@article {pmid38603592, year = {2024}, author = {Ranjan, R and Koffel, T and Klausmeier, CA}, title = {The three-species problem: Incorporating competitive asymmetry and intransitivity in modern coexistence theory.}, journal = {Ecology letters}, volume = {27}, number = {4}, pages = {e14426}, doi = {10.1111/ele.14426}, pmid = {38603592}, issn = {1461-0248}, support = {//Niedersächsisches Ministerium für Wissenschaft und Kultur/ ; //Deutsches Zentrum für integrative Biodiversitätsforschung Halle-Jena-Leipzig/ ; EF-2124800//National Science Foundation/ ; //Volkswagen Foundation/ ; }, abstract = {While natural communities can contain hundreds of species, modern coexistence theory focuses primarily on species pairs. Alternatively, the structural stability approach considers the feasibility of equilibria, gaining scalability to larger communities but sacrificing information about dynamic stability. Three-species competitive communities are a bridge to more-diverse communities. They display novel phenomena while remaining amenable to mathematical analysis, but remain incompletely understood. Here, we combine these approaches to identify the key quantities that determine three-species competition outcomes. We show that pairwise niche overlap and fitness differences are insufficient to completely characterize competitive outcomes, which requires a strictly triplet-wise quantity: cyclic asymmetry, which underlies intransitivity. Low pairwise niche overlap stabilizes the triplet, while high fitness differences promote competitive exclusion. The effect of cyclic asymmetry on stability is complex and depends on pairwise niche overlap. In summary, we elucidate how pairwise niche overlap, fitness differences and cyclic asymmetry determine three-species competition outcomes.}, } @article {pmid38600958, year = {2024}, author = {Visagie, CM and Yilmaz, N and Kocsubé, S and Frisvad, JC and Hubka, V and Samson, RA and Houbraken, J}, title = {A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species.}, journal = {Studies in mycology}, volume = {107}, number = {}, pages = {1-66}, pmid = {38600958}, issn = {0166-0616}, abstract = {The order Eurotiales is diverse and includes species that impact our daily lives in many ways. In the past, its taxonomy was difficult due to morphological similarities, which made accurate identification of species difficult. This situation improved and stabilised with recent taxonomic and nomenclatural revisions that modernised Aspergillus, Penicillium and Talaromyces. This was mainly due to the availability of curated accepted species lists and the publication of comprehensive DNA sequence reference datasets. This has also led to a sharp increase in the number of new species described each year with the accepted species lists in turn also needing regular updates. The focus of this study was to review the 160 species described between the last list of accepted species published in 2020 until 31 December 2022. To review these species, single-gene phylogenies were constructed and GCPSR (Genealogical Concordance Phylogenetic Species Recognition) was applied. Multi-gene phylogenetic analyses were performed to further determine the relationships of the newly introduced species. As a result, we accepted 133 species (37 Aspergillus, two Paecilomyces, 59 Penicillium, two Rasamsonia, 32 Talaromyces and one Xerochrysium), synonymised 22, classified four as doubtful and created a new combination for Paraxerochrysium coryli, which is classified in Xerochrysium. This brings the number of accepted species to 453 for Aspergillus, 12 for Paecilomyces, 535 for Penicillium, 14 for Rasamsonia, 203 for Talaromyces and four for Xerochrysium. We accept the newly introduced section Tenues (in Talaromyces), and series Hainanici (in Aspergillus sect. Cavernicolarum) and Vascosobrinhoana (in Penicillium sect. Citrina). In addition, we validate the invalidly described species Aspergillus annui and A. saccharicola, and series Annuorum (in Aspergillus sect. Flavi), introduce a new combination for Dichlaena lentisci (type of the genus) and place it in a new section in Aspergillus subgenus Circumdati, provide an updated description for Rasamsonia oblata, and list excluded and recently synonymised species that were previously accepted. This study represents an important update of the accepted species lists in Eurotiales. Taxonomic novelties: New sections: Aspergillus section Dichlaena Visagie, Kocsubé & Houbraken. New series: Aspergillus series Annuorum J.J. Silva, B.T. Iamanaka, Frisvad. New species: Aspergillus annui J.J. Silva, M.H.P. Fungaro, Frisvad, M.H. Taniwaki & B.T. Iamanaka; Aspergillus saccharicola J.J. Silva, Frisvad, M.H.P. Fungaro, M.H. Taniwaki & B.T. Iamanaka. New combinations: Aspergillus lentisci (Durieu & Mont.) Visagie, Malloch, L. Kriegsteiner, Samson & Houbraken; Xerochrysium coryli (Crous & Decock) Visagie & Houbraken. Citation: Visagie CM, Yilmaz N, Kocsubé S, Frisvad JC, Hubka V, Samson RA, Houbraken J (2024). A review of recently introduced Aspergillus, Penicillium, Talaromyces and other Eurotiales species. Studies in Mycology 107: 1-66. doi: 10.3114/sim.2024.107.01.}, } @article {pmid38585620, year = {2024}, author = {Huymann, LR and Hannecker, A and Giovanni, T and Liimatainen, K and Niskanen, T and Probst, M and Peintner, U and Siewert, B}, title = {Revised taxon definition in European Cortinarius subgenus Dermocybe based on phylogeny, chemotaxonomy, and morphology.}, journal = {Mycological progress}, volume = {23}, number = {1}, pages = {26}, pmid = {38585620}, issn = {1617-416X}, abstract = {UNLABELLED: Cortinarius (Fr.) Fr. is one of the most species-rich genera in the Agaricales (Basidiomycota). Cortinarius subgen. Dermocybe (Fr.) Trog includes brightly coloured Cortinarii with anthraquinone pigments. The chemotaxonomic approach has always been as important as classical methods for species definition of Dermocybe and helped to improve overall species concepts. However, some species concepts within this group remain unclear. We therefore address this topic based on a combined phylogenetic, morphological, and pigment-chemical approach. For this, sequence data, HPLC-MS pigment profiles and spore sizes were included were included to obtain a better resolution of taxa. The study was based on 173 recent collections and 12 type specimens. A total of 117 rDNA ITS sequences were produced from the collections in this study, 102 sequences were retrieved from databases. We could detect and clearly delimit 19 Dermocybe species occurring in central European habitats, from which 16 are discussed in detail. Additionally, we grouped the detected anthraquinone pigments into four groups. This detailed analysis of dermocyboid Cortinarius species occurring in a restricted number of habitat types confirmed our hypothesis that species diversity is much higher than currently assumed. This high diversity is blurred by too wide and incorrect species concepts of several classical species like C. croceus and C. cinnamomeus. Molecular and chemotaxonomical studies carried out together with careful phenotypical analyses resulted in a good differentiation of species. A key is presented for these taxa to allow a better identification of Cortinarius subgenus Dermocybe spp. occurring in Central Europe mainly in the alpine range.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11557-024-01959-z.}, } @article {pmid38574082, year = {2024}, author = {Tiktak, GP and Gabb, A and Brandt, M and Diz, FR and Bravo-Vásquez, K and Peñaherrera-Palma, C and Valdiviezo-Rivera, J and Carlisle, A and Melling, LM and Cain, B and Megson, D and Preziosi, R and Shaw, KJ}, title = {Genetic identification of three CITES-listed sharks using a paper-based Lab-on-a-Chip (LOC).}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0300383}, doi = {10.1371/journal.pone.0300383}, pmid = {38574082}, issn = {1932-6203}, abstract = {Threatened shark species are caught in large numbers by artisanal and commercial fisheries and traded globally. Monitoring both which shark species are caught and sold in fisheries, and the export of CITES-restricted products, are essential in reducing illegal fishing. Current methods for species identification rely on visual examination by experts or DNA barcoding techniques requiring specialist laboratory facilities and trained personnel. The need for specialist equipment and/or input from experts means many markets are currently not monitored. We have developed a paper-based Lab-on-a-Chip (LOC) to facilitate identification of three threatened and CITES-listed sharks, bigeye thresher (Alopias superciliosus), pelagic thresher (A. pelagicus) and shortfin mako shark (Isurus oxyrinchus) at market source. DNA was successfully extracted from shark meat and fin samples and combined with DNA amplification and visualisation using Loop Mediated Isothermal Amplification (LAMP) on the LOC. This resulted in the successful identification of the target species of sharks in under an hour, with a working positive and negative control. The LOC provided a simple "yes" or "no" result via a colour change from pink to yellow when one of the target species was present. The LOC serves as proof-of-concept (PoC) for field-based species identification as it does not require specialist facilities. It can be used by non-scientifically trained personnel, especially in areas where there are suspected high frequencies of mislabelling or for the identification of dried shark fins in seizures.}, } @article {pmid38542144, year = {2024}, author = {Cruz, H and Pinheiro, M and Borges, V}, title = {ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious Agents.}, journal = {International journal of molecular sciences}, volume = {25}, number = {6}, pages = {}, doi = {10.3390/ijms25063172}, pmid = {38542144}, issn = {1422-0067}, support = {DURABLE (Project no. 101102733)//European Commission/ ; EU4H-2022-DGA-MS-IBA-1//European Comission/ ; }, abstract = {In response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we introduce ReporType, a versatile bioinformatics pipeline designed for targeted loci screening and typing of infectious agents. Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and/or screening of specific genomic loci. The pipeline accommodates a range of input formats, from Illumina or Oxford Nanopore Technology (ONT) reads (FASTQ) to Sanger sequencing files (AB1), or FASTA files, making it flexible for application in multiple pathogens and with different purposes. ReporType is released with pre-prepared databases for some viruses and bacteria, yet it remains easily configurable to handle custom databases. ReporType performance and functionality were validated through proof-of-concept exercises, encompassing diverse pathogenic species, including viruses such as measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV) and Human T-Cell Lymphotropic virus type 1 (HTLV-1), as well as bacteria like Chlamydia trachomatis and Legionella pneumophila. In summary, ReporType emerges as a simple, dynamic and pan-pathogen tool, poised to evolve in tandem with the ever-changing needs of the fields of pathogen genomics, infectious disease epidemiology, and one health bioinformatics. ReporType is freely available at GitHub.}, } @article {pmid38503840, year = {2024}, author = {Duran, DP and Laroche, RA and Roman, SJ and Godwin, W and Herrmann, DP and Bull, E and Egan, SP}, title = {Species delimitation, discovery and conservation in a tiger beetle species complex despite discordant genetic data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6617}, pmid = {38503840}, issn = {2045-2322}, abstract = {In an age of species declines, delineating and discovering biodiversity is critical for both taxonomic accuracy and conservation. In recent years, there has been a movement away from using exclusively morphological characters to delineate and describe taxa and an increase in the use of molecular markers to describe diversity or through integrative taxonomy, which employs traditional morphological characters, as well as genetic or other data. Tiger beetles are charismatic, of conservation concern, and much work has been done on the morphological delineation of species and subspecies, but few of these taxa have been tested with genetic analyses. In this study, we tested morphologically based taxonomic hypotheses of polymorphic tiger beetles in the Eunota circumpicta (LaFerté-Sénectère, 1841) species complex using multilocus genomic and mtDNA analyses. We find multiple cryptic species within the previous taxonomic concept of Eunota circumpicta, some of which were historically recognized as subspecies. We found that the mtDNA and genomic datasets did not identify the same taxonomic units and that the mtDNA was most at odds with all other genetic and morphological patterns. Overall, we describe new cryptic diversity, which raises important conservation concerns, and provide a working example for testing species and subspecies validity despite discordant data.}, } @article {pmid38480821, year = {2024}, author = {Fujita, H and Shimada, D and Kudo, J and Kosha, K and Kakuyama, S and Terasaki, H and Kunishima, M}, title = {Carbocationoids, a concept for controlling highly reactive cationic species.}, journal = {Communications chemistry}, volume = {7}, number = {1}, pages = {55}, pmid = {38480821}, issn = {2399-3669}, support = {21H02603//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 17H03970//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 26670001//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {Carbocations, which are positively charged highly electrophilic intermediates, are efficacious for the direct alkylation of low-reactive nucleophiles. The utilization of carbocations in SN1 reactions relies on the activation of their precursors in the presence of a nucleophile. However, undesirable interactions between the nucleophile and the leaving group activator limit the scope of acceptable nucleophiles. Here we report a strategy to conduct SN1 reactions involving unstable carbocations in an alternative stepwise procedure, which was demonstrated by the benzylation of various neutral nucleophiles. In the first step, carbocations were accumulated in a nucleophile-free solution in the form of carbocationoids utilizing the coordinative stabilization of triazinediones. Subsequently, the addition of these solutions in the second step enabled room-temperature alkylation without the need for acidic additives. This methodology overcomes the inherent challenges of carbocations in SN1 reactions.}, } @article {pmid38480402, year = {2024}, author = {Wood, TJ}, title = {New Asian Andrena species, with notes on the subgenus Cnemidandrena (Hymenoptera: Andrenidae).}, journal = {Zootaxa}, volume = {5404}, number = {1}, pages = {167-188}, doi = {10.11646/zootaxa.5404.1.11}, pmid = {38480402}, issn = {1175-5334}, abstract = {Asia is the worlds largest continent and comprises most of the Holarctic biogeographic region. The genus Andrena is principally distributed through the Holarctic, but it remains understudied in Asia. The subgenus Cnemidandrena Hedicke, 1933 is distributed across Asia with some species reaching south to the Tibetan Plateau. However, some southern members display an unusual morphology, including A. (Cnemidandrena) kishidai chagyabensis Wu, 1982 (newly recorded for Bhutan, India, and Nepal) and A. (Cnemidandrena) granulitergorum Tadauchi & Xu, 2002 (newly recorded for Nepal). The male of A. granulitergorum is described for the first time, A. (Cnemidandrena) rufina Morawitz, 1876 is reported from Kyrgyzstan, Afghanistan, and Kashmir for the first time, and possible senior synonyms for Asian A. (Cnemidandrena) are suggested. To contribute to an improved understanding of localised Asian Andrena diversity, the following new species are described: A. (Cnemidandrena) textrix sp. nov. from China, A. (incertae sedis) liebigi sp. nov. and A. (Troandrena) monfaredi sp. nov. from Iran, and A. (incertae sedis) quercorum sp. nov. from Turkey. These results further confirm that additional taxonomic work is needed to harmonise Andrena species concepts across the different biogeographic regions of Asia.}, } @article {pmid38480389, year = {2024}, author = {Hendrix, SV and Bartlett, CR}, title = {Redescription and revised genus placement of Oliarus pinicolus Osborn, 1926, with notes on Antillean Pentastirini (Hemiptera: Fulgoromorpha: Cixiidae).}, journal = {Zootaxa}, volume = {5405}, number = {2}, pages = {209-226}, doi = {10.11646/zootaxa.5405.2.3}, pmid = {38480389}, issn = {1175-5334}, abstract = {Oliarus pinicolus Osborn, 1926 is a little-known planthopper described from western Cuba on Cuban pine (Pinus cubensis). As part of a review of the sprawling New World cixiid genus Melanoliarus Fennah, 1945, the species is herein redescribed and illustrated for the first time, including the male terminalia. After comparison to similar species in the region, we transfer the species to Nivcentia Holzinger, 2004, as Nivcentia pinicolus comb. nov., based on characteristics of the male terminalia and provide an amended description of the genus. We also designate a lectotype for Oliarus pinicolus to ensure the stability of the species concept described here. A checklist of Antillean Pentastirini is included with taxonomic comments on the species and genera of the region. The pentastirine species of Cuba are illustrated.}, } @article {pmid38469542, year = {2023}, author = {Tembrock, LR and Wilson, CR and Zink, FA and Timm, AE and Gilligan, TM and Konstantinov, AS and Tishechkin, AK}, title = {CO1 barcodes resolve an asymmetric biphyletic clade for Diabrotica undecimpunctata subspecies and provide nucleotide variants for differentiation from related lineages using real-time PCR.}, journal = {Frontiers in insect science}, volume = {3}, number = {}, pages = {1168586}, pmid = {38469542}, issn = {2673-8600}, abstract = {Diabrotica undecimpunctata is a multivoltine polyphagous beetle species that has long been documented as a significant agricultural pest throughout its native range in North America. This beetle can vector bacterial and viral plant pathogens that result in major losses to crops such as cucumber and soybean. Many countries outside the Americas treat D. undecimpunctata as a species of quarantine importance, while in the USA only the subspecies D. u. duodecimnotata is subject to quarantine, to prevent introduction from Mexico. Identification of D. undecimpunctata on the basis of morphology alone can be complicated given the use of conflicting characters in the description of some subspecific taxa. To better understand relationships among D. undecimpunctata subspecies and other related species, we sequenced mitochondrial cytochrome oxidase 1 (CO1) and nuclear internal transcribed spacer 2 (ITS2) DNA from individuals in different subspecific taxa and across different parts of the species range using museum samples and interceptions. When our data were combined with publicly available Diabrotica data, no pattern of divergence consistent with the currently recognized subspecific designations was found. In addition, we compared phylogenetic patterns in CO1 data from the congener D. virgifera to demonstrate the utility of mitochondrial data in resolving subspecies. From the CO1 data, a diagnostic real-time PCR assay was developed that could successfully identify all haplotypes within the large D. undecimpunctata clade for use in surveys and identification at ports of entry. These findings underscore the need to resolve molecular and morphological datasets into cogent, lineage-based groupings. Such efforts will provide an evolutionary context for the study of agriculturally important attributes of Diabrotica such as host preferences, xenobiotic metabolism, and natural and anthropogenic patterns of dispersal.}, } @article {pmid38456839, year = {2024}, author = {Chávez-Tinoco, M and García-Ortega, LF and Mancera, E}, title = {Genetic modification of Candida maltosa, a non-pathogenic CTG species, reveals EFG1 function.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {3}, pages = {}, doi = {10.1099/mic.0.001447}, pmid = {38456839}, issn = {1465-2080}, abstract = {Candida maltosa is closely related to important pathogenic Candida species, especially C. tropicalis and C. albicans, but it has been rarely isolated from humans. For this reason, through comparative studies, it could be a powerful model to understand the genetic underpinnings of the pathogenicity of Candida species. Here, we generated a cohesive assembly of the C. maltosa genome and developed genetic engineering tools that will facilitate studying this species at a molecular level. We used a combination of short and long-read sequencing to build a polished genomic draft composed of 14 Mbp, 45 contigs and close to 5700 genes. This assembly represents a substantial improvement from the currently available sequences that are composed of thousands of contigs. Genomic comparison with C. albicans and C. tropicalis revealed a substantial reduction in the total number of genes in C. maltosa. However, gene loss seems not to be associated to the avirulence of this species given that most genes that have been previously associated with pathogenicity were also present in C. maltosa. To be able to edit the genome of C. maltosa we generated a set of triple auxotrophic strains so that gene deletions can be performed similarly to what has been routinely done in pathogenic Candida species. As a proof of concept, we generated gene knockouts of EFG1, a gene that encodes a transcription factor that is essential for filamentation and biofilm formation in C. albicans and C. tropicalis. Characterization of these mutants showed that Efg1 also plays a role in biofilm formation and filamentous growth in C. maltosa, but it seems to be a repressor of filamentation in this species. The genome assembly and auxotrophic mutants developed here are a key step forward to start using C. maltosa for comparative and evolutionary studies at a molecular level.}, } @article {pmid38443925, year = {2024}, author = {Moragues-Solanas, L and Le-Viet, T and McSorley, E and Halford, C and Lockhart, DS and Aydin, A and Kay, GL and Elumogo, N and Mullen, W and O'Grady, J and Gilmour, MW}, title = {Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection.}, journal = {BMC medical genomics}, volume = {17}, number = {1}, pages = {71}, pmid = {38443925}, issn = {1755-8794}, support = {MR/R015937/1/MRC_/Medical Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011011/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011011/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: The timely and accurate diagnosis of bloodstream infection (BSI) is critical for patient management. With longstanding challenges for routine blood culture, metagenomics is a promising approach to rapidly provide sequence-based detection and characterisation of bloodborne bacteria. Long-read sequencing technologies have successfully supported the use of clinical metagenomics for syndromes such as respiratory illness, and modified approaches may address two requisite factors for metagenomics to be used as a BSI diagnostic: depletion of the high level of host DNA to then detect the low abundance of microbes in blood.

METHODS: Blood samples from healthy donors were spiked with different concentrations of four prevalent causative species of BSI. All samples were then subjected to a modified saponin-based host DNA depletion protocol and optimised DNA extraction, whole genome amplification and debranching steps in preparation for sequencing, followed by bioinformatical analyses. Two related variants of the protocol are presented: 1mL of blood processed without bacterial enrichment, and 5mL of blood processed following a rapid bacterial enrichment protocol-SepsiPURE.

RESULTS: After first identifying that a large proportion of host mitochondrial DNA remained, the host depletion process was optimised by increasing saponin concentration to 3% and scaling the reaction to allow more sample volume. Compared to non-depleted controls, the 3% saponin-based depletion protocol reduced the presence of host chromosomal and mitochondrial DNA < 10[6] and < 10[3] fold respectively. When the modified depletion method was further combined with a rapid bacterial enrichment method (SepsiPURE; with 5mL blood samples) the depletion of mitochondrial DNA improved by a further > 10X while also increasing detectable bacteria by > 10X. Parameters during DNA extraction, whole genome amplification and long-read sequencing were also adjusted, and subsequently amplicons were detected for each input bacterial species at each of the spiked concentrations, ranging from 50-100 colony forming units (CFU)/mL to 1-5 CFU/mL.

CONCLUSION: In this proof-of-concept study, four prevalent BSI causative species were detected in under 12 h to species level (with antimicrobial resistance determinants) at concentrations relevant to clinical blood samples. The use of a rapid and precise metagenomic protocols has the potential to advance the diagnosis of BSI.}, } @article {pmid38436469, year = {2024}, author = {van der Gulik, PTS and Hoff, WD and Speijer, D}, title = {The contours of evolution: In defence of Darwin's tree of life paradigm.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2400012}, doi = {10.1002/bies.202400012}, pmid = {38436469}, issn = {1521-1878}, abstract = {Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights into widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.}, } @article {pmid38435991, year = {2024}, author = {Yu, KP and Kuntner, M}, title = {Discovering unknown Madagascar biodiversity: integrative taxonomy of raft spiders (Pisauridae: Dolomedes).}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16781}, doi = {10.7717/peerj.16781}, pmid = {38435991}, issn = {2167-8359}, abstract = {Madagascar is a global biodiversity hotspot, but its biodiversity continues to be underestimated and understudied. Of raft spiders, genus Dolomedes Latreille, 1804, literature only reports two species on Madagascar. Our single expedition to humid forests of eastern and northern Madagascar, however, yielded a series of Dolomedes exemplars representing both sexes of five morphospecies. To avoid only using morphological diagnostics, we devised and tested an integrative taxonomic model for Dolomedes based on the unified species concept. The model first determines morphospecies within a morphometrics framework, then tests their validity via species delimitation using COI. It then incorporates habitat preferences, geological barriers, and dispersal related traits to form hypotheses about gene flow limitations. Our results reveal four new Dolomedes species that we describe from both sexes as Dolomedes gregoric sp. nov., D. bedjanic sp. nov., D. hydatostella sp. nov., and D. rotundus sp. nov. The range of D. kalanoro Silva & Griswold, 2013, now also known from both sexes, is expanded to eastern Madagascar. By increasing the known raft spider diversity from one valid species to five, our results merely scratch the surface of the true Dolomedes species diversity on Madagascar. Our integrative taxonomic model provides the framework for future revisions of raft spiders anywhere.}, } @article {pmid38426894, year = {2024}, author = {Dong, Y and Zhang, Q and Mao, Y and Wu, M and Wang, Z and Chang, L and Zhang, J}, title = {Control of two insect pests by expression of a mismatch corrected double-stranded RNA in plants.}, journal = {Plant biotechnology journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/pbi.14321}, pmid = {38426894}, issn = {1467-7652}, support = {32102297//National Natural Science Foundation of China/ ; 32271912//National Natural Science Foundation of China/ ; 32272634//National Natural Science Foundation of China/ ; }, abstract = {RNA interference (RNAi) has emerged as an efficient technology for pest control by silencing the essential genes of targeted insects. Owing to its nucleotide sequence-guided working mechanism, RNAi has a high degree of species-specificity without impacts on non-target organisms. However, as plants are inevitably under threat by two or more insect pests in nature, the species-specific mode of RNAi-based technology restricts its wide application for pest control. In this study, we artificially designed an intermediate dsRNA (iACT) targeting two β-Actin (ACT) genes of sap-sucking pests Bemisia tabaci and Myzus persicae by mutual correction of their mismatches. When expressing hairpin iACT (hpiACT) from tobacco nuclear genome, transgenic plants are well protected from both B. tabaci and M. persicae, either individually or simultaneously, as evidenced by reduced fecundity and suppressed ACT gene expression, whereas expression of hpRNA targeting BtACT or MpACT in transgenic tobacco plants could only confer specific resistance to either B. tabaci or M. persicae, respectively. In sum, our data provide a novel proof-of-concept that two different insect species could be simultaneously controlled by artificial synthesis of dsRNA with sequence optimization, which expands the range of transgenic RNAi methods for crop protection.}, } @article {pmid38421416, year = {2024}, author = {Monecke, S}, title = {Threatened chronotopes: can chronobiology help endangered species?.}, journal = {Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology}, volume = {}, number = {}, pages = {}, pmid = {38421416}, issn = {1432-1351}, abstract = {Pittendrigh and Daan's 1976 article "Pacemaker structure: A clock for all seasons" marks the foundation of modern seasonal chronobiology. It proposed the internal coincidence model comprised of a Morning (M) and Evening (E) oscillator, which are coupled but synchronized separately by dawn and dusk. It has become an attractive model to explain the seasonal adaptation of circadian rhythms. Using the example of the European hamster, this article connects the classical entrainment concept to species decline and, ultimately, conservation concepts. Seasonality of this species is well studied and circannual rhythms have been described in at least 32 parameters. The European hamster is listed as critically endangered on the International Union for Conservation of Nature (IUCN) red list. Changes in the temporal structure of the environment (the chronotope) caused by climate change and light pollution might be responsible for the global decline. The article shows that classical chronobiological concepts such as the internal coincidence model (Pittendrigh and Daan Pittendrigh and Daan, J Comp Physiol [a] 106:333-355, 1976) are helpful to understand the (chronobiological) causes of the decline and can potentially support species conservation. Knowing the species' physiological limitations as well as its adaptation capacities can potentially prevent its extinction at a time when classical conservation concepts have reached their limits.}, } @article {pmid38392811, year = {2024}, author = {Wang, S and Jiang, N and Ma, R}, title = {Morphology and Phylogeny Reveal Three New Species of Cytospora Associated with Tree Cankers in China.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/jof10020139}, pmid = {38392811}, issn = {2309-608X}, support = {31960316//National Natural Science Foundation of China/ ; }, abstract = {Cytospora (Cytosporaceae, Diaporthales) is a fungal genus that usually inhabits plants as endophytes, saprobes, as well as pathogens. Species of this genus are characterized by possessing allantoid hyaline conidia and ascospores. Samples with typical Cytospora canker symptoms on Prunus davidiana, P. padus and Salix sp. were collected in Tibet and Xinjiang, China. Species were identified using both morphological and molecular approaches of combined loci of internal transcribed spacer region rDNA (ITS), the partial actin (act) region, RNA polymerase II second largest subunit (rpb2), the translation elongation factor 1-alpha (tef1) gene and the partial be-ta-tubulin (tub2) gene. Six isolates in the present study formed three distinct clades from previously known species. Cytospora hejingensis sp. nov. from Salix sp., C. jilongensis sp. nov. from P. davidiana and C. kunsensis from P. padus were proposed herein. The current study improves the understanding of species concept in Cytospora.}, } @article {pmid38377202, year = {2024}, author = {Lukhtanov, VA}, title = {Polytypic species concept and subspecies in the genomic era.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {9}, pages = {e2317038121}, doi = {10.1073/pnas.2317038121}, pmid = {38377202}, issn = {1091-6490}, } @article {pmid38349782, year = {2024}, author = {Koch Bach, R and Murithi, HM and Slocum, CR and Coyne, D and Clough, S}, title = {Remarkably high ITS haplotype diversity of the fungal Select Agent Coniothyrium glycines discovered throughout its range in sub-Saharan Africa.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-09-23-0315-KC}, pmid = {38349782}, issn = {0031-949X}, abstract = {Red leaf blotch of soybean, caused by the fungus Coniothyrium glycines, is a foliar disease characterized by blotching, necrosis, and defoliation, which has only been reported from Africa. The species is listed as a Select Agent by the Federal Select Agent Program due to its potentially devastating impacts to soybean production should it spread to the U.S. Despite its potential import, very few isolates are available for study. Herein, we obtained 96 new C. glycines isolates from six soybean-producing countries throughout sub-Saharan Africa. Along with 12 previously collected ones, we sequenced each at the internal transcribed spacer (ITS) region. Between all isolates, we identified a total of 28 single nucleotide polymorphisms and 23 haplotypes. One hypothesis to explain the tremendous diversity uncovered at the ITS-which is generally conserved within a species-is that our current species concept of C. glycines is too broad, and that there may be multiple species that cause RLB. Zambia contained the highest haplotype diversity, a significant fraction of which remains unsampled. Most haplotypes were specific to a single country, except for two, which were found in Zambia and either neighboring Mozambique or Zimbabwe. This geographic specificity indicates that the ITS region may be useful in identifying source populations or routes of transmission should this pathogen spread beyond Africa. The observed geographic partitioning of this pathogen is likely the result of millions of years of replication on little-studied native hosts, given that soybean has only been cultivated in Africa since the early 1900s.}, } @article {pmid38338696, year = {2024}, author = {Maggisano, V and Capriglione, F and Mio, C and Bulotta, S and Damante, G and Russo, D and Celano, M}, title = {RNA Profile of Cell Bodies and Exosomes Released by Tumorigenic and Non-Tumorigenic Thyroid Cells.}, journal = {International journal of molecular sciences}, volume = {25}, number = {3}, pages = {}, doi = {10.3390/ijms25031407}, pmid = {38338696}, issn = {1422-0067}, abstract = {Tumor cells release exosomes, extracellular vesicle containing various bioactive molecules such as protein, DNA and RNA. The analysis of RNA molecules packaged in exosomes may provide new potential diagnostic or prognostic tumor biomarkers. The treatment of radioiodine-refractory aggressive thyroid cancer is still an unresolved clinical challenge, and the search for biomarkers that are detectable in early phase of the disease has become a fundamental goal for thyroid cancer research. By using transcriptome analysis, this study aimed to analyze the gene expression profiles of exosomes secreted by a non-tumorigenic thyroid cell line (Nthy-ori 3.1-exo) and a papillary thyroid cancer (TPC-1-exo) cell line, comparing them with those of cell bodies (Nthy-ori 3.1-cells and TPC-1-cells). A total of 9107 transcripts were identified as differentially expressed when comparing TPC-1-exo with TPC-1-cells and 5861 when comparing Nthy-ori 3.1-exo with Nthy-ori 3.1-cells. Among them, Sialic acid-binding immunoglobulin-like lectins 10 and 11 (SIGLEC10, SIGLEC11) and Keratin-associated protein 5 (KRTAP5-3) transcripts, genes known to be involved in cancer progression, turned out to be up-regulated only in TPC-1-exo. Gene ontology analysis revealed significantly enriched pathways, and only in TPC-1-exo were the differential expressed genes associated with an up-regulation in epigenetic processes. These findings provide a proof of concept that some mRNA species are specifically packaged in tumor-cell-derived exosomes and may constitute a starting point for the identification of new biomarkers for thyroid tumors.}, } @article {pmid38333362, year = {2023}, author = {Smith, JE and Gabbaï, FP}, title = {Are Ar3SbCl2 Species Lewis Acidic? Exploration of the Concept and Pnictogen Bond Catalysis Using a Geometrically Constrained Example.}, journal = {Organometallics}, volume = {42}, number = {3}, pages = {240-245}, doi = {10.1021/acs.organomet.2c00565}, pmid = {38333362}, issn = {0276-7333}, abstract = {As part of our investigations into the Lewis acidic behavior of antimony derivatives, we have decided to study the properties of 5-phenyl-5,5-dichloro-λ[5]-dibenzostibole (1), a dichlorostiborane with an antimony atom confined to a five-membered heterocycle. Our work shows that the resulting geometrical constraints elevate the Lewis acidity of the antimony atom, as confirmed by the crystal structure of 1-THF and the solution study of the interaction of 1 with Ph3PO. The enhanced Lewis acidic properties of 1, which exceed those of simple dichlorostiboranes such as Ph3SbCl2, also become manifest in pnictogen bonding catalysis experiments involving the reductions of imines with Hantzsch ester. The influence of geometrical constraints in the chemistry of this compound is also supported by a computational activation strain analysis as well as by an energy decomposition analysis of a model Me3PO adduct.}, } @article {pmid30313177, year = {2018}, author = {Gippoliti, S and Groves, CP}, title = {Overlooked mammal diversity and conservation priorities in Italy: Impacts of taxonomic neglect on a Biodiversity Hotspot in Europe.}, journal = {Zootaxa}, volume = {4434}, number = {3}, pages = {511-528}, doi = {10.11646/zootaxa.4434.3.7}, pmid = {30313177}, issn = {1175-5334}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources ; Europe ; Italy ; *Mammals ; Phylogeny ; }, abstract = {For more than half a century, little taxonomic revisionary work has been directed towards extant European mammals so that the limits of most geographically widespread polytypic species remained scientifically untested. Occasionally, taxonomic changes have been proposed and several new species have been resurrected / discovered in the last decades mainly on the basis of genetic studies, often considered the only tool to establish objective species boundaries. Nevertheless, the precise details of species boundaries, subspecific variation and phylogenetic relationships remain unknown for several European mammal taxa. The inadequacies of outdated, incomplete taxonomic knowledge reach an extreme in southern Europe, and notably Italy, where cryptic species abound and specimen-based research is scanty. The state of mammalian taxonomic knowledge in Italy shows that Linnaean and Wallacean shortfalls are no means restricted to hyperdiverse, understudied tropics. They undermine our knowledge of temperate regions, with severe consequences for biodiversity conservation policies in Europe, where conservation assessments overlook significant endemic biodiversity. European mammalogy stands to benefit from an infusion of the tree-thinking philosophy that undergirds evolutionary theory and particularly phylogenetic methods systematics. Furthermore, it is important that taxonomic research be seen as a normal part of scientific advancement and of critical importance as the basis of a sound biodiversity conservation policy.}, } @article {pmid38311795, year = {2024}, author = {Petrović, K and Orzali, L and Krsmanović, S and Valente, MT and Tolimir, M and Pavlov, J and Riccioni, L}, title = {Genetic diversity and pathogenicity of the Fusarium species complex on soybean in Serbia.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-11-23-2450-RE}, pmid = {38311795}, issn = {0191-2917}, abstract = {Using morphological and cultural characteristics for identification, 36 Fusarium isolates were recovered from diseased roots, stems, and seeds of soybean from several localities throughout Vojvodina Province, Serbia, were identified as Fusarium spp. Based on molecular characterization, 12 Fusarium species were identified: F. acuminatum, F. avenaceum, F. commune, F. equiseti, F. graminearum, F. incarnatum, F. oxysporum, F. proliferatum, F. solani, F. sporotrichioides, F. subglutinans, and F. tricinctum. The EF-1α based-phylogeny grouped the isolates into 12 well-supported clades, but the polymorphisms among sequences in some clades suggested the use of the species complex concept: (1) FIESC - F. incarnatum and F. equiseti; (2) FOSC - F. oxysporum; (3) FSSC - F. solani; and (4) FAATSC - F. acuminatum, F. avenaceum and F. tricinctum. Pathogenicity tests showed that the most aggressive species causing soybean seed rot were F. sporotrichioides, F. graminearum, FIESC, and F. avenaceum. Furthermore, F. subglutinans, FSSC, and F. proliferatum, showed a high percentage of pathogenicity on soybean seeds (80-100%), while variability in pathogenicity occurred within isolates of F. tricinctum species has occurred variability in the virulence of different isolates. FOSC, F. commune and F. acuminatum had the lowest pathogenicity degree. To our knowledge, this is the first study of the characterization of Fusarium complex species on soybean in Serbia. This study provides valuable information about the structure composition of Fusarium complex species and pathogenicity that will be used in further research on soybean resistance to Fusarium-based diseases.}, } @article {pmid38308632, year = {2024}, author = {Zhang, N and Xue, Z and Shi, L and Luo, G}, title = {Unveiling the Detailed Mechanism and Origins of Chemo-, Regio-, and Stereoselectivity of Rare-Earth Catalyzed Alternating Copolymerization of Polar and Nonpolar Olefins.}, journal = {Inorganic chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.inorgchem.3c04428}, pmid = {38308632}, issn = {1520-510X}, abstract = {The direct copolymerization of polar and nonpolar olefins is of great interest and significance, as it is the most atom-economical and straightforward strategy for the synthesis of functional polyolefin materials. Despite considerable efforts, the precise control of monomer-sequence and their regio- and stereochemistry is full of challenges, and the related mechanistic origins are still in their infancy to date. Herein, the mechanistic studies on the model reaction of Sc-catalyzed co-syndiospecific alternating copolymerization of anisylpropylene (AP) and styrene were performed by DFT calculations. The results suggest that the subtle balance between electronic and steric factors plays an important role during monomer insertions, and a new amino-dissociated mechanism was proposed for AP insertion at chain initiation. AP insertion follows the 2,1-si-insertion pattern, which is mainly controlled by steric factors caused by the restricted MeO···Sc interaction. As for styrene insertion, it prefers the 2,1-re-insertion manner and its regio- and stereoselectivities are influenced by steric repulsions between the inserting styrene and the polymer chain or the ligand. More interestingly, it is found that the alternating monomer-sequence is mainly determined by the "steric matching" principle, which is quantitatively expressed by the buried volume of the metal center of the preinserted species. The concept of steric pocket has been successfully applied to explain the different performances of several catalysts and other alternating copolymerization reactions. The insightful mechanistic findings and the quantitative steric pocket model present here are expected to promote rational design of new rare-earth catalysts for developing regio-, stereo-, and sequence-controlled copolymerization of specific polar and nonpolar olefins.}, } @article {pmid38306290, year = {2024}, author = {Campos, LR and Trefflich, S and Morais, DA and Imparato, DO and Chagas, VS and Albanus, RD and Dalmolin, RJ and Castro, MA}, title = {Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analysis.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msae019}, pmid = {38306290}, issn = {1537-1719}, abstract = {Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key concept behind this strategy is that orthologous genes share ancestry to some extent. While reconstructing the history of a single gene is feasible with the existing computational resources, the reconstruction of entire biological systems remains challenging. Here we present Bridge, a new algorithm designed to infer the evolutionary root of orthologous genes in large-scale evolutionary analysis. The Bridge algorithm infers the evolutionary root of a given gene based on the distribution of its orthologs in a species tree. The Bridge algorithm is implemented in R and can be used either to assess genetic changes across the evolutionary history of orthologous groups or to infer the onset of specific traits in a biological system.}, } @article {pmid38298569, year = {2023}, author = {Abad, ZG and Burgess, TI and Bourret, T and Bensch, K and Cacciola, SO and Scanu, B and Mathew, R and Kasiborski, B and Srivastava, S and Kageyama, K and Bienapfl, JC and Verkleij, G and Broders, K and Schena, L and Redford, AJ}, title = {Phytophthora : taxonomic and phylogenetic revision of the genus.}, journal = {Studies in mycology}, volume = {106}, number = {}, pages = {259-348}, doi = {10.3114/sim.2023.106.05}, pmid = {38298569}, issn = {0166-0616}, abstract = {Many members of the Oomycota genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of regulatory concern around the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for 20 species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani, P. honggalleglyana (Synonym: P. hydropathica), P. megakarya, P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. ×multiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated multigene phylogeny and molecular toolbox with seven genes (ITS rDNA, β-tub, COI, EF1α, HSP90, L10, and YPT1) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 species, are associated with the "IDphy: molecular and morphological identification of Phytophthora based on the types" online resource (https://idtools.org/tools/1056/index.cfm). The first version of the IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic molecular toolbox with seven genes that includes the two metabarcoding genes (ITS and COI) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora, widely considered one of the most important genera of plant pathogens. Taxonomic novelties: New species: Phytophthora cajani K.S. Amin, Baldev & F.J. Williams ex Abad, Phytophthora honggalleglyana Abad, Phytophthora megakarya Brasier & M.J. Griffin ex Abad, Phytophthora pisi Heyman ex Abad, Phytophthora pseudopolonica W.W. Li, W.X. Huai & W.X. Zhao ex Abad & Kasiborski; New combinations: Phytophthora ×multiformis (Brasier & S.A. Kirk) Abad, Phytophthora uniformis (Brasier & S.A. Kirk) Abad; Epitypifications (basionyms): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora inundata Brasier et al., Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Lectotypifications (basionym): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Neotypifications (basionym): Phloeophthora syringae Kleb., Phytophthora meadii McRae Citation: Abad ZG, Burgess TI, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl JC, Verkleij G, Broders K, Schena L, Redford AJ (2023). Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology 106: 259-348. doi: 10.3114/sim.2023.106.05.}, } @article {pmid38289357, year = {2024}, author = {Horstmann, M and Quarles, CD and Happel, S and Sperling, M and Faust, A and Rahbar, K and Clases, D and Karst, U}, title = {Quantification of [[99]Tc]TcO4[-] in urine by means of anion-exchange chromatography-aerosol desolvation nebulization-inductively coupled plasma-mass spectrometry.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, pmid = {38289357}, issn = {1618-2650}, support = {CRC 1450 - 431460824//Deutsche Forschungsgemeinschaft/ ; }, abstract = {To sensitively determine [99]Tc, a new method for internal quantification of its most common and stable species, [[99]Tc]Tc[Formula: see text], was developed. Anion-exchange chromatography (IC) was coupled to inductively coupled plasma-mass spectrometry (ICP-MS) and equipped with an aerosol desolvation system to provide enhanced detection power. Due to a lack of commercial Tc standards, an isotope dilution-like approach using a Ru spike and called isobaric dilution analysis (IBDA) was used for internal quantification of [99]Tc. This approach required knowledge of the sensitivities of [99]Ru and [99]Tc in ICP-MS. The latter was determined using an in-house prepared standard manufactured from decayed medical [99m]Tc-generator eluates. This standard was cleaned and preconcentrated using extraction chromatography with TEVA resin and quantified via total reflection X-ray fluorescence (TXRF) analysis. IC coupled to ICP-MS enabled to separate, detect and quantify [[99]Tc]Tc[Formula: see text] as most stable Tc species in complex environments, which was demonstrated in a proof of concept. We quantified this species in untreated and undiluted raw urine collected from a patient, who previously underwent scintigraphy with a [99m]Tc-tracer, and determined a concentration of 19.6 ± 0.5 ng L[-1]. The developed method has a high utility to characterize a range of Tc-based radiopharmaceuticals, to determine concentrations, purity, and degradation products in complex samples without the need to assess activity parameters of [99(m)]Tc.}, } @article {pmid38287267, year = {2024}, author = {Angeler, DG and Fried-Petersen, HB}, title = {Parallels of quantum superposition in ecological models: from counterintuitive patterns to eco-evolutionary interpretations of cryptic species.}, journal = {BMC ecology and evolution}, volume = {24}, number = {1}, pages = {15}, pmid = {38287267}, issn = {2730-7182}, abstract = {BACKGROUND: Superposition, i.e. the ability of a particle (electron, photon) to occur in different states or positions simultaneously, is a hallmark in the subatomic world of quantum mechanics. Although counterintuitive at first sight, the quantum world has potential to inform macro-systems of people and nature. Using time series and spatial analysis of bird, phytoplankton and benthic invertebrate communities, this paper shows that superposition can occur analogously in redundancy analysis (RDA) frequently used by ecologists.

RESULTS: We show that within individual ecosystems single species can be associated simultaneously with different orthogonal axes in RDA models, which suggests that they operate in more than one niche spaces. We discuss this counterintuitive result in relation to the statistical and mathematical features of RDA and the recognized limitations with current traditional species concepts based on vegetative morphology.

CONCLUSION: We suggest that such "quantum weirdness" in the models is reconcilable with classical ecosystems logic when the focus of research shifts from morphological species to cryptic species that consist of genetically and ecologically differentiated subpopulations. We support our argument with theoretical discussions of eco-evolutionary interpretations that should become testable once suitable data are available.}, } @article {pmid38273563, year = {2024}, author = {Saccò, M and Mammola, S and Altermatt, F and Alther, R and Bolpagni, R and Brancelj, A and Brankovits, D and Fišer, C and Gerovasileiou, V and Griebler, C and Guareschi, S and Hose, GC and Korbel, K and Lictevout, E and Malard, F and Martínez, A and Niemiller, ML and Robertson, A and Tanalgo, KC and Bichuette, ME and Borko, Š and Brad, T and Campbell, MA and Cardoso, P and Celico, F and Cooper, SJB and Culver, D and Di Lorenzo, T and Galassi, DMP and Guzik, MT and Hartland, A and Humphreys, WF and Ferreira, RL and Lunghi, E and Nizzoli, D and Perina, G and Raghavan, R and Richards, Z and Reboleira, ASPS and Rohde, MM and Fernández, DS and Schmidt, SI and van der Heyde, M and Weaver, L and White, NE and Zagmajster, M and Hogg, I and Ruhi, A and Gagnon, MM and Allentoft, ME and Reinecke, R}, title = {Groundwater is a hidden global keystone ecosystem.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17066}, doi = {10.1111/gcb.17066}, pmid = {38273563}, issn = {1365-2486}, support = {GA N°101052342//Biodiversa+/ ; //School of Molecular and Life Sciences, Curtin University/ ; }, abstract = {Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.}, } @article {pmid38263700, year = {2024}, author = {Cheng, R and Luo, A and Orr, M and Ge, D and Hou, Z and Qu, Y and Guo, B and Zhang, F and Sha, Z and Zhao, Z and Wang, M and Shi, X and Han, H and Zhou, Q and Li, Y and Liu, X and Shao, C and Zhang, A and Zhou, X and Zhu, C}, title = {Cryptic diversity begets challenges and opportunities in biodiversity research.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12809}, pmid = {38263700}, issn = {1749-4877}, support = {NGSB20211405//Ningxia Hui Autonomous Region Agricultural Science and Technology Independent Innovation Fund/ ; 2008DP173354//Key Laboratory of the Zoological Systematics and Evolution of the Chinese Academy of Sciences/ ; ZL202203601//Survey of Wildlife Resources in Key Areas of Tibet/ ; }, abstract = {How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.}, } @article {pmid38261918, year = {2024}, author = {Godarzi, B and Chandler, F and van der Linden, A and Sikkema, RS and de Bruin, E and Veldhuizen, E and van Amerongen, A and Gröne, A}, title = {A species-independent lateral flow microarray immunoassay to detect WNV and USUV NS1-specific antibodies in serum.}, journal = {One health (Amsterdam, Netherlands)}, volume = {18}, number = {}, pages = {100668}, doi = {10.1016/j.onehlt.2023.100668}, pmid = {38261918}, issn = {2352-7714}, abstract = {Arboviruses such as West Nile Virus (WNV) and Usutu Virus (USUV) are emerging pathogens that circulate between mosquitoes and birds, occasionally spilling over into humans and horses. Current serological screening methods require access to a well-equipped laboratory and are not currently available for on-site analysis. As a proof of concept, we propose here a species-independent lateral flow microarray immunoassay (LMIA) able to quickly detect and distinguish between WNV Non-Structural 1 (NS1) and USUV NS1-specific antibodies. A double antigen approach was used to test sera collected from humans, horses, European jackdaws (Corvus monedula), and common blackbirds (Turdus merula). Optimization of the concentration of capture antigen spotted on the LMIA membrane and the amount of detection antigen conjugated to detector particles indicated that maximizing both parameters increased assay sensitivity. Upon screening of a larger serum panel, the optimized LMIA showed significantly higher spot intensity for a homologous binding event. Using a Receiver Operating Characteristics (ROC) curve, WNV NS1 LMIA results in humans, horses, and C. monedula showed good correlation when compared to "gold standard" WNV FRNT90. The most optimal derived sensitivity and specificity of the WNV NS1 LMIA relative to corresponding WNV FRNT90-confirmed sera were determined to be 96% and 86%, respectively. While further optimization is required, this study demonstrates the feasibility of developing a species-independent LMIA for on-site analysis of WNV, USUV, and other arboviruses. Such a tool would be useful for the on-site screening and monitoring of relevant species in more remote or low-income regions.}, } @article {pmid38234382, year = {2022}, author = {Reschke, K and Morozova, OV and Dima, B and Cooper, JA and Corriol, G and Biketova, AY and Piepenbring, M and Noordeloos, ME}, title = {Phylogeny, taxonomy, and character evolution in Entoloma subgenus Nolanea.}, journal = {Persoonia}, volume = {49}, number = {}, pages = {136-170}, pmid = {38234382}, issn = {0031-5850}, abstract = {Nolanea is a well-known and long-established subgenus of the genus Entoloma traditionally defined mainly by the mycenoid basidiocarps of the included species. Until now, revisions of this subgenus including molecular data exist only on a regional scale. In this study, the phylogeny of species of Nolanea is analysed based on multi-gene DNA sequences including data of specimens from all continents. New primers are designed for the mitochondrial small subunit and RPB2. The performance of the DNA loci in reconstructing the phylogeny in subg. Nolanea is evaluated. An ancestral state reconstruction is used to infer the character state evolution as well as the importance and reliability of morphological characters used to define subclades below subgeneric rank. Based on the results, seven sections are recognised in Nolanea: the sections Holoconiota, Infularia, Mammosa, Nolanea, Papillata, Staurospora, and the newly described sect. Elegantissima. A large phylogeny based on the fungal barcode rDNA ITS with numerous type sequences is used to evaluate current species concepts. Several names are revealed to be synonyms of older names. Four species new to science are described, namely E. altaicum, E. argillaceum, E. cornicolor, and E. incognitum. Lectotypes, epitypes or neotypes are designated for E. cetratum, E. clandestinum, E. conferendum, E. cuspidiferum, E. hebes, E. minutum, E. nitens, and E. rhodocylix. The re-evaluation of the limits of subg. Nolanea leads to an altered concept excluding species with distinct, lageniform cheilocystidia. The section Ameides is placed in subg. Leptonia. For several species formerly accommodated in Nolanea, but excluded now, viz., E. lepiotoides, E. rhombisporum, E. subelegans, and E. velenovskyi the taxonomic position remains unclear, because of the yet unresolved phylogeny of the whole genus Entoloma. Citation: Reschke K, Morozova OV, Dima B, et al. 2022. Phylogeny, taxonomy, and character evolution in Entoloma subgenus Nolanea. Persoonia 49: 136-170. https://doi.org/10.3767/persoonia.2022.49.04.}, } @article {pmid38230379, year = {2024}, author = {Miller, KB and Michat, MC and Ferreira, N}, title = {Reclassification of Cybistrinae Sharp, 1880 in the Neotropical Region (Coleoptera, Adephaga, Dytiscidae), with description of new taxa.}, journal = {ZooKeys}, volume = {1188}, number = {}, pages = {125-168}, pmid = {38230379}, issn = {1313-2989}, abstract = {The classification of the Neotropical Cybistrinae Sharp, 1880 (Coleoptera: Adephaga: Dytiscidae) is extensively revised based on a phylogenetic analysis of morphological features of the group. A new genus, Nilssondytesgen. nov. is described for a unique new species, Nilssondytesdiversussp. nov. from Venezuela. The New World genus, Megadytes Sharp, 1882, with several subgenera, was found to not be monophyletic. The type species of Megadytes, Dytiscuslatus Fabricius, 1801 and the species Cybisterparvus Trémouilles, 1984 were found to be monophyletic together, and phylogenetically more closely related to Cybister Curtis, 1827 than to other species assigned to Megadytes sensu stricto, which were found to also be monophyletic. The name Megadytes is here restricted to include only Megadyteslatus and Megadytesparvus. These two species assigned to this newly restricted genus concept are reviewed and diagnosed. A new genus, Metaxydytesgen. nov., is erected to include all the other species currently assigned to Megadytes sensu stricto. The current subgenus names assigned to Megadytes, Bifurcitus Brinck, 1945, Paramegadytes Trémouilles & Bachmann, 1980, and Trifurcitus Brinck, 1945, are elevated to genus rank since they are variously paraphyletic. The two species assigned to Cybister (Neocybister) Miller, Bergsten & Whiting, 2007, Cybister (Neocybister) festae Griffini, 1895, and Cybister (Neocybister) puncticollis (Brullé, 1837) re reviewed and diagnosed with the former redescribed and its type specimens considered for the first time since its description. Another evidently new species and possible new genus, Megadytes species, IR57 (Ribera et al. 2008), from Peru, is also characterized, but not formally treated because of lack of important data for the single, partial specimen. Diagnostic features are illustrated for the entire group.}, } @article {pmid38221381, year = {2023}, author = {Hilburn, BG and Janosik, AM and Johnston, CE}, title = {Incipient speciation in allopatric Etheostoma rupestre (Percidae: Etheostomatinae) lineages, with the description of three new subspecies.}, journal = {Zootaxa}, volume = {5343}, number = {2}, pages = {151-172}, doi = {10.11646/zootaxa.5343.2.3}, pmid = {38221381}, issn = {1175-5334}, abstract = {In recent years, new species descriptions for the North American darters have proliferated. Most species concepts accepted by contemporary ichthyologists require that a valid species be both monophyletic and diagnoseable, yet many lineages exhibit modal or range differences in morphological characteristics without individuals being diagnosable. Such scenarios present difficulties with regards to proper taxonomic recognition of divergent lineages and often prohibit appropriate conservation action. Following the example of recent authors, we provide meristic, geometric morphometric, and pigmentation data to support the recognition of three subspecies of Etheostoma rupestre, a species endemic to the Mobile Basin. These morphological data cohere with previous genetic work for E. rupestre. The nominate subspecies Etheostoma rupetsre rupestre (Tsais Rock Darter) is endemic to the Tombigbee River and Black Warrior River watersheds in Alabama and Mississippi and is characterized by having lower numbers of lateral blotches, lower range and mean of lateral line scales, lower modal number of scales above the lateral line, and lower degrees of nape squamation than other subspecies. Etheostoma rupestre piersoni (Shamrock Darter), ssp. nov., is endemic to the Cahaba and Alabama River Watersheds in Alabama and is characterized by intermediate counts of lateral blotches and higher scale counts and nape squamation than E. r. rupestre. Etheostoma rupestre uphapeense (Jade Darter), ssp. nov., is restricted to several small, disjunct populations in the Coosa and Tallapoosa watersheds in Alabama, Georgia, and Tennessee. Etheostoma r. uphapeense is characterized by having a higher mean number of lateral blotches than both other subspecies and higher scale counts than E. r. rupestre. While E. r. rupestre and E. r. piersoni are widespread and abundant within their respective ranges, E. r. uphapeense has a disjunct range and is often uncommon where it occurs. Etheostoma r. uphapeense should be monitored where it occurs to discern population trends.}, } @article {pmid38221354, year = {2023}, author = {Hoare, RJB and Patrick, BH and Buckley, TR and Brav-Cubitt, T}, title = {Wing pattern variation and DNA barcodes defy taxonomic splitting in the New Zealand Pimelea Looper Notoreas perornata (Walker) (Lepidoptera: Geometridae: Larentiinae): the importance of populations as conservation units.}, journal = {Zootaxa}, volume = {5346}, number = {1}, pages = {1-27}, doi = {10.11646/zootaxa.5346.1.1}, pmid = {38221354}, issn = {1175-5334}, abstract = {The endemic Notoreas perornata (Walker, 1863) complex (Lepidoptera: Geometridae: Larentiinae) from the North Island and northern South Island of New Zealand is reviewed. Larvae feed on Pimelea spp. (Thymelaeaceae), frequently in highly fragmented and threatened shrubland habitats. Allopatric populations tend to differ in size and wing pattern characteristics, but not in genitalia; moreover extensive variation renders recognition of subspecies / allopatric species based on any species concept problematic. A mitochondrial DNA gene tree is not congruent with morphology and indicates rapid recent divergence that has not settled into diagnosable lineages. Based on our results, we synonymise Notoreas simplex Hudson, 1898 with N. perornata (Walker, 1863), and retain N. perornata as a single, highly diverse but monotypic species. All known populations are illustrated to display variation. For conservation purposes, we recommend the continued recognition within the species of 10 populations or groups of populations that appear to be on the way to diverging at subspecific level based on morphological and/or DNA data. The conservation status of all these populations is reviewed. One conservation unit, comprising the populations from Westland, has not been seen since 1998 and is feared possibly extinct.}, } @article {pmid38217397, year = {2024}, author = {Martin, JM and Leece, AB and Baker, SE and Herries, AIR and Strait, DS}, title = {A lineage perspective on hominin taxonomy and evolution.}, journal = {Evolutionary anthropology}, volume = {}, number = {}, pages = {e22018}, doi = {10.1002/evan.22018}, pmid = {38217397}, issn = {1520-6505}, support = {DFG FOR 2237//Deutsche Forschungsgemeinschaft/ ; Discovery Grant DP170100056//Australian Research Council/ ; }, abstract = {An uncritical reliance on the phylogenetic species concept has led paleoanthropologists to become increasingly typological in their delimitation of new species in the hominin fossil record. As a practical matter, this approach identifies species as diagnosably distinct groups of fossils that share a unique suite of morphological characters but, ontologically, a species is a metapopulation lineage segment that extends from initial divergence to eventual extinction or subsequent speciation. Working from first principles of species concept theory, it is clear that a reliance on morphological diagnosabilty will systematically overestimate species diversity in the fossil record; because morphology can evolve within a lineage segment, it follows that early and late populations of the same species can be diagnosably distinct from each other. We suggest that a combination of morphology and chronology provides a more robust test of the single-species null hypothesis than morphology alone.}, } @article {pmid38202336, year = {2023}, author = {Cai, ZY and Xia, NH}, title = {A Novel Elucidation for Synflorescences of Chinese Bamboos.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {38202336}, issn = {2223-7747}, support = {31670196//National Natural Science Foundation of China/ ; 32270227//National Natural Science Foundation of China/ ; }, abstract = {The objective of this work is to elucidate the flowering structures of Chinese bamboos applying the synflorescence concept. To keep in line with grasses, the bamboo synflorescence is defined as a whole culm or a whole branch terminating in an inflorescence. For the first time, the repetitive and fundamental unit of bamboo synflorescences is clearly identified and termed as the "basic flowering branch". The basic flowering branch could be considered as the most simplified synflorescence for a bamboo species. Applying the synflorescence concept, the pseudospikelet is interpreted as a sort of basic flowering branch rather than a spikelet. Consequently, the synflorescence development pattern is consistent throughout the whole family. This study also marks the first recognition of both pseudospikelets and true spikelet flowering branches within the same bamboo synflorescence, which is observed in the genera Brachystachyum, Semiarundinaria and Menstruocalamus.}, } @article {pmid38191639, year = {2024}, author = {Torresani, M and Rocchini, D and Ceola, G and de Vries, JPR and Feilhauer, H and Moudrý, V and Bartholomeus, H and Perrone, M and Anderle, M and Gamper, HA and Chieffallo, L and Guatelli, E and Gatti, RC and Kleijn, D}, title = {Grassland vertical height heterogeneity predicts flower and bee diversity: an UAV photogrammetric approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {809}, pmid = {38191639}, issn = {2045-2322}, support = {862480//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; 862480//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; 862480//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; 862480//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; }, abstract = {The ecosystem services offered by pollinators are vital for supporting agriculture and ecosystem functioning, with bees standing out as especially valuable contributors among these insects. Threats such as habitat fragmentation, intensive agriculture, and climate change are contributing to the decline of natural bee populations. Remote sensing could be a useful tool to identify sites of high diversity before investing into more expensive field survey. In this study, the ability of Unoccupied Aerial Vehicles (UAV) images to estimate biodiversity at a local scale has been assessed while testing the concept of the Height Variation Hypothesis (HVH). This hypothesis states that the higher the vegetation height heterogeneity (HH) measured by remote sensing information, the higher the vegetation vertical complexity and the associated species diversity. In this study, the concept has been further developed to understand if vegetation HH can also be considered a proxy for bee diversity and abundance. We tested this approach in 30 grasslands in the South of the Netherlands, where an intensive field data campaign (collection of flower and bee diversity and abundance) was carried out in 2021, along with a UAV campaign (collection of true color-RGB-images at high spatial resolution). Canopy Height Models (CHM) of the grasslands were derived using the photogrammetry technique "Structure from Motion" (SfM) with horizontal resolution (spatial) of 10 cm, 25 cm, and 50 cm. The accuracy of the CHM derived from UAV photogrammetry was assessed by comparing them through linear regression against local CHM LiDAR (Light Detection and Ranging) data derived from an Airborne Laser Scanner campaign completed in 2020/2021, yielding an [Formula: see text] of 0.71. Subsequently, the HH assessed on the CHMs at the three spatial resolutions, using four different heterogeneity indices (Rao's Q, Coefficient of Variation, Berger-Parker index, and Simpson's D index), was correlated with the ground-based flower and bee diversity and bee abundance data. The Rao's Q index was the most effective heterogeneity index, reaching high correlations with the ground-based data (0.44 for flower diversity, 0.47 for bee diversity, and 0.34 for bee abundance). Interestingly, the correlations were not significantly influenced by the spatial resolution of the CHM derived from UAV photogrammetry. Our results suggest that vegetation height heterogeneity can be used as a proxy for large-scale, standardized, and cost-effective inference of flower diversity and habitat quality for bees.}, } @article {pmid38162573, year = {2023}, author = {Cook, CN and Redford, KH and Schwartz, MW}, title = {Species conservation in the era of genomic science.}, journal = {Bioscience}, volume = {73}, number = {12}, pages = {885-890}, doi = {10.1093/biosci/biad098}, pmid = {38162573}, issn = {0006-3568}, abstract = {The exponential increase in the availability of genomic data, derived from sequencing thousands of loci or whole genomes, provides exciting new insights into the diversity of life. However, it can also challenge established species concepts and existing management regimes derived from these concepts. Genomic data can help inform decisions about how to manage genetic diversity, but policies that protect identified taxonomic entities can generate conflicting recommendations that create challenges for practitioners. We outline three dimensions of management concern that arise when facing new and potentially conflicting interpretations of genomic data: defining conservation entities, deciding how to manage diversity, and evaluating the risks and benefits of management actions. We highlight the often-underappreciated role of values in influencing management choices made by individuals, scientists, practitioners, the public, and other stakeholders. Such values influence choices through mechanisms such as the Rashomon effect, whereby management decisions are complicated by conflicting perceptions of the causes and consequences of the conservation problem. To illustrate how this might operate, we offer a hypothetical example of this effect for the interpretation of genomic data and its implications for conservation management. Such value-based decisions can be challenged by the rigidity of existing management regimes, making it difficult to achieve the necessary flexibility to match the changing biological understanding. We finish by recommending that both conservation geneticists and practitioners reflect on their respective values, responsibilities, and roles in building a more robust system of species management. This includes embracing the inclusion of stakeholders in decision-making because, as in many cases, there are not objectively defensible right or wrong decisions.}, } @article {pmid38152478, year = {2023}, author = {Noble, PJ and Seitz, C and Lee, SS and Manoylov, KM and Chandra, S}, title = {Characterization of algal community composition and structure from the nearshore environment, Lake Tahoe (United States).}, journal = {Frontiers in ecology and evolution}, volume = {10}, number = {}, pages = {1-16}, doi = {10.3389/fevo.2022.1053499}, pmid = {38152478}, issn = {2296-701X}, abstract = {Periphyton assemblages from the nearshore environment of the west (California) side of Lake Tahoe, were analyzed to determine their taxonomic composition and community structure across habitats and seasons. Lake Tahoe is the second deepest lake in the US and an iconic oligotrophic subalpine lake with remarkable transparency. It has experienced offshore cultural eutrophication since the 1960s with observations of nuisance nearshore algal growth since the mid 2000s attributed to anthropogenic stressors. Samplings from November 2019-September 2020 provide useful snapshots against which older monitoring may be contextualized. A voucher flora, complete with descriptions, photo-documentation and referencing to species concepts employed, was created as a method of providing reproducible identification and enumeration of algal species, and more seamless reconciliation of detailed taxonomic data with future monitoring projects. The eulittoral zone (0-2 m) is seasonally dominated by elongate araphid (Synedra, Ulnaria) and stalked or entubed diatoms (Gomphonema, Cymbella, Encyonema). The sublittoral zone (>2 m) is dominated by a nitrogen-fixing Epithemia-cyanobacteria assemblage with less seasonal changes in dominance and composition that expanded to impinge on the 2 m depths of the eulittoral zone in the Fall. Sublittoral epipsammic samples, despite their proximity to rocks, had a very distinct diatom composition and high species dominance, similar to what was seen in the Fall eulittoral samples, with high numbers of Staurosirella chains and small biraphid diatoms. The deeper samples at 30 and 50 m contained high numbers of live Epithemia, and indicate a thriving sublittoral assemblage at these greater depths, but with less biomass. The 2019-20 data show many of the same diatom taxa observed in the 1970's and 1980's but with changes in species dominance. Notably, there was less of the green alga Mougeotia, when compared to the 1970's data, and a higher dominance by nitrogen fixing Epithemia in the sublittoral zone, persisting year-round. These new data show roughly double the algal species biodiversity that had been documented previously in the Lake Tahoe nearshore, and is largely attributed to the methods employed. Adopting these new methods in future monitoring efforts should improve harmonization of taxonomic data and help advance our knowledge of the contributions to nearshore cultural eutrophication.}, } @article {pmid38127644, year = {2023}, author = {Harrington, TC and Ferreira, MA and Somasekhara, YM and Vickery, J and Mayers, CG}, title = {An expanded concept of Ceratocystis manginecans and five new species in the Latin American Clade of Ceratocystis.}, journal = {Mycologia}, volume = {}, number = {}, pages = {1-29}, doi = {10.1080/00275514.2023.2284070}, pmid = {38127644}, issn = {1557-2536}, abstract = {The genus Ceratocystis contains a number of emerging plant pathogens, mostly members of the Latin American Clade (LAC), in which there are several unresolved taxonomic controversies. Among the most important are Brazilian pathogens in the C. fimbriata complex, C. manginecans and C. eucalypticola. Representatives of C. manginecans and C. eucalypticola from India and China, respectively, were shown to be fully interfertile in laboratory matings, and hybrids between the putative species were identified on Punica in India. An Indian tester strain was sexually compatible with representatives of what has been considered C. fimbriata on numerous hosts across Brazil. In this revision of the LAC, the name C. fimbriata is restricted to the widely dispersed Ipomoea strain, and C. manginecans is recognized as a Brazilian species that is important on Mangifera, Eucalyptus, and many other crops. C. mangivora and C. mangicola are also considered synonyms of C. manginecans. Based on phylogenetics and mating studies, two other Brazilian species are recognized: C. atlantica, sp. nov., and C. alfenasii, sp. nov., each with wide host ranges. Three new Caribbean species are recognized based on phylogenetics and earlier inoculation studies: C. costaricensis, sp. nov., on Coffea, C. cubensis, sp. nov., on Spathodea, and C. xanthosomatis, sp. nov., on the vegetatively propagated aroids Xanthosoma and Syngonium. Some of the other Ceratocystis species were based primarily on unique internal transcribed spacer (ITS) rDNA sequences, but the unreliability of rDNA sequences was demonstrated when intraspecific crossing of isolates with differing ITS sequences generated single-ascospore progeny with intragenomic variation in ITS sequences and others with new ITS sequences. Species recognition in Ceratocystis should use phenotype, including intersterility tests, to help identify which lineages are species. Although some species remain under-studied, we recognize 16 species in the LAC, all believed to be native to Latin America, the Caribbean region, or eastern USA.}, } @article {pmid38104322, year = {2023}, author = {Rodriguez Gutierrez, G and Ortiz Perez, A and Palzer, S}, title = {Integrated, Selective, Simultaneous Multigas Sensing Based on Nondispersive Infrared Spectroscopy-Type Photoacoustic Spectroscopy.}, journal = {ACS sensors}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssensors.3c01285}, pmid = {38104322}, issn = {2379-3694}, abstract = {Most chemical sensing scenarios require the selective and simultaneous determination of the concentrations of multiple gas species. In order to enable large-scale monitoring, reliability, robustness, and the potential for integration and miniaturization are key parameters that next-generation sensing technologies must comply with. Due to their superior sensitivity and selectivity as compared to standard NDIR-type systems, photoacoustic NDIR-approaches offer a means for selective detection at much reduced system dimensions such that microintegration becomes feasible. This contribution presents an acoustic frequency multiplexing method to integrate sensing capabilities for the parallel analysis of multiple gases in a single device without loss in selectivity via sound frequency separation. The approach is demonstrated using mid-infrared light emitting diodes and a multigas photoacoustic detector to monitor some of the most important greenhouse gases: carbon dioxide and methane. The number of gas species the sensor concept is able to detect simultaneously can be expanded without increasing the size of the system or its complexity. Additionally, the results demonstrate that the integrated device features the same selectivity and sensitivity as the currently used single gas photoacoustic NDIR systems. Furthermore, the possibility of an extension to any number of gas species is argued.}, } @article {pmid38096265, year = {2023}, author = {Zhu, LR and Wang, ZY and Luo, JJ and Zheng, YJ and Zou, HL and Luo, HQ and Zhao, LB and Li, NB and Li, BL}, title = {Mercury-Mediated Epitaxial Accumulation of Au Atoms for Stained Hydrogel-Improved On-Site Mercury Monitoring.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.3c04338}, pmid = {38096265}, issn = {1520-6882}, abstract = {Trivalent Au ions are easily reduced to be zerovalent atoms by coexisting reductant reagents, resulting in the subsequent accumulation of Au atoms and formation of plasmonic nanostructures. In the absence of stabilizers or presence of weak stabilizers, aggregative growth of Au nanoparticles (NPs) always occurs, and unregular multidimensional Au materials are consequently constructed. Herein, the addition of nanomole-level mercury ions can efficiently prevent the epitaxial accumulation of Au atoms, and separated Au NPs with mediated morphologies and superior plasmonic characteristics are obtained. Experimental results and theoretical simulation demonstrate the Hg-concentration-reliant formation of plasmonic nanostructures with their mediated sizes and shapes in the presence of weak reductants. Moreover, the sensitive plasmonic responses of reaction systems exhibit selectivity comparable to that of Hg species. As a concept of proof, polymeric carbon dots (CDs) were used as the initial reductant, and the reactions between trivalent Au and CDs were studies. Significantly, Hg atoms prevent the epitaxial accumulation of Au atoms, and plasmonic NPs with decreased sizes were in situ synthesized, corresponding to varied surface plasmonic resonance absorption performance of the CD-induced hybrids. Moreover, with the integration of sensing substrates of CD-doped hydrogels, superior response stabilities, analysis selectivity, and sensitivity of Hg[2+] ions were achieved on the basis of the mercury-mediated in situ chemical reactions between trivalent Au ions and reductant CDs. Consequently, a high-performance sensing strategy with the use of Au NP-staining hydrogels (nanostaining hydrogels) was exhibited. In addition to Hg sensing, the nanostaining hydrogels facilitated by doping of emerging materials and advanced chem/biostrategies can be developed as high-performance on-site monitoring routes to various pollutant species.}, } @article {pmid38067426, year = {2023}, author = {Shentu, J and Lu, Y and Li, Y and Li, J and Mao, Y and Li, X}, title = {Compact Combustion Mechanisms of Typical n-Alkanes Developed by the Minimized Reaction Network Method.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {23}, pages = {}, doi = {10.3390/molecules28237695}, pmid = {38067426}, issn = {1420-3049}, support = {No. 91741201//National Natural Science Foundation of China/ ; }, abstract = {The existing combustion kinetic modeling method which aims at developing phenomenological combustion mechanisms characterized by multiple reactions confronts several challenges, including the conflicts between computing resources and mechanism scales during numerical simulation, etc. In order to address these issues, the minimized reaction network method for complex combustion system modeling based on the principle of simultaneous chemical equilibrium is proposed, which is aimed to develop combustion mechanisms with minimal reaction steps under a limited number of species. The concept of mechanism resolution is proposed in this method, and the reaction network with minimal reaction steps under a given mechanism resolution is constructed so that the scale of mechanisms is compressed greatly. Meanwhile, distinguishing from other mechanisms, the reversible form of elementary reactions is adopted and the classical two-parameter (A, Ea) Arrhenius equation fits the rate constants. Typical n-alkanes including n-butane, n-heptane, n-octane, n-decane, n-dodecane and n-hexadecane were taken as examples to indicate the development process of mechanisms and systematic kinetic validations were carried out. Results show that this method leads to very compact mechanisms with satisfactory accuracy, and it eliminates the process of mechanism reduction and is beneficial for mechanism optimization. This method and the derived kinetic mechanisms are hoped to contribute to combustion engineering applications.}, } @article {pmid38052444, year = {2023}, author = {Logan, RK and Vaudo, JJ and Wetherbee, BM and Shivji, MS}, title = {Seasonally mediated niche partitioning in a vertically compressed pelagic predator guild.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2012}, pages = {20232291}, doi = {10.1098/rspb.2023.2291}, pmid = {38052444}, issn = {1471-2954}, abstract = {Niche partitioning among closely related, sympatric species is a fundamental concept in ecology, and its mechanisms are of broad interest for understanding ecosystem functioning and predicting the impacts of human-driven environmental change. However, identifying mechanisms by which top marine predators partition available resources has been especially challenging given the difficulty of quantifying resource use of large pelagic animals. In the eastern tropical Pacific (ETP), three large, highly mobile and ecologically similar pelagic predators (blue marlin (Makaira nigricans), black marlin (Istiompax indica) and sailfish (Istiophorus platypterus)) coexist in a vertically compressed habitat. To evaluate each species' ecological niche, we leveraged a decade of recreational fisheries data, multi-year satellite tracking with high-resolution dive data, and stable isotope analysis. Fishery interaction and telemetry-based three-dimensional seasonal utilization distributions suggested high spatial and temporal overlap among species; however, seasonal and diel variability in diving behaviour produced spatial partitioning, leading to low trophic overlap among species. Expanding oxygen minimum zones will reduce the available vertical habitat within predator guilds, likely leading to increases in interspecific competition. Thus, understanding the mechanisms of habitat partitioning among predators in the vertically compressed ETP can provide insight into how predators in other ocean regions may respond to vertically limited habitats.}, } @article {pmid38006418, year = {2023}, author = {Li, WJ and Li, FF and Bai, J and Liang, K and Li, K and Qin, GQ and Zhang, YL and Li, XJ}, title = {Isolation and characterization of intestinal bacteria associated with cellulose degradation in grasshoppers (Orthoptera).}, journal = {Journal of insect science (Online)}, volume = {23}, number = {6}, pages = {}, doi = {10.1093/jisesa/iead101}, pmid = {38006418}, issn = {1536-2442}, support = {32070473//National Natural Science Foundation of China/ ; //Hebei Provincial Innovation Capacity Enhancement Program-Special Project/ ; 225A2904D//High-level Talent Team Building/ ; }, abstract = {Insect gut bacteria play an essential role in the nutritional metabolism, growth, and development of insects. Grasshoppers (Orthoptera) are cellulose-rich plant-feeding pests. Although the biological potential of grasshopper gut microorganisms to assist cellulose decomposition is well established, microbial resources for efficient degradation of cellulose biomass are still scarce and need to be developed. In this study, we used selective media to isolate cellulose-degrading bacteria from the intestines of Atractomorpha sinensis, Trilophidia annulata, Sphingonotus mongolicus, and Calliptamus abbreviatus. Phylogenetic analysis based on the maximum likelihood method using 16S rDNA sequencing sequences to identify bacteria revealed the isolation of 11 strains belonging to 3 genera, including Klebsiella, Aeromonas, and Bacillus. The degradability of the isolates to cellulose was then determined by the DNS colorimetric method, and the results showed that Bacillus had the highest degradation rate. The elucidation of microbial cellulose degradation capacity in grasshoppers not only contributes to the understanding of multiple plant-insect-microbe interactions, but also provides a valuable microbial resource for solving the biomass conversion of cellulose species problem.}, } @article {pmid37988674, year = {2023}, author = {Kuang, X and Liu, Y and Luo, H and Li, Q and Wu, F and Fan, C and Liu, J}, title = {Triggerable Prodrug Nanocoating Enables On-Demand Activation of Microbial and Small-Molecular Therapeutics for Combination Treatment.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.3c10015}, pmid = {37988674}, issn = {1520-5126}, abstract = {The synergy of living microbial and small-molecular therapeutics has been widely explored for treating a variety of diseases, while current combination strategies often suffer from low bioavailability, heterogeneous spatiotemporal distribution, and premature drug release. Here, the use of a triggerable prodrug nanocoating is reported to enable the on-demand activation of microbial and small-molecular therapeutics for combination treatment. As a proof-of-concept study, a reactive oxygen species-responsive aromatic thioacetal linker is employed to prepare cationic chitosan-drug conjugates, which can form a nanocoating on the surface of living bacteria via electrostatic interaction. Following administration, the wrapped bacteria can be prevented from in vivo insults by the shielding effect of the nanocoating and be co-delivered with the conjugated drug in a spatiotemporally synchronous manner. Upon reaching the lesion site, the upgraded reactive oxygen species trigger in situ cleavage of the thioacetal linker, resulting in the release of the conjugated drug and a linker-derived therapeutic cinnamaldehyde. Meanwhile, a charge reversal achieved by the generation of negatively charged thiolated chitosan induces the dissociation of the nanocoating, leading to synchronous release of the living bacteria. The adequate activation of the combined therapeutics at the lesion site exhibits superior synergistic treatment efficacy, as demonstrated by an in vivo assessment using a mouse model of colitis. This work presents an appealing approach to combine living microbial and small-molecular therapeutics for advanced therapy of diseases.}, } @article {pmid37983640, year = {2023}, author = {Wang, MZ and Wu, J and Zhang, SL and Mao, LM and Ohi-Toma, T and Takano, A and Zhang, YH and Cameron, KM and Li, P}, title = {Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/cla.12565}, pmid = {37983640}, issn = {1096-0031}, support = {31970225//National Natural Science Foundation of China/ ; }, abstract = {Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as "East Asian tulips" has a number of cryptic species and a huge genome size (1C = 21.48-57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within Amana are challenging. Here we included all species and 84 populations of Amana, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in Amana. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA-BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, Amana polymorpha, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.}, } @article {pmid37961924, year = {2023}, author = {Karnbrock, SBH and Alcarazo, M}, title = {Cooperation between p-Block Elements and Redox-Active Ligands: Stoichiometric and Catalytic Transformations.}, journal = {Chemistry (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e202302879}, doi = {10.1002/chem.202302879}, pmid = {37961924}, issn = {1521-3765}, abstract = {The relevance acquired by redox-active ligands in modern catalysis stems from their facile delivery and acceptance of electrons, either to the metal they coordinate or directly to an incoming substrate that also binds the central metal. Doing that, they generate coordinated radicals and provide access to more than one spin state during the catalytic cycle. As consequence, the new reaction barriers get reduced when compared to similar processes that are restricted to a single spin surface. The principles that govern this genuine approach to catalyst design are well-established, and their implementation has allowed the development of synthetically useful catalytic transformations; however, the extension of the concept to species in which p-block elements take the role of central atoms remains largely underdeveloped. Through the discussion of the key achievements and recent progress, this Concept Article highlights this original approach to design (organo)catalysts, discloses the progress achieved, and also reveals the many shortcomings still existing in the field.}, } @article {pmid37960608, year = {2023}, author = {Pezoa, JE and Ramírez, DA and Godoy, CA and Saavedra, MF and Restrepo, SE and Coelho-Caro, PA and Flores, CA and Pérez, FG and Torres, SN and Urbina, MA}, title = {A Spatial-Spectral Classification Method Based on Deep Learning for Controlling Pelagic Fish Landings in Chile.}, journal = {Sensors (Basel, Switzerland)}, volume = {23}, number = {21}, pages = {}, doi = {10.3390/s23218909}, pmid = {37960608}, issn = {1424-8220}, support = {ANID FONDEF IDeA IT20i0032//Agencia Nacional de Investigación y Desarrollo/ ; ANID ANILLO ACT210073//Agencia Nacional de Investigación y Desarrollo/ ; ANID FONDECYT Iniciación 11221231//Agencia Nacional de Investigación y Desarrollo/ ; ANID FONDECYT Postdoctorado 3220368//Agencia Nacional de Investigación y Desarrollo/ ; ANID FONDECYT Postdoctorado 3220803//Agencia Nacional de Investigación y Desarrollo/ ; }, abstract = {Fishing has provided mankind with a protein-rich source of food and labor, allowing for the development of an important industry, which has led to the overexploitation of most targeted fish species. The sustainable management of these natural resources requires effective control of fish landings and, therefore, an accurate calculation of fishing quotas. This work proposes a deep learning-based spatial-spectral method to classify five pelagic species of interest for the Chilean fishing industry, including the targeted Engraulis ringens, Merluccius gayi, and Strangomera bentincki and non-targeted Normanichthtys crockeri and Stromateus stellatus fish species. This proof-of-concept method is composed of two channels of a convolutional neural network (CNN) architecture that processes the Red-Green-Blue (RGB) images and the visible and near-infrared (VIS-NIR) reflectance spectra of each species. The classification results of the CNN model achieved over 94% in all performance metrics, outperforming other state-of-the-art techniques. These results support the potential use of the proposed method to automatically monitor fish landings and, therefore, ensure compliance with the established fishing quotas.}, } @article {pmid37938655, year = {2022}, author = {Ferchiou, S and Caza, F and de Boissel, PGJ and Villemur, R and St-Pierre, Y}, title = {Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {61}, pmid = {37938655}, issn = {2730-6151}, support = {RGPIN-2019-06607//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; RGPIN-2019-06607//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; RGPIN-2019-06607//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; RGPIN-2019-06607//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; }, abstract = {Liquid biopsy (LB) is a concept that is rapidly gaining ground in the biomedical field. Its concept is largely based on the detection of circulating cell-free DNA (ccfDNA) fragments that are mostly released as small fragments following cell death in various tissues. A small percentage of these fragments are from foreign (nonself) tissues or organisms. In the present work, we applied this concept to mussels, a sentinel species known for its high filtration capacity of seawater. We exploited the capacity of mussels to be used as natural filters to capture environmental DNA fragments of different origins to provide information on the biodiversity of marine coastal ecosystems. Our results showed that hemolymph of mussels contains DNA fragments that varied considerably in size, ranging from 1 to 5 kb. Shotgun sequencing revealed that a significant amount of DNA fragments had a nonself microbial origin. Among these, we found DNA fragments derived from bacteria, archaea, and viruses, including viruses known to infect a variety of hosts that commonly populate coastal marine ecosystems. Taken together, our study shows that the concept of LB applied to mussels provides a rich and yet unexplored source of knowledge regarding the microbial biodiversity of a marine coastal ecosystem.}, } @article {pmid37924375, year = {2023}, author = {Francischini, DDS and Arruda, MAZ}, title = {One-point calibration and matrix-matching concept for quantification of potentially toxic elements in wood by LA-ICP-MS.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, pmid = {37924375}, issn = {1618-2650}, support = {303231/2020-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 2014/50867-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/50085-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2018/25207-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/000//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, abstract = {The aim of this work is to evaluate two quantitative methods, based on the external calibration applied in laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analysis, known as (i) analytical curve and (ii) one-point calibration, using the concept of matrix matching to quantify three potentially toxic elements (PTEs) in wood samples. These can biologically register changes in the abiotic environment and be applied to monitoring climate change or environmental toxicity. In this case, standard sample preparation was evaluated to prepare the standard pellets using Pinus taeda species as a matrix-matching concept. Six pellets of P. taeda, with different Pb, Cd, and Ba concentrations, were prepared to build the analytical curve and one-point calibration strategies. The LA-ICP-MS parameters were optimised for [206]Pb, [208]Pb, [112]Cd, [114]Cd, [137]Ba, and [138]Ba isotope analysis in wood samples. The two calibration strategies provided 74-110% analytical recovery from certified reference materials and similar results to those obtained by ICP-MS through the acid digestion of environmental wood samples from São Paulo City (Brazil). This demonstrated the applicability of the one-point calibration strategy in quantifying PTEs in wood samples, which could be used with environmental analyses. Differences observed between the Ba isotope results obtained via LA-ICP-MS and ICP-MS quantification were related to sampling by LA-ICP-MS and the ICP-MS sample introduction, as well as to laser matrix and transport effects because of the difference between the wood species evaluated.}, } @article {pmid37915996, year = {2023}, author = {Hübner, J and Chemyreva, VG and Notton, DG}, title = {Taxonomic and nomenclatural notes on Geodiaprialongiceps Kieffer, 1911 (Hymenoptera, Diapriidae) and synonymy of the genus Geodiapria Kieffer, 1910.}, journal = {ZooKeys}, volume = {1183}, number = {}, pages = {1-11}, pmid = {37915996}, issn = {1313-2989}, abstract = {This paper reviews the status of Geodiapria and its nominotypical and only included species G.longiceps. Geodiapria was previously understood to be very similar to, and doubtfully separated from the genus Basalys. We use integrative taxonomy (morphology, DNA-barcoding, phylogenetic tree building) to show that the valid name for what was G.longiceps Kieffer, 1911 is now Basalysrufocinctus (Kiefer, 1911) and that Geodiapria is consequently a junior synonym of Basalyssyn. nov. The following taxa are new synonyms of B.rufocinctus: Loxotropalongiceps Wasmann, 1909, syn. nov., G.longiceps Kieffer, 1911, syn. nov., L.rufosignata Kieffer, 1911, syn. nov. Basalysrufocinctus is newly reported from Corsica, Germany, Norway and Spain.}, } @article {pmid37897602, year = {2024}, author = {Sakala, J}, title = {Fossil Wood Analyses: Several Examples from Five Case Studies in the Area of Central and NW Bohemia, Czech Republic.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2722}, number = {}, pages = {89-104}, pmid = {37897602}, issn = {1940-6029}, abstract = {In the area of the Central and NW Bohemia, Czech Republic, the fossil wood is quite abundant, found in different states of preservation and present from Paleozoic (Pennsylvanian), through Mesozoic (Upper Cretaceous), to Cenozoic (upper Eocene to lower Miocene). So, this small area is ideal to demonstrate various aspects of the fossil wood analyses, including anatomy (unifacial vs. bifacial cambium, formation of tyloses and its significance, early vs. late wood, unambiguity of scientific terminology, stem vs. root wood), taphonomy (completeness of fossil record, influence of environment on mode of preservation, influence of preservation on wood anatomy and preservation potential, discrepancy between the record of wood and other organs), systematics (stem vs. crown group, wide concept of fossil wood genera, "mosaic" species, wood of extinct plants), and palaeoclimatic reconstruction (definition of "wood type," subjective vs. objective methods). The majority of the studied woods were thin-sectioned following the standard techniques and observed with a compound light microscope.}, } @article {pmid37894058, year = {2023}, author = {Chen, P and Abeywickrama, PD and Ji, S and Zhou, Y and Li, X and Zhang, W and Yan, J}, title = {Molecular Identification and Pathogenicity of Diaporthe eres and D. hongkongensis (Diaporthales, Ascomycota) Associated with Cherry Trunk Diseases in China.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, doi = {10.3390/microorganisms11102400}, pmid = {37894058}, issn = {2076-2607}, support = {KJCX20210403//Beijing Academy of Agricultural and Forestry Sciences/ ; BAIC08-2023//Beijing Innovation Team of the Modern Agricultural Research System/ ; }, abstract = {This study aimed to identify fungal species associated with trunk diseases of sweet cherries (Prunus avium) in several commercial cherry orchards in Beijing, Guizhou and Shandong provinces, China. In total, eighteen fungal strains that fitted well into the species concept of Diaporthe were isolated. Based on both morphological and multi-locus phylogenetic analyses of internal transcribed spacer region (ITS), beta-tubulin (tub-2), calmodulin (Cal) and translation elongation factor 1-α (tef1-α) sequencing data, fourteen isolates were identified as Diaporthe eres, while four isolates were classified as D. hongkongensis. Here, we report D. hongkongensis causing sweet cherry branch dieback disease and, further, we confirmed the host association of D. eres with sweet cherries in China. A pathogenicity assay revealed the ability of both D. eres and D. hongkongensis to cause shoot necrosis and stem lesions on Prunus avium cv. 'Brooks' (mean lesion lengths of 1.86 cm and 1.56 cm, respectively). The optimal temperature for the growth of both Diaporthe species was tested. The optimal growth temperature for D. hongkongensis was 30 °C, and the 25-28 °C temperatures were the most favorable for the growth of D. eres strains. This research advances the understanding of fungal trunk diseases in fruit crops, particularly gummosis and branch dieback disease in Chinese cherry orchards, and will aid growers in making decisions about cultural practices and disease management.}, } @article {pmid37889725, year = {2023}, author = {Wang, Y and Shi, J and Wu, Y and Zhang, W and Yang, X and Lv, H and Xia, S and Zhao, S and Tian, J and Cui, P and Xu, J}, title = {Selection of Flagship Species and Their Use as Umbrellas in Bird Conservation: A Case Study in Lishui, Zhejiang Province, China.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/ani13111825}, pmid = {37889725}, issn = {2076-2615}, support = {HXYJCP2021110648//Project of Biodiversity Conservation in Lishui, Zhejiang Province;/ ; 2110404//Project supported by the biodiversity investigation, observation and assessment program (2019-2023) of Ministry of Ecology and Environment of China/ ; }, abstract = {The concept of flagship species is widely used in conservation biology. Flagship birds play a key role in raising conservation funds, increasing awareness of biodiversity conservation, and maintaining ecosystem services. This study selected flagship bird species in Lishui, Zhejiang Province, China, and assessed their conservation effectiveness and ability to serve as umbrella species. A regional bird survey program from 2019-2022 recorded 361 bird species in Lishui. This study constructed a framework of flagship species selection based on social, ecological, economic, and cultural criteria. The analytic hierarchy process-entropy weight method (AHP-EM) was used to rank the score of 361 bird species, and the MaxEnt model was used to analyze the suitable distribution areas of these species. Finally, 10 species, which covered the distribution sites of all 361 bird species, were selected as the flagship species of Lishui. The distribution areas covered all the nature reserves and the priority areas of biodiversity of Lishui, in which these 10 species can also serve as umbrella species to protect local biodiversity. The methodology and ideas in this study could provide insights into the application of conservation concepts at the local level, as well as suggest possible recommendations for local governments to select flagship species for conservation.}, } @article {pmid37865244, year = {2023}, author = {Chen, SP and Liu, WT and Cheng, FY and Wang, CH and Huang, SM and Wang, JL}, title = {Ozone containment through selective mitigation measures on precursors of volatile organic compounds.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {167953}, doi = {10.1016/j.scitotenv.2023.167953}, pmid = {37865244}, issn = {1879-1026}, abstract = {Abatement of volatile organic compounds (VOCs) ozone reduction is usually carried out by reducing the total amount of VOCs without considering reactivity between different species. This study incorporates the concept of maximum incremental reactivity (MIR) and speciation profiles into the industrial emission inventory of Taiwan to target organic species from industrial sources with the greatest ozone formation potentials (OFPs). These high OFP sources/species are then mitigated to assess the O3 reduction amount (ΔO3) with Community Multiscale Air Quality (CMAQ) modeling under VOC-limited conditions. The objective is to minimize the number of target sources/species and their tonnage while achieving maximum O3 reduction. This approach is referred to as the Selective Precursor Mitigation (SPM). A case study of a high ozone episode (September 4-10, 2020) was chosen for illustration, during which a relatively stagnant atmospheric condition with minimal transboundary ozone occurred. A series of scenarios to target the highest OFP chemicals/industries for mitigation are compared for the achievable max. ΔO3, areas affected (area coverage), and reduction efficiency. For instance, by reducing the ten leading industry classes with the island's highest OFPs (OFPind), up to 19 % of max. 1-h ΔO3 can be expected. If, however, the same tonnage of VOCs as that of OFPind is distributed to all industries without considering the reactivity, called the overall mitigation (OM), comparable results to those of OFPind were found, but the number of sources needed to be managed with OM would increase by nearly three times (29,662 for OM vs. 11,981 for OFPind). Further reducing the management scale by only zooming in the ten highest OFP chemicals within the ten leading OFP industries (OFPsp) would result in relatively limited area coverage. Still, major ozone hot spots could be alleviated. Although the domain is set on the island of Taiwan, the SPM approach is universally applicable to other regions worldwide to gain the maximum ozone reduction effect at a minimized societal cost.}, } @article {pmid37862543, year = {2023}, author = {Nordmann, T and Wickenhagen, S and Doležal, M and Mehlstäubler, TE}, title = {Bichromatic UV detection system for atomically-resolved imaging of ions.}, journal = {The Review of scientific instruments}, volume = {94}, number = {6}, pages = {}, doi = {10.1063/5.0145409}, pmid = {37862543}, issn = {1089-7623}, abstract = {We present a compact bichromatic imaging system, located outside of the vacuum chamber of a trapped ion apparatus that collects the fluorescence of 230.6 and 369.5 nm photons simultaneously on a shared electron-multiplying charge-coupled device (EMCCD) camera. The system contains two lens doublets, consisting of a sphere and an asphere. They provide a numerical aperture of 0.45 and 0.40 at 230.6 and 369.5 nm, respectively, and enable spatially resolved state detection with a large field of view of 300 μm for long 115In+/172Yb+ Coulomb crystals. Instead of diffraction-limited imaging for one wavelength, the focus in this system is on simultaneous single-ion resolved imaging of both species over a large field, with special attention to the deep UV wavelength (230.6 nm) and the low scattering rate of In+ ions. The introduced concept is applicable to other dual-species applications.}, } @article {pmid37849422, year = {2023}, author = {Melekhin, M and Potekhin, A and Gentekaki, E and Chantangsi, C}, title = {Paramecium (Oligohymenophorea, Ciliophora) diversity in Thailand sheds light on the genus biogeography and reveals new phylogenetic lineages.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {e13004}, doi = {10.1111/jeu.13004}, pmid = {37849422}, issn = {1550-7408}, support = {075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 122031100281-5//Zoological Institute RAS/ ; }, abstract = {Paramecium (Ciliophora, Oligohymenophorea) is a good model to study ciliate biogeography. Extensive sampling mainly in northern hemisphere has led to 16 valid morphological species description thus far. However, a majority of hard-to-reach regions, including South East Asia, are underinvestigated. Our study combined traditional morphological and molecular approaches to reveal the biodiversity of Paramecium in Thailand from more than 110 samples collected in 10 provinces. Representatives of seven morphological species were identified from our collection, including the rare species, such as P. gigas and P. jenningsi. Additionally, we detected five different sibling species of the P. aurelia complex, described a new cryptic species P. hiwatashii n. sp. phylogenetically related to P. caudatum, and discovered a potentially new genetic species of the P. bursaria species complex. We also documented a variety of bacterial cytoplasmic symbionts from at least nine monoclonal cultures of Paramecium.}, } @article {pmid37849900, year = {2020}, author = {Ibarra-Chávez, R and Haag, AF and Dorado-Morales, P and Lasa, I and Penadés, JR}, title = {Rebooting Synthetic Phage-Inducible Chromosomal Islands: One Method to Forge Them All.}, journal = {Biodesign research}, volume = {2020}, number = {}, pages = {5783064}, pmid = {37849900}, issn = {2693-1257}, abstract = {Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in Saccharomyces cerevisiae based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from Staphylococcus aureus and Escherichia coli and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.}, } @article {pmid37845589, year = {2023}, author = {Yong, RQ and Martin, SB and Smit, NJ}, title = {A new species of Siphoderina Manter, 1934 (Digenea: Cryptogonimidae) infecting the Dory Snapper Lutjanus fulviflamma (Teleostei: Lutjanidae) from the east coast of South Africa.}, journal = {Systematic parasitology}, volume = {}, number = {}, pages = {}, pmid = {37845589}, issn = {1573-5192}, abstract = {Parasitological assessment of marine fishes at Sodwana Bay in the iSimangaliso Marine Protected Area on the east coast of South Africa revealed a new species of cryptogonimid trematode infecting the pyloric caeca of the Dory Snapper, Lutjanus fulviflamma (Forsskål) (Lutjanidae). The new species is morphologically consistent with the concept of the large genus Siphoderina Manter, 1934; its phylogenetic position within this genus was validated through molecular sequencing of the ITS2 and partial 28S ribosomal DNA sub-regions. We name this species Siphoderina nana n. sp. and comment on the current state of understanding for this genus of cryptogonimids.}, } @article {pmid37843973, year = {2023}, author = {Li, F and Hou, L and Liu, W and Jin, Y and Lu, J and Li, B}, title = {Carbon Vacancy-Enhanced Activity of Fe-N-C Single Atom Catalysts toward Luminol Chemiluminescence in the Absence of H2O2.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.3c03972}, pmid = {37843973}, issn = {1520-6882}, abstract = {The classic luminol-H2O2 chemiluminescence (CL) systems suffer from easy self-decomposition of H2O2 at room temperature, hindering the practical applications of the luminol-H2O2 CL system. In this work, unexpectedly, we found that the carbon vacancy-modified Fe-N-C single atom catalysts (VC-Fe-N-C SACs) can directly trigger a luminol solution to generate strong CL emission in the absence of H2O2. The Fe-based SACs were prepared through the conventional pyrolysis of zeolitic imidazolate frameworks. The massive carbon vacancies were readily introduced into Fe-N-C SACs through a tannic acid-etching process. Carbon vacancy significantly enhanced the catalytic activity of Fe-N-C SACs on the CL reaction of luminol-dissolved oxygen. The VC-Fe-N-C SACs performed a 13.4-fold CL enhancement compared with the classic luminol-Fe[2+] system. It was found that the introduction of a carbon vacancy could efficiently promote dissolved oxygen to convert to reactive oxygen species. As a proof of concept, the developed CL system was applied to detect alkaline phosphatase with a linear range of 0.005-1 U/L as well as a detection limit of 0.003 U/L. This work demonstrated that VC-Fe-N-C SAC is a highly efficient CL catalyst that can promote the analytic application of the luminol CL system.}, } @article {pmid37836089, year = {2023}, author = {Boltenkov, EV}, title = {Resolving the Puzzle of Iris maackii (Iridaceae): A Morphological Insight into Its Taxonomy.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {19}, pages = {}, doi = {10.3390/plants12193349}, pmid = {37836089}, issn = {2223-7747}, abstract = {Since the early 20th century, Iris maackii (Iridaceae) has been considered a synonym of I. laevigata, a synonym of I. pseudacorus, or an accepted species. The current concept of I. maackii in the literature and databases is often applied to yellow-flowered plants with prominently veined rosette leaves, which are diagnostic features of I. pseudacorus growing in Northeast Asia. Therefore, the objective was to clarify the taxonomic identity of I. maackii. This study is based on a critical examination of the literature, on the observed morphological characters in the holotype of I. maackii, and on a morphological comparison of I. maackii with living plants of I. laevigata and I. pseudacorus. Additionally, a morphometric comparison of the seed characters was carried out to clarify the morphological distinction among I. maackii, I. laevigata, and I. pseudacorus. A careful study demonstrated that the rosette leaf texture and the morphology of the flowering stem, fruit, and seeds of I. maackii are identical to or within the variation range of I. laevigata. Thus, I. maackii is morphologically non-distinct from I. laevigata and should be recognized as a taxonomic synonym of the latter. An image of the holotype of I. maackii is provided along with detailed illustrations of I. laevigata and I. pseudacorus.}, } @article {pmid37818247, year = {2023}, author = {Shukla, I and Gaynor, KM and Worm, B and Darimont, CT}, title = {The diversity of animals identified as keystone species.}, journal = {Ecology and evolution}, volume = {13}, number = {10}, pages = {e10561}, pmid = {37818247}, issn = {2045-7758}, abstract = {Although the keystone species concept was conceived of over 50 years ago, contemporary efforts to synthesize related literature have been limited. Our objective was to create a list of keystone animal species identified in the literature and to examine the variation in the traits of species and the ecosystem influences they elicit. We documented 230 species considered keystones. A clustering analysis classified them into five archetypes based on combinations of their taxonomic class, body size, trophic level, and role (consumers, modifiers, or prey). Although conservation and public perception of keystones primarily focuses on large vertebrate consumers, our analysis reveals that researchers have defined a wide diversity of keystone species, with large variation in associated ecosystem processes. Future research may confront ambiguity in the definition of keystone status, as well as clarify the type, abundance, and quality of data required to assign the term. Identifying keystones with increased rigor would not only enrich the literature but also inform intervention to safeguard threatened keystones and their associated influences on ecosystems.}, } @article {pmid37799270, year = {2018}, author = {Carlisle, JD and Keinath, DA and Albeke, SE and Chalfoun, AD}, title = {Identifying Holes in the Greater Sage-Grouse Conservation Umbrella.}, journal = {The Journal of wildlife management}, volume = {82}, number = {5}, pages = {948-957}, pmid = {37799270}, issn = {0022-541X}, abstract = {The umbrella species concept, wherein multiple species are indirectly protected under the umbrella of a reserve created for one, is intended to enhance conservation efficiency. Although appealing in theory and common in practice, empirical tests of the concept have been scarce. We used a real-world, semi-protected reserve established to protect a high-profile umbrella species (greater sage-grouse [Centrocercus urophasianus]) to investigate 2 potential mechanisms underlying the concept's successful application: reserve size and species similarity. We estimated how much habitat protection the established reserve provided to 52 species of conservation concern associated with vegetation communities where greater sage-grouse occur. To illustrate the importance of reserve size, we compared the effectiveness of the established reserve to alternative greater sage-grouse reserves of various sizes and to simulated reserves of equal size but sited with no regard for greater sage-grouse. We further assessed whether key species' traits were associated with different levels of protection under the umbrella reserve. The established umbrella reserve protected 82% of the state's greater sage-grouse population and 0-63% of the habitat of the background species examined. The reserve outperformed equally sized, simulated reserves for only 12 of 52 background species. As expected, larger alternative reserves served as better umbrellas, but regardless of reserve size, not all species received equal protection. The established reserve was most effective at protecting the habitat of species that were most similar to the umbrella species (i.e., avian species, those highly associated with sagebrush plant communities, and those with widespread habitat). In contrast, the habitat of species with restricted distributions, particularly when combined with vegetation associations not closely matching the umbrella species, was not protected as well by the umbrella reserve. Such species require additional, targeted attention to achieve conservation objectives. Successful application of the umbrella species concept requires careful consideration of the characteristics of the umbrella species, the reserve delineated on its behalf, and the similarity of the umbrella species to its purported background species.}, } @article {pmid37799165, year = {2017}, author = {Carlisle, JD and Stewart, DR and Chalfoun, AD}, title = {AN INVERTEBRATE ECOSYSTEM ENGINEER UNDER THE UMBRELLA OF SAGE-GROUSE CONSERVATION.}, journal = {Western North American naturalist}, volume = {77}, number = {4}, pages = {450-463}, pmid = {37799165}, issn = {1527-0904}, abstract = {Conservation practitioners often rely on areas designed to protect species of greatest conservation priority to also conserve co-occurring species (i.e., the umbrella species concept). The extent to which vertebrate species may serve as suitable umbrellas for invertebrate species, however, has rarely been explored. Sage-grouse (Centrocercus spp.) have high conservation priority throughout much of the rangelands of western North America and are considered an umbrella species through which the conservation of entire rangeland ecosystems can be accomplished. Harvester ants are ecosystem engineers and play important roles in the maintenance and function of rangeland ecosystems. We compared indices of the abundance of western harvester ants (Pogonomyrmex occidentalis) and Greater Sage-Grouse (Centrocercus urophasianus) at 72 sites in central Wyoming, USA in 2012. The abundance of harvester ant mounds was best predicted by a regression model that included a combination of local habitat characteristics and the abundance of sage-grouse. When controlling for habitat-related factors, areas with higher abundances of sage-grouse pellets (an index of sage-grouse abundance and/or habitat use) had higher abundances of ant mounds than areas with lower abundances of sage-grouse pellets. The causal mechanism underlying this positive relationship between sage-grouse and ant mound abundance at the fine scale could be indirect (e.g., both species prefer similar environmental conditions) or direct (e.g., sage-grouse prefer areas with a high abundance of ant mounds because ants are an important prey item during certain life stages). We observed no relationship between a broad-scale index of breeding sage-grouse density and the abundance of ant mounds. We suspect that consideration of the non-breeding habitat of sage-grouse and finer-scale measures of sage-grouse abundance are critical to the utility of sage-grouse as an umbrella species for the conservation of harvester ants and their important role in rangeland ecosystems.}, } @article {pmid37796448, year = {2023}, author = {Eggertson, QA and Rintoul, TL and Lévesque, CA}, title = {Resolving the Globisporangium ultimum (Pythium ultimum) species complex.}, journal = {Mycologia}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/00275514.2023.2241980}, pmid = {37796448}, issn = {1557-2536}, abstract = {The Globisporangium ultimum (formerly Pythium ultimum) species complex was previously composed of two morphological varieties: var. ultimum and var. sporangiiferum. Prior attempts to resolve this morphology-based species complex using molecular techniques have been inconclusive or conflicting. The increased availability of sequenced genomes and isolates identified as G. ultimum var. ultimum and var. sporangiiferum has allowed us to examine these relationships at a higher resolution and with a broader scope than previously possible. Using comparative genomics, we identified highly variable gene regions and designed primers for four new protein-coding genes for phylogenetics. These were then used alongside three known markers to generate a nuclear multigene genealogy of the species complex. From a collection of 163 isolates belonging to the target taxa, a subset of 29 was chosen to be included in this study (verified with nuclear rDNA internal transcribed spacer 1 [ITS1] and mitochondrial cytochrome c oxidase subunit 1 [cox1] sequences). Seventeen isolates of var. ultimum were selected to be representative of variations in genotype, morphology, and geographic collection location. The 12 isolates of var. sporangiiferum included all available specimens identified either morphologically (in previous studies) or through sequence similarity with ITS1 and cox1. Based on the fulfillment of reciprocal monophyly and observed genealogical concordance under the genealogical concordance phylogenetic species recognition, we determined that the Globisporangium ultimum species complex is composed of four genetically distinct species: Globisporangium ultimum, Globisporangium sporangiiferum, Globisporangium solveigiae, and Globisporangium bothae.}, } @article {pmid37775924, year = {2023}, author = {Abachi, H and Moallem, M and Taghavi, SM and Hamidizade, M and Soleimani, A and Fazliarab, A and Portier, P and Osdaghi, E}, title = {Garlic Bulb Decay and Soft Rot Caused by the Cross-Kingdom Pathogen Burkholderia gladioli.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-08-23-1603-RE}, pmid = {37775924}, issn = {0191-2917}, abstract = {In 2021, two Gram-negative bacterial strains were isolated from garlic (Allium sativum) bulbs showing decay and soft rot symptoms in central Iran. The bacterial strains were aggressively pathogenic on cactus, garlic, gladiolus, onion, potato, and saffron plants, and induced soft rot symptoms on carrot, cucumber, potato and radish discs. Furthermore, they were pathogenic on sporophore of cultivated and wild mushrooms. Phylogenetic analyses revealed that the bacterial strains belong to Burkholderia gladioli species. Garlic bulb rot caused by B. gladioli has rarely been reported in the literature. Historically, B. gladioli strains had been assigned to four pathovars i.e. B. gladioli pv. alliicola, B. gladioli pv. gladioli, B. gladioli pv. agaricicola, and B. gladioli pv. cocovenenans infecting onion, Gladiolus sp., mushrooms, and poisoning foods, respectively. Multilocus (i.e., 16S rRNA, atpD, gyrB, and lepA genes) sequence-based phylogenetic investigations including reference strains of B. gladioli pathovars showed that the two garlic strains belong to phylogenomic clade 2 of the species which includes the pathotype strain of B. gladioli pv. alliicola. Although the garlic strains were phylogenetically closely related to the B. gladioli pv. alliicola reference strains, they possessed pathogenicity characteristics that overlapped with three of the four historical pathovars including the ability to rot onion (pv. alliicola), gladiolus (pv. gladioli) and mushrooms (pv. agaricicola). Further, pathotype of each pathovar could infect the hosts of other pathovars, undermining the utility of pathovar concept in this species. Overall, using phenotypic pathovar-oriented assays to classify B. gladioli strains should be replaced by phylogenetic or phylogenomic analysis.}, } @article {pmid37760039, year = {2023}, author = {Cortese-Krott, MM}, title = {The Reactive Species Interactome in Red Blood Cells: Oxidants, Antioxidants, and Molecular Targets.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, doi = {10.3390/antiox12091736}, pmid = {37760039}, issn = {2076-3921}, support = {263779315, 220652768, 521638178 and 386517575.//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Beyond their established role as oxygen carriers, red blood cells have recently been found to contribute to systemic NO and sulfide metabolism and act as potent circulating antioxidant cells. Emerging evidence indicates that reactive species derived from the metabolism of O2, NO, and H2S can interact with each other, potentially influencing common biological targets. These interactions have been encompassed in the concept of the reactive species interactome. This review explores the potential application of the concept of reactive species interactome to understand the redox physiology of RBCs. It specifically examines how reactive species are generated and detoxified, their interactions with each other, and their targets. Hemoglobin is a key player in the reactive species interactome within RBCs, given its abundance and fundamental role in O2/CO2 exchange, NO transport/metabolism, and sulfur species binding/production. Future research should focus on understanding how modulation of the reactive species interactome may regulate RBC biology, physiology, and their systemic effects.}, } @article {pmid37755002, year = {2023}, author = {Jiménez-Gaona, Y and Vivanco-Galván, O and Cruz, D and Armijos-Carrión, A and Suárez, JP}, title = {Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota).}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, doi = {10.3390/jof9090894}, pmid = {37755002}, issn = {2309-608X}, abstract = {BACKGROUND: The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella.

OBJECTIVES: The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella.

METHODOLOGY: Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale.

RESULTS AND CONCLUSIONS: The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.}, } @article {pmid37746130, year = {2023}, author = {Wang, Z and Kim, W and Wang, YW and Yakubovich, E and Dong, C and Trail, F and Townsend, JP and Yarden, O}, title = {The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.}, journal = {Frontiers in fungal biology}, volume = {4}, number = {}, pages = {1214537}, pmid = {37746130}, issn = {2673-6128}, abstract = {Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.}, } @article {pmid37728195, year = {2023}, author = {Biswas, R and Batista Da Rocha, C and Bennick, RA and Zhang, J}, title = {Water-Soluble Fullerene Monoderivatives for Biomedical Applications.}, journal = {ChemMedChem}, volume = {}, number = {}, pages = {e202300296}, doi = {10.1002/cmdc.202300296}, pmid = {37728195}, issn = {1860-7187}, abstract = {Monoderivatives of fullerenes functionalized with hydrophilic groups make them water soluble, while preserving the hydrophobic fullerene cage. This class of molecules have intriguing biomedical applications, including drug delivery, photodynamic therapy (PDT), antiviral and antimicrobial activity and reactive oxygen species (ROS)-scavenging abilities. In this Concept we discuss the synthesis and biomedical applications of water-soluble fullerene monoderivatives and their biological behavior based on their structures.}, } @article {pmid37720058, year = {2023}, author = {Pollmann, M and Kuhn, D and König, C and Homolka, I and Paschke, S and Reinisch, R and Schmidt, A and Schwabe, N and Weber, J and Gottlieb, Y and Steidle, JLM}, title = {New species based on the biological species concept within the complex of Lariophagus distinguendus (Hymenoptera, Chalcidoidea, Pteromalidae), a parasitoid of household pests.}, journal = {Ecology and evolution}, volume = {13}, number = {9}, pages = {e10524}, pmid = {37720058}, issn = {2045-7758}, abstract = {The pteromalid parasitoid Lariophagus distinguendus (Foerster) belongs to the Hymenoptera, a megadiverse insect order with high cryptic diversity. It attacks stored product pest beetles in human storage facilities. Recently, it has been shown to consist of two separate species. To further study its cryptic diversity, strains were collected to compare their relatedness using barcoding and nuclear genes. Nuclear genes identified two clusters which agree with the known two species, whereas the barcode fragment determined an additional third Clade. Total reproductive isolation (RI) according to the biological species concept (BSC) was investigated in crossing experiments within and between clusters using representative strains. Sexual isolation exists between all studied pairs, increasing from slight to strong with genetic distance. Postzygotic barriers mostly affected hybrid males, pointing to Haldane's rule. Hybrid females were only affected by unidirectional Spiroplasma-induced cytoplasmic incompatibility and behavioural sterility, each in one specific strain combination. RI was virtually absent between strains separated by up to 2.8% COI difference, but strong or complete in three pairs from one Clade each, separated by at least 7.2%. Apparently, each of these clusters represents one separate species according to the BSC, highlighting cryptic diversity in direct vicinity to humans. In addition, these results challenge the recent 'turbo-taxonomy' practice of using 2% COI differences to delimitate species, especially within parasitic Hymenoptera. The gradual increase in number and strength of reproductive barriers between strains with increasing genetic distance also sheds light on the emergence of barriers during the speciation process in L. distinguendus.}, } @article {pmid37705950, year = {2023}, author = {Fowers, BJ and Novak, LF and Kiknadze, NC and Selim, M}, title = {Is the concept of personality capacious enough to incorporate virtues?.}, journal = {Frontiers in psychology}, volume = {14}, number = {}, pages = {1232637}, doi = {10.3389/fpsyg.2023.1232637}, pmid = {37705950}, issn = {1664-1078}, abstract = {We will consider four answers to the question about whether the concept of personality is capacious enough to incorporate virtues. The simplest is that the concept of personality encompasses all individual variations in persons. It follows from this answer that virtues would, as individual differences, be incorporated into personality. Unfortunately, definitions of personality do not always invoke such capaciousness, and, in practice, most scholars limit their work to the Big Five or HEXACO models, which do not incorporate virtues. The second answer is that the concept of personality incorporates all trait or dimension level variations across persons, with some exceptions, such as intelligence, attachment style, and psychopathy. Following this definition, virtues, as traits, would be incorporated into such a broad definition of personality. Unfortunately, the boundaries for inclusion and exclusion into personality are fuzzy in this case, and there is no extant definition of personality that solves this problem. The third answer is that personality traits and virtue traits are similar, but distinct concepts. This article presents conceptual and empirical arguments for this similarity in seeing traits as a higher order concept that includes the species of personality and the species of virtue. The fourth answer is that personality and virtue are unrelated. This answer is dismissed because there are many studies that indicate that they are correlated, and few advocate such a clear differentiation. The conclusion is that, pending conceptual and empirical results indicating otherwise, the genus-species relationship seems most fitting where traits are a genus, and personality and virtue are each a species within that genus.}, } @article {pmid37693498, year = {2023}, author = {Thomas, GWC and Hughes, JJ and Kumon, T and Berv, JS and Erik Nordgren, C and Lampson, M and Levine, M and Searle, JB and Good, JM}, title = {The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.28.555178}, pmid = {37693498}, abstract = {A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.}, } @article {pmid37680314, year = {2023}, author = {Mercogliano, R and Dongo, D}, title = {Fish welfare during slaughter: the European Council Regulation 1099/09 application.}, journal = {Italian journal of food safety}, volume = {12}, number = {3}, pages = {10926}, doi = {10.4081/ijfs.2023.10926}, pmid = {37680314}, issn = {2239-7132}, abstract = {The Treaty of Lisbon states that animals are sentient beings. Fish species show physiological differences from terrestrial animals and are slaughtered and killed in a very different context. Many existing commercial killing methods expose fish to extensive suffering over a prolonged period of time, and some of the slaughtering practices they experience can cause pain and distress. This study highlights the limited feasibility of European Council Regulation 1099/09 requirements on welfare when killing cephalopods and crustaceans. Sentience is the animal's capacity to have positive (comfort, excitement) and negative (pain, anxiety, distress, or harm) feelings. Considerable evidence is now showing that the major commercial fish species, including cephalopods and crustaceans, possess complex neurological substrates supporting pain sensitivity and conscious experiences. In the legislation applied to scientific procedures, the concept of sentience in these species is important. Therefore, it would be appropriate to acknowledge current scientific evidence and establish reference criteria for fish welfare. For the welfare of fish species during slaughter, European Council Regulation 1099/09 applicability is limited. Fish welfare during slaughter is more than just an ethical problem. According to the One-Health approach, food safety should also include the concept of sentience for fish welfare. Pending studies that dispel all doubt, the precautionary principle of European Council Regulation 178/04 remains valid and should be applied to fish welfare.}, } @article {pmid37676702, year = {2023}, author = {Ansari, L and Asgari, B and Zare, R and Zamanizadeh, HR}, title = {Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.006028}, pmid = {37676702}, issn = {1466-5034}, abstract = {During a survey of species diversity of Penicillium and Talaromyces in sugarcane (Saccharum officinarum) rhizosphere in the Khuzestan province of Iran [1], 195 strains were examined, from which 187 belonged to Penicillium (11 species) and eight to Talaromyces (one species). In the present study, three strains of Penicillium belonging to section Exilicaulis series Restricta, identified as P. restrictum by Ansari et al. [1], were subjected to a phylogenetic study. The multilocus phylogeny of partial β-tubulin, calmodulin and RNA polymerase II second largest subunit genes enabled the recognition of one new phylogenetic species that is here formally described as Penicillium rhizophilum sp. nov. This species is phylogenetically distinct in series Restricta, but it does not show significant morphological differences from other species previously classified in the series. Therefore, we here placed bias on the phylogenetic species concept. The holotype of Penicillium rhizophilum sp. nov. is IRAN 18169F and the ex-type culture is LA30[T] (=IRAN 4042C[T]=CBS 149737[T]).}, } @article {pmid37650771, year = {2023}, author = {Sen, A and Ansari, A and Swain, A and Pandey, B and Rajaraman, G}, title = {Probing the Origins of Puzzling Reactivity in Fe/Mn-Oxo/Hydroxo Species toward C-H Bonds: A DFT and Ab Initio Perspective.}, journal = {Inorganic chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.inorgchem.3c01632}, pmid = {37650771}, issn = {1520-510X}, abstract = {Activation of C-H bonds using an earth-abundant metal catalyst is one of the top challenges of chemistry, where high-valent Mn/Fe-oxo(hydroxo) biomimic species play an important role. There are several open questions related to the comparative oxidative abilities of these species, and a unifying concept that could accommodate various factors influencing reactivity is lacking. To shed light on these open questions, here, we have used a combination of density functional theory (DFT) (B3LYP-D3/def2-TZVP) and ab initio (CASSCF/NEVPT2) calculations to study a series of high-valent metal-oxo species [M[n+]H3buea(O/OH)] (M = Mn and Fe, n = II to V; H3buea = tris[(N'-tert-butylureaylato)-N-ethylene)]aminato towards the activation of dihydroanthracene (DHA). The H-bonding network in the ligand architecture influences the ground state-excited state gap and brings several excited states of the same spin multiplicity closer in energy, which triggers reactivity via one of those excited states, reducing the kinetic barriers for the C-H bond activation and rationalizing several puzzling reactivity trends observed in various high-valent Mn/Fe-oxo(hydroxo) species.}, } @article {pmid37638478, year = {2023}, author = {Génin, F and Rambeloarivony, H and Silvestro, D and Masters, JC}, title = {Ontogeny and phylogeny of mating behaviour: social heteroch rony in primates.}, journal = {Theoretical biology forum}, volume = {116}, number = {1-2}, pages = {15-50}, doi = {10.19272/202311402002}, pmid = {37638478}, issn = {2282-2593}, abstract = {Based on the Recognition Concept of species, the specific-mate contact model posits that mating systems develop as combinations of two fundamental courtship strategies that we interpret here in terms of behavioural heterochrony: territorial mate-attraction evolved as an effect of peramorphosis whereas group-living mate-seeking evolved as an effect of paedomorphosis. We tested this hypothesis on primates in a phylogenetic and paleo-climatic context. Our results suggest that primate promiscuity (both males and females are mate-seekers) evolved with group-living from ancestral pair-living monogamy (both males and females are mate-attractors) in the Palaeogene, as the result of a slowdown in growth (neoteny) caused by increased environmental predictability. A secondary return to territorial monogamy probably evolved as the result of accelerated growth driven by seasonality (acceleration). Polygamy evolved in the Neogene during periods of forest fragmentation and environmental unpredictability. Small monogamous ancestors evolved seasonal polyandry (female attraction) as an effect of truncated development (progenesis). Large promiscuous, neotenic ancestors evolved non-seasonal polygyny (male attraction) as an effect of prolonged development (hypermorphosis) in males. We conclude that social heterochrony offers alternative explanations for the coevolution of life history and mating be-haviour; and we discuss the implications of our model for human social evolution.}, } @article {pmid37627695, year = {2023}, author = {Xesfyngi, Y and Georgoutsou-Spyridonos, M and Tripathy, A and Milionis, A and Poulikakos, D and Mastellos, DC and Tserepi, A}, title = {A High-Performance Antibacterial Nanostructured ZnO Microfluidic Device for Controlled Bacterial Lysis and DNA Release.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {8}, pages = {}, doi = {10.3390/antibiotics12081276}, pmid = {37627695}, issn = {2079-6382}, support = {MIS 5002567//Operational Programme "Competitiveness, Entrepreneurship and Innovation" (NSRF 2014-2020) and co-financed by Greece and the European Union (European Regional Development Fund)/ ; }, abstract = {In this work, the antibacterial properties of nanostructured zinc oxide (ZnO) surfaces are explored by incorporating them as walls in a simple-to-fabricate microchannel device. Bacterial cell lysis is demonstrated and quantified in such a device, which functions due to the action of its nanostructured ZnO surfaces in contact with the working fluid. To shed light on the mechanism responsible for lysis, E. coli bacteria were incubated in zinc and nanostructured ZnO substrates, as well as the here-investigated ZnO-based microfluidic devices. The unprecedented killing efficiency of E. coli in nanostructured ZnO microchannels, effective after a 15 min incubation, paves the way for the implementation of such microfluidic chips in the disinfection of bacteria-containing solutions. In addition, the DNA release was confirmed by off-chip PCR and UV absorption measurements. The results indicate that the present nanostructured ZnO-based microfluidic chip can, under light, achieve partial inactivation of the released bacterial DNA via reactive oxygen species-mediated oxidative damage. The present device concept can find broader applications in cases where the presence of DNA in a sample is not desirable. Furthermore, the present microchannel device enables, in the dark, efficient release of bacterial DNA for downstream genomic DNA analysis. The demonstrated potential of this antibacterial device for tailored dual functionality in light/dark conditions is the main novel contribution of the present work.}, } @article {pmid37626983, year = {2023}, author = {Jabin, G and Joshi, BD and Wang, MS and Mukherjee, T and Dolker, S and Wang, S and Chandra, K and Chinnadurai, V and Sharma, LK and Thakur, M}, title = {Mid-Pleistocene Transitions Forced Himalayan ibex to Evolve Independently after Split into an Allopatric Refugium.}, journal = {Biology}, volume = {12}, number = {8}, pages = {}, doi = {10.3390/biology12081097}, pmid = {37626983}, issn = {2079-7737}, support = {NMHS/2017-18/LG09/02/476//Ministry of Environment, Forests and Climate Change/ ; }, abstract = {Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8-0.5 mya and c. 50-30 kya, with an intermediate large population expansion c. 0.2-0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale.}, } @article {pmid37586095, year = {2023}, author = {Carrasco, RA and Breen, KM}, title = {Allostasis in Neuroendocrine Systems Controlling Reproduction.}, journal = {Endocrinology}, volume = {}, number = {}, pages = {}, doi = {10.1210/endocr/bqad125}, pmid = {37586095}, issn = {1945-7170}, abstract = {Allostasis provides a supporting role to the homeostatic control of biological variables in mammalian species. While the concept of homeostasis is related to the control of variables within a set point or range that are essential to life, allostasis refers to systems that facilitate adaptation to challenges that the organism faces and the new requirements for survival. Essential for such adaptation is the role played by the brain in eliciting neural and neuroendocrine responses. Reproductive function is fundamental for the survival of species but is costly in energetic terms and requires a synchrony with an ever-changing environment. Thus, in many species reproductive function is blocked or delayed over immediate challenges. This review will cover the physiological systems and neuroendocrine pathways that supply allostatic control over reproductive neuroendocrine systems. Light, hypoxia, temperature, nutrition, psychosocial, and immune mediators influence the neuroendocrine control of reproductive functions through pathways that are confluent at the paraventricular nucleus; however, understanding of the integrative responses to these stimuli has not been clarified. Likely, the ultimate consequence of these allostatic mechanisms is the modification of kisspeptin and gonadotropin-releasing hormone neuronal activity, thus compromising reproduction function in the short term, while preserving species survivability.}, } @article {pmid37553336, year = {2023}, author = {Weiss, AS and Niedermeier, LS and von Strempel, A and Burrichter, AG and Ring, D and Meng, C and Kleigrewe, K and Lincetto, C and Hübner, J and Stecher, B}, title = {Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4780}, pmid = {37553336}, issn = {2041-1723}, support = {SFB 1371 (395357507, 279971426 and 315980449//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 865615//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.}, } @article {pmid37504686, year = {2023}, author = {Wang, XC and Zhuang, WY and Zhao, RL}, title = {Species Diversity of Helvella lacunosa Clade (Pezizales, Ascomycota) in China and Description of Sixteen New Species.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {7}, pages = {}, doi = {10.3390/jof9070697}, pmid = {37504686}, issn = {2309-608X}, support = {32270008//National Natural Science Foundation of China/ ; 31750001//National Natural Science Foundation of China/ ; QYZDY-SSW-SMC029//Key Research Program of Frontier Science, Chinese Academy of Sciences/ ; 2019HJ2096001006//The Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China/ ; }, abstract = {Helvella lacunosa and its allies are widely distributed in the Northern Hemisphere and perform important functions in ecosystems. A comprehensive study on 101 collections of Helvella lacunosa, including those deposited in four Chinese fungaria or collected recently from 10 provinces, was conducted based on morphological and molecular characteristics. Phylogenies of "Helvella lacunosa clade" inferred from Hsp90, ITS, LSU, and TEF were reconstructed with 49 lineages recognized, of which 25 lineages occurred in China, and each represented an individual species. Sixteen new species were determined with detailed descriptions and illustrations. Two new Chinese records were reported. Species concepts and their distinctions in macro- and micro-features were discussed.}, } @article {pmid37494414, year = {2023}, author = {Huang, GJ and Li, CW and Lee, PY and Su, JX and Chao, KC and Chu, LA and Chiang, AS and Cheng, JX and Chen, BH and Lu, CH and Chu, SW and Yang, SD}, title = {Electronic Preresonance Stimulated Raman Scattering Spectromicroscopy Using Multiple-Plate Continuum.}, journal = {The journal of physical chemistry. B}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jpcb.3c02629}, pmid = {37494414}, issn = {1520-5207}, abstract = {Stimulated Raman scattering (SRS) spectromicroscopy is a powerful technique that enables label-free detection of chemical bonds with high specificity. However, the low Raman cross section due to typical far-electronic resonance excitation seriously restricts the sensitivity and undermines its application to bio-imaging. To address this bottleneck, the electronic preresonance (EPR) SRS technique has been developed to enhance the Raman signals by shifting the excitation frequency toward the molecular absorption. A fundamental weakness of the previous demonstration is the lack of dual-wavelength tunability, making EPR-SRS only applicable to a limited number of species in the proof-of-concept experiment. Here, we demonstrate the EPR-SRS spectromicroscopy using a multiple-plate continuum (MPC) light source able to examine a single vibration mode with independently adjustable pump and Stokes wavelengths. In our experiments, the C═C vibration mode of Alexa 635 is interrogated by continuously scanning the pump-to-absorption frequency detuning throughout the entire EPR region enabled by MPC. The results exhibit 150-fold SRS signal enhancement and good agreement with the Albrecht A-term preresonance model. Signal enhancement is also observed in EPR-SRS images of the whole Drosophila brain stained with Alexa 635. With the improved sensitivity and potential to implement hyperspectral measurement, we envision that MPC-EPR-SRS spectromicroscopy can bring the Raman techniques closer to a routine in bio-imaging.}, } @article {pmid37486130, year = {2023}, author = {Cobo-Simón, M and Hart, R and Ochman, H}, title = {Gene flow and species boundaries of the genus Salmonella.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0029223}, doi = {10.1128/msystems.00292-23}, pmid = {37486130}, issn = {2379-5077}, abstract = {The genus Salmonella comprises two species, Salmonella bongori and Salmonella enterica, which are infectious to a wide variety of animal hosts. The diversity within S. enterica has been further partitioned into 6-10 subspecies based on such features as host range, geography, and most recently, genetic relatedness and phylogenetic affiliation. Although Salmonella pathogenicity is attributable to large numbers of acquired virulence factors, the extent of homologous exchange in the species at large is apparently constrained such that the species and subspecies form distinct clusters of strains. To explore the extent of gene flow within and among subspecies, and to ultimately define true biological species, we evaluated patterns of recombination in over 1,000 genomes currently assigned to the genus. Those Salmonella subspecies containing sufficient numbers of sequenced genomes to allow meaningful analysis-i.e., subsp. enterica and diarizonae-were found to be reproductively isolated from one another and from all other subspecies. Based on the configuration of genomic sequence divergence among subspecies, it is expected that each of the other Salmonella subspecies will also represent a biological species. Our findings argue against the application of prescribed nucleotide-identity thresholds to delineate bacterial species and contend that the Biological Species Concept should not be disregarded for bacteria, even those, like Salmonella, that demonstrate complex patterns of species and subspecies divergence. IMPORTANCE The Biological Species Concept (BSC), which defines species boundaries based on the capacity for gene exchange, is widely used to classify sexually reproducing eukaryotes but is generally thought to be inapplicable to bacteria due to their completely asexual mode of reproduction. We show that the genus Salmonella, whose thousands of described serovars were formerly considered to be strictly clonal, undergoes sufficient levels of homologous recombination to be assigned to species according to the BSC. Aside from the two recognized species, Salmonella enterica and Salmonella bongori, several (and likely all) of the subspecies within S. enterica are reproductively isolated from one another and should each be considered a separate biological species. These findings demonstrate that species barriers in bacteria can form despite high levels of nucleotide identity and that commonly applied thresholds of genomic sequence identity are not reliable indicators of bacterial species status.}, } @article {pmid37481056, year = {2023}, author = {Tong, S and Samet, JM and Steffen, W and Kinney, PL and Frumkin, H}, title = {Solidarity for the anthropocene: From the widening inequity to climate change and beyond.}, journal = {Environmental research}, volume = {}, number = {}, pages = {116716}, doi = {10.1016/j.envres.2023.116716}, pmid = {37481056}, issn = {1096-0953}, abstract = {Social solidarity is essential to large-scale collective action, but the need for solidarity has received little attention from scholars of Earth Systems, sustainability and public health. Now, the need for solidarity requires recognition. We have entered a new planetary epoch - the Anthropocene - in which human-induced global changes are occurring at an unprecedented scale. There are multiple health crises facing humanity - widening inequity, climate change, biodiversity loss, diminishing resources, persistent poverty, armed conflict, large-scale migration, and others. These global challenges are so far-reaching, and call for such extensive, large-scale action, that solidarity is a sine qua non for tackling these challenges. However, the heightened need for solidarity has received little attention in the context of the Anthropocene and, in particular, how it can be created and nurtured has been overlooked. In this commentary, we explore the concept of solidarity from inter-species, intra-generational and inter-generational perspectives. We also propose strategies to enhance solidarity in the Anthropocene.}, } @article {pmid37466780, year = {2023}, author = {Lisboa, TP and de Faria, LV and de Oliveira, WBV and Oliveira, RS and Matos, MAC and Dornellas, RM and Matos, RC}, title = {Cost-effective protocol to produce 3D-printed electrochemical devices using a 3D pen and lab-made filaments to ciprofloxacin sensing.}, journal = {Mikrochimica acta}, volume = {190}, number = {8}, pages = {310}, pmid = {37466780}, issn = {1436-5073}, support = {3038115/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 150604/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; E-26/211.465/2019//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-33/201.429/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/205.806/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 205.807/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {A novel conductive filament based on graphite (Gr) dispersed in polylactic acid polymer matrix (PLA) is described to produce 3D-electrochemical devices (Gr/PLA). This conductive filament was used to additively manufacture electrochemical sensors using the 3D pen. Thermogravimetric analysis confirmed that Gr was successfully incorporated into PLA, achieving a composite material (40:60% w/w, Gr and PLA, respectively), while Raman and scanning electron microscopy revealed the presence of defects and a high porosity on the electrode surface, which contributes to improved electrochemical performance. The 3D-printed Gr/PLA electrode provided a more favorable charge transfer (335 Ω) than the conventional glassy carbon (1277 Ω) and 3D-printed Proto-pasta® (3750 Ω) electrodes. As a proof of concept, the ciprofloxacin antibiotic, a species of multiple interest, was selected as a model molecule. Thus, a square wave voltammetry (SWV) method was proposed in the potential range + 0.9 to + 1.3 V (vs Ag|AgCl|KCl(sat)), which provided a wide linear working range (2 to 32 µmol L[-1]), 1.79 µmol L[-1] limit of detection (LOD), suitable precision (RSD < 7.9%), and recovery values from 94 to 109% when applied to pharmaceutical and milk samples. Additionally, the sensor is free from the interference of other antibiotics routinely employed in veterinary practices. This device is disposable, cost-effective, feasibly produced in financially limited laboratories, and consequently promising for evaluation of other antibiotic species in routine applications.}, } @article {pmid37463717, year = {2023}, author = {Graves, JL}, title = {Favored Races in the Struggle for Life: Racism and the Speciation Concept.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/cshperspect.a041454}, pmid = {37463717}, issn = {1943-0264}, abstract = {Evolutionary speciation, whether it be cladistic or phyletic, has always been associated with race concepts. Biological races are conceived as definable stages of divergence from a common ancestor. However, the species concept in Western science began within a special creationist framework. The sixteenth century European voyages of discovery resulted in special creationist schemes explaining the origin of the new peoples encountered. These were designed to provide the moral justification for their colonization and enslavement. By the seventeenth century, European naturalists were beginning to seriously question the meaning of the variation within the animals and plants they observed within the context of God's role in creation. By the middle of the nineteenth century, "the species question" was the most important intellectual enterprise within biology. Here I discuss how notions of speciation influenced and were influenced by conceptions of race within Homo sapiens.}, } @article {pmid37455851, year = {2023}, author = {Bhat, AH and Machado, RAR and Abolafia, J and Askary, TH and Půža, V and Ruiz-Cuenca, AN and Rana, A and Sayed, S and Al-Shuraym, LA}, title = {Multigene Sequence-Based and Phenotypic Characterization Reveals the Occurrence of a Novel Entomopathogenic Nematode Species, Steinernema anantnagense n. sp.}, journal = {Journal of nematology}, volume = {55}, number = {1}, pages = {20230029}, pmid = {37455851}, issn = {0022-300X}, abstract = {Three entomopathogenic nematode populations were isolated from agricultural fields in the Anantnag district of Jammu and Kashmir (India). Sequences of multiple gene regions and phenotypic features show that they are conspecific and represent a novel species. Molecular and morphological features provided evidence for placing the new species into the "Kushidai" clade. Within this clade, analysis of sequence data of the internal transcribed spacer (ITS) gene, the D2D3 region of the 28S rRNA gene, the mitochondrial cytochrome oxidase I (mtCOI) gene, and the mitochondrial 12S (mt12S) gene depicted the novel species as a distinctive entity closely related to Steinernema akhursti, S. kushidai, and S. populi. Phylogenetic analyses also show that the new species is a sister species to S. akhursti, and these two species are closely related to S. kushidai and S. populi. Additionally, the new species does not mate or produce fertile progeny with any of the closely related species, reinforcing its uniqueness from a biological species concept standpoint. The new species is further characterized by the third-stage infective juveniles with almost straight bodies (0.7-0.8 mm length), poorly developed stoma and pharynx, and conoid-elongate tail (49-66 µm) with hyaline posterior part. Adult females are characterized by short and conoid tails bearing a short mucron in the first generation and long conoid tails with thin mucron in the second generation. Adult males have ventrally curved spicules in both generations. Moreover, the first-generation male has rounded manubrium, fusiform gubernaculum, conoid and slightly ventrally curved tails with minute mucron, and the second generation has rhomboid manubrium anteriorly ventrad bent, and tails with long and robust mucron. The morphological, morphometrical, molecular, and phylogenetic analyses support the new species status of this nematode, which is hereby described as Steinernema anantnagense n. sp. The bacterial symbiont associated with S. anantnagense n. sp. represents a novel species, closely related to Xenorhabdus japonica. These findings shed light on the diversity of entomopathogenic nematodes and their symbiotic bacteria, providing valuable information for future studies in this field.}, } @article {pmid37455023, year = {2023}, author = {Poorter, L and Amissah, L and Bongers, F and Hordijk, I and Kok, J and Laurance, SGW and Lohbeck, M and Martínez-Ramos, M and Matsuo, T and Meave, JA and Muñoz, R and Peña-Claros, M and van der Sande, MT}, title = {Successional theories.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.12995}, pmid = {37455023}, issn = {1469-185X}, support = {Aspasia 015.014.006/NWO_/Dutch Research Council/Netherlands ; NWO-VI.Veni.192.027/NWO_/Dutch Research Council/Netherlands ; }, abstract = {Succession is a fundamental concept in ecology because it indicates how species populations, communities, and ecosystems change over time on new substrate or after a disturbance. A mechanistic understanding of succession is needed to predict how ecosystems will respond to land-use change and to design effective ecosystem restoration strategies. Yet, despite a century of conceptual advances a comprehensive successional theory is lacking. Here we provide an overview of 19 successional theories ('models') and their key points, group them based on conceptual similarity, explain conceptual development in successional ideas and provide suggestions how to move forward. Four groups of models can be recognised. The first group (patch & plants) focuses on plants at the patch level and consists of three subgroups that originated in the early 20th century. One subgroup focuses on the processes (dispersal, establishment, and performance) that operate sequentially during succession. Another subgroup emphasises individualistic species responses during succession, and how this is driven by species traits. A last subgroup focuses on how vegetation structure and underlying demographic processes change during succession. A second group of models (ecosystems) provides a more holistic view of succession by considering the ecosystem, its biota, interactions, diversity, and ecosystem structure and processes. The third group (landscape) considers a larger spatial scale and includes the effect of the surrounding landscape matrix on succession as the distance to neighbouring vegetation patches determines the potential for seed dispersal, and the quality of the neighbouring patches determines the abundance and composition of seed sources and biotic dispersal vectors. A fourth group (socio-ecological systems) includes the human component by focusing on socio-ecological systems where management practices have long-lasting legacies on successional pathways and where regrowing vegetations deliver a range of ecosystem services to local and global stakeholders. The four groups of models differ in spatial scale (patch, landscape) or organisational level (plant species, ecosystem, socio-ecological system), increase in scale and scope, and reflect the increasingly broader perspective on succession over time. They coincide approximately with four periods that reflect the prevailing view of succession of that time, although all views still coexist. The four successional views are: succession of plants (from 1910 onwards) where succession was seen through the lens of species replacement; succession of communities and ecosystems (from 1965 onwards) when there was a more holistic view of succession; succession in landscapes (from 2000 onwards) when it was realised that the structure and composition of landscapes strongly impact successional pathways, and increased remote-sensing technology allowed for a better quantification of the landscape context; and succession with people (from 2015 onwards) when it was realised that people and societal drivers have strong effects on successional pathways, that ecosystem processes and services are important for human well-being, and that restoration is most successful when it is done by and for local people. Our review suggests that the hierarchical successional framework of Pickett is the best starting point to move forward as this framework already includes several factors, and because it is flexible, enabling application to different systems. The framework focuses mainly on species replacement and could be improved by focusing on succession occurring at different hierarchical scales (population, community, ecosystem, socio-ecological system), and by integrating it with more recent developments and other successional models: by considering different spatial scales (landscape, region), temporal scales (ecosystem processes occurring over centuries, and evolution), and by taking the effects of the surrounding landscape (landscape integrity and composition, the disperser community) and societal factors (previous and current land-use intensity) into account. Such a new, comprehensive framework could be tested using a combination of empirical research, experiments, process-based modelling and novel tools. Applying the framework to seres across broadscale environmental and disturbance gradients allows a better insight into what successional processes matter and under what conditions.}, } @article {pmid37438215, year = {2023}, author = {Cannon, CH and Lerdau, M}, title = {Conservation should not make 'perfect' an enemy of 'good'.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2023.06.010}, pmid = {37438215}, issn = {1878-4372}, } @article {pmid37403035, year = {2023}, author = {Flütsch, S and Wiestner, F and Butticaz, L and Moor, D and Stölting, KN}, title = {Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {375}, pmid = {37403035}, issn = {1471-2164}, abstract = {BACKGROUND: Vibrio spp. are a diverse group of ecologically important marine bacteria responsible for several foodborne outbreaks of gastroenteritis around the world. Their detection and characterization are moving away from conventional culture-based methods towards next generation sequencing (NGS)-based approaches. However, genomic methods are relative in nature and suffer from technical biases arising from library preparation and sequencing. Here, we introduce a quantitative NGS-based method that enables the quantitation of Vibrio spp. at the limit of quantification (LOQ) through artificial DNA standards and their absolute quantification via digital PCR (dPCR).

RESULTS: We developed six DNA standards, called Vibrio-Sequins, together with optimized TaqMan assays for their quantification in individually sequenced DNA libraries via dPCR. To enable Vibrio-Sequin quantification, we validated three duplex dPCR methods to quantify the six targets. LOQs were ranging from 20 to 120 cp/µl for the six standards, whereas the limit of detection (LOD) was ~ 10 cp/µl for all six assays. Subsequently, a quantitative genomics approach was applied to quantify Vibrio-DNA in a pooled DNA mixture derived from several Vibrio species in a proof-of-concept study, demonstrating the increased power of our quantitative genomic pipeline through the coupling of NGS and dPCR.

CONCLUSIONS: We significantly advance existing quantitative (meta)genomic methods by ensuring metrological traceability of NGS-based DNA quantification. Our method represents a useful tool for future metagenomic studies aiming at quantifying microbial DNA in an absolute manner. The inclusion of dPCR into sequencing-based methods supports the development of statistical approaches for the estimation of measurement uncertainties (MU) for NGS, which is still in its infancy.}, } @article {pmid37390550, year = {2023}, author = {Johnson, A and Miller, EA and Weber, B and Figueroa, CF and Aguayo, JM and Johny, AK and Noll, S and Brannon, J and Kozlowicz, B and Johnson, TJ}, title = {Evidence of host specificity in Lactobacillus johnsonii genomes and its influence on probiotic potential in poultry.}, journal = {Poultry science}, volume = {102}, number = {9}, pages = {102858}, doi = {10.1016/j.psj.2023.102858}, pmid = {37390550}, issn = {1525-3171}, abstract = {To date, the selection of candidate strains for probiotic development in production animals has been largely based upon screens for desired phenotypic traits. However, increasing evidence indicates that the use of host-specific strains may be important, because coevolution with the animal host better prepares a bacterial strain to colonize and succeed in its respective host animal species. This concept was applied to Lactobacillus johnsonii in commercial poultry production because of its previous correlation with enhanced bird performance. Using 204 naturally isolated chicken- and turkey-source L. johnsonii, we demonstrate that there is a strong phylogenetic signal for coevolution with the animal host. These isolates differ phenotypically, even within host source, and these differences can be correlated with certain L. johnsonii phylogenetic clades. In commercial turkey poults, turkey-specific strains with strong in vitro phenotypes performed better early in life than strains lacking those phenotypes. A follow-up performance trial in broiler chickens demonstrated that chicken-specific strains result in better overall bird performance than nonchicken-specific strains. Collectively, this work provides evidence for the impact of host adaptation on a probiotic strain's potential. Furthermore, this top-down approach is useful for screening larger numbers of isolates for probiotic candidates.}, } @article {pmid37351543, year = {2023}, author = {Han, SL and Wang, MM and Ma, ZY and Raza, M and Zhao, P and Liang, JM and Gao, M and Li, YJ and Wang, JW and Hu, DM and Cai, L}, title = {Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus.}, journal = {Studies in mycology}, volume = {104}, number = {}, pages = {87-148}, doi = {10.3114/sim.2022.104.02}, pmid = {37351543}, issn = {0166-0616}, abstract = {Fusarium species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of Fusarium diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 Fusarium strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated Fusarium species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one Fusarium species, and the detailed associations are discussed. Following Koch's postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the "narrow" generic concept of Fusarium (= Gibberella). This study represents one of the most comprehensive surveys of cereal Fusarium diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated Fusarium species, as well as largely clarifies the phylogenetic relationships within the genus. Taxonomic novelties: New species: Fusarium erosum S.L. Han, M.M. Wang & L. Cai, Fusarium fecundum S.L. Han, M.M. Wang & L. Cai, Fusarium jinanense S.L. Han, M.M. Wang & L. Cai, Fusarium mianyangense S.L. Han, M.M. Wang & L. Cai, Fusarium nothincarnatum S.L. Han, M.M. Wang & L. Cai, Fusarium planum S.L. Han, M.M. Wang & L. Cai, Fusarium sanyaense S.L. Han, M.M. Wang & L. Cai, Fusarium weifangense S.L. Han, M.M. Wang & L. Cai. Citation: Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Studies in Mycology 104: 87-148. doi: 10.3114/sim.2022.104.02.}, } @article {pmid37342155, year = {2022}, author = {Réblová, M and Hernández-Restrepo, M and Sklenář, F and Nekvindová, J and Réblová, K and Kolařík, M}, title = {Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys.}, journal = {Studies in mycology}, volume = {103}, number = {}, pages = {87-212}, pmid = {37342155}, issn = {0166-0616}, abstract = {Chloridium is a little-studied group of soil- and wood-inhabiting dematiaceous hyphomycetes that share a rare mode of phialidic conidiogenesis on multiple loci. The genus has historically been divided into three morphological sections, i.e. Chloridium, Gongromeriza, and Psilobotrys. Sexual morphs have been placed in the widely perceived genus Chaetosphaeria, but unlike their asexual counterparts, they show little or no morphological variation. Recent molecular studies have expanded the generic concept to include species defined by a new set of morphological characters, such as the collar-like hyphae, setae, discrete phialides, and penicillately branched conidiophores. The study is based on the consilience of molecular species delimitation methods, phylogenetic analyses, ancestral state reconstruction, morphological hypotheses, and global biogeographic analyses. The multilocus phylogeny demonstrated that the classic concept of Chloridium is polyphyletic, and the original sections are not congeneric. Therefore, we abolish the existing classification and propose to restore the generic status of Gongromeriza and Psilobotrys. We present a new generic concept and define Chloridium as a monophyletic, polythetic genus comprising 37 species distributed in eight sections. In addition, of the taxa earlier referred to Gongromeriza, two have been redisposed to the new genus Gongromerizella. Analysis of published metabarcoding data showed that Chloridium is a common soil fungus representing a significant (0.3 %) proportion of sequence reads in environmental samples deposited in the GlobalFungi database. The analysis also showed that they are typically associated with forest habitats, and their distribution is strongly influenced by climate, which is confirmed by our data on their ability to grow at different temperatures. We demonstrated that Chloridium forms species-specific ranges of distribution, which is rarely documented for microscopic soil fungi. Our study shows the feasibility of using the GlobalFungi database to study the biogeography and ecology of fungi. Taxonomic novelties: New genus: Gongromerizella Réblová; New sections: Chloridium section Cryptogonytrichum Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Gonytrichopsis Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Metachloridium Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Volubilia Réblová, Hern.-Restr., M. Kolařík & F. Sklenar; New species: Chloridium bellum Réblová & Hern.-Restr., Chloridium biforme Réblová & Hern.-Restr., Chloridium detriticola Réblová & Hern.-Restr., Chloridium gamsii Réblová & Hern.-Restr., Chloridium guttiferum Réblová & Hern.-Restr., Chloridium moratum Réblová & Hern.-Restr., Chloridium peruense Réblová & Hern.-Restr., Chloridium novae-zelandiae Réblová & Hern.-Restr., Chloridium elongatum Réblová & Hern.-Restr., Chloridium volubile Réblová & Hern.-Restr.; New varieties: Chloridium bellum var. luteum Réblová & Hern.-Restr., Chloridium detriticola var. effusum Réblová & Hern.-Restr., Chloridium chloridioides var. convolutum Réblová & Hern.-Restr.; New combinations: Chloridium section Gonytrichum (Nees & T. Nees) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Mesobotrys (Sacc.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Pseudophialocephala (M.S. Calabon et al.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium simile (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium chloridioides (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium subglobosum (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium fuscum (Corda) Réblová & Hern.-Restr., Chloridium ypsilosporum (Hol.-Jech.) Réblová & Hern.-Restr., Chloridium costaricense (G. Weber et al.) Réblová & Hern.-Restr., Chloridium cuneatum (N.G. Liu et al.) Réblová & Hern.-Restr., Fusichloridium cylindrosporum (W. Gams & Hol.-Jech.) Réblová, Gongromeriza myriocarpa (Fr.) Réblová, Gongromeriza pygmaea (P. Karst.) Réblová, Gongromerizella lignicola (F. Mangenot) Réblová, Gongromerizella pachytrachela (W. Gams & Hol.-Jech) Réblová, Gongromerizella pini (Crous & Akulov) Réblová; New name: Chloridium pellucidum Réblová & Hern.-Restr.; Epitypifications (basionyms): Chaetopsis fusca Corda, Gonytrichum caesium var. subglobosum W. Gams & Hol.-Jech.; Lectotypification (basionym): Gonytrichum caesium Nees & T. Nees. Citation: Réblová M, Hernández-Restrepo M, Sklenář F, Nekvindová J, Réblová K, Kolařík M (2022). Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys. Studies in Mycology 103: 87-212. doi: 10.3114/sim.2022.103.04.}, } @article {pmid37330325, year = {2023}, author = {Jiang, Y and Wu, R and Zhang, W and Xin, F and Jiang, M}, title = {Construction of stable microbial consortia for effective biochemical synthesis.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2023.05.008}, pmid = {37330325}, issn = {1879-3096}, abstract = {Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.}, } @article {pmid37313763, year = {2023}, author = {Gouvêa, DY and Brigandt, I}, title = {Against unifying homology concepts: Redirecting the debate.}, journal = {Journal of morphology}, volume = {284}, number = {7}, pages = {e21599}, doi = {10.1002/jmor.21599}, pmid = {37313763}, issn = {1097-4687}, abstract = {The term "homology" is persistently polysemous, defying the expectation that extensive scientific research should yield semantic stability. A common response has been to seek a unification of various prominent definitions. This paper proposes an alternative strategy, based on the insight that scientific concepts function as tools for research: When analyzing various conceptualizations of homology, we should preserve those distinguishing features that support particular research goals. We illustrate the fruitfulness of our strategy by application to two cases. First, we revisit Lankester's celebrated evolutionary reappraisal of homology and argue that his analysis has been distorted by assimilation to modern agendas. His "homogeny" does not mean the same thing as modern evolutionary "homology," and his "homoplasy" is no mere antonym. Instead, Lankester uses both new terms to pose a question that remains strikingly relevant-how do mechanistic and historical causes of morphological resemblance interact? Second, we examine the puzzle of avian digit homology, which exemplifies disciplinary differences in homology conceptualization and assessment. Recent progress has been fueled by the development of new tools within the relevant disciplines (paleontology and developmental biology) and especially by increasing interdisciplinary cooperation. Conceptual unification has played very little role in this work, which instead seeks concrete evolutionary scenarios that integrate all the available evidence. Together these cases indicate the complex relationship between concepts and other tools in homology research.}, } @article {pmid37284912, year = {2023}, author = {Kock, A and Pheiffer, W and Wepener, V and Smit, NJ and Taylor, JC}, title = {Using Confocal Microscopy and Pigment Analyses to Detect Adverse Insecticide Effects in non-target Freshwater Diatom species - a proof-of-concept Using Nitzschia palea.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {110}, number = {6}, pages = {107}, pmid = {37284912}, issn = {1432-0800}, abstract = {The persistence of insecticides in aquatic environments is a cause of concern and to date hardly any studies have focused on the effects that DDT and deltamethrin have on non-target freshwater diatom communities. The application of diatoms in ecotoxicological studies is well acknowledged and therefore this study used laboratory bioassays to determine the effects that DDT and deltamethrin have on a monoculture of a diatom indicator species, Nitzschia palea. The insecticides affected the morphology of chloroplasts at all exposure concentrations. These effects were a maximum reduction in chlorophyll concentrations (4.8% and 2.3%), cell viability (51% and 42%), and increases in cell deformities (3.6% and 1.6%) following exposure to DDT and deltamethrin respectively. Based on the results we propose that methods, such as confocal microscopy, chlorophyll-α analysis and cell deformities are useful tools in assessing the effects of insecticides on diatoms.}, } @article {pmid37251510, year = {2023}, author = {Cocquyt, C and Verschuren, D}, title = {Checklist of the diatoms (Bacillariophyta) from Lake Naivasha, Kenya, with some historical notes.}, journal = {PhytoKeys}, volume = {224}, number = {}, pages = {101-174}, pmid = {37251510}, issn = {1314-2011}, abstract = {Lake Naivasha is one of only two large freshwater lakes in the Eastern Rift Valley of Kenya, East Africa. Together with its satellite lakes Crescent Island Crater, Oloidien and Sonachi, it comprises a great variety of pelagic and benthic habitats for aquatic biota, and its sediment record represents a unique archive of past climate change and long-term ecosystem dynamics in equatorial East Africa. This is particularly so because local paleoenvironmental reconstructions can be checked against historical data on the composition of aquatic fauna and flora collected in Lake Naivasha since the early 20[th] century. Some of the most prominent biological proxies for reconstructing past changes in lakes are diatoms (Bacillariophyta), a group of unicellular autotrophic eukaryotes of which the siliceous skeletons (valves) preserve well in lake sediments and are good indicators for, among others, climate-driven changes in salinity. However, diatom taxonomy and species concepts have changed a lot in recent decades, making it sometimes difficult for non-taxonomists to know which species are concerned in different published studies. This paper provides the currently accepted taxonomic names of the 310 specific and infraspecific diatom taxa reported from Lake Naivasha and its satellite lakes to date, together with their synonyms used in literature concerning these lakes as well as other, commonly used synonyms. Further, a short overview is given of the history of diatom research conducted on materials from Lake Naivasha and its satellite lakes. The present checklist may facilitate the identification and interpretation aspects of future diatom studies on the wider Lake Naivasha ecosystem and on other East African lakes that are less well studied.}, } @article {pmid37234963, year = {2023}, author = {Amézquita, A and Mazariegos-H, LA and Cañaveral, S and Orejuela, C and Barragán-Contreras, LA and Daza, JM}, title = {Species richness under a vertebral stripe: integrative taxonomy uncovers three additional species of Pholidobolus lizards (Sauria, Squamata, Gymnophthalmidae) from the north-western Colombian Andes.}, journal = {ZooKeys}, volume = {1141}, number = {}, pages = {119-148}, doi = {10.3897/zookeys.1141.94774}, pmid = {37234963}, issn = {1313-2989}, abstract = {The systematic study of biodiversity underlies appropriate inference in most other fields of biological research, yet it remains hampered by disagreements on both theoretical and empirical issues such as the species concept and the operational diagnosis of a species. Both become particularly challenging in those lineages where morphological traits are evolutionarily constrained by their adaptive value. For instance, cryptic organisms often conserve or converge in their external appearance, which hinders the recognition of species boundaries. An integrative approach has been adopted to study microgeographic variation in the leaf-litter lizard Pholidobolusvertebralis and test three predictions derived from the evolutionary species concept. Molecular data provided unambiguous evidence of divergence among the three recovered new clades and a common evolutionary history for each of them. The broadly sympatric clades were indeed diagnosable from externally visible traits, such as head scales, adult size, and sexually dimorphic ventral colouration. Also, they barely overlapped on the phenotypic space that summarised 39 morphometric and meristic traits. These clades are described as three species and an available name is suggested for a recovered fourth clade. The geographic distribution of the new and proximate species suggests a role for elevation on evolutionary divergence; it also raises interesting questions on the speciation pattern of an otherwise underestimated cryptic lineage.}, } @article {pmid37218757, year = {2023}, author = {Eilertsen, HC and Strømholt, J and Bergum, JS and Eriksen, GK and Ingebrigtsen, R}, title = {Mass Cultivation of Microalgae: II. A Large Species Pulsing Blue Light Concept.}, journal = {Biotech (Basel (Switzerland))}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/biotech12020040}, pmid = {37218757}, issn = {2673-6284}, abstract = {If mass cultivation of photoautotrophic microalgae is to gain momentum and find its place in the new "green future", exceptional optimizations to reduce production costs must be implemented. Issues related to illumination should therefore constitute the main focus, since it is the availability of photons in time and space that drives synthesis of biomass. Further, artificial illumination (e.g., LEDs) is needed to transport enough photons into dense algae cultures contained in large photobioreactors. In the present research project, we employed short-term O2 production and 7-day batch cultivation experiments to evaluate the potential to reduce illumination light energy by applying blue flashing light to cultures of large and small diatoms. Our results show that large diatom cells allow more light penetration for growth compared to smaller cells. PAR (400-700 nm) scans yielded twice as much biovolume-specific absorbance for small biovolume (avg. 7070 μm[3]) than for large biovolume (avg. 18,703 μm[3]) cells. The dry weight (DW) to biovolume ratio was 17% lower for large than small cells, resulting in a DW specific absorbance that was 1.75 times higher for small cells compared to large cells. Blue 100 Hz square flashing light yielded the same biovolume production as blue linear light in both the O2 production and batch experiments at the same maximum light intensities. We therefore suggest that, in the future, more focus should be placed on researching optical issues in photobioreactors, and that cell size and flashing blue light should be central in this.}, } @article {pmid37214460, year = {2023}, author = {Raclariu-Manolică, AC and Mauvisseau, Q and de Boer, HJ}, title = {Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1179099}, doi = {10.3389/fphar.2023.1179099}, pmid = {37214460}, issn = {1663-9812}, abstract = {Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.}, } @article {pmid37202254, year = {2023}, author = {Pacheco, MA and Escalante, AA}, title = {Origin and diversity of malaria parasites and other Haemosporida.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2023.04.004}, pmid = {37202254}, issn = {1471-5007}, abstract = {Symbionts, including parasites, are ubiquitous in all world ecosystems. Understanding the diversity of symbiont species addresses diverse questions, from the origin of infectious diseases to inferring processes shaping regional biotas. Here, we review the current approaches to studying Haemosporida's species diversity and evolutionary history. Despite the solid knowledge of species linked to diseases, such as the agents of human malaria, studies on haemosporidian phylogeny, diversity, ecology, and evolution are still limited. The available data, however, indicate that Haemosporida is an extraordinarily diverse and cosmopolitan clade of symbionts. Furthermore, this clade seems to have originated with their vertebrate hosts, particularly birds, as part of complex community level processes that we are still characterizing.}, } @article {pmid37186410, year = {2023}, author = {Li, M and Li, H and Zhang, X and Wang, X and Tao, Y}, title = {Mechanistic insight into anion-binding catalytic living cationic polymerization.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202303237}, doi = {10.1002/anie.202303237}, pmid = {37186410}, issn = {1521-3773}, abstract = {Exploiting non-covalent interactions to catalyze challenging ionic polymerizations is an ambitious goal but is in its infancy. We recently demonstrated non-covalent anion-binding catalysis as an effective methodology to enable living cationic polymerization (LCP) of vinyl ethers in an environmentally benign manner. Here, we further elucidate the structure-reactivity relationships of the elaborately designed seleno-cyclodiphosph(V)azanes catalysts and the roles of anion-binding interactions by a combined theoretical DFT study and experimental study. The investigation suggests that the distinct cis-cyclodiphosph(V)azane framework combined with "selenium effect" and electron-withdrawing 3,5-(CF3)2-Phenyl substitution pattern in catalyst enables a critical contribution to accessing excellent stability, anion affinity and solubility under polymerization conditions. Thus, the catalyst could leverage anion-binding interactions to precisely control reversible and transient dormant-active species equilibrium, allowing it to dynamically bind, recognize and pre-organize propagating ionic species and monomer, thereby facilitating efficient chain propagation and minimizing irreversible chain transfer events under mild conditions. The more in-depth understanding of the mechanism for anion-binding catalytic LCP reported herein should help to guide future catalyst design and to extend this concept to broader polymerization systems where ionic species serve as crucial intermediates.}, } @article {pmid37186045, year = {2023}, author = {Temraleeva, AD and Portnaya, EA}, title = {Morphological and Molecular Genetic Analyses of the Genus Vischeria (Eustigmatophyceae, Ochrophyta) in the Algal Collection of Soil Science Institute.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {508}, number = {1}, pages = {20-31}, pmid = {37186045}, issn = {1608-3105}, abstract = {Four soil eustigmatophyte algal strains isolated from gray forest soils in Moscow and Tula regions of Russia and deposited in the Algal Collection of Soil Science Institute (ACSSI) were examined by morphological and molecular genetic methods. The strains were assigned to the genus Vischeria on evidence of 18S rRNA gene and ITS2 phylogeny. The strains were morphologically similar to V. magna. However, only one of them, ACSSI 026, clustered with the authentic strain SAG 2554, while the other strains formed a separate independent group. The taxonomy of the genus is problematic because its phylogenetic tree based on the 18S rRNA gene and ITS2 is unresolved, the variable regions V4-V5 and V8-V9 of the 18S rRNA gene are noninformative, and the compensatory base change (CBC) concept fails to work (the concept states that closely related species are distinct if even a single CBC occurs in conserved secondary structure regions of ITS2). The concept of species is presumably possible to develop for Eustigmatophyceae and the genus Vischeria in particular when a greater number of eustigmatophyte algal strains are isolated from various biotopes; plastid genes are used or the total plastid genome is deeply sequenced; and ultrastructural, physiological, and biochemical characteristics are studied in more detail.}, } @article {pmid37168247, year = {2023}, author = {Iwamoto, Y and Degawa, Y and Nakayama, T}, title = {Re-examination of a rare protosteloid amoeba Schizoplasmodiopsis micropunctata, and the revision of Tychosporium (Cavosteliida, Variosea, Amoebozoa).}, journal = {Mycoscience}, volume = {64}, number = {2}, pages = {63-68}, doi = {10.47371/mycosci.2023.01.002}, pmid = {37168247}, issn = {1618-2545}, abstract = {The genus Schizoplasmodiopsis is one of the most morphologically diverse groups among the class Variosea. Recent phylogenetic studies suggest that Schizoplasmodiopsis is polyphyletic, but there are few taxonomic studies of this genus. We established S. micropunctata strain YIP-40, observed in detail its of morphology and lifecycle, and conducted a phylogenetic analysis. The phylogenetic analysis revealed that S. micropunctata was sister to Tychosporium acutostipes. Scanning electron microscopy showed S. micropunctata had a non-deciduous hilum structure that is unique to Tychosporium. The morphology of amoebae, mitotic behavior, and prespore cells of S. micropunctata also supported the close relationship to Tychosporium. We propose to transfer S. micropunctata to Tychosporium and emend the generic concept of Tychosporium to include this species.}, } @article {pmid37147058, year = {2023}, author = {Jeanroy, F and Demontrond, F and Vidal, FX and Gueyrard, D and Vidal, S and Demesmay, C and Dugas, V}, title = {Deciphering dynamic combinatorial libraries of glycoclusters with miniaturized weak affinity chromatography coupled with mass spectrometry (nano-FAC-MS).}, journal = {Analytica chimica acta}, volume = {1261}, number = {}, pages = {341227}, doi = {10.1016/j.aca.2023.341227}, pmid = {37147058}, issn = {1873-4324}, abstract = {We report an original methodology based on affinity chromatography coupled with mass spectrometry to decipher the complexity of dynamic combinatorial libraries (DCLs) of glycoclusters. Such libraries are intended to boost the design of potential therapeutic anti-infectious agents targeting Pseudomonas aeruginosa, which is responsible for numerous diseases, mostly found in hospitals as major a cause of nosocomial infections. Dynamic combinatorial chemistry provides a rapid access to an equilibrating mixture of glycocluster candidates through the formation of reversible covalent bonds under thermodynamic control. Identifying each molecule in the complex mixture overcomes challenges due to the dynamic process. Selection of glycoclusters candidates was first realized on a model lectin (Concanavalin A, ConA). Home-made affinity nanocolumns, containing covalently immobilized ConA and have volumes in the microliter range, were used to separate DCLs of glycoclusters with respect to their specific lectin binding properties under buffered aqueous conditions. Miniaturization facilitates the inline coupling with MS detection in such purely aqueous and buffered conditions and reduces target protein consumption. Monolithic lectin-affinity columns prepared by immobilization of ConA were first characterized using a known ligand. The amount of active binding immobilized lectin is 61 ± 5 pmol on 8.5-cm length column. We demonstrated the ability of our approach to evaluate individual dissociation constants of species directly in the complex mixture. The concept was then successfully applied to the screening of DCLs of more complex glycoclusters to identify (by mass spectrometry) and rank the ligands (by relative breakthrough curve delay) according to their affinity for the immobilized lectin in a single experiment.}, } @article {pmid37143529, year = {2023}, author = {Nascimento Brito, V and Lana Alves, J and Sírio Araújo, K and de Souza Leite, T and Borges de Queiroz, C and Liparini Pereira, O and de Queiroz, MV}, title = {Endophytic Trichoderma species from rubber trees native to the Brazilian Amazon, including four new species.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1095199}, pmid = {37143529}, issn = {1664-302X}, abstract = {Fungi belonging to the genus Trichoderma have been widely recognized as efficient controllers of plant diseases. Although the majority of isolates currently deployed, thus far, have been isolated from soil, endophytic Trichoderma spp. is considered to be a promising option for application in biocontrol. In this study, 30 endophytic Trichoderma isolates-obtained from the leaves, stems, and roots of wild Hevea spp. in the Brazilian Amazon-were analyzed using specific DNA barcodes: sequences of internal transcribed spacers 1 and 2 of rDNA (ITS region), genes encoding translation elongation factor 1-α (TEF1-α), and the second largest subunit of RNA polymerase II (RPB2). The genealogical concordance phylogenetic species recognition (GCPSR) concept was used for species delimitation. A phylogenetic analysis showed the occurrence of Trichoderma species, such as T. erinaceum, T. ovalisporum, T. koningiopsis, T. sparsum, T. lentiforme, T. virens, and T. spirale. Molecular and morphological features resulted in the discovery of four new species, such as T. acreanum sp. nov., T. ararianum sp. nov., T. heveae sp. nov., and T. brasiliensis sp. nov. The BI and ML analyses shared a similar topology, providing high support to the final trees. The phylograms show three distinct subclades, namely, T. acreanum and T. ararianum being paraphyletic with T. koningiopsis; T. heveae with T. subviride; and T. brasiliensis with T. brevicompactum. This study adds to our knowledge of the diversity of endophytic Trichoderma species in Neotropical forests and reveals new potential biocontrol agents for the management of plant diseases.}, } @article {pmid37097257, year = {2023}, author = {Ballego-Campos, I and Bonifácio, SKV and Assis, LCS}, title = {A unified view of homology.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/cla.12541}, pmid = {37097257}, issn = {1096-0031}, abstract = {As it spread through time and into distinct areas of science-from comparative anatomy to evolutionary biology, cladistics, developmental and molecular biology-the homology concept has changed considerably, presenting various meanings. Despite many attempts at developing a comprehensive understanding of the concept, this context-sensitive notion of homology has been a subject of an ongoing debate. Inspired by that and following Kevin de Queiroz and Richard Mayden's view on species concept and delimitation, we presented in this article an attempt to systematize and advance the understanding of the homology problem. Our main goals were: (i) to present a comprehensive checklist of 'concepts of homology'; (ii) to identify which are really concepts with ontological definitions (theoretically rooted in structural correspondence and common ancestry), and which are, in fact, not concepts, but epistemological (empirical and methodological) criteria of homology delimitation; (iii) to provide a synonymy of the concepts and criteria of homology delimitation; (iv) to present a hierarchy of homology concepts within Hennig's hologenetic system; and (v) to endorse the adoption of a unified view of homology by treating homology as a correspondence of spatio-temporal properties (genetic, epigenetic, developmental and positional) at the level of the individual, species or monophyletic group. We found 59 'concepts of homology' in the literature, from which 34 were categorically treated as concepts, 17 as criteria of homology delimitation, Four were excluded from our treatment, and Müller's five concepts were rather treated as approaches to homology. Homology concepts and criteria were synonymized based on structural correspondence, replicability, common ancestry, genetic and epigenetic developmental causes, position and optimization. Regarding the synonymy, we conclusively recognized 21 different concepts of homology, and five empirical and four methodological criteria. Hierarchical ontological aspects of homology were systematized under Hennig's hologenetic system, based on the existence of ontogenetic, tokogenetic and phylogenetic levels of homology. The delimitation of tokogenetic and phylogenetic homologies depends on optimization criteria. The unified view of homology is discussed in the context of the ancestral angiosperm flower.}, } @article {pmid37089520, year = {2022}, author = {Shibata, S and Hirooka, Y}, title = {Taxonomy and phylogeny of Exobasidium pentasporium causing witches' broom of Rhododendron species.}, journal = {Mycoscience}, volume = {63}, number = {6}, pages = {247-253}, pmid = {37089520}, issn = {1340-3540}, abstract = {Exobasidium pentasporium was first found on Rhododendron kaempferi in Nikko, Tochigi Prefecture, Japan and described only with a brief mentions and illustration of a specimen in 1896. This fungus causes a witches' broom disease of Rhododendron species. To stabilize the concept of this species, the specimen in the protologue was located, carefully examined, and illustrated. In addition, the name was epitypified based on a newly collected topotype specimen. A phylogenetic tree using ITS and LSU sequences showed that our isolates of E. pentasporium grouped with other Exobasidium species on Rhododendron forming a monophyletic clade with strong statistical support and were unrelated to E. nobeyamense, another causal agent of witches' broom disease on Rhododendron species.}, } @article {pmid37079045, year = {2023}, author = {Liberles, DA}, title = {A Genomic Conceptualization of Species.}, journal = {Journal of molecular evolution}, volume = {}, number = {}, pages = {}, pmid = {37079045}, issn = {1432-1432}, abstract = {Species concepts have been defined through a number of lenses, but are almost entirely empirical in nature. Fundamentally linked to various existing species concepts, an interpretation of genomic data through a species classification filter based upon a theoretical genotype-phenotype map with a monophyly requirement is discussed.}, } @article {pmid37066658, year = {2023}, author = {Bangal, P and Sridhar, H}, title = {Revisiting the 'nuclear species' concept: do we really know what we think we know?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {378}, number = {1878}, pages = {20220108}, doi = {10.1098/rstb.2022.0108}, pmid = {37066658}, issn = {1471-2970}, abstract = {The idea of 'nuclear species' has received a lot of attention in mixed-species flock research. Our impression of this literature is that referenced statements tend to cite the same papers in support of a small set of ideas, and often there is a mismatch between what papers contain and what they're cited for. Motivated by these impressions, we built and quantitatively examined a database of referenced statements about nuclearity in flocks. This confirmed our impression quantitatively, but more strikingly, a single paper stood out in its influence on ideas around nuclearity in flocks. Moynihan's 1962 monograph on mixed-species flocks in Panama, 'The organization and probable evolution of some mixed-species flocks of neotropical birds' published in Smithsonian Miscellaneous Collections, was cited twice as much as the next most-cited paper and was the most-cited paper for 10 out of 15 most-discussed ideas related to nuclearity. Further, a number of other highly cited papers are strongly influenced by Moynihan's ideas, i.e. its influence is much greater than what a count of citations conveys. We also found that Moynihan was mis-cited frequently. We juxtapose what we found from the citation analysis with what the paper actually contains to better understand the nature of support that Moynihan provides, and discuss the implications of our findings for what we know about and how we research nuclearity in flocks. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.}, } @article {pmid37052581, year = {2023}, author = {De León, ME and Wilson, HS and Jospin, G and Eisen, JA}, title = {Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, doi = {10.1099/mgen.0.000971}, pmid = {37052581}, issn = {2057-5858}, abstract = {Violacein is a water-insoluble violet pigment produced by various Gram-negative bacteria. The compound and the bacteria that produce it have been gaining attention due to the antimicrobial and proposed antitumour properties of violacein and the possibility that strains producing it may have broad industrial uses. Bacteria that produce violacein have been isolated from diverse environments including fresh and ocean waters, glaciers, tropical soils, trees, fish and the skin of amphibians. We report here the isolation and characterization of six violacein-producing bacterial strains and three non-violacein-producing close relatives, each isolated from either an aquatic environment or moist food materials in northern California, USA. For each isolate, we characterized traditional phenotypes, generated and analysed draft genome sequences, and carried out multiple types of taxonomic, phylogenetic and phylogenomic analyses. Based on these analyses we assign putative identifications to the nine isolates, which include representatives of the genera Chromobacterium, Aquitalea, Iodobacter, Duganella, Massilia and Janthinobacterium. In addition, we discuss the utility of various metrics for taxonomic assignment in these groups including average nucleotide identity, whole genome phylogenetic analysis and extent of recent homologous recombination using the software program PopCOGenT.}, } @article {pmid37045753, year = {2023}, author = {Winsor, MP}, title = {Darwin's dark matter: utter extinction.}, journal = {Annals of science}, volume = {}, number = {}, pages = {1-33}, doi = {10.1080/00033790.2023.2194889}, pmid = {37045753}, issn = {1464-505X}, abstract = {Species that died without leaving descendants Darwin called 'utterly extinct'. They far outnumber the ancestors of all living things, so they resemble the dark matter of modern cosmology, which far outweighs visible matter. He realized in 1837 that their absence is what creates the groups in a natural classification. In his Notebook B he combined the idea that species multiply with the idea that ancestors' relatives must mostly be extinct. The fossil Megatherium was utterly extinct. The iconic branching 'I think' diagram shows extinction causing the origin of genera by eliminating intermediate species. Darwin's concept of taxonomic ranks, starting with the genus, was informed by his interaction with taxonomists. Based on his familiarity with demography, Darwin reasoned that the survival of transitional forms was unlikely, which helped him decide to focus at the species level. When drafting his theory in the 1840s, he left out these speculative ideas, but they emerged again in the 1850s when he realized his theory needed a cause for branches to diverge. His ecological answer worked at the species level, but his Principle of Divergence was unconvincing at higher taxonomic levels. In the Origin, Darwin repeatedly insisted on the importance of utter extinction..}, } @article {pmid37045431, year = {2022}, author = {Yan, M and Bao, J and Luo, M and Gao, Y and Dietrich, CH and Duan, Y}, title = {Phylogenetic analyses and species delimitation of Aconurella Ribaut (Hemiptera: Cicadellidae: Deltocephalinae: Chiasmini) in China based on molecular data.}, journal = {Zootaxa}, volume = {5205}, number = {3}, pages = {281-296}, doi = {10.11646/zootaxa.5205.3.6}, pmid = {37045431}, issn = {1175-5334}, abstract = {The grassland leafhopper genus Aconurella is widespread in the Old World. Species of this genus are difficult to identify by traditional morphological characters but the morphology-based species classification in this genus has not previously been tested using molecular data. This study analysed DNA sequence data from two mitochondrial genes (COI, 16S) and one nuclear gene (ITS2) to infer the phylogenetic relationships and status of five previously recognized Aconurella species and compare the performance of different molecular species-delimitation methods using single and multiple loci. The analysis divided the included haplotypes into five well-supported subclades, most corresponding to existing morphology-based species concepts. However, different molecular species delimitation methods (jMOTU, ABGD, bPTP, GMYC and BPP) yielded somewhat different results, suggesting the presence of between 4 and 8 species, sometimes lumping the haplotypes of Aconurella diplachnis and Aconurella sibirica into a single species or recognizing multiple putative species within Aconurella prolixa. Considering the different results yielded by various methods employing single loci, the BPP method, which combines data from multiple loci, may be more reliable for delimiting species of Aconurella. Our results suggest that the morphological characters previously used to identify these species are reliable and adequately reflect boundaries between genetically distinct taxa.}, } @article {pmid37045293, year = {2022}, author = {Uluar, O and Yahyaoğlu, Ö and Çiplak, B}, title = {Anatolian endemic genus Bolua (Orthoptera: Tettigoniidae: Tettigoniinae): genetic and phenotypic data indicate inconsistent diversity and evolutionary patterns.}, journal = {Zootaxa}, volume = {5195}, number = {3}, pages = {224-240}, doi = {10.11646/zootaxa.5195.3.2}, pmid = {37045293}, issn = {1175-5334}, abstract = {Anatolia harbours diverse and unique biodiversity. Nearly half of the genera and more than 80% of the species belonging to the tettigoniid subfamily Tettigoniinae are endemic to Anatolia. Although the Anatolian Tettigoniinae have been well studied, proper documentation of Tettigoniinae biodiversity requires studies using contemporary approaches and techniques. We attempted to study the taxonomy, phylogeny, and phylogeography of the Bolua, a monotypic genus endemic to northwest Anatolia. Species delimitation tests applied to three mitochondrial and two nuclear gene segments indicated three putative species in the genus. Analyses suggested inversely related genetic and phenotypic divergence. By integrating these results, we reached the following conclusions. (i) The plausible taxonomic composition recognizes three species in the genus; the type species Bolua turkiyae and two new species B. balikesirensis sp. n. and B. bursaensis sp. n., (ii) the radiation steps in Bolua correspond to the starting of the Pliocene, Mid Pleistocene Transition (MPT) and end of cold periods of Günz and Riss glacial. By considering intra generic divergence steps and habitat preference plus the distribution pattern of the species, ecological speciation seems to be the mode of generic radiation, (iii) possibly due to habitat conservatism, the isolated relict populations on highlands evolved under similar selection pressures, and this led to a conserved phenotype, consequently morphologically poorly diverged species, though genetic divergence is deep and (iv) although morphological diagnoses is poor, genetic divergence between species is deep, and each species fulfils the criteria of several species concepts.}, } @article {pmid37045148, year = {2023}, author = {Abo-Shnaf, R and Castilho, RC and Marticorena, JLM and DE Moraes, GJ}, title = {A new genus and three new species of mites, with a revised concept of the family Ameroseiidae (Acari: Mesostigmata: Ascoidea).}, journal = {Zootaxa}, volume = {5231}, number = {3}, pages = {249-272}, doi = {10.11646/zootaxa.5231.3.2}, pmid = {37045148}, issn = {1175-5334}, abstract = {This paper describes a new genus and three new species of mites found in litter and soil samples from Brazil and Egypt. Endopodoseius Abo-Shnaf & Moraes n. gen., Endopodoseius erikae Abo-Shnaf & Marticorena n. sp., Endopodoseius zaheri Abo-Shnaf & Moraes n. sp. and Endopodoseius edmilsoni Abo-Shnaf & Castilho n. sp. are considered to belong to the Superfamily Ascoidea and the Family Ameroseiidae. The concept of the family is expanded to include species with one or more of the following character states-the podonotal and opisthonotal shields partially or totally separate; poroid iv1 absent; dorsal idiosomal setae J1, J5 and R1 present; genital seta st5 inserted outside the epigynal shield; opisthogaster with 7-10 pairs of setae; and femur II with 11 setae.}, } @article {pmid37045079, year = {2023}, author = {Tishechkin, DY}, title = {An enigma of Handianus Ribaut, 1942 (Hemiptera: Cicadellidae: Deltocephalinae: Athysanini): identical host preferences and male calling signals in two morphologically distinctive sympatric species.}, journal = {Zootaxa}, volume = {5239}, number = {4}, pages = {585-592}, doi = {10.11646/zootaxa.5239.4.9}, pmid = {37045079}, issn = {1175-5334}, abstract = {Handianus eurotiae and H. fartilis distinctly differ in the forewing venation and the male genitalia shape, but have strongly overlapping ranges, do not differ in ecological preferences, feed on the same host plant, Krascheninnikovia ceratoides, and produce almost identical male calling signals. They were never found in the same biotope, although the mechanism of such vicariation is not clear. According to Mayr's biological species concept, such taxa are good species, but Paterson's species recognition concept is inapplicable in this case. Similar examples in Orthoptera and Auchenorrhyncha are considered.}, } @article {pmid37044546, year = {2022}, author = {Bartlett, JS and Lambkin, CL}, title = {Australian Opilonini (Coleoptera: Cleridae: Clerinae) part I: A revised taxonomy for Australian Opilo Latreille including descriptions of new genera and species.}, journal = {Zootaxa}, volume = {5220}, number = {1}, pages = {1-81}, doi = {10.11646/zootaxa.5220.1.1}, pmid = {37044546}, issn = {1175-5334}, abstract = {The species- and genus-level taxonomy of Australian species assigned to Opilo Latreille is assessed and revised in the context of a morphological species concept. Australian species are deemed not congeneric with Opilo mollis (Linnaeus), the type species of Opilo Latreille. Species are grouped into genera by degree of difference observed in states of the tegmen, median lobe, antennal scape, basitarsi, hindwing, elytral striae and pronotal disc. Examination of 1,259 specimens resulted in recognition of 6 genera and 44 species, 36 of which are new to science. The following new genera are proposed: Ancyropilus gen. nov.; Culcipternulus gen. nov.; Infectostriatus gen. nov.; Monilonotum gen. nov.; Notopilo gen. nov.; Platynotum gen. nov.. Three infraspecific taxa described as 'varieties', viz, Opilo congruus var. abdominalis Schenkling, 1901, Notoxus congruus var. femoralis Westwood, 1849 and Opilo pascoei var. doddi Schenkling, 1906, are elevated to species status, with Opilo abdominalis (occupied by Opilo abdominalis Fairmaire, 1891) requiring a replacement name. The 44 species recognised in this revision are: Ancyropilus brigalowae sp. nov.; Ancyropilus emmotti sp. nov.; Ancyropilus exossuarius sp. nov.; Ancyropilus hornensis sp. nov.; Ancyropilus labris sp. nov.; Ancyropilus monteithi sp. nov.; Ancyropilus noonbahensis sp. nov.; Ancyropilus packsaddlensis sp. nov.; Ancyropilus simplex sp. nov.; Ancyropilus tricolor sp. nov.; Culcipternulus mareebensis sp. nov.; Infectostriatus absentis sp. nov.; Infectostriatus differens sp. nov.; Monilonotum bunyense sp. nov.; Monilonotum doddi (Schenkling, 1906) stat. rev., comb. nov. (transferred from Opilo); Monilonotum eburneocincta (Gorham, 1878) comb. nov. (transferred from Opilo); Monilonotum pascoei (Gorham, 1876) comb. nov. (transferred from Opilo); Monilonotum rufiventre (Gerstmeier, 1990) comb. nov. (transferred from Olesterus); Monilonotum sundholmi sp. nov.; Notopilo beswickensis sp. nov.; Notopilo brevistriatus sp. nov.; Notopilo calicis sp. nov.; Notopilo cambageicola sp. nov.; Notopilo confusus sp. nov.; Notopilo congruus (Newman) comb. nov. (transferred from Opilo); Notopilo elstoni sp. nov.; Notopilo eremosus sp. nov.; Notopilo gerstmeieri sp. nov.; Notopilo interfabulatus sp. nov.; Notopilo katherinensis sp. nov.; Notopilo lawnhillensis sp. nov.; Notopilo magnus sp. nov.; Notopilo obesus sp. nov.; Notopilo reduncus stat, rev., nom. nov. (replacement name for Opilo abdominalis Schenkling, 1901); Notopilo tanybasilaris sp. nov.; Notopilo tompricensis sp. nov.; Notopilo variipes (Chevrolat) comb. nov. (transferred from Opilo); Notopilo xanthoimprocerus sp. nov.; Notopilo xanthoprolatus sp. nov.; Platynotum bulli sp. nov.; Platynotum culgoense sp. nov.; Platynotum femorale (Westwood) stat. rev., comb. nov. (transferred from Opilo); Platynotum foveosetosa sp. nov.; Platynotum gracile sp. nov.. The available names Opilus congruus Newman, 1842 and Opilus femoralis Westwood, 1849, are respectively corrected to Opilo congruus Newman, 1842 and Opilo femoralis Westwood, 1849 in accordance with Article 11.9.3.2 of the Code (ICZN 1999). Lectotypes are designated for Opilo abdominalis Schenkling, 1901, Opilo congruus Newman, 1842, Opilo femoralis Westwood, 1849, Opilo variipes Chevrolat, Opilo doddi Schenkling, 1906 and Opilo pascoei Gorham, 1876.}, } @article {pmid37044430, year = {2023}, author = {Huo, QB and Zhao, MY and DU, YZ and Murányi, D and Zhu, BQ and Yu, L}, title = {The intraspecific morphological variability of Styloperla Wu, 1935 (Plecoptera: Styloperlidae).}, journal = {Zootaxa}, volume = {5249}, number = {1}, pages = {125-137}, doi = {10.11646/zootaxa.5249.1.7}, pmid = {37044430}, issn = {1175-5334}, abstract = {Intraspecific morphological variability of four Styloperla Wu, 1935 species are described and discussed in this paper. The males of each species have variable specializations present at their basal cercal process, including the variable number of branches or differing degrees of curvature at the apical spines. A generalization on the species definition of Plecoptera, especially a new concept of conspecificity is also provided herein.}, } @article {pmid37023708, year = {2023}, author = {Hanganu-Opatz, IL and Klausberger, T and Sigurdsson, T and Nieder, A and Jacob, SN and Bartos, M and Sauer, JF and Durstewitz, D and Leibold, C and Diester, I}, title = {Resolving the prefrontal mechanisms of adaptive cognitive behaviors: A cross-species perspective.}, journal = {Neuron}, volume = {111}, number = {7}, pages = {1020-1036}, doi = {10.1016/j.neuron.2023.03.017}, pmid = {37023708}, issn = {1097-4199}, abstract = {The prefrontal cortex (PFC) enables a staggering variety of complex behaviors, such as planning actions, solving problems, and adapting to new situations according to external information and internal states. These higher-order abilities, collectively defined as adaptive cognitive behavior, require cellular ensembles that coordinate the tradeoff between the stability and flexibility of neural representations. While the mechanisms underlying the function of cellular ensembles are still unclear, recent experimental and theoretical studies suggest that temporal coordination dynamically binds prefrontal neurons into functional ensembles. A so far largely separate stream of research has investigated the prefrontal efferent and afferent connectivity. These two research streams have recently converged on the hypothesis that prefrontal connectivity patterns influence ensemble formation and the function of neurons within ensembles. Here, we propose a unitary concept that, leveraging a cross-species definition of prefrontal regions, explains how prefrontal ensembles adaptively regulate and efficiently coordinate multiple processes in distinct cognitive behaviors.}, } @article {pmid37016427, year = {2023}, author = {van der Wal, FJ and Achterberg, RP and van der Goot, JA and Dinkla, A and Bossers-de Vries, R and van Solt-Smits, C and Bossers, A and Heijne, M}, title = {Proof of concept for multiplex detection of antibodies against Chlamydia species in chicken serum using a bead-based suspension array with peptides as antigens.}, journal = {Veterinary research}, volume = {54}, number = {1}, pages = {31}, pmid = {37016427}, issn = {1297-9716}, abstract = {The available differentiating tests for Chlamydia are based on detection of genetic material and only give information about the actual infection status, but reveal nothing of past infections. As the use of serological methods increases the window of detection, the goal of this study was to investigate if it is possible to develop a differentiating serological test for antibodies against Chlamydia species in chicken sera. Focus was on C. psittaci, C. gallinacea, and two closely related species, i.e. C. abortus and C. avium. To enable differentiating serology, a bead-based Luminex suspension array was constructed, using peptides as antigens, derived from known immunoreactive Chlamydia proteins. For the majority of these peptides, species-specific seroreactivity in mammalian sera has been reported in literature. The suspension array correctly identified antibodies against various Chlamydia species in sera from experimentally infected mice, and was also able to differentiate between antibodies against C. psittaci and C. gallinacea in sera from experimentally infected chickens. In field sera, signals were difficult to interpret as insufficient sera from experimentally infected chickens were available for evaluating the seroreactivity of all peptides. Nevertheless, results of the suspension array with field sera are supported by published data on the occurrence of C. gallinacea in Dutch layers, thereby demonstrating the proof of concept of multiplex serology for Chlamydial species in poultry.}, } @article {pmid37015274, year = {2023}, author = {Caicoya, AL and Schaffer, A and Holland, R and von Fersen, L and Colell, M and Amici, F}, title = {Innovation across 13 ungulate species: problem solvers are less integrated in the social group and less neophobic.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1996}, pages = {20222384}, doi = {10.1098/rspb.2022.2384}, pmid = {37015274}, issn = {1471-2954}, abstract = {Innovation is the ability to solve new problems or find novel solutions to familiar problems, and it is known to provide animals with crucial fitness benefits. Although this ability has been extensively studied in some taxa, the factors that predict innovation within and across species are still largely unclear. In this study, we used a novel foraging task to test 111 individuals belonging to 13 ungulate species-a still understudied taxon. To solve the task, individuals had to open transparent and opaque cups with food rewards, by removing their cover. We assessed whether individual factors (neophobia, social integration, sex, age, rank) and socio-ecological factors (dietary breadth, fission-fusion dynamics, domestication, group size) predicted participation and performance in the task. Using a phylogenetic approach, we showed that success was higher for less neophobic and socially less integrated individuals. Moreover, less neophobic individuals, individuals of domesticated species and having higher fission-fusion dynamics were more likely to participate in the task. These results are in line with recent literature suggesting a central role of sociality and personality traits to successfully deal with novel challenges, and confirm ungulates as a promising taxon to test evolutionary theories with a comparative approach.}, } @article {pmid36994538, year = {2023}, author = {Qiu, L and Dong, J and Li, X and Parey, SH and Tan, K and Orr, M and Majeed, A and Zhang, X and Luo, S and Zhou, X and Zhu, C and Ji, T and Niu, Q and Liu, S and Zhou, X}, title = {Defining honeybee subspecies in an evolutionary context warrants strategized conservation.}, journal = {Zoological research}, volume = {44}, number = {3}, pages = {483-493}, doi = {10.24272/j.issn.2095-8137.2022.414}, pmid = {36994538}, issn = {2095-8137}, abstract = {Despite the urgent need for conservation consideration, strategic action plans for the preservation of the Asian honeybee, Apis cerana Fabricius, 1793, remain lacking. Both the convergent and divergent adaptations of this widespread insect have led to confusing phenotypical traits and inconsistent infraspecific taxonomy. Unclear subspecies boundaries pose a significant challenge to honeybee conservation efforts, as it is difficult to effectively prioritize conservation targets without a clear understanding of subspecies identities. Here, we investigated genome variations in 362 worker bees representing almost all populations of mainland A. cerana to understand how evolution has shaped its population structure. Whole-genome single nucleotide polymorphisms (SNPs) based on nuclear sequences revealed eight putative subspecies, with all seven peripheral subspecies exhibiting mutually exclusive monophyly and distinct genetic divergence from the widespread central subspecies. Our results demonstrated that most classic morphological traits, including body size, were related to the climatic variables of the local habitats and did not reflect the true evolutionary history of the organism. Thus, such morphological traits were not suitable for subspecific delineation. Conversely, wing vein characters showed relative independence to the environment and supported the subspecies boundaries inferred from nuclear genomes. Mitochondrial phylogeny further indicated that the present subspecies structure was a result of multiple waves of population divergence from a common ancestor. Based on our findings, we propose that criteria for subspecies delineation should be based on evolutionary independence, trait distinction, and geographic isolation. We formally defined and described eight subspecies of mainland A. cerana. Elucidation of the evolutionary history and subspecies boundaries enables a customized conservation strategy for both widespread and endemic honeybee conservation units, guiding colony introduction and breeding.}, } @article {pmid36983491, year = {2023}, author = {Du, Z and Li, Y and Wang, XC and Wang, K and Yao, YJ}, title = {Re-Examination of the Holotype of Ganoderma sichuanense (Ganodermataceae, Polyporales) and a Clarification of the Identity of Chinese Cultivated Lingzhi.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {3}, pages = {}, doi = {10.3390/jof9030323}, pmid = {36983491}, issn = {2309-608X}, abstract = {The widely cultivated Chinese Lingzhi is a famous fungus with significant medicinal and economic value, which has commonly been misidentified as Ganoderma lucidum for a long period of time. The scientific binomial of the fungus is always a hotly debated question that revolves around G. lingzhi and G. sichuanense. To interpret the species concept of the taxon, six specific primers for G. sichuanense and one universal primer were designed. Through directed and nested PCRs, we obtained nine ITS sequences from the holotype (HMAS 42798) of G. sichuanense. By genome sequencing, the ITS sequence of the first cultivated Lingzhi (HMAS 25103) was assembled. Based on a phylogenetic study of the genus Ganoderma, the correct name for widely cultivated Ganoderma species in China was confirmed as G. sichuanense, and G. lingzhi should be a later synonym.}, } @article {pmid36979054, year = {2023}, author = {Żabicka, J and Kirschey, T and Migdałek, G and Słomka, A and Kuta, E}, title = {Genetic Variation versus Morphological Variability in European Peatland Violets (Viola epipsila-V. palustris Group).}, journal = {Biology}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/biology12030362}, pmid = {36979054}, issn = {2079-7737}, abstract = {In Europe, the V. epipsila-V. palustris group comprises V. epipsila Ledeb., V. palustris L., V. pubifolia (Kuta) G. H. Loos (=V. palustris subsp. pubifolia Kuta), interspecific hybrids, and putative introgressants. The genetic affinity of V. pubifolia to V. palustris, and their shared origin via hybridization followed by polyploidization, were confirmed using inter simple sequence repeat (ISSR) markers, restriction site-associated DNA sequencing (RAD-Seq), and a low-copy nuclear gene, GPI, which encodes glucose-6-phosphate isomerase. The other taxa of subsect. Stolonosae were not identified as putative parents of V. pubifolia by GPI. Our analyses indicated that V. pubifolia can be included in the morphological and genetic variation of V. palustris. The ISSR, RAD-Seq, and genome size value separated well V. palustris from V. epipsila and hybrids. The results also reopen the discussion on intraspecific variation in the context of taxa ranks and species concepts. The reduced tolerance of V. epipsila in Europe to changing environmental conditions might result from low genetic differentiation and heterozygosity, as well as the increased number of interspecific hybrids (V. epipsila × V. palustris), and eventually can possibly lead to its extinction. The disappearance of populations/individuals of this species may indicate anthropogenic changes occurring in peatlands.}, } @article {pmid36944262, year = {2023}, author = {Milner, DS and Galindo, LJ and Irwin, NAT and Richards, TA}, title = {Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes.}, journal = {Annual review of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-micro-032421-115538}, pmid = {36944262}, issn = {1545-3251}, abstract = {Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the functional factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, } @article {pmid36920650, year = {2023}, author = {Konashev, MB}, title = {The Russian Backdrop to Dobzhansky's Genetics and the Origin of Species.}, journal = {Journal of the history of biology}, volume = {}, number = {}, pages = {}, pmid = {36920650}, issn = {1573-0387}, abstract = {Theodosius Dobzhansky was one of the principal 'founding fathers' of the modern 'synthetic theory of evolution' and the 'biological species' concept, first set forth in his classic book, Genetics and the Origin of Species (1937). Much of the discussion of Dobzhansky's work by historians has focused on English-accessible sources, and has emphasized the roles of the Morgan School, and figures such as Sewall Wright, and Leslie C. Dunn. This article uses Dobzhansky's Russian articles that are unknown to English-speaking readers, and his late 1920s to early 1930s correspondence with colleagues and friends in the Soviet Union, to clarify some of the Russian influences on Dobzhansky's evolving evolutionary views, particularly the development of his views on species and speciation. For Dobzhansky, as for Darwin, the problem of species and speciation was crucial for his theoretical explanation of evolution.}, } @article {pmid36890896, year = {2023}, author = {Bai, S and Han, X and Feng, D}, title = {Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1139744}, pmid = {36890896}, issn = {1664-462X}, abstract = {High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.}, } @article {pmid36876315, year = {2023}, author = {Wang, MZ and Fan, XK and Zhang, YH and Wu, J and Mao, LM and Zhang, SL and Cai, MQ and Li, MH and Zhu, ZS and Zhao, MS and Liu, LX and Cameron, KM and Li, P}, title = {Phylogenomics and integrative taxonomy reveal two new species of Amana (Liliaceae).}, journal = {Plant diversity}, volume = {45}, number = {1}, pages = {54-68}, pmid = {36876315}, issn = {2468-2659}, abstract = {Until now the genus Amana (Liliaceae), known as 'East Asian tulips', has contained just seven species. In this study, a phylogenomic and integrative taxonomic approach was used to reveal two new species, Amana nanyueensis from Central China and A. tianmuensis from East China. A. nanyueensis resembles Amana edulis in possessing a densely villous-woolly bulb tunic and two opposite bracts, but differs in its leaves and anthers. Amana tianmuensis resembles Amana erythronioides in possessing three verticillate bracts and yellow anthers, but differs in aspects of its leaves and bulbs. These four species are clearly separated from each other in principal components analysis based on morphology. Phylogenomic analyses based on plastid CDS further support the species delimitation of A. nanyueensis and A. tianmuensis and suggests they are closely related to A. edulis. Cytological analysis shows that A. nanyueensis and A. tianmuensis are both diploid (2n = 2x = 24), different from A. edulis, which is either diploid (northern populations) or tetraploid (southern populations, 2n = 4x = 48). The pollen morphology of A. nanyueensis is similar to other Amana species (single-groove germination aperture), but A. tianmuensis is quite different because of the presence of a sulcus membrane, which creates the illusion of double grooves. Ecological niche modelling also revealed a niche differentiation between A. edulis, A. nanyueensis and A. tianmuensis.}, } @article {pmid36876113, year = {2023}, author = {Anderson, BD and Bisanz, JE}, title = {Challenges and opportunities of strain diversity in gut microbiome research.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1117122}, pmid = {36876113}, issn = {1664-302X}, abstract = {Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.}, } @article {pmid36845931, year = {2023}, author = {Zuo, J and Zhu, E and Yin, W and Yao, C and Liao, J and Ping, X and Zhu, Y and Cai, X and Rao, Y and Feng, H and Zhang, K and Qian, Z}, title = {Long-term spatiotemporal and highly specific imaging of the plasma membrane of diverse plant cells using a near-infrared AIE probe.}, journal = {Chemical science}, volume = {14}, number = {8}, pages = {2139-2148}, pmid = {36845931}, issn = {2041-6520}, abstract = {Fluorescent probes are valuable tools to visualize plasma membranes intuitively and clearly and their related physiological processes in a spatiotemporal manner. However, most existing probes have only realized the specific staining of the plasma membranes of animal/human cells within a very short time period, while almost no fluorescent probes have been developed for the long-term imaging of the plasma membranes of plant cells. Herein, we designed an AIE-active probe with NIR emission to achieve four-dimensional spatiotemporal imaging of the plasma membranes of plant cells based on a collaboration approach involving multiple strategies, demonstrated long-term real-time monitoring of morphological changes of plasma membranes for the first time, and further proved its wide applicability to plant cells of different types and diverse plant species. In the design concept, three effective strategies including the similarity and intermiscibility principle, antipermeability strategy and strong electrostatic interactions were combined to allow the probe to specifically target and anchor the plasma membrane for an ultralong amount of time on the premise of guaranteeing its sufficiently high aqueous solubility. The designed APMem-1 can quickly penetrate cell walls to specifically stain the plasma membranes of all plant cells in a very short time with advanced features (ultrafast staining, wash-free, and desirable biocompatibility) and the probe shows excellent plasma membrane specificity without staining other areas of the cell in comparison to commercial FM dyes. The longest imaging time of APMem-1 can be up to 10 h with comparable performance in both imaging contrast and imaging integrity. The validation experiments on different types of plant cells and diverse plants convincingly proved the universality of APMem-1. The development of plasma membrane probes with four-dimensional spatial and ultralong-term imaging ability provides a valuable tool to monitor the dynamic processes of plasma membrane-related events in an intuitive and real-time manner.}, } @article {pmid36842092, year = {2023}, author = {Kious, BM}, title = {Suffering and the dilemmas of pediatric care: a response to Tyler Tate.}, journal = {Theoretical medicine and bioethics}, volume = {}, number = {}, pages = {}, pmid = {36842092}, issn = {1573-0980}, abstract = {In a recent article, Tyler Tate argues that the suffering of children - especially children with severe cognitive impairments - should be regarded as the antithesis of flourishing, where flourishing is relative to one's individual characteristics and essentially involves receiving care from others. Although initially persuasive, Tate's theory is ambiguous in several ways, leading to significant conceptual problems. By identifying flourishing with receiving care, Tate raises questions about the importance of care that he does not address, giving rise to a bootstrapping problem. By making flourishing relative to an individual's circumstances, Tate is forced to confront questions about exactly how relative it can be, suggesting the possibility that, on his view, to flourish is simply to be however one is. In an attempt to surmount these problems, I offer a revision and restatement of Tate's view that defines the relationship between individualized flourishing and the more conventional, species-relative concept, and describe more clearly the role that care should play with respect to flourishing - one that is instrumental and not merely constitutive. Even this restated view, however, fails to answer difficult questions about how one should respond to the medical needs of some children, highlighting the fact that a conceptual analysis of suffering may do little, in the end, to untangle ethical dilemmas in the care of severely ill children.}, } @article {pmid36793683, year = {2023}, author = {Korshunova, T and Lundin, K and Malmberg, K and Martynov, A}, title = {Narrowly defined taxa on a global scale: The phylogeny and taxonomy of the genera Catriona and Tenellia (Nudibranchia, Trinchesiidae) favours fine-scale taxonomic differentiation and dissolution of the "lumpers & splitters" dilemma.}, journal = {Evolutionary applications}, volume = {16}, number = {2}, pages = {428-460}, pmid = {36793683}, issn = {1752-4571}, abstract = {By applying morphological and molecular data on two genera of the nudibranch molluscs it is shown that the tension between taxonomic practice and evolutionary processes persists. A review of the related genera Catriona and Tenellia is used to demonstrate that the fine-scale taxonomic differentiation is an important tool in the integration of morphological and molecular data. This is highlighted by the hidden species problem and provides strong argument that the genus must be kept as a maximally narrowly-defined entity. Otherwise, we are forced to compare a highly disparate species under the putatively lumped name "Tenellia". We demonstrate this in the present study by applying a suite of delimitation methods and describing a new species of Tenellia from the Baltic Sea. The new species possesses fine-scale morphological distinguishing features, which were not investigated before. The true, narrowly defined genus Tenellia represents a peculiar taxon with a clearly expressed paedomorphic characters and predominantly brackish-water habitats. The phylogenetically related genus Catriona, of which three new species are described here, clearly demonstrates different features. A lumping decision to call many morphologically and evolutionary different taxa as "Tenellia" will downgrade the taxonomic and phylogenetic resolution of the entire family Trinchesiidae to just a single genus. The dissolution of the dilemma of "lumpers & splitters", which still significantly affects taxonomy, will further help to make systematics a true evolutionary discipline.}, } @article {pmid36775928, year = {2023}, author = {Sherratt, E and Kraatz, B}, title = {Multilevel analysis of integration and disparity in the mammalian skull.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/evolut/qpad020}, pmid = {36775928}, issn = {1558-5646}, abstract = {Biological variation is often considered in a scalable hierarchy, e.g., within the individual, within the populations, above the species level. Morphological integration, the concept of covariation among constituent parts of an organism, is also hierarchical; the degree to which these 'modules' covary is a matter of the scale of the study as well as underlying processes driving the covariation. Multilevel analyses of trait covariation are a valuable tool to infer the origins and historical persistence of morphological diversity. Here we investigate concordance in patterns of integration and modularity across three biological levels of variation: within a species, within two genera-level radiations, and among species at the family level. We demonstrate this approach using the skull of mammalian family Leporidae (rabbits and hares), which is morphologically diverse and has a rare-among-mammals functional signal of locomotion adaptation. We tested three alternative hypotheses of modularity; from the most supported we investigated disparity and integration of each module to infer which is most responsible for patterns of cranial variation across these levels, and whether variation is partitioned consistently across levels. We found a common pattern of modularity underlies leporid cranial diversity, though there is inconsistency across levels in each module's disparity and integration. The face module contributes the most to disparity at all levels, which we propose is facilitating evolutionary diversity in this clade. Therefore, the distinctive facial tilt of leporids is an adaptation to locomotory behavior facilitated by a modular system that allows lineages to respond differently to selection pressures.}, } @article {pmid36765984, year = {2023}, author = {Fraiture, MA and D'aes, J and Guiderdoni, E and Meunier, AC and Delcourt, T and Hoffman, S and Vandermassen, E and De Keersmaecker, SCJ and Vanneste, K and Roosens, NHC}, title = {Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/foods12030455}, pmid = {36765984}, issn = {2304-8158}, abstract = {Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) organisms and their derived food/feed products commercialized on the European Union market fall within the scope of European Union Directive 2001/18/EC. Consequently, their control in the food/feed chain by GMO enforcement laboratories is required by the competent authorities to guarantee food/feed safety and traceability (2003/1829/EC; 2003/1830/EC). However, their detection is potentially challenging at both the analytical and interpretation levels since this requires methodological approaches that can target and detect a specific single nucleotide variation (SNV) introduced into a GE organism. In this study, we propose a targeted high-throughput sequencing approach, including (i) a prior PCR-based enrichment step to amplify regions of interest, (ii) a sequencing step, and (iii) a data analysis methodology to identify SNVs of interest. To investigate if the performance of this targeted high-throughput sequencing approach is compatible with the performance criteria used in the GMO detection field, several samples containing different percentages of a GE rice line carrying a single adenosine insertion in OsMADS26 were prepared and analyzed. The SNV of interest in samples containing the GE rice line could successfully be detected, both at high and low percentages. No impact related to food processing or to the presence of other crop species was observed. The present proof-of-concept study has allowed us to deliver the first experimental-based evidence indicating that the proposed targeted high-throughput sequencing approach may constitute, in the future, a specific and sensitive tool to support the safety and traceability of the food/feed chain regarding GE plants carrying SNVs.}, } @article {pmid36761452, year = {2022}, author = {Sharkey, MJ and Tucker, EM and Baker, A and Smith, MA and Ratnasingham, S and Manjunath, R and Hebert, P and Hallwachs, W and Janzen, D}, title = {More discussion of minimalist species descriptions and clarifying some misconceptions contained in Meier et al. 2021.}, journal = {ZooKeys}, volume = {1110}, number = {}, pages = {135-149}, pmid = {36761452}, issn = {1313-2989}, abstract = {This is a response to a preprint version of "A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science", https://www.biorxiv.org/content/10.1101/2021.04.28.441626v2. Meier et al. strongly criticized Sharkey et al.'s publication in which 403 new species were deliberately minimally described, based primarily on COI barcode sequence data. Here we respond to these criticisms. The following points are made: 1) Sharkey et al. did not equate BINs with species, as demonstrated in several examples in which multiple species were found to be in single BINs. 2) We reiterate that BINs were used as a preliminary sorting tool, just as preliminary morphological identification commonly sorts specimens based on color and size into unit trays; despite BINs and species concepts matching well over 90% of species, this matching does not equate to equality. 3) Consensus barcodes were used only to provide a diagnosis to conform to the rules of the International Code of Zoological Nomenclature just as consensus morphological diagnoses are. The barcode of a holotype is definitive and simply part of its cellular morphology. 4) Minimalist revisions will facilitate and accelerate future taxonomic research, not hinder it. 5) We refute the claim that the BOLD sequences of Plesiocoelusvanachterbergi are pseudogenes and demonstrate that they simply represent a frameshift mutation. 6) We reassert our observation that morphological evidence alone is insufficient to recognize species within species-rich higher taxa and that its usefulness lies in character states that are congruent with molecular data. 7) We show that in the cases in which COI barcodes code for the same amino acids in different putative species, data from morphology, host specificity, and other ecological traits reaffirm their utility as indicators of genetically distinct lineages.}, } @article {pmid36761113, year = {2022}, author = {Brunke, AJ}, title = {A world generic revision of Quediini (Coleoptera, Staphylinidae, Staphylininae), part 1. Early diverging Nearctic lineages.}, journal = {ZooKeys}, volume = {1134}, number = {}, pages = {129-170}, pmid = {36761113}, issn = {1313-2989}, abstract = {Several phylogenetically isolated, early diverging lineages of rove beetle tribe Quediini, all endemic to the western Nearctic, have recently been revealed by phylogenomic systematics. These three lineages, currently treated as either Quedius (Raphirus) or Q. (Paraquedius) warrant recognition at the genus level in the ongoing effort to achieve reciprocal monophyly of genera in Quediini. The three lineages were each morphologically studied in detail, with the following results: Paraquedius Casey, stat. res. is re-elevated to genus rank, Quediellus Casey, stat. res. is resurrected from synonymy and redefined, and Iratiquedius gen. nov. is described for the species of the Amabilis and Prostans groups. A morphological diagnosis is provided for each genus at both the global and regional (Nearctic) level. Species level revisions, with keys, are provided for Iratiquedius, Paraquedius, and Quediellus with the following results: Iratiquediusuncifer sp. nov. and Paraquediusmarginicollis sp. nov. are described, Quediellusnanulus Casey is treated as syn. nov. of Quediellusdebilis (Horn), and I.amabilis (Smetana), I.mutator (Smetana), and P.puncticeps (Horn) are substantially redefined. Where possible, CO1 barcode sequence data are integrated with the morphological species concepts used herein and their clusters were found to be congruent.}, } @article {pmid36761034, year = {2022}, author = {Boza Espinoza, TE and Kessler, M}, title = {A monograph of the genus Polylepis (Rosaceae).}, journal = {PhytoKeys}, volume = {203}, number = {}, pages = {1-274}, pmid = {36761034}, issn = {1314-2011}, abstract = {We present a monograph of the high Andean tree genus Polylepis (Rosaceae), based on a species concept considering morphological, climatic and biogeographic distinctness as indicators of evolutionary independence. In total, we recognize 45 species of Polylepis, grouped in five sections. Polylepissect.Sericeae is represented by 15 species in four subsections, P.sect.Reticulatae by seven species, P.sect.Subsericantes by three species, P.sect.Australes by two species and P.sect.Incanaee by three subsections with 18 species. We describe seven new species, one from Colombia (P.frontinensis), one from Ecuador (P.simpsoniae) and five from Peru (P.acomayensis, P.fjeldsaoi, P.occidentalis, P.pilosissima and P.sacra). Three species from Peru (P.albicans, P.pallidistigma and P.serrata) are re-instated as valid species. Two taxa from Bolivia (P.incanoides and P.nana) are elevated from subspecies to species rank. The morphology, habitat, distribution, ecology and conservation status of each species are documented. We also provide an identification key to the species of the genus and general introductions on taxonomic history, morphology, evolution, ecology and conservation.}, } @article {pmid36760461, year = {2022}, author = {Sklenář, F and Glässnerová, K and Jurjević, Ž and Houbraken, J and Samson, RA and Visagie, CM and Yilmaz, N and Gené, J and Cano, J and Chen, AJ and Nováková, A and Yaguchi, T and Kolařík, M and Hubka, V}, title = {Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability.}, journal = {Studies in mycology}, volume = {102}, number = {}, pages = {53-93}, pmid = {36760461}, issn = {0166-0616}, abstract = {Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera. Citation: Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102 : 53-93. doi: 10.3114/sim.2022.102.02.}, } @article {pmid36719249, year = {2023}, author = {Rivi, V and Benatti, C and Rigillo, G and Blom, JMC}, title = {Invertebrates as models of learning and memory: investigating neural and molecular mechanisms.}, journal = {The Journal of experimental biology}, volume = {226}, number = {3}, pages = {}, doi = {10.1242/jeb.244844}, pmid = {36719249}, issn = {1477-9145}, abstract = {In this Commentary, we shed light on the use of invertebrates as model organisms for understanding the causal and conserved mechanisms of learning and memory. We provide a condensed chronicle of the contribution offered by mollusks to the studies on how and where the nervous system encodes and stores memory and describe the rich cognitive capabilities of some insect species, including attention and concept learning. We also discuss the use of planarians for investigating the dynamics of memory during brain regeneration and highlight the role of stressful stimuli in forming memories. Furthermore, we focus on the increasing evidence that invertebrates display some forms of emotions, which provides new opportunities for unveiling the neural and molecular mechanisms underlying the complex interaction between stress, emotions and cognition. In doing so, we highlight experimental challenges and suggest future directions that we expect the field to take in the coming years, particularly regarding what we, as humans, need to know for preventing and/or delaying memory loss. This article has an associated ECR Spotlight interview with Veronica Rivi.}, } @article {pmid36716112, year = {2023}, author = {Manoj, KM}, title = {Murburn posttranslational modifications of proteins: Cellular redox processes and murzyme-mediated metabolo-proteomics.}, journal = {Journal of cellular physiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jcp.30954}, pmid = {36716112}, issn = {1097-4652}, abstract = {Murburn concept constitutes the thesis that diffusible reactive species or DRS are obligatorily involved in routine metabolic and physiological activities. Murzymes are defined as biomolecules/proteins that generate/modulate/sustain/utilize DRS. Murburn posttranslational modifications (PTMs) result because murburn/murzyme functionalism is integral to cellular existence. Cells must incorporate the inherently stochastic nature of operations mediated by DRS. Due to the earlier/inertial stigmatic perception that DRS are mere agents of chaos, several such outcomes were either understood as deterministic modulations sponsored by house-keeping enzymes or deemed as unregulated nonenzymatic events resulting out of "oxidative stress". In the current review, I dispel the myths around DRS-functions, and undertake systematic parsing and analyses of murburn modifications of proteins. Although it is impossible to demarcate all PTMs into the classical or murburn modalities, telltale signs of the latter are evident from the relative inaccessibility of the locus, non-specificities and mechanistic details. It is pointed out that while many murburn PTMs may be harmless, some others could have deleterious or beneficial physiological implications. Some details of reversible/irreversible modifications of amino acid residues and cofactors that may be subjected to phosphorylation, halogenation, glycosylation, alkylation/acetylation, hydroxylation/oxidation, etc. are listed, along with citations of select proteins where such modifications have been reported. The contexts of these modifications and their significance in (patho)physiology/aging and therapy are also presented. With more balanced explorations and statistically verified data, a definitive understanding of normal versus pathological contexts of murburn modifications would be obtainable in the future.}, } @article {pmid36714688, year = {2022}, author = {Chang, JT and Chao, CT and Nakamura, K and Liu, HL and Luo, MX and Liao, PC}, title = {Corrigendum: Divergence with gene flow and contrasting population size blur the species boundary in Cycas Sect. Asiorientales, as inferred from morphology and RAD-seq data.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1081728}, doi = {10.3389/fpls.2022.1081728}, pmid = {36714688}, issn = {1664-462X}, abstract = {[This corrects the article DOI: 10.3389/fpls.2022.824158.].}, } @article {pmid36700086, year = {2021}, author = {Yoshimura, Y and Hamada, A and Augey, Y and Akiyama, M and Sakakibara, Y}, title = {Genomic style: yet another deep-learning approach to characterize bacterial genome sequences.}, journal = {Bioinformatics advances}, volume = {1}, number = {1}, pages = {vbab039}, pmid = {36700086}, issn = {2635-0041}, abstract = {MOTIVATION: Biological sequence classification is the most fundamental task in bioinformatics analysis. For example, in metagenome analysis, binning is a typical type of DNA sequence classification. In order to classify sequences, it is necessary to define sequence features. The k-mer frequency, base composition and alignment-based metrics are commonly used. On the other hand, in the field of image recognition using machine learning, image classification is broadly divided into those based on shape and those based on style. A style matrix was introduced as a method of expressing the style of an image (e.g. color usage and texture).

RESULTS: We propose a novel sequence feature, called genomic style, inspired by image classification approaches, for classifying and clustering DNA sequences. As with the style of images, the DNA sequence is considered to have a genomic style unique to the bacterial species, and the style matrix concept is applied to the DNA sequence. Our main aim is to introduce the genomics style as yet another basic sequence feature for metagenome binning problem in replace of the most commonly used sequence feature k-mer frequency. Performance evaluations showed that our method using a style matrix has the potential for accurate binning when compared with state-of-the-art binning tools based on k-mer frequency.

The source code for the implementation of this genomic style method, along with the dataset for the performance evaluation, is available from https://github.com/friendflower94/binning-style.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, } @article {pmid36696515, year = {2023}, author = {Le Bras, Z and Bouchet, S and Winkel, LHE}, title = {Sensitive and High-Throughput Analysis of Volatile Organic Species of S, Se, Br, and I at Trace Levels in Water and Atmospheric Samples by Thermal Desorption Coupled to Gas Chromatography and Inductively Coupled Plasma Mass Spectrometry.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.2c04751}, pmid = {36696515}, issn = {1520-6882}, abstract = {Emissions of volatile organic sulfur (S), selenium (Se), bromine (Br), and iodine (I) species from aquatic ecosystems represent an important source of these elements into the atmosphere. Available methods to measure these species are either not sensitive enough or not automated, which hinder a full understanding of species distribution and production mechanisms. Here, we present a sensitive and high-throughput method for the simultaneous and comprehensive quantification of S, Se, Br, and I volatile organic species in atmospheric and aqueous samples using a preconcentration step onto sorbent tubes and subsequent analysis by thermal desorption coupled to gas chromatography and inductively coupled plasma mass spectrometry (TD-GC-ICP-MS). Selected commercially available sorbent tubes, consisting of mixed porous polymer and graphitized black carbon, offered the highest trapping capacity and lowest loss of species when stored at -20 °C for 28 days after sampling. After optimization of the TD-GC-ICP-MS method, absolute detection limits were better than 3.8 pg, 9.1 fg, 313 fg, and 50 fg, respectively, for S, Se, Br, and I species. As a proof of concept, the concentrations of target species were determined in aqueous and continuously collected atmospheric samples during a cruise in the Baltic and North Seas. Moreover, unknown S, Br, and I volatile species were detected in both aqueous and atmospheric samples demonstrating the full potential of the method.}, } @article {pmid36696419, year = {2023}, author = {Chen, SW and Zheng, ZY and Mahfut, FB and Yang, Y and Ogino, M and Okada, K and Sato, K and Zhang, W}, title = {Leveraging an advanced simulated moving bed approach to achieve 3-component separation for enhanced impurity removal in a non-affinity cation exchange capture step.}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0280760}, doi = {10.1371/journal.pone.0280760}, pmid = {36696419}, issn = {1932-6203}, abstract = {One of the key challenges in downstream bioprocessing is to obtain products of high purity in a productive fashion through the effective removal of process and product related impurities. While a classical simulated moving bed (SMB) system operation can typically achieve a 2-component separation between the weakly bound impurities and target species, here we present an advanced SMB approach that can achieve a 3-component separation, including the removal of the strongly bound impurities from the target species. As a proof-of-concept, we demonstrate the enhanced removal of strongly bound host cell proteins (HCP) from the target monoclonal antibody (mAb) through the utilisation of the advanced SMB approach in a non-affinity cation exchange (CEX) capture step. In this way, 1 less polishing step was required to achieve the therapeutic requirements of < 100 ppm HCP and the overall process recovery was increased by ~ 6% compared to the corresponding process that utilised a batch CEX operation. The non-affinity CEX capture platform technology established through the utilisation of the advanced SMB approach presented here can potentially be further applied to address the downstream processing challenges presented by other challenging biotherapeutic modalities to yield a final target product with improved purity and recovery.}, } @article {pmid36671828, year = {2023}, author = {Bateman, RM and Rudall, PJ}, title = {Morphological Continua Make Poor Species: Genus-Wide Morphometric Survey of the European Bee Orchids (Ophrys L.).}, journal = {Biology}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/biology12010136}, pmid = {36671828}, issn = {2079-7737}, abstract = {Despite (or perhaps because of) intensive multidisciplinary research, opinions on the optimal number of species recognised within the Eurasian orchid genus Ophrys range from nine to at least 400. The lower figure of nine macrospecies is based primarily on seeking small but reliable discontinuities in DNA 'barcode' regions, an approach subsequently reinforced and finessed via high-throughput sequencing studies. The upper figure of ca. 400 microspecies reflects the morphological authoritarianism of traditional taxonomy combined with belief in extreme pollinator specificity caused by reliance on pollination through pseudo-copulation, enacted by bees and wasps. Groupings of microspecies that are less inclusive than macrospecies are termed mesospecies. Herein, we present multivariate morphometric analyses based on 51 characters scored for 457 individual plants that together span the full morphological and molecular diversity within the genus Ophrys, encompassing 113 named microspecies that collectively represent all 29 mesospecies and all nine macrospecies. We critique our preferred morphometric approach of accumulating heterogeneous data and analysing them primarily using principal coordinates, noting that our conclusions would have been strengthened by even greater sampling and the inclusion of data describing pseudo-pheromone cocktails. Morphological variation within Ophrys proved to be exceptionally multidimensional, lacking strong directional trends. Multivariate clustering of plants according to prior taxonomy was typically weak, irrespective of whether it was assessed at the level of macrospecies, mesospecies or microspecies; considerable morphological overlap was evident even between subsets of the molecularly differentiable macrospecies. Characters supporting genuine taxonomic distinctions were often sufficiently subtle that they were masked by greater and more positively correlated variation that reflected strong contrasts in flower size, tepal colour or, less often, plant size. Individual macrospecies appear to represent morphological continua, within which taxonomic divisions are likely to prove arbitrary if based exclusively on morphological criteria and adequately sampled across their geographic range. It remains unclear how much of the mosaic of subtle character variation among the microspecies reflects genetic versus epigenetic or non-genetic influences and what proportion of any contrasts observed in gene frequencies can be attributed to the adaptive microevolution that is widely considered to dictate speciation in the genus. Moreover, supplementing weak morphological criteria with extrinsic criteria, typically by imposing constraints on geographic location and/or supposed pollinator preference, assumes rather than demonstrates the presence of even the weakest of species boundaries. Overall, it is clear that entities in Ophrys below the level of macrospecies have insufficiently structured variation, either phenotypic or genotypic, to be resolved into discrete, self-circumscribing ("natural") entities that can legitimately be equated with species as delimited within other less specialised plant genera. Our search for a non-arbitrary (meso)species concept competent to circumscribe an intermediate number of species has so far proven unsuccessful.}, } @article {pmid36657627, year = {2023}, author = {Dai, C and Feng, P}, title = {Multiple concordant cytonuclear divergences and potential hybrid speciation within a species complex in Asia.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {107709}, doi = {10.1016/j.ympev.2023.107709}, pmid = {36657627}, issn = {1095-9513}, abstract = {Various environmental factors impact the distribution, population structure, demography and evolutionary trajectory of a bird species, leading to genetic and morphological divergences between populations across its distribution. The Paradoxornis webbianus species complex is found throughout much of East Asia, where its geographically distinct populations exhibit dramatic morphological variation. This has resulted in a hotly debated taxonomy. This study intended to identify genetic divergence patterns and their underlying contributing factors for this species complex. We collected 243 birds, whose data was combined with those available in GenBank to perform phylogeographic analyses using one mitochondrial and six nuclear loci. Six mitochondrial clades were observed in the species complex, while individual-based Bayesian clustering using nuclear markers showed multiple congruent breaks. Overall, the six molecular lineages could be recognized as independent species under the lineage species concept in view of genetic divergence, clade-specific morphological changes and distribution: P. webbianus, P. w. bulomachus, P. alphonsianus, P. a. ganluoensis, P. brunneus brunneus and P. b. ricketti. The estimated divergence times range from 0.46 to 3.36 million years ago, suggesting it was likely impacted by paleoclimatic changes. Interestingly, P. alphonsianus carries two divergent mitochondrial lineages shared with P. webbianus and P. a. ganluoensis, respectively, and analyses based on nuclear loci found a similar pattern. We discussed the various hypotheses for this pattern and argued that P. alphonsianus was likely the result of hybridization between P. webbianus and P. a. ganluoensis. Further data on genome, transcriptome and breeding ecology are needed to address the hypothesis of hybrid speciation and its underlying mechanisms.}, } @article {pmid36655041, year = {2023}, author = {Kim, JG and Cho, K and Yoon, SM and Lee, J}, title = {Taxonomic review of the genus Stenocaris Sars (Copepoda, Harpacticoida, Cylindropsyllidae), with (re)descriptions of two Stenocaris species from the Far East.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14623}, pmid = {36655041}, issn = {2167-8359}, abstract = {The taxonomic concept of the genus Stenocaris Sars, 1909 is uncertain because none of the synapomorphies for the species of Stenocaris are defined. Detailed comparison of previous records of Stenocaris minor (T. Scott, 1892) from different localities reveals that this species represents a species complex composed of two species, S. minor s. str. and S. minor sensu Cottarelli & Venanzetti, 1989. Because the latter species has fundamental differences in the nature of the fifth leg in females and the sexual dimorphism of the second leg in males, we propose a new species for S. minor sensu Cottarelli & Venanzetti, 1989, S. figaroloensis sp. nov. We also suggest that S. minor sensu Apostolov, 1971, S. minor sensu Marinov, 1971, and S. minor sensu Apostolov & Marinov, 1988 from the Black Sea and S. minor sensu Wilson, 1932 from North America should be relegated to species inquirenda in the genus. Taxonomic review of the morphology of all Stenocaris species indicated that the generic concept must be restricted to accommodate S. minor s. str., S. gracilis Sars, 1909, S. intermedia Itô, 1972, S. figaroloensis sp. nov., and the South Korean new species, S. marcida sp. nov., based on the synapomorphic condition of the confluent fifth leg in males. As a result of our analysis, two Stenocaris species, S. baltica Arlt, 1983 and S. pygmaea Noodt, 1955, are transferred to the genus Vermicaris Kornev & Chertoprud, 2008 as V. baltica (Arlt, 1983) comb. nov. and V. pygmaea (Noodt, 1955) comb. nov. based on the synapomorphic characters of a reduced condition of the second and fifth legs. Additionally, S. arenicola Wilson, 1932 and S. kliei (Kunz, 1938) are allocated to a new genus, Huysicaris gen. nov., mainly characterized by obvious caudal rami with a recurved dorsal spinous process and convex inner margins, as H. arenicola (Wilson, 1932) comb. nov. and H. kliei (Kunz, 1938) comb. nov. A marine interstitial harpacticoid collected from the subtidal substrate off Dok-do Island in the East Sea of South Korea is proposed as S. marcida sp. nov. and the distribution of S. intermedia, originally known from its type locality in Japanese waters only, is extended to the East Sea of Korea and Russia. We provide their detailed descriptions and illustrations and discuss the morphological characters supporting their identities.}, } @article {pmid36622661, year = {2022}, author = {Bolnick, DI and Hund, AK and Nosil, P and Peng, F and Ravinet, M and Stankowski, S and Subramanian, S and Wolf, JBW and Yukilevich, R}, title = {A multivariate view of the speciation continuum.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/evolut/qpac004}, pmid = {36622661}, issn = {1558-5646}, support = {/ERC_/European Research Council/International ; }, abstract = {The concept of a "speciation continuum" has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.}, } @article {pmid36620432, year = {2021}, author = {Hajdari, A and Pulaj, B and Schmiderer, C and Mala, X and Wilson, B and Lluga-Rizani, K and Mustafa, B}, title = {A phylogenetic analysis of the wild Tulipa species (Liliaceae) of Kosovo based on plastid and nuclear DNA sequence.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {2}, number = {3}, pages = {e202100016}, pmid = {36620432}, issn = {2641-6573}, abstract = {In Kosovo, the genus Tulipa is represented by eight taxa, most of which form a species complex surrounding Tulipa scardica. To investigate the phylogenetic relationship of these Tulipa species a Bayesian analysis was undertaken using the ITS nuclear marker and trnL-trnF, rbcL and psbA-trnH plastid markers. The resulting phylogenetic trees show that Kosovarian Tulipa species consistently group into two main clades, the subgenera Eriostemones and Tulipa. Furthermore, our analyses provide some evidence that the subspecies of Tulipa sylvestris are genetically distinguishable, however not significantly enough to support their reclassification as species. In contrast, the markers provide some novel information to reassess the species concepts of the T. scardica complex. Our data provide support for the synonymisation of Tulipa luanica and Tulipa kosovarica under the species Tulipa serbica. Resolution and sampling limitations hinder any concrete conclusion about whether Tulipa albanica and T. scardica are true species, yet our data do provide some support that these are unique taxa and therefore should continue to be treated as such until further clarification. Overall, our work shows that genetic data will be important in determining species concepts in this genus, however, even with a molecular perspective pulling apart closely related taxa can be extremely challenging.}, } @article {pmid36585846, year = {2022}, author = {Cobo-Simón, M and Hart, R and Ochman, H}, title = {Escherichia coli: What is and Which are?.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msac273}, pmid = {36585846}, issn = {1537-1719}, abstract = {Escherichia coli have served as important model organisms for over a century-used to elucidate key aspects of genetics, evolution, molecular biology, and pathogenesis. However, defining which strains actually belong to this species is erratic and unstable due to shifts in the characters and criteria used to distinguish bacterial species. Additionally, many isolates designated as E. coli are genetically more closely related to strains of Shigella than to other E. coli, creating a situation in which the entire genus of Shigella and its four species are encompassed within the single species E. coli. We evaluated all complete genomes assigned to E. coli and its closest relatives according to the Biological Species Concept (BSC), using evidence of reproductive isolation and gene flow (i.e., homologous recombination in the case of asexual bacteria) to ascertain species boundaries. The BSC establishes a uniform, consistent and objective principle that allows species-level classification across all Domains of Life and does not rely on either phenotypic or genotypic similarity to a defined type-specimen for species membership. Analyzing a total of 1887 sequenced genomes and comparing our results to other genome-based classification methods, we found few barriers to gene flow among the strains, clades, phylogroups or species within E. coli and Shigella. Due to the utility in recognizing which strains constitute a true biological species, we designate genomes that form a genetic cohesive group as members of E. coliBIO.}, } @article {pmid36558823, year = {2022}, author = {Carrillo-Bilbao, G and Navarro, JC and Martin-Solano, S and Chávez-Larrea, MA and Cholota-Iza, C and Saegerman, C}, title = {First Molecular Identification of Trypanosomes and Absence of Babesia sp. DNA in Faeces of Non-Human Primates in the Ecuadorian Amazon.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, doi = {10.3390/pathogens11121490}, pmid = {36558823}, issn = {2076-0817}, abstract = {Trypanosomes are a group of pathogens distributed in the continents of Africa, America, Asia and Europe, and they affect all vertebrates including the neotropical primate group. Information about the trypanosome's diversity, phylogeny, ecology and pathology in non-human primates (NHPs) from the neotropical region is scarce. The objective of the study was to identify Trypanosoma and Babesia molecularly in NHPs under the phylogenetic species concept. We extracted DNA from a total of 76 faecal samples collected between 2019 and 2021, from a total of 11 non-human primate species of which 46 are from captive NHPs and 30 are free-living NHPs in the Western Amazon region of Ecuador. We did not detect DNA of Babesia sp. by polymerase chain reaction test in any of the faecal samples. However, the nested-PCR-based method revealed Trypanosoma parasites by ITS gene amplification in two faecal samples; one for the species Leontocebus lagonotus (from the captive population) and a second one for Cebus albifrons (from the free-ranging population). Maximum parsimony and likelihood methods with the Kimura2+G+I model inferred the evolutionary history of the two records, which showed an evolutionary relationship with the genus Trypanosoma. Two sequences are monophyletic with Trypanosoma. However, the number of sequences available in GenBank for their species identification is limited. The two samples present different molecular identifications and evolutionary origins in the tree topology. We are most likely referring to two different species, and two different localities of infection. We suggest that health management protocols should be implemented to prevent the transmission of blood-borne pathogens such as Trypanosoma sp. among captive populations. In addition, these protocols also protect the personnel of wildlife rehabilitation centers working in close proximity to NHPs and vice versa.}, } @article {pmid36511814, year = {2022}, author = {Deepak, V and Gower, DJ and Cooper, N}, title = {Diet and habit explain head-shape convergences in natricine snakes.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeb.14139}, pmid = {36511814}, issn = {1420-9101}, abstract = {The concept of ecomorphs, whereby species with similar ecologies have similar phenotypes regardless of their phylogenetic relatedness, is often central to discussions regarding the relationship between ecology and phenotype. However, some aspects of the concept have been questioned, and sometimes species have been grouped as ecomorphs based on phenotypic similarity without demonstrating ecological similarity. Within snakes, similar head shapes have convergently evolved in species living in comparable environments and/or with similar diets. Therefore, ecomorphs could exist in some snake lineages, but this assertion has rarely been tested for a wide-ranging group within a single framework. Natricine snakes (Natricinae) are ecomorphologically diverse and currently distributed in Asia, Africa, Europe and north-central America. They are primarily semiaquatic or ground-dwelling terrestrial snakes, but some are aquatic, burrowing or aquatic and burrowing in habit and may be generalist or specialist in diet. Thus, natricines present an interesting system to test whether snakes from different major habit categories represent ecomorphs. We quantify morphological similarity and disparity in head shape among 191 of the ca. 250 currently recognized natricine species and apply phylogenetic comparative methods to test for convergence. Natricine head shape is largely correlated with habit, but in some burrowers is better explained by dietary specialism. Convergence in head shape is especially strong for aquatic burrowing, semiaquatic and terrestrial ecomorphs and less strong for aquatic and burrowing ecomorphs. The ecomorph concept is useful for understanding natricine diversity and evolution, though would benefit from further refinement, especially for aquatic and burrowing taxa.}, } @article {pmid36502470, year = {2022}, author = {Manoj, KM and Gideon, DA and Bazhin, NM and Tamagawa, H and Nirusimhan, V and Kavdia, M and Jaeken, L}, title = {Na,K-ATPase: A murzyme facilitating thermodynamic equilibriums at the membrane-interface.}, journal = {Journal of cellular physiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jcp.30925}, pmid = {36502470}, issn = {1097-4652}, abstract = {The redox metabolic paradigm of murburn concept advocates that diffusible reactive species (DRS, particularly oxygen-centric radicals) are mainstays of physiology, and not mere pathological manifestations. The murburn purview of cellular function also integrates the essential principles of bioenergetics, thermogenesis, homeostasis, electrophysiology, and coherence. In this context, any enzyme that generates/modulates/utilizes/sustains DRS functionality is called a murzyme. We have demonstrated that several water-soluble (peroxidases, lactate dehydrogenase, hemogoblin, etc.) and membrane-embedded (Complexes I-V in mitochondria, Photosystems I/II in chloroplasts, rhodopsin/transducin in rod cells, etc.) proteins serve as murzymes. The membrane protein of Na,K-ATPase (NKA, also known as sodium-potassium pump) is the focus of this article, owing to its centrality in neuro-cardio-musculo electrophysiology. Herein, via a series of critical queries starting from the geometric/spatio-temporal considerations of diffusion/mass transfer of solutes in cells to an update on structural/distributional features of NKA in diverse cellular systems, and from various mechanistic aspects of ion-transport (thermodynamics, osmoregulation, evolutionary dictates, etc.) to assays/explanations of inhibitory principles like cardiotonic steroids (CTS), we first highlight some unresolved problems in the field. Thereafter, we propose and apply a minimalist murburn model of trans-membrane ion-differentiation by NKA to address the physiological inhibitory effects of trans-dermal peptide, lithium ion, volatile anesthetics, confirmed interfacial DRS + proton modulators like nitrophenolics and unsaturated fatty acid, and the diverse classes of molecules like CTS, arginine, oximes, etc. These explanations find a pan-systemic connectivity with the inhibitions/uncouplings of other membrane proteins in cells.}, } @article {pmid36470606, year = {2022}, author = {Tester, PA and Litaker, RW and Soler-Onís, E and Fernández-Zabala, J and Berdalet, E}, title = {Using artificial substrates to quantify Gambierdiscus and other toxic benthic dinoflagellates for monitoring purposes.}, journal = {Harmful algae}, volume = {120}, number = {}, pages = {102351}, doi = {10.1016/j.hal.2022.102351}, pmid = {36470606}, issn = {1878-1470}, mesh = {*Dinoflagellida ; Ecosystem ; Biomass ; }, abstract = {Collecting methods generally used to determine cell abundances of toxic benthic dinoflagellates (BHAB) use cells dislodged from either macrophytes or artificial substrates. This article compares the advantages of the macrophyte and artificial substrate methods and discusses which method is more appropriate for use in monitoring programs that focus on toxic BHAB species identification and quantification. The concept of benthic dinoflagellate "preference" for specific macrophytes was also reviewed. Examination of data from 75 field studies showed macrophytes with higher surface area per unit biomass harbored higher concentrations of Gambierdiscus cells. There was no definitive evidence that cells were actively selecting one macrophyte over another. This observation supports the use of artificial substrates (AS) as a means of assessing cell abundances in complex habitats because cell counts are normalized to a standardized surface area, not macrophyte biomass. The artificial substrate method represents the most robust approach, currently available, for collecting toxic, benthic dinoflagellates for a cell-based early warning system.}, } @article {pmid36465531, year = {2022}, author = {Hohenwallner, K and Troppmair, N and Panzenboeck, L and Kasper, C and El Abiead, Y and Koellensperger, G and Lamp, LM and Hartler, J and Egger, D and Rampler, E}, title = {Decoding Distinct Ganglioside Patterns of Native and Differentiated Mesenchymal Stem Cells by a Novel Glycolipidomics Profiling Strategy.}, journal = {JACS Au}, volume = {2}, number = {11}, pages = {2466-2480}, pmid = {36465531}, issn = {2691-3704}, abstract = {Gangliosides are an indispensable glycolipid class concentrated on cell surfaces with a critical role in stem cell differentiation. Nonetheless, owing to the lack of suitable methods for scalable analysis covering the full scope of ganglioside molecular diversity, their mechanistic properties in signaling and differentiation remain undiscovered to a large extent. This work introduces a sensitive and comprehensive ganglioside assay based on liquid chromatography, high-resolution mass spectrometry, and multistage fragmentation. Complemented by an open-source data evaluation workflow, we provide automated in-depth lipid species-level and molecular species-level annotation based on decision rule sets for all major ganglioside classes. Compared to conventional state-of-the-art methods, the presented ganglioside assay offers (1) increased sensitivity, (2) superior structural elucidation, and (3) the possibility to detect novel ganglioside species. A major reason for the highly improved sensitivity is the optimized spectral readout based on the unique capability of two parallelizable mass analyzers for multistage fragmentation. We demonstrated the high-throughput universal capability of our novel analytical strategy by identifying 254 ganglioside species. As a proof of concept, 137 unique gangliosides were annotated in native and differentiated human mesenchymal stem cells including 78 potential cell-state-specific markers and 38 previously unreported gangliosides. A general increase of the ganglioside numbers upon differentiation was observed as well as cell-state-specific clustering based on the ganglioside species patterns. The combination of the developed glycolipidomics assay with the extended automated annotation tool enables comprehensive in-depth ganglioside characterization as shown on biological samples of interest. Our results suggest ganglioside patterns as a promising quality control tool for stem cells and their differentiation products. Additionally, we believe that our analytical workflow paves the way for probing glycolipid-based biochemical processes shedding light on the enigmatic processes of gangliosides and glycolipids in general.}, } @article {pmid36461060, year = {2022}, author = {Alcántara-Salinas, G and Hunn, ES and Ibáñez-Bravo, ME and Aldasoro-Maya, EM and Flores-Hernández, N and Pérez-Sato, JA and Real-Luna, N and Trujillo, RAM and Lope-Alzina, D and Rivera-Hernández, JE}, title = {Bird conservation status and cultural values in Indigenous Mexican communities: towards a bioculturally informed conservation policy.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {18}, number = {1}, pages = {69}, pmid = {36461060}, issn = {1746-4269}, mesh = {Humans ; Animals ; Mexico ; *Birds ; *Policy ; Biodiversity ; Endangered Species ; }, abstract = {BACKGROUND: We summarize comparative ethnoornithological data for ten Mexican Indigenous communities, an initial step towards a comprehensive archive of the avian diversity conserved within Mexico's Indigenous territories. We do so by counting highlighted species listed for bird conservation status on widely recognized "red lists" and their cultural value to build biocultural policies in Mexico for their conservation.

METHODS: Indigenous bird names for each study site were determined to allow calculation of the "Scientific Species Recognition Ratio" (SSRR) for high cultural value birds obtained across communities. This demonstrated patterns of cultural prominence. A matrix of 1275 bird versus seven biocultural values was analysed using a correspondence analysis (InfoStat/L-v2020) to illustrate patterns of concordance between bird conservation status and cultural values.

RESULTS: This paper contributes to quantitative and qualitative data on the role of ethnoornithology and ethnobiology in biocultural conservation. The areas studied provide refugia for almost 70% of the Mexican avifauna within a fraction of 1% of the national territory, that is 769 bird species recorded for all communities. The global correspondence of regions of biological and linguistic megadiversity is well established, while linguistic diversity is widely accepted as a good proxy for general cultural diversity. Our correspondence analysis explained 81.55% of the variation, indicating a strong relation between cultural importance and bird conservation status. We propose three main categories to establish a bioculturally informed public policy in Mexico for the conservation of what we described as high, medium, and bioculturally prominent bird species all include cultural value in any material or symbolic aspect. High are those species appearing on any threatened list, but also considered in any endemic status, while medium include threatened listed species. The last category included species not necessarily listed on any threat list, but with a wide range of social and cultural uses. We suggest that the concept might be extended to other species of biocultural importance.

CONCLUSIONS: We argue that bird conservation policies should be biocultural, that is they should recognize birds of cultural value on a par with bird species "of special interest" because they are most critical for biodiversity conservation. The desire of local people to protect their traditional community lands and livelihoods can be an effective biodiversity conservation strategy, which should be recognized in national biocultural policies.}, } @article {pmid36449568, year = {2022}, author = {Stagg, O and Morris, K and Townsend, LT and Kvashnina, KO and Baker, ML and Dempsey, RL and Abrahamsen-Mills, L and Shaw, S}, title = {Sulfidation and Reoxidation of U(VI)-Incorporated Goethite: Implications for U Retention during Sub-Surface Redox Cycling.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.2c05314}, pmid = {36449568}, issn = {1520-5851}, abstract = {Over 60 years of nuclear activity have resulted in a global legacy of contaminated land and radioactive waste. Uranium (U) is a significant component of this legacy and is present in radioactive wastes and at many contaminated sites. U-incorporated iron (oxyhydr)oxides may provide a long-term barrier to U migration in the environment. However, reductive dissolution of iron (oxyhydr)oxides can occur on reaction with aqueous sulfide (sulfidation), a common environmental species, due to the microbial reduction of sulfate. In this work, U(VI)-goethite was initially reacted with aqueous sulfide, followed by a reoxidation reaction, to further understand the long-term fate of U species under fluctuating environmental conditions. Over the first day of sulfidation, a transient release of aqueous U was observed, likely due to intermediate uranyl(VI)-persulfide species. Despite this, overall U was retained in the solid phase, with the formation of nanocrystalline U(IV)O2 in the sulfidized system along with a persistent U(V) component. On reoxidation, U was associated with an iron (oxyhydr)oxide phase either as an adsorbed uranyl (approximately 65%) or an incorporated U (35%) species. These findings support the overarching concept of iron (oxyhydr)oxides acting as a barrier to U migration in the environment, even under fluctuating redox conditions.}, } @article {pmid36447513, year = {2022}, author = {Stork, S and Jalinsky, J and Neiman, M}, title = {Evidence for stronger discrimination between conspecific and heterospecific mating partners in sexual vs. asexual female freshwater snails.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14470}, pmid = {36447513}, issn = {2167-8359}, abstract = {Once-useful traits that no longer contribute to fitness tend to decay over time. Here, we address whether the expression of mating-related traits that increase the fitness of sexually reproducing individuals but are likely less useful or even costly to asexual counterparts seems to exhibit decay in the latter. Potamopyrgus antipodarum is a New Zealand freshwater snail characterized by repeated transitions from sexual to asexual reproduction. The frequent coexistence of sexual and asexual lineages makes P. antipodarum an excellent model for the study of mating-related trait loss. Under the presumption (inherent in the Biological Species Concept) that failure to discriminate between conspecific and heterospecific mating partners represents a poor mate choice, we used a mating choice assay including sexual and asexual P. antipodarum females and conspecific (presumed better choice) vs. heterospecific (presumed worse choice) males to evaluate the loss of behavioral traits related to sexual reproduction. We found that sexual females engaged in mating behaviors with conspecific mating partners more frequently and for a greater duration than with heterospecific mating partners. By contrast, asexual females mated at similar frequency and duration as sexual females, but did not mate more often or for longer duration with conspecific vs. heterospecific males. While further confirmation will require inclusion of a more diverse array of sexual and asexual lineages, these results are consistent with a scenario where selection acting to maintain effective mate discrimination in asexual P. antipodarum is weak or ineffective relative to sexual females and, thus, where asexual reproduction is associated with the evolutionary decay of mating-related traits in this system.}, } @article {pmid36398197, year = {2022}, author = {Bergmann, A and Burchardt, LS and Wimmer, B and Kugelschafter, K and Gloza-Rausch, F and Knörnschild, M}, title = {The soundscape of swarming: Proof of concept for a noninvasive acoustic species identification of swarming Myotis bats.}, journal = {Ecology and evolution}, volume = {12}, number = {11}, pages = {e9439}, pmid = {36398197}, issn = {2045-7758}, abstract = {Bats emit echolocation calls to orientate in their predominantly dark environment. Recording of species-specific calls can facilitate species identification, especially when mist netting is not feasible. However, some taxa, such as Myotis bats can be hard to distinguish acoustically. In crowded situations where calls of many individuals overlap, the subtle differences between species are additionally attenuated. Here, we sought to noninvasively study the phenology of Myotis bats during autumn swarming at a prominent hibernaculum. To do so, we recorded sequences of overlapping echolocation calls (N = 564) during nights of high swarming activity and extracted spectral parameters (peak frequency, start frequency, spectral centroid) and linear frequency cepstral coefficients (LFCCs), which additionally encompass the timbre (vocal "color") of calls. We used this parameter combination in a stepwise discriminant function analysis (DFA) to classify the call sequences to species level. A set of previously identified call sequences of single flying Myotis daubentonii and Myotis nattereri, the most common species at our study site, functioned as a training set for the DFA. 90.2% of the call sequences could be assigned to either M. daubentonii or M. nattereri, indicating the predominantly swarming species at the time of recording. We verified our results by correctly classifying the second set of previously identified call sequences with an accuracy of 100%. In addition, our acoustic species classification corresponds well to the existing knowledge on swarming phenology at the hibernaculum. Moreover, we successfully classified call sequences from a different hibernaculum to species level and verified our classification results by capturing swarming bats while we recorded them. Our findings provide a proof of concept for a new noninvasive acoustic monitoring technique that analyses "swarming soundscapes" by combining classical acoustic parameters and LFCCs, instead of analyzing single calls. Our approach for species identification is especially beneficial in situations with multiple calling individuals, such as autumn swarming.}, } @article {pmid36349407, year = {2022}, author = {Hu, J and Vandenkoornhuyse, P and Khalfallah, F and Causse-Védrines, R and Mony, C}, title = {Ecological corridors homogenize plant root endospheric mycobiota.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.18606}, pmid = {36349407}, issn = {1469-8137}, abstract = {Ecological corridors promote species coexistence in fragmented habitats where dispersal limits species fluxes. The corridor concept was developed and investigated with macroorganisms in mind while microorganisms, the invisible majority of biodiversity, were disregarded. We analyzed the effect of corridors on the dynamics of endospheric fungal assemblages associated with plant roots at the scale of one meter over two years (i.e. at five time points) by combining an experimental corridor-mesocosm with high-throughput amplicon sequencing. We show that the plant root endospheric mycobiota was sensitive to corridor effects when the corridors were set up at a small spatial scale. The endospheric mycobiota of connected plants had higher species richness, lower beta-diversity, and more deterministic assembly than the mycobiota of isolated plants. These effects became more pronounced with the development of host plants. Biotic corridors composed of host plants may thus play a key role in the spatial dynamics of microbial communities and may influence microbial diversity and related ecological functions.}, } @article {pmid36324542, year = {2022}, author = {Portillo, JTDM and Barbo, FE and Sawaya, RJ}, title = {Climatic niche breadths of the Atlantic Forest snakes do not increase with increasing latitude.}, journal = {Current zoology}, volume = {68}, number = {5}, pages = {535-540}, pmid = {36324542}, issn = {1674-5507}, abstract = {The climatic niche is a central concept for understanding species distribution, with current and past climate interpreted as strong drivers of present and historical-geographical ranges. Our aim is to understand whether Atlantic Forest snakes follow the general geographical pattern of increasing species climatic niche breadths with increasing latitude. We also tested if there is a tradeoff between temperature and precipitation niche breadths of species in order to understand if species with larger breadths of one niche dimension have stronger dispersal constraints by the other due to narrower niche breadths. Niche breadths were calculated by the subtraction of maximal and minimal values of temperature and precipitation across species ranges. We implemented Phylogenetic Generalized Least Squares to measure the relationship between temperature and precipitation niche breadths and latitude. We also tested phylogenetic signals by Lambda statistics to analyze the degree of phylogenetic niche conservatism to both niche dimensions. Temperature niche breadths were not related to latitude. Precipitation niche breadths decreased with increasing latitude and presented a high phylogenetic signal, that is, significant phylogenetic niche conservatism. We rejected the tradeoff hypotheses of temperature and precipitation niche breadths. Our results also indicate that precipitation should be an important ecological constraint affecting the geographical distribution of snake lineages across the South American Atlantic Forest. We then provide a general view of how phylogenetic niche conservatism could impact the patterns of latitudinal variation of climatic niches across this biodiversity hotspot.}, } @article {pmid36307232, year = {2022}, author = {Berns, GS}, title = {Deciphering the dog brain with fMRI.}, journal = {Trends in neurosciences}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tins.2022.10.005}, pmid = {36307232}, issn = {1878-108X}, abstract = {fMRI has been increasingly used to study brain function in domestic dogs trained to lie still in MRI scanners. These studies highlight both similarities and differences between dogs and humans when presented with the same stimuli, raising intriguing questions about the concept of functional homologies in a coevolved species that shares the human environment.}, } @article {pmid36294662, year = {2022}, author = {Peçanha, PM and Peçanha-Pietrobom, PM and Grão-Velloso, TR and Rosa Júnior, M and Falqueto, A and Gonçalves, SS}, title = {Paracoccidioidomycosis: What We Know and What Is New in Epidemiology, Diagnosis, and Treatment.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {10}, pages = {}, pmid = {36294662}, issn = {2309-608X}, abstract = {Paracoccidioidomycosis (PCM) is a systemic mycosis endemic to Latin America caused by thermodimorphic fungi of the genus Paracoccidioides. In the last two decades, enhanced understanding of the phylogenetic species concept and molecular variations has led to changes in this genus' taxonomic classification. Although the impact of the new species on clinical presentation and treatment remains unclear, they can influence diagnosis when serological methods are employed. Further, although the infection is usually acquired in rural areas, the symptoms may manifest years or decades later when the patient might be living in the city or even in another country outside the endemic region. Brazil accounts for 80% of PCM cases worldwide, and its incidence is rising in the northern part of the country (Amazon region), owing to new settlements and deforestation, whereas it is decreasing in the south, owing to agriculture mechanization and urbanization. Clusters of the acute/subacute form are also emerging in areas with major human intervention and climate change. Advances in diagnostic methods (molecular and immunological techniques and biomarkers) remain scarce, and even the reference center's diagnostics are based mainly on direct microscopic examination. Classical imaging findings in the lungs include interstitial bilateral infiltrates, and eventually, enlargement or calcification of adrenals and intraparenchymal central nervous system lesions are also present. Besides itraconazole, cotrimoxazole, and amphotericin B, new azoles may be an alternative when the previous ones are not tolerated, although few studies have investigated their use in treating PCM.}, } @article {pmid36290373, year = {2022}, author = {Ali, F and Khan, N and Rahmonov, O}, title = {Ecosystem Services and Linkages of Naturally Managed Monotheca buxifolia (Falc.) A. DC. Forests with Local Communities across Contiguous Mountainous Ranges in Pakistan.}, journal = {Biology}, volume = {11}, number = {10}, pages = {}, pmid = {36290373}, issn = {2079-7737}, abstract = {The local community of the Suleiman and Hindukush mountain systems in Pakistan has largely depended on the natural resources of the environment since ancient times. The ecosystem of these regions is under huge pressure due to a lack of awareness and the uncontrolled interference of communal, commercial, security, political, and ecological conditions. The present study was designed to illuminate the link between mountain society and the consumption of the benefits from Monotheca phytocoenoses using the ecosystem services concept from the sphere of the socio-ecological system to cultural relations. The use of this approach is very important due to the visible role and dominant status of Monotheca vegetation within the ecological system of the region. M. buxifolia is strongly connected with both local and cultural traditions and is counted as a key species, particularly for high-mountain inhabitants. We report that Monotheca phytocoenoses provide several services including shelter, food, fodder, medicines, and wood, etc., to the indigenous community and is highly valued in the local culture because of the poor economic condition of the society. The concept of this cultural keystone species is crucial for understanding ecosystem services and must be considered for the protection and conservation of these habitats. The results of field and social studies have shown that the stable maintenance of Monotheca phytocoenosis forests ensures the existence of key species as the most important providers of ecosystem services, e.g., provisioning, regulation, maintenance and cultural services, indicating the close relations between society and the protection of mountain areas. According to the results obtained, the mountains community of the studied area believes that tree species like M. buxifolia, F. palmata, O. ferruginea, P. granatum, A. modesta, J. regia, etc., are the key components contributing to the function of both the mountain ecosystem and communities' well-being. This approach will be extremely useful for ensuring an inclusive management of the socio-ecological system of the Hindukush and Suleiman Mountain ranges of Pakistan.}, } @article {pmid36273538, year = {2023}, author = {Lamattina, D and Salomón, OD}, title = {Triatoma infestans, to be or not to be autogenic?.}, journal = {Acta tropica}, volume = {237}, number = {}, pages = {106727}, doi = {10.1016/j.actatropica.2022.106727}, pmid = {36273538}, issn = {1873-6254}, mesh = {Animals ; Female ; *Triatoma ; *Triatominae ; Nymph ; Feeding Behavior ; Nutritional Status ; }, abstract = {Autogeny, the ability to develop eggs without a meal in the adult stage, has been described in several groups of arthropods, especially hematophagous Diptera Nematocera. In obligate hematophagous hemimetabolous insects that feed on blood in all their instars, such as Triatominae, this concept gives rise to species with apparently facultative autogeny, such as Triatoma infestans. Generalized linear models were applied to explain egg production by the predictor variables molting weight as a proxy of nymphal accumulated reserves and digested blood weight as an indicator of adult reserve in fasted, incompletely fed and engorged at repletion females. The relationship between these indicators of nutritional status and egg development turned out to be a continuous function in which, with molting weights greater than 254 mg, the insects are autogenic, but for the first batch of eggs with molting weights between 132 and 253 mg, they require one adult meal of at least 202 mg, and with molting weights less than 131 mg at least two meals are required. Both molting weight and blood intake could determine oocyte production in an additive manner, thus the concept of autogeny as a switch on-off phenomenon is not directly applicable to Triatominae. Nevertheless, autogenic ability would allow Triatominae with relatively long cycles to accelerate population growth under favorable or low competition conditions during colonization or recovery after a control intervention.}, } @article {pmid36255144, year = {2022}, author = {Wang, S and Qian, YQ and Zhao, RP and Chen, LL and Song, JM}, title = {Graph-based pan-genome: increased opportunities in plant genomics.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erac412}, pmid = {36255144}, issn = {1460-2431}, abstract = {Due to the development of sequencing technology and the great reduction in sequencing costs, the genomes of an increasing number of plant species have been assembled, and the numerous genomes have revealed large amounts of variation. However, a single reference genome does not allow the exploration of species diversity; therefore, the concept of the pan-genome was developed. A pan-genome is a collection of all sequences available for a species, including a large number of consensus sequences, large structural variations (SVs), and small variations, including single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). A simple linear pan-genome does not allow these SVs to be intuitively characterized, so graph-based pan-genomes have been developed. These pan-genomes store sequence and SV information in the form of nodes and paths to store and display species variation information in a more intuitive manner. The key role of graph-based pan-genome is to expand the coordinate system of the linear reference genome to accommodate more regions of genetic diversity. Here, we review the origin and development of graph-based pan-genomes, explore their application in plant research, and further highlight the application of graph-based pan-genomes for future plant breeding.}, } @article {pmid36247363, year = {2022}, author = {Rocchini, D and Santos, MJ and Ustin, SL and Féret, JB and Asner, GP and Beierkuhnlein, C and Dalponte, M and Feilhauer, H and Foody, GM and Geller, GN and Gillespie, TW and He, KS and Kleijn, D and Leitão, PJ and Malavasi, M and Moudrý, V and Müllerová, J and Nagendra, H and Normand, S and Ricotta, C and Schaepman, ME and Schmidtlein, S and Skidmore, AK and Šímová, P and Torresani, M and Townsend, PA and Turner, W and Vihervaara, P and Wegmann, M and Lenoir, J}, title = {The Spectral Species Concept in Living Color.}, journal = {Journal of geophysical research. Biogeosciences}, volume = {127}, number = {9}, pages = {e2022JG007026}, pmid = {36247363}, issn = {2169-8953}, abstract = {Biodiversity monitoring is an almost inconceivable challenge at the scale of the entire Earth. The current (and soon to be flown) generation of spaceborne and airborne optical sensors (i.e., imaging spectrometers) can collect detailed information at unprecedented spatial, temporal, and spectral resolutions. These new data streams are preceded by a revolution in modeling and analytics that can utilize the richness of these datasets to measure a wide range of plant traits, community composition, and ecosystem functions. At the heart of this framework for monitoring plant biodiversity is the idea of remotely identifying species by making use of the 'spectral species' concept. In theory, the spectral species concept can be defined as a species characterized by a unique spectral signature and thus remotely detectable within pixel units of a spectral image. In reality, depending on spatial resolution, pixels may contain several species which renders species-specific assignment of spectral information more challenging. The aim of this paper is to review the spectral species concept and relate it to underlying ecological principles, while also discussing the complexities, challenges and opportunities to apply this concept given current and future scientific advances in remote sensing.}, } @article {pmid36240488, year = {2022}, author = {Tong, KKH and Riisom, M and Leung, E and Hanif, M and Söhnel, T and Jamieson, SMF and Hartinger, CG}, title = {Impact of Coordination Mode and Ferrocene Functionalization on the Anticancer Activity of N-Heterocyclic Carbene Half-Sandwich Complexes.}, journal = {Inorganic chemistry}, volume = {61}, number = {43}, pages = {17226-17241}, doi = {10.1021/acs.inorgchem.2c02832}, pmid = {36240488}, issn = {1520-510X}, mesh = {Metallocenes/pharmacology ; *Coordination Complexes/pharmacology ; Reactive Oxygen Species ; Methane/pharmacology ; *Antineoplastic Agents/pharmacology ; Ligands ; }, abstract = {The substitution of phenyl rings in established drugs with ferrocenyl moieties has been reported to yield compounds with improved biological activity and alternative modes of action, often involving the formation of reactive oxygen species (ROS). Translating this concept to N-heterocyclic carbene (NHC) complexes, we report here organometallics with a piano-stool structure that feature di- or tridentate ligand systems. The ligands impacted the cytotoxic activity of the NHC complexes, but the coordination modes seemed to have a limited influence, which may be related to the propensity of forming the same species in solution. In general, the stability of the complexes in an aqueous environment and their reactivity to selected biomolecules were largely dominated by the nature of the metal center. While the complexes promoted the formation of ROS, the levels did not correlate with their cytotoxic activity. However, the introduction of ferrocenyl moieties had a significant impact on the antiproliferative potency of the complexes and, in particular, some of the ferrocenyl-functionalized compounds yielded IC50 values in the low μM range.}, } @article {pmid36223598, year = {2022}, author = {Bradshaw, MJ and Braun, U and Pfister, DH}, title = {Phylogeny and taxonomy of the genera of Erysiphaceae, part 1: Golovinomyces.}, journal = {Mycologia}, volume = {114}, number = {6}, pages = {964-993}, doi = {10.1080/00275514.2022.2115419}, pmid = {36223598}, issn = {1557-2536}, mesh = {Phylogeny ; *Plant Diseases/microbiology ; DNA, Fungal/genetics ; *Ascomycota/genetics ; DNA, Ribosomal/genetics ; Plants/microbiology ; }, abstract = {Powdery mildews are a monophyletic group of obligate plant pathogenic fungi in the family Erysiphaceae. Powdery mildews are economically important in that they cause damage to many agriculturally significant crops and plants in ecologically important habitats. In this contribution, we introduce a new series of publications focusing on the phylogeny and taxonomy of this group, with an emphasis on specimens collected from North America. The first part of the series focuses on the genus Golovinomyces and includes a section detailing the powdery mildew species concept. We conducted analyses of Golovinomyces spp. with available rDNA sequence data from GenBank and supplemented the data set with rDNA (ITS, 28S, IGS) as well as protein-coding (GAPDH) data from 94 North American collections. Many of the species evaluated are included in phylogenetic and morphological analyses for the first time, including the American species G. americanus, G. brunneopunctatus, G. californicus, G. greeneanus, G. hydrophyllacearum, and G. sparsus. A special emphasis was placed on acquiring ex-type or ex-epitype sequences or presenting reference sequences for phylogenetic-taxonomic purposes. Three new species, G. eurybiarum, G. galiorum, and G. malvacearum, are described, and the new combinations G. fuegianus, G. mutisiae, and G. reginae are introduced. Ex-holotype sequences of Erysiphe sparsa (≡ G. sparsus) reveal that it should be reduced to synonymy with G. ambrosiae, and ex-epitype sequences of G. valerianae reveal that it should be reduced to synonymy with G. orontii. Multiple epitypes are designated with ex-epitype sequences.}, } @article {pmid36211486, year = {2022}, author = {Wallingford, JC and Neve Myers, P and Barber, CM}, title = {Effects of addition of 2-fucosyllactose to infant formula on growth and specific pathways of utilization by Bifidobacterium in healthy term infants.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {961526}, pmid = {36211486}, issn = {2296-861X}, abstract = {Oligosaccharides in human milk support health via intestinal microbiome. We studied effects of addition of 2-fucosyllactose (2'FL) to the infant formula on infant growth, occurrence of adverse events (AE), and infant microbiome, including expression of microbial genes that metabolize 2'FL. Our hypothesis was that while 2'FL would not affect growth, it would cause changes in microbiome metabolism. In a double-blinded randomized controlled study fashion, the infant formula ± 2'FL or human milk was fed to healthy term infants for 16 weeks. Fecal samples obtained at baseline and week 16 were analyzed for microbial populations, metagenomic species concept (MGS), and genetics of gut metabolic modules (GMMs). There were no effects of addition of 2'FL on growth or AEs. There were no significant differences by feeding group in MGS richness or Shannon diversity at baseline, but formula groups each had significantly greater richness (p < 0.05) and diversity (p < 0.05) after 16 weeks of feeding than the breastfed group. While two glycosyl hydrolase (GH) families (GH42 and GH112) were significantly increased, two other GH families (GH20 and GH2) were significantly decreased in the test formula group compared to the control formula group; although modest, addition of 2'FL resulted in changes in microbiome in the direction of breastfed infants, consistent with internal metabolism of HMOs by Bifidobacterium.}, } @article {pmid36203732, year = {2022}, author = {Oppong, SO and Twum, F and Hayfron-Acquah, JB and Missah, YM}, title = {A Novel Computer Vision Model for Medicinal Plant Identification Using Log-Gabor Filters and Deep Learning Algorithms.}, journal = {Computational intelligence and neuroscience}, volume = {2022}, number = {}, pages = {1189509}, pmid = {36203732}, issn = {1687-5273}, mesh = {Algorithms ; Artificial Intelligence ; *Deep Learning ; Humans ; Neural Networks, Computer ; *Plants, Medicinal ; }, abstract = {Computer vision is the science that enables computers and machines to see and perceive image content on a semantic level. It combines concepts, techniques, and ideas from various fields such as digital image processing, pattern matching, artificial intelligence, and computer graphics. A computer vision system is designed to model the human visual system on a functional basis as closely as possible. Deep learning and Convolutional Neural Networks (CNNs) in particular which are biologically inspired have significantly contributed to computer vision studies. This research develops a computer vision system that uses CNNs and handcrafted filters from Log-Gabor filters to identify medicinal plants based on their leaf textural features in an ensemble manner. The system was tested on a dataset developed from the Centre of Plant Medicine Research, Ghana (MyDataset) consisting of forty-nine (49) plant species. Using the concept of transfer learning, ten pretrained networks including Alexnet, GoogLeNet, DenseNet201, Inceptionv3, Mobilenetv2, Restnet18, Resnet50, Resnet101, vgg16, and vgg19 were used as feature extractors. The DenseNet201 architecture resulted with the best outcome of 87% accuracy and GoogLeNet with 79% preforming the worse averaged across six supervised learning algorithms. The proposed model (OTAMNet), created by fusing a Log-Gabor layer into the transition layers of the DenseNet201 architecture achieved 98% accuracy when tested on MyDataset. OTAMNet was tested on other benchmark datasets; Flavia, Swedish Leaf, MD2020, and the Folio dataset. The Flavia dataset achieved 99%, Swedish Leaf 100%, MD2020 99%, and the Folio dataset 97%. A false-positive rate of less than 0.1% was achieved in all cases.}, } @article {pmid36182674, year = {2022}, author = {Zheng, W and Chen, Y and Fu, H and Yan, Z and Lei, Z and Duan, W and Feng, C}, title = {Reactive species conversion into [1]O2 promotes substantial inhibition of chlorinated byproduct formation during electrooxidation of phenols in Cl[-]-laden wastewater.}, journal = {Water research}, volume = {225}, number = {}, pages = {119143}, doi = {10.1016/j.watres.2022.119143}, pmid = {36182674}, issn = {1879-2448}, mesh = {Waste Water/chemistry ; Chlorine/chemistry ; *Water Purification/methods ; Phenol/chemistry ; Hydrogen Peroxide/chemistry ; Phenols ; Halogens/chemistry ; Oxidation-Reduction ; Chlorides ; *Water Pollutants, Chemical/chemistry ; Ultraviolet Rays ; }, abstract = {The generation of chlorinated byproducts during the electrochemical oxidation (EO) of Cl[-]-laden wastewater is a significant concern. We aim to propose a concept of converting reactive species (e.g., reactive chlorines and HO[•] resulting from electrolysis) into [1]O2 via the addition of H2O2, which substantially alleviates chlorinated organic formation. When phenol was used as a model organic compound, the results showed that the H2O2-involving EO system outperformed the H2O2-absent system in terms of higher rate constants (5.95 × 10[-2] min[-1]vs. 2.97 × 10[-2] min[-1]) and a much lower accumulation of total organic chlorinated products (1.42 mg L[-1]vs. 8.18 mg L[-1]) during a 60 min operation. The rate constants of disappearance of a variety of phenolic compounds were positively correlated with the Hammett constants (σ), suggesting that the reactive species preferred oxidizing phenols with electron-rich groups. After the identification of [1]O2 that was abundant in the bulk solution with the use of electron paramagnetic resonance and computational kinetic simulation, the routes of [1]O2 generation were revealed. Despite the consensus as to the contribution of reaction between H2O2 and ClO[-] to [1]O2 formation, we conclude that the predominant pathway is through H2O2 reaction with electrogenerated HO[•] or chlorine radicals (Cl[•] and Cl2[•][-]) to produce O2[•][-], followed by self-combination. Density functional theory calculations theoretically showed the difficulty in forming chlorinated byproducts for the [1]O2-initiated phenol oxidation in the presence of Cl[-], which, by contrast, easily occurred for the Cl[•]-or HO[•]-initiated phenol reaction. The experiments run with real coking wastewater containing high-concentration phenols further demonstrated the superiority of the H2O2-involving EO system. The findings imply that this unique method for treating Cl[-]-laden organic wastewater is expected to be widely adopted for generalizing EO technology for environmental applications.}, } @article {pmid36121444, year = {2022}, author = {Rauf, S and Hanif, MB and Mushtaq, N and Tayyab, Z and Ali, N and Shah, MAKY and Motola, M and Saleem, A and Asghar, MI and Iqbal, R and Yang, C and Xu, W}, title = {Modulating the Energy Band Structure of the Mg-Doped Sr0.5Pr0.5Fe0.2Mg0.2Ti0.6O3-δ Electrolyte with Boosted Ionic Conductivity and Electrochemical Performance for Solid Oxide Fuel Cells.}, journal = {ACS applied materials & interfaces}, volume = {14}, number = {38}, pages = {43067-43084}, pmid = {36121444}, issn = {1944-8252}, abstract = {Achieving fast ionic conductivity in the electrolyte at low operating temperatures while maintaining the stable and high electrochemical performance of solid oxide fuel cells (SOFCs) is challenging. Herein, we propose a new type of electrolyte based on perovskite Sr0.5Pr0.5Fe0.4Ti0.6O3-δ for low-temperature SOFCs. The ionic conducting behavior of the electrolyte is modulated using Mg doping, and three different Sr0.5Pr0.5Fe0.4-xMgxTi0.6O3-δ (x = 0, 0.1, and 0.2) samples are prepared. The synthesized Sr0.5Pr0.5Fe0.2Mg0.2Ti0.6O3-δ (SPFMg0.2T) proved to be an optimal electrolyte material, exhibiting a high ionic conductivity of 0.133 S cm[-1] along with an attractive fuel cell performance of 0.83 W cm[-2] at 520 °C. We proved that a proper amount of Mg doping (20%) contributes to the creation of an adequate number of oxygen vacancies, which facilitates the fast transport of the oxide ions. Considering its rapid oxide ion transport, the prepared SPFMg0.2T presented heterostructure characteristics in the form of an insulating core and superionic conduction via surface layers. In addition, the effect of Mg doping is intensively investigated to tune the band structure for the transport of charged species. Meanwhile, the concept of energy band alignment is employed to interpret the working principle of the proposed electrolyte. Moreover, the density functional theory is utilized to determine the perovskite structures of SrTiO3-δ and Sr0.5Pr0.5Fe0.4-xMgxTi0.6O3-δ (x = 0, 0.1, and 0.2) and their electronic states. Further, the SPFMg0.2T with 20% Mg doping exhibited low dissociation energy, which ensures the fast and high ionic conduction in the electrolyte. Inclusively, Sr0.5Pr0.5Fe0.4Ti0.6O3-δ is a promising electrolyte for SOFCs, and its performance can be efficiently boosted via Mg doping to modulate the energy band structure.}, } @article {pmid36101245, year = {2022}, author = {Moravec, JI and Wiesner, J and Jocque, M}, title = {New or rare Madagascar tiger beetles26. A new species of the genus Pogonostoma Klug from northwestern Madagascar and a revised key to the Pogonostoma (P.) srnkai species-group (Coleoptera: Cicindelidae).}, journal = {Zootaxa}, volume = {5169}, number = {2}, pages = {165-176}, doi = {10.11646/zootaxa.5169.2.4}, pmid = {36101245}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; *Coleoptera ; Madagascar ; }, abstract = {A new species of the genus Pogonostoma Klug, 1835, P. (Pogonostoma) mahimborondrense Moravec Wiesner sp. nov. is described as new to science from the Mahimborondro protected area in Northern Highlands, northwestern Madagascar. By its unique complex of diagnostic characters, the new species is incomparable to any other species within the genus. It is placed here into the Pogonostoma (P.) srnkai species-group (in the concept presented in the monograph of the genus by Moravec 2007). A revised key to species of the species-group is presented in order to supplement the key in the monograph. Habitus and diagnostic characters of the new species are illustrated in colour photographs. Maps and photos of the occurrence of the new species in Mahimborondro are also presented.}, } @article {pmid36095810, year = {2022}, author = {Lair, X and Ropars, L and Skevington, JH and Kelso, S and Geslin, B and Minssieux, E and Nve, G}, title = {Revision of the genus Pelecocera Meigen, 1822 (Diptera: Syrphidae) from France: taxonomy, ecology and distribution.}, journal = {Zootaxa}, volume = {5141}, number = {1}, pages = {1-24}, doi = {10.11646/zootaxa.5141.1.1}, pmid = {36095810}, issn = {1175-5334}, mesh = {Animals ; *Diptera ; France ; }, abstract = {The occurrence and distribution of the various species of the genus Pelecocera Meigen, 1822 (Diptera: Syrphidae) occurring in France are revised and a new species, Pelecocera garrigae Lair Nve, 2022 sp. nov., is described from Mediterranean France. Distribution and ecological data of the six French species of Pelecocera are provided and an identification key is given to all these species. Sequences of the cytochrome c oxidase subunit I (COI) from all European Pelecocera species support the morphological species concept, except for Pelecocera scaevoides (Falln, 1817). The binomen Pelecocera lugubris Perris, 1839 is recovered to name the Pelecocera lusitanica (Mik, 1898) of authors in France.}, } @article {pmid36095753, year = {2022}, author = {Philips, TK and Mudge, AD and Orozco, J and Neidlinger, R and Beinhundner, G and Joly, C}, title = {A rich and diverse fauna: an illustrated guide to the cetoniines of Ghana with comparisons to Ivory Coast and Benin (Coleoptera: Scarabaeidae: Cetoniinae).}, journal = {Zootaxa}, volume = {5150}, number = {2}, pages = {151-188}, doi = {10.11646/zootaxa.5150.2.1}, pmid = {36095753}, issn = {1175-5334}, mesh = {Animals ; Benin ; *Coleoptera ; Cote d'Ivoire ; Ghana ; }, abstract = {The currently known cetoniine fauna of Ghana is discussed and illustrated. It now includes 60 genera and 148 taxa, including 9 subspecies. Comparison to the adjacent countries of Ivory Coast and nearby Benin gives evidence that the faunas of all three countries surprisingly may still be grossly under-sampled and hence poorly known for what is considered a relatively well-known group of beetles. At least 22 species known from both Ivory Coast and Benin are expected to be found in Ghana but still have yet to be reported. Notes on several species concepts and the alternate use of names are also given to clarify the taxonomy of the taxa known from this area.}, } @article {pmid36093929, year = {2022}, author = {Green, WH}, title = {Concluding remarks: Faraday Discussion on unimolecular reactions.}, journal = {Faraday discussions}, volume = {238}, number = {0}, pages = {741-766}, doi = {10.1039/d2fd00136e}, pmid = {36093929}, issn = {1364-5498}, abstract = {This Faraday Discussion, marking the centenary of Lindemann's explanation of the pressure-dependence of unimolecular reactions, presented recent advances in measuring and computing collisional energy transfer efficiencies, microcanonical rate coefficients, and pressure-dependent (phenomenological) rate coefficients, and the incorporation of these rate coefficients in kinetic models. Several of the presentations featured systems where breakdown of the Born-Oppenheimer approximation is key to understanding the measured rates/products. Many of the reaction systems presented were quite complex, which can make it difficult to go from "plausible proposed explanation" to "quantitative agreement between model and experiment". This complexity highlights the need for better automation of the calculations, better documentation and benchmarking to catch any errors and to make the calculations more easily reproducible, and continued (and even closer) cooperation of experimentalists and modelers. In some situations the correct definition of a "species" is debatable, since the population distributions and time evolution are so distorted from the perfect-Boltzmann Lewis-structure zero-order concept of a chemical species. Despite all these challenges, the field has made tremendous advances, and several cases were presented which demonstrated both excellent understanding of very complicated reaction chemistry and quantitatively accurate predictions of complicated experiments. Some of the interesting contributions to this Discussion are highlighted here, with some comments and suggestions for next steps.}, } @article {pmid36079936, year = {2022}, author = {Polivtseva, S and Kois, J and Kruzhilina, T and Kaupmees, R and Klopov, M and Molaiyan, P and van Gog, H and van Huis, MA and Volobujeva, O}, title = {Solution-Mediated Inversion of SnSe to Sb2Se3 Thin-Films.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {12}, number = {17}, pages = {}, pmid = {36079936}, issn = {2079-4991}, abstract = {New facile and controllable approaches to fabricating metal chalcogenide thin films with adjustable properties can significantly expand the scope of these materials in numerous optoelectronic and photovoltaic devices. Most traditional and especially wet-chemical synthetic pathways suffer from a sluggish ability to regulate the composition and have difficulty achieving the high-quality structural properties of the sought-after metal chalcogenides, especially at large 2D length scales. In this effort, and for the first time, we illustrated the fast and complete inversion of continuous SnSe thin-films to Sb2Se3 using a scalable top-down ion-exchange approach. Processing in dense solution systems yielded the formation of Sb2Se3 films with favorable structural characteristics, while oxide phases, which are typically present in most Sb2Se3 films regardless of the synthetic protocols used, were eliminated. Density functional theory (DFT) calculations performed on intermediate phases show strong relaxations of the atomic lattice due to the presence of substitutional and vacancy defects, which likely enhances the mobility of cationic species during cation exchange. Our concept can be applied to customize the properties of other metal chalcogenides or manufacture layered structures.}, } @article {pmid36072310, year = {2022}, author = {Doyle, JJ}, title = {Cell types as species: Exploring a metaphor.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {868565}, pmid = {36072310}, issn = {1664-462X}, abstract = {The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.}, } @article {pmid36065479, year = {2022}, author = {Lachance, MA}, title = {Phylogenies in yeast species descriptions: In defense of neighbor-joining.}, journal = {Yeast (Chichester, England)}, volume = {39}, number = {10}, pages = {513-520}, doi = {10.1002/yea.3812}, pmid = {36065479}, issn = {1097-0061}, mesh = {*Algorithms ; Evolution, Molecular ; *Models, Genetic ; Phylogeny ; }, abstract = {The neighbor-joining (NJ) method of tree inference is examined, with special attention to its use in yeast species descriptions. How the often-vilified method works is often misunderstood. More importantly, given the right kind of data, its output is a phylogram that illustrates a hypothetical phylogeny that is just as credible as that obtained by any other method. And as with any other method, the result is greatly affected by sampling intensity, particularly the number of aligned positions used for analysis. I address various allegations, including the claim that the method is phenetic, and, therefore, not phylogenetic. I argue that NJ is the most suitable tree inference method to use in yeast species descriptions, primarily because it is best at visually preserving the extent of sequence divergence between close relatives, which continues to be the primary criterion for yeast species delineation. The relevance of bootstraps in the application of the phylogenetic species concept is discussed.}, } @article {pmid36063161, year = {2022}, author = {Mallet, J and Mullen, SP}, title = {Reproductive isolation is a heuristic, not a measure: a commentary on Westram et al., 2022.}, journal = {Journal of evolutionary biology}, volume = {35}, number = {9}, pages = {1175-1182}, doi = {10.1111/jeb.14052}, pmid = {36063161}, issn = {1420-9101}, mesh = {Gene Flow ; *Genetic Speciation ; Heuristics ; *Reproductive Isolation ; Sympatry ; }, abstract = {Reproductive isolation is the heuristic basis of the biological species concept, but what is it? Westram et al. (this issue) propose that it is a measurable quantity, "barrier strength," that prevents gene flow among populations. However, their attempt to make the concept of reproductive isolation more scientific is unlikely to satisfy the diverse opinions of all evolutionary biologists. There are many different opinions about the nature of species, even under the biological species concept. Complete reproductive isolation, where gene flow is effectively zero, is regarded by some biologists as an important end point of speciation. Others, including Westram et al., argue for a more nuanced approach, and they also suggest that reproductive isolation may differ in different parts of the genome due to variation in genetic linkage to divergently selected loci. In contrast to both these approaches, we favour as a key criterion of speciation the stable coexistence of divergent populations in sympatry. Obviously, such populations must be reproductively isolated in some sense, but neither the fraction of the genome that is exchanged, nor measures of overall barrier strength acting on neutral variation will yield very precise predictions as to species status. Although an overall measure of reproductive isolation is virtually unattainable for these reasons, its early generation components, such as assortative mating, divergent selection, or hybrid inviability and sterility are readily measurable and remain informative. For example, we can make the prediction that to remain divergent in sympatry, almost all sexual species will require strong assortative mating, as well as some sort of ecological or intrinsic selection against hybrids and introgressed variants.}, } @article {pmid36027870, year = {2022}, author = {Kudryavtsev, A}, title = {From Argentine Abyssal Plain to farmed turbot in Spain: A ubiquitous amoeba species Vannella robusta sp. nov. (Amoebozoa, Vannellida).}, journal = {European journal of protistology}, volume = {85}, number = {}, pages = {125912}, doi = {10.1016/j.ejop.2022.125912}, pmid = {36027870}, issn = {1618-0429}, mesh = {Amebiasis/*veterinary/virology ; Amoebozoa/classification/*isolation & purification ; Animals ; Argentina ; Atlantic Ocean ; Electron Transport Complex IV/genetics ; Fish Diseases/*virology ; Flatfishes/genetics/*parasitology ; Phylogeny ; RNA, Ribosomal/genetics ; Seawater/parasitology ; Sequence Analysis, DNA ; Spain ; Species Specificity ; }, abstract = {A strain with the characters of the genus Vannella was isolated from the water layer immediately above the deep-sea sediment collected in the south-western Atlantic Ocean, ca. 4.6 km deep. Small-subunit ribosomal RNA (SSU rRNA) and cytochrome c oxidase (Cox1) gene phylogenetic analyses showed that the new strain branches within the clade of previously isolated unnamed Vannella strains from different marine fish and invertebrate hosts. Although the SSU rRNA gene sequences of these strains show variability within 2% of all nucleotide positions without any regular pattern, the available Cox1 gene sequences from within this clade are identical. Given the morphological homogeneity of the revealed clade, all of its strains can be assigned under the same species name, and the variation of their SSU rRNA is comparable to its intragenomic variation, as shown by molecular cloning of the PCR amplicons. High variability of the SSU rRNA gene sequences within and between independently isolated morphologically identical strains in combination with highly conserved Cox1 gene sequences may be a feature in some clades of Vannella, but is not a general rule for this genus, as SSU rRNA genes conserved between different morphospecies occur in several other clades within Vannella.}, } @article {pmid36004556, year = {2022}, author = {Pizzato, J and Tang, W and Bernabeu, S and Bonnin, RA and Bille, E and Farfour, E and Guillard, T and Barraud, O and Cattoir, V and Plouzeau, C and Corvec, S and Shahrezaei, V and Dortet, L and Larrouy-Maumus, G}, title = {Discrimination of Escherichia coli, Shigella flexneri, and Shigella sonnei using lipid profiling by MALDI-TOF mass spectrometry paired with machine learning.}, journal = {MicrobiologyOpen}, volume = {11}, number = {4}, pages = {e1313}, pmid = {36004556}, issn = {2045-8827}, support = {105603/Z/14/Z/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria ; Escherichia coli ; *Escherichia coli Infections ; Humans ; Lipids ; Machine Learning ; RNA, Ribosomal, 16S ; *Shigella ; Shigella flexneri ; Shigella sonnei ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a staple in clinical microbiology laboratories. Protein-profiling of bacteria using this technique has accelerated the identification of pathogens in diagnostic workflows. Recently, lipid profiling has emerged as a way to complement bacterial identification where protein-based methods fail to provide accurate results. This study aimed to address the challenge of rapid discrimination between Escherichia coli and Shigella spp. using MALDI-TOF MS in the negative ion mode for lipid profiling coupled with machine learning. Both E. coli and Shigella species are closely related; they share high sequence homology, reported for 16S rRNA gene sequence similarities between E. coli and Shigella spp. exceeding 99%, and a similar protein expression pattern but are epidemiologically distinct. A bacterial collection of 45 E. coli, 48 Shigella flexneri, and 62 Shigella sonnei clinical isolates were submitted to lipid profiling in negative ion mode using the MALDI Biotyper Sirius® system after treatment with mild-acid hydrolysis (acetic acid 1% v/v for 15 min at 98°C). Spectra were then analyzed using our in-house machine learning algorithm and top-ranked features used for the discrimination of the bacterial species. Here, as a proof-of-concept, we showed that lipid profiling might have the potential to differentiate E. coli from Shigella species using the analysis of the top five ranked features obtained by MALDI-TOF MS in the negative ion mode of the MALDI Biotyper Sirius® system. Based on this new approach, MALDI-TOF MS analysis of lipids might help pave the way toward these goals.}, } @article {pmid35993885, year = {2022}, author = {Chambers, EA and Marshall, TL and Hillis, DM}, title = {The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation.}, journal = {Systematic biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/sysbio/syac056}, pmid = {35993885}, issn = {1076-836X}, abstract = {With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability to draw accurate species boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa can determine if assortative mating or selection against hybrids exists (supporting the presence of two distinct species), or alternatively if mating is random among genotypes and admixture among adjacent populations is gradual and continuous (supporting geographic variation within a single species). Here, we test two alternative hypotheses for two pairs of named taxa at contact zones within the American milksnake (Lampropeltis triangulum) complex. A prior morphological analysis found areas of gradual intergradation among named taxa, and concluded that the taxa represented geographical races of a single polytypic species. In contrast, a subsequent analysis of gene sequence data, but with limited sampling near the contact zones, hypothesized distinct boundaries between species at the contact zones. At the contact zone between proposed species L. triangulum and L. gentilis, we examined a ∼700 km-wide transect across the states of Kansas and Missouri, with thorough sampling and reduced-representation genomic-level sequencing, to test the two opposing taxonomic hypotheses. Our transect analyses included examinations of population structure, fixed differences, cline-fitting, and an admixture index analysis. These analyses all supported a gradual and continuous geographic cline across a broad intergrade zone between two geographic forms of L. triangulum, thus providing strong support for a single species in this region (and no support for the recognition of L. gentilis as a distinct species). At a second contact zone between proposed species L. triangulum and L. elapsoides (but variously treated as species or subspecies by different researchers) in Kentucky and Tennessee, we re-evaluated morphological data. In this case, the contact zone analysis indicated sympatry and reproductive isolation of the two taxa, and thus strongly supported L. triangulum and L. elapsoides as distinct species. We conclude that detailed studies of contact zones, based on either genetic or morphological data, are essential for distinguishing intraspecific from interspecific variation in the case of widely and continuously distributed taxa.}, } @article {pmid35988118, year = {2022}, author = {Kekäläinen, J}, title = {Cryptic female choice within individual males - A neglected component of the postmating sexual selection?.}, journal = {Journal of evolutionary biology}, volume = {35}, number = {11}, pages = {1407-1413}, doi = {10.1111/jeb.14081}, pmid = {35988118}, issn = {1420-9101}, mesh = {Male ; Female ; Animals ; *Sexual Selection ; *Semen ; Fertilization ; Spermatozoa ; Reproduction ; }, abstract = {Cryptic female choice (CFC) is commonly assumed to act only in polyandrous mating systems, which allows females to bias fertilization towards the sperm of particular males. However, accumulated evidence has demonstrated that sperm show significant phenotypic and genotypic variation also within single ejaculates, which have important consequences for offspring phenotype and fitness. Here, I argue that these neglected sources of intra-male sperm variation often allow CFC to act also within individual males and facilitate fertilization bias towards genetically compatible (or otherwise preferred) sperm haplotypes. In this article, I explain prerequisites for within-male CFC, the criteria for demonstrating it and summarize accumulated evidence for this emerging selection process. Then, I evaluate prevalence of within-male CFC and review its potential evolutionary consequences. The aim of this article is to broaden the current definition of CFC by demonstrating that CFC has potential to act in all mating systems, in both internally and externally fertilizing species. Incorporation of the within-male CFC concept into the current models of sexual selection may provide novel insights into the deeper understanding of selective factors driving the evolution of mating systems and reproductive proteins. Finally, within-male CFC towards particular sperm haplotypes may increase our understanding of non-Mendelian inheritance.}, } @article {pmid35963148, year = {2022}, author = {Harbuzov, Z and Farberova, V and Tom, M and Pallavicini, A and Stanković, D and Lotan, T and Lubinevsky, H}, title = {Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition.}, journal = {Marine genomics}, volume = {65}, number = {}, pages = {100980}, doi = {10.1016/j.margen.2022.100980}, pmid = {35963148}, issn = {1876-7478}, mesh = {Base Composition ; Gene Library ; *High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; }, abstract = {The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470-490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342-3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.}, } @article {pmid35952411, year = {2022}, author = {Qi, L and Qiao, J}, title = {Progress of chiral ligand-exchange capillary electrophoresis for enantioseparation.}, journal = {Journal of chromatography. A}, volume = {1679}, number = {}, pages = {463381}, doi = {10.1016/j.chroma.2022.463381}, pmid = {35952411}, issn = {1873-3778}, mesh = {*Electrophoresis, Capillary ; Ligands ; Stereoisomerism ; }, abstract = {Chiral ligand exchange capillary electrophoresis (CLE-CE) has become an area of tremendous interest in chiral separation science, particularly in life science and pharmaceutical, due to its notable simplicity, tunable migration order, and outstanding performance. This approach effectively separates enantiomers in drugs, food products and bio-samples. Nevertheless, the main challenges in CLE-CE are the limited chiral ligand-species, unclear mechanism of thermodynamic enantioseparation and unsatisfactory enantioseparation efficiency, which restrict its applications. Designing desirable chiral ligand-species and exploring profitable central metal ions are considered to be efficient strategies for addressing these obstacles, which can improve the performance of CLE-CE and expand its application in living bio-systems. This review introduces the concept of desirable chiral ligand species and highlights the latest CLE-CE research in the last decade, with special emphasis on boosting its enantioseparation efficiency and expanding its cutting-edge application. Moreover, further research in the CLE-CE field is prospected.}, } @article {pmid35923138, year = {2022}, author = {Zhou, H and Lu, X and Du, C and Zhou, Z and Feng, J and Liang, Z and Xu, Y and Qiu, X and Shen, Z}, title = {Cycloacceleration of Reactive Oxygen Species Generation Based on Exceedingly Small Magnetic Iron Oxide Nanoparticles for Tumor Ferroptosis Therapy.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {18}, number = {35}, pages = {e2202705}, doi = {10.1002/smll.202202705}, pmid = {35923138}, issn = {1613-6829}, mesh = {Cell Line, Tumor ; Contrast Media ; *Ferroptosis ; Humans ; Magnetic Iron Oxide Nanoparticles ; *Nanoparticles ; *Neoplasms/diagnostic imaging/drug therapy/pathology ; Reactive Oxygen Species ; Tumor Microenvironment ; }, abstract = {Because of the insufficiency of hydrogen peroxide, the relatively low rate of Fenton reaction, and the active glutathione (GSH) peroxidase 4 (GPX4) in tumor cells, it is difficult to achieve a desirable efficacy of ferroptosis therapy (FT) for tumors based on nanomaterials. Inspired by the concept of "cyclotron" in physics, in this study, a new concept of cycloacceleration of reactive oxygen species (ROS) generation in tumor cells to realize high-performance FT of tumors is proposed. Typically, a magnetic resonance imaging (MRI) contrast agent of dotted core-shell Fe3 O4 /Gd2 O3 hybrid nanoparticles (FGNPs) is prepared based on exceedingly small magnetic iron oxide nanoparticles (ES-MIONs). Sorafenib (SFN) is loaded and poly(ethylene glycol) methyl ether-poly(propylene sulfide)-NH2 (mPEG-PPS-NH2) is grafted on the surface of FGNP to generate SA-SFN-FGNP via self-assembly. The results of in vitro and in vivo demonstrate SA-SFN-FGNP can work with the acidic tumor microenvironment and endosomal conditions, Fenton reaction and system XC [-] , and generate cyclic reactions in tumor cells, resulting in specific cycloacceleration of ROS generation for high-performance FT of tumors. The very high longitudinal relaxivity (r1 , 33.43 mM[-1] s[-1] , 3.0 T) makes sure that the SA-SFN-FGNP can be used for MRI-guided FT of tumors.}, } @article {pmid35906926, year = {2022}, author = {Leducq, JB and Sneddon, D and Santos, M and Condrain-Morel, D and Bourret, G and Martinez-Gomez, NC and Lee, JA and Foster, JA and Stolyar, S and Shapiro, BJ and Kembel, SW and Sullivan, JM and Marx, CJ}, title = {Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity.}, journal = {Genome biology and evolution}, volume = {14}, number = {8}, pages = {}, pmid = {35906926}, issn = {1759-6653}, mesh = {Ecosystem ; *Methylobacterium ; Phylogeny ; Plant Leaves ; Plants/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer (HGT). We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content, and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.}, } @article {pmid35890512, year = {2022}, author = {Ott, T and Schall, M and Vogt, R and Oberprieler, C}, title = {The Warps and Wefts of a Polyploidy Complex: Integrative Species Delimitation of the Diploid Leucanthemum (Compositae, Anthemideae) Representatives.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {14}, pages = {}, pmid = {35890512}, issn = {2223-7747}, abstract = {Species delimitation-owing to the paramount role of the species rank in evolutionary, ecological, and nature conservation studies-is an essential contribution of taxonomy to biodiversity research. In an 'integrative taxonomy' approach to species delimitation on the diploid level, we searched for evolutionary significant units (the warps and wefts) that gave rise to the polyploid complex of European ox-eye daisies (Leucanthemum; Compositae-Anthemideae). Species discovery and validation methods based on genetic, ecological, geographical, and morphometric datasets were applied to test the currently accepted diploid morpho-species, i.e., morphologically delimited species, in Leucanthemum. Novel approaches were taken in the analyses of RADseq data (consensus clustering), morphometrics of reconstructed leaf silhouettes from digitized herbarium specimens, and quantification of species-distribution overlaps. We show that 17 of the 20 Leucanthemum morpho-species are supported by genetic evidence. The taxonomic rank of the remaining three morpho-species was resolved by combining genealogic, ecologic, geographic, and morphologic data in the framework of von Wettstein's morpho-geographical species concept. We herewith provide a methodological pipeline for the species delimitation in an 'integrative taxonomy' fashion using sources of evidence from genealogical, morphological, ecological, and geographical data in the philosophy of De Queiroz's "Unified Species Concept".}, } @article {pmid35868886, year = {2022}, author = {Connolly, JB and Romeis, J and Devos, Y and Glandorf, DCM and Turner, G and Coulibaly, MB}, title = {Gene drive in species complexes: defining target organisms.}, journal = {Trends in biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tibtech.2022.06.013}, pmid = {35868886}, issn = {1879-3096}, abstract = {Engineered gene drives, which bias their own inheritance to increase in frequency in target populations, are being developed to control mosquito malaria vectors. Such mosquitoes can belong to complexes of both vector and nonvector species that can produce fertile interspecific hybrids, making vertical gene drive transfer (VGDT) to sibling species biologically plausible. While VGDT to other vectors could positively impact human health protection goals, VGDT to nonvectors might challenge biodiversity ones. Therefore, environmental risk assessment of gene drive use in species complexes invites more nuanced considerations of target organisms and nontarget organisms than for transgenes not intended to increase in frequency in target populations. Incorporating the concept of target species complexes offers more flexibility when assessing potential impacts from VGDT.}, } @article {pmid35860537, year = {2022}, author = {Smith, LT and Magdalena, C and Przelomska, NAS and Pérez-Escobar, OA and Melgar-Gómez, DG and Beck, S and Negrão, R and Mian, S and Leitch, IJ and Dodsworth, S and Maurin, O and Ribero-Guardia, G and Salazar, CD and Gutierrez-Sibauty, G and Antonelli, A and Monro, AK}, title = {Revised Species Delimitation in the Giant Water Lily Genus Victoria (Nymphaeaceae) Confirms a New Species and Has Implications for Its Conservation.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {883151}, pmid = {35860537}, issn = {1664-462X}, abstract = {Reliably documenting plant diversity is necessary to protect and sustainably benefit from it. At the heart of this documentation lie species concepts and the practical methods used to delimit taxa. Here, we apply a total-evidence, iterative methodology to delimit and document species in the South American genus Victoria (Nymphaeaceae). The systematics of Victoria has thus far been poorly characterized due to difficulty in attributing species identities to biological collections. This research gap stems from an absence of type material and biological collections, also the confused diagnosis of V. cruziana. With the goal of improving systematic knowledge of the genus, we compiled information from historical records, horticulture and geography and assembled a morphological dataset using citizen science and specimens from herbaria and living collections. Finally, we generated genomic data from a subset of these specimens. Morphological and geographical observations suggest four putative species, three of which are supported by nuclear population genomic and plastid phylogenomic inferences. We propose these three confirmed entities as robust species, where two correspond to the currently recognized V. amazonica and V. cruziana, the third being new to science, which we describe, diagnose and name here as V. boliviana Magdalena and L. T. Sm. Importantly, we identify new morphological and molecular characters which serve to distinguish the species and underpin their delimitations. Our study demonstrates how combining different types of character data into a heuristic, total-evidence approach can enhance the reliability with which biological diversity of morphologically challenging groups can be identified, documented and further studied.}, } @article {pmid35845367, year = {2022}, author = {Burbrink, FT and Crother, BI and Murray, CM and Smith, BT and Ruane, S and Myers, EA and Pyron, RA}, title = {Empirical and philosophical problems with the subspecies rank.}, journal = {Ecology and evolution}, volume = {12}, number = {7}, pages = {e9069}, pmid = {35845367}, issn = {2045-7758}, abstract = {Species-level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species "concepts." These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what "kind" of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.}, } @article {pmid35842034, year = {2022}, author = {Kurtz, MA and Khullar, P and Gilbert, JL}, title = {Cathodic activation and inflammatory species are critical to simulating in vivo Ti-6Al-4V selective dissolution.}, journal = {Acta biomaterialia}, volume = {149}, number = {}, pages = {399-409}, doi = {10.1016/j.actbio.2022.07.020}, pmid = {35842034}, issn = {1878-7568}, mesh = {*Alloys ; Corrosion ; Humans ; *Hydrogen Peroxide ; Materials Testing/methods ; Solubility ; Surface Properties ; Titanium ; }, abstract = {In vivo retrievals of metallic orthopedic implants have shown selective dissolution of Ti-6Al-4V, where the vanadium-rich β phase preferentially corrodes from the surface. This damage, typically observed in crevices, is not directly caused by wear mechanics and the underlying electrochemical mechanism remains poorly understood. Previous studies show that fretting corrosion can cause negative potential drops, resulting in a decrease in surface oxide passivation resistance and the electrochemical generation of reactive oxygen species (ROS) at metallic surfaces. In this study, we combine cathodic activation and hydrogen peroxide to induce selective dissolution in vitro. After a 600 s -1 V hold and 4 h recovery in 20 °C 1 M H2O2 solution, the Ti-6Al-4V β phase was preferentially dissolved. An initial activation threshold of -0.5 V induced a significant increase in β dissolution (p = 0.000). Above this threshold, little selective dissolution occurred. In an Arrhenius-like fashion, decreasing solution concentration to 0.1 M required 72 h to generate β dissolution instead of 4 h at 1 M. Heating 0.1 M solution to body temperature (37 °C) resulted in a decrease in the time needed to replicate a similar level of β dissolution (>90%). Electrochemical impedance shows that both cathodic activation and inflammatory species are necessary to induce selective dissolution, where the combinatorial effect causes a significant drop in oxide passivation resistance from 106 to 102 (p = 0.000). STATEMENT OF SIGNIFICANCE: Though hip arthroplasties are considered a successful procedure, revision rates of 2-4% result in tens of thousands of additional surgeries within the United States, subjecting patients to increased risk of complications. Corrosion is associated with implant failure and retrieval studies show that titanium and its alloys can severely corrode in vivo in ways not yet duplicated in vitro. Here, we reproduce selective dissolution of Ti-6Al-4V β phase simulating key characteristics of in vivo degradation observed in orthopedic retrievals. We establish both cathodically activated corrosion, a relatively unexplored concept, and the presence of inflammatory species as prerequisites, furthering our understanding of this clinically relevant damage mode. We introduce an Arrhenius-based approach to assess the concentration-temperature-time interactions present.}, } @article {pmid35837745, year = {2022}, author = {Barrett, CF and Santee, MV and Fama, NM and Freudenstein, JV and Simon, SJ and Sinn, BT}, title = {Lineage and role in integrative taxonomy of a heterotrophic orchid complex.}, journal = {Molecular ecology}, volume = {31}, number = {18}, pages = {4762-4781}, pmid = {35837745}, issn = {1365-294X}, support = {U54 GM104942/GM/NIGMS NIH HHS/United States ; P20 GM121299/GM/NIGMS NIH HHS/United States ; P20 GM103434/GM/NIGMS NIH HHS/United States ; }, mesh = {*Orchidaceae/genetics ; Oregon ; Phylogeny ; Species Specificity ; }, abstract = {Lineage-based species definitions applying coalescent approaches to species delimitation have become increasingly popular. Yet, the application of these methods and the recognition of lineage-only definitions have recently been questioned. Species delimitation criteria that explicitly consider both lineages and evidence for ecological role shifts provide an opportunity to incorporate ecologically meaningful data from multiple sources in studies of species boundaries. Here, such criteria were applied to a problematic group of mycoheterotrophic orchids, the Corallorhiza striata complex, analysing genomic, morphological, phenological, reproductive-mode, niche, and fungal host data. A recently developed method for generating genomic polymorphism data-ISSRseq-demonstrates evidence for four distinct lineages, including a previously unidentified lineage in the Coast Ranges and Cascades of California and Oregon, USA. There is divergence in morphology, phenology, reproductive mode, and fungal associates among the four lineages. Integrative analyses, conducted in population assignment and redundancy analysis frameworks, provide evidence of distinct genomic lineages and a similar pattern of divergence in the extended data, albeit with weaker signal. However, none of the extended data sets fully satisfy the condition of a significant role shift, which requires evidence of fixed differences. The four lineages identified in the current study are recognized at the level of variety, short of comprising different species. This study represents the most comprehensive application of lineage + role to date and illustrates the advantages of such an approach.}, } @article {pmid35837665, year = {2022}, author = {Brunke, AJ}, title = {Revision of rove beetle genus Bolitogyrus Chevrolat (Staphylininae, Cyrtoquediini). Supplement 1.}, journal = {ZooKeys}, volume = {1096}, number = {}, pages = {1-16}, pmid = {35837665}, issn = {1313-2989}, abstract = {Bolitogyrus is a moderately diverse genus of 78 species that are widely disjunct in the subtropical and tropical forests of the Neotropical and Oriental regions. Following recent revisions of both the Neotropical and Oriental species, this study provides new distributional data, a revised species concept for Bolitogyrusstrigifrons (Wendeler) sensu nov., and the description of B.pseudostrigifrons sp. nov. and B.nigropolitoides sp. nov., bringing the total number of Bolitogyrus species to 80. Several keys are updated to reflect the newly available data and new species.}, } @article {pmid35780503, year = {2022}, author = {Wang, M and Mao, X and Liu, J and Deng, B and Deng, S and Jin, S and Li, W and Gong, J and Deng, R and Zhu, J}, title = {A Versatile 3D-Confined Self-Assembly Strategy for Anisotropic and Ordered Mesoporous Carbon Microparticles.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {9}, number = {25}, pages = {e2202394}, pmid = {35780503}, issn = {2198-3844}, mesh = {*Carbon/chemistry ; Catalysis ; *Metal Nanoparticles/chemistry ; Platinum/chemistry ; Polymers/chemistry ; }, abstract = {Mesoporous carbon microparticles (MCMPs) with anisotropic shapes and ordered structures are attractive materials that remain challenging to access. In this study, a facile yet versatile route is developed to prepare anisotropic MCMPs by combining neutral interface-guided 3D confined self-assembly (3D-CSA) of block copolymer (BCP) with a self-templated direct carbonization strategy. This route enables pre-engineering BCP into microparticles with oblate shape and hexagonal packing cylindrical mesostructures, followed by selective crosslinking and decorating of their continuous phase with functional species (such as platinum nanoparticles, Pt NPs) via in situ growth. To realize uniform in situ growth, a "guest exchange" strategy is proposed to make room for functional species and a pre-crosslinking strategy is developed to preserve the structural stability of preformed BCP microparticles during infiltration. Finally, Pt NP-loaded MCMPs are derived from the continuous phase of BCP microparticles through selective self-templated direct carbonization without using any external carbon source. This study introduces an effective concept to obtain functional species-loaded and N-doped MCMPs with oblate shape and almost hexagonal structure (p6mm), which would find important applications in fuel cells, separation, and heterogeneous catalysis.}, } @article {pmid35775956, year = {2022}, author = {Fang, G and Chen, H and Shao, X and Wang, H and Zhan, D and Wang, R and Meng, P and Fang, H and Liu, F and Ling, P and Wu, Z and Diao, J and Yao, Q and Chen, Q}, title = {Single Image Capture of Bioactive Ion Crosstalk within Inter-Organelle Membrane Contacts at Nanometer Resolution.}, journal = {Small methods}, volume = {6}, number = {8}, pages = {e2200321}, doi = {10.1002/smtd.202200321}, pmid = {35775956}, issn = {2366-9608}, mesh = {Cell Physiological Phenomena ; *Lysosomes/metabolism ; Mitochondria ; Mitochondrial Membranes ; *Organelles/chemistry ; }, abstract = {Rapid bioactive ion exchange is a form of communication that regulates a wide range of biological processes. Despite advances in super-resolution optical microscopy, visualizing ion exchange remains challenging due to the extremely fast nature of these events. Here, a "converting a dynamic event into a static image construction" (CDtSC) strategy is developed that uses the color transformation of a single dichromatic molecular probe to visualize bioactive ion inter-organelle exchange in live cells. As a proof of concept, a reactive sulfur species (RSS) is analyzed at the mitochondria-lysosome contact sites (MLCs). A non-toxic and sensitive probe based on coumarin-hemicyanine structure is designed that responds to RSS localized in both mitochondria and lysosomes while fluorescing different colors. Using this probe, RSS give-and-take at MLCs is visualized, thus providing the first evidence that RSS is involved in inter-organelle contacts and communication. Taken together, the CDtSC provides a strategy to visualize and analyze rapid inter-organelle ion exchange events in live cells at nanometer resolution.}, } @article {pmid35760130, year = {2022}, author = {Sreedhar, A and Hoai Ta, QT and Noh, JS}, title = {Role of p-n junction initiated mixed-dimensional 0D/2D, 1D/2D, and 2D/2D BiOX (X = Cl, Br, and I)/TiO2 nanocomposite interfaces for environmental remediation applications: A review.}, journal = {Chemosphere}, volume = {305}, number = {}, pages = {135478}, doi = {10.1016/j.chemosphere.2022.135478}, pmid = {35760130}, issn = {1879-1298}, mesh = {Catalysis ; *Environmental Restoration and Remediation ; *Nanocomposites ; Titanium ; Water ; }, abstract = {Nowadays, we are critically facing various environmental issues. Among these, water contamination is the foremost issue, which worsens our health and living organisms in the water. Thus, it is necessary to provide an avenue to minimize the toxic matter through the development of facile technique and harmless photocatalyst. In this review, we intended to uncover the findings associated with various 0D, 1D, and 2D nanostructures featured photocatalysts for advancements in interfacial characteristics and toxic matter degradation. In this context, we evaluated the promising mixed-dimensional 0D/2D, 1D/2D, and 2D/2D bismuth oxyhalides BiOX (X = Cl, Br, and I) integrated TiO2 nanostructure interfaces. Tunable mixed-dimensional interfaces highlighted with higher surface area, more heterojunctions, variation in the conduction and valence band potential, narrowed band gap, and built-in electric field formation between BiOX and TiO2, which exhibits remarkable toxic dye, heavy metals, and antibiotics degradation. Further, this review further examines insights into the charge carrier generation, separation, and shortened charge transfer path at reduced recombination. Considering the advantages of type-II, S-scheme, and Z-scheme charge transfer mechanisms in the BiOX/TiO2, we heightened the combination of various reactive species generation. In a word, the concept of mixed-dimensional BiOX/TiO2 heterojunction interface endows toxic matter adsorption and decomposition into useful products. Challenges and future perspectives are also provided.}, } @article {pmid35754287, year = {2022}, author = {Salvatore, MF and Soto, I and Kasanga, EA and James, R and Shifflet, MK and Doshier, K and Little, JT and John, J and Alphonso, HM and Cunningham, JT and Nejtek, VA}, title = {Establishing Equivalent Aerobic Exercise Parameters Between Early-Stage Parkinson's Disease and Pink1 Knockout Rats.}, journal = {Journal of Parkinson's disease}, volume = {12}, number = {6}, pages = {1897-1915}, pmid = {35754287}, issn = {1877-718X}, mesh = {Animals ; Exercise Test ; Exercise Therapy/methods ; Heart Rate ; Humans ; Infant ; *Parkinson Disease/genetics ; Rats ; }, abstract = {BACKGROUND: Rodent Parkinson's disease (PD) models are valuable to interrogate neurobiological mechanisms of exercise that mitigate motor impairment. Translating these mechanisms to human PD must account for physical capabilities of the patient.

OBJECTIVE: To establish cardiovascular parameters as a common metric for cross-species translation of aerobic exercise impact.

METHOD: We evaluated aerobic exercise impact on heart rate (HR) in 21 early-stage PD subjects (Hoehn Yahr ≤1.5) exercising in non-contact boxing training for ≥3 months, ≥3x/week. In 4-month-old Pink1 knockout (KO) rats exercising in a progressively-increased treadmill speed regimen, we determined a specific treadmill speed that increased HR to an extent similar in human subjects.

RESULTS: After completing aerobic exercise for ∼30 min, PD subjects had increased HR∼35% above baseline (∼63% maximum HR). Motor and cognitive test results indicated the exercising subjects completed the timed up and go (TUG) and trail-making test (TMT-A) in significantly less time versus exercise-naïve PD subjects. In KO and age-matched wild-type (WT) rats, treadmill speeds of 8-10 m/min increased HR up to 25% above baseline (∼67% maximum HR), with no further increases up to 16 m/min. Exercised KO, but not WT, rats showed increased locomotor activity compared to an age-matched exercise-naïve cohort at 5 months old.

CONCLUSION: These proof-of-concept results indicate HR is a cross-species translation parameter to evaluate aerobic exercise impact on specific motor or cognitive functions in human subjects and rat PD models. Moreover, a moderate intensity exercise regimen is within the physical abilities of early-stage PD patients and is therefore applicable for interrogating neurobiological mechanisms in rat PD models.}, } @article {pmid35736076, year = {2022}, author = {Cavender, JC and Vadell, EM and Perrigo, AL and Landolt, JC and Stephenson, SL and Liu, P}, title = {Four New Species of Dictyostelids from Soil Systems in Northern Thailand.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {6}, pages = {}, pmid = {35736076}, issn = {2309-608X}, abstract = {Dictyostelid cellular slime molds (dictyostelids) are ubiquitous microorganisms found in the uppermost layers of most soils. Reports on the species diversity of dictyostelids in Southeast Asia, particularly Thailand, are few in number. A survey for dictyostelids performed in northern Thailand in 2008 recovered 15 distinctive forms, including several common species and a number of forms morphologically different from anything already described. Five of the latter were formally described as new to science in a previous paper. An additional five isolates appeared to be morphologically distinct, and this was supported by DNA sequence data and phylogenetic analysis. These isolates representing four species are described herein as species new to science. Detailed descriptions and illustrations of these new species are provided.}, } @article {pmid35718755, year = {2022}, author = {Estes, JA and Vermeij, GJ}, title = {History's legacy: Why future progress in ecology demands a view of the past.}, journal = {Ecology}, volume = {103}, number = {11}, pages = {e3788}, doi = {10.1002/ecy.3788}, pmid = {35718755}, issn = {1939-9170}, mesh = {Animals ; *Ecosystem ; Food Chain ; Hydrogen-Ion Concentration ; Kelp ; Otters ; Seawater ; *Ecology/methods/standards ; }, abstract = {History has profoundly affected the composition, distribution, and abundances of species in contemporary ecosystems. A full understanding of how ecosystems work and change must therefore take history into account. We offer four well-studied examples illustrating how a knowledge of history has strengthened interpretations of modern systems: the development of molluscan antipredatory defenses in relation to shell-breaking predators; the North Pacific kelp ecosystem with sea otters, smaller predators, sea urchins, and large herbivores; estuarine ecosystems affected by the decline in oysters and other suspension feeders; and the legacy of extinct large herbivores and frugivores in tropical American forests. Many current ecological problems would greatly benefit from a historical perspective. We highlight four of these: soil depletion and tree stunting in forests related to the disappearance of large consumers; the spread of anoxic dead zones in the ocean, which we argue could be mitigated by restoring predator and suspension-feeding guilds; ocean acidification, which would be alleviated by more nutrient recycling by consumers in the aerobic ecosystem; and the relation between species diversity and keystone predators, a foundational concept that is complicated by simplified trophic relationships in modern ecosystems.}, } @article {pmid35705651, year = {2022}, author = {Sharwani, AA and Narayanan, KB and Khan, ME and Han, SS}, title = {Photocatalytic degradation activity of goji berry extract synthesized silver-loaded mesoporous zinc oxide (Ag@ZnO) nanocomposites under simulated solar light irradiation.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10017}, pmid = {35705651}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/chemistry/pharmacology ; Catalysis ; Coloring Agents ; Congo Red ; Gram-Negative Bacteria ; Gram-Positive Bacteria ; *Lycium ; *Metal Nanoparticles/chemistry ; Methylene Blue ; *Nanocomposites/chemistry ; Plant Extracts/chemistry/pharmacology ; Silver/chemistry ; Zinc ; *Zinc Oxide/chemistry ; }, abstract = {Different approaches have been developed for the synthesis of various nanostructured materials with unique morphologies. This study demonstrated the photocatalytic and antimicrobial abilities of silver-loaded zinc oxide nanocomposites (Ag@ZnO NCs). Initially, ZnO with a unique mesoporous ellipsoidal morphology in the size range of 0.59 ± 0.11 × 0.33 ± 0.09 µm (length × width) was synthesized using aqueous precipitation in a mild hydrothermal condition (80 °C) with the aqueous fruit extract of goji berry (GB) (as an additive) and calcined in air at 200 °C/2 h and 250 °C/3 h. Powder X-ray diffraction (XRD) revealed the formation of a hexagonal phase of the wurtzite (WZ) structure. The average crystallite size of ZnO was 23.74 ± 4.9 nm as calculated using Debye-Scherrer's equation. It also possesses higher thermal stability with the surface area, pore volume, and pore size of 11.77 m[2]/g, 0.027 cm[3]/g, and 9.52 nm, respectively. Furthermore, different mesoporous Ag@ZnO NCs loaded with face-centered cubic (fcc) silver nanoparticles (Ag NPs) in the range of 90-160 nm were synthesized by GB extract as a reducing and capping agent on the surface of ZnO after calcination in air. The immobilization of Ag NPs was confirmed by XRD, X-ray photoelectron spectroscopy (XPS), field-emission scanning electron microscopy (FE-SEM), FE-transmission electron microscopy (FE-TEM), and energy-dispersive X-ray spectroscopy (EDS). It was found that Ag0.2@ZnO NC (0.2 wt% of Ag) showed excellent photocatalytic degradation of both methylene blue (MB) (cationic) and congo red (CR) (anionic) dyes under simulated solar irradiation. The photocatalytic degradation of 99.3 ± 0.35% MB and 98.5 ± 1.3% CR occurred in 90 and 55 min, respectively, at room temperature by Ag0.2@ZnO NC. Besides, these NCs also showed broad-spectrum antibacterial activity against both Gram-positive and Gram-negative bacteria. The mechanistic concept of generating reactive oxygen species (ROS) by electron and hole charge (e‾/h[+]) carriers seems to be responsible for the photocatalytic degradation of commercial dyes and antibacterial activities by Ag@ZnO NCs. Thus, these silver-loaded mesoporous ellipsoidal ZnO NCs are promising candidates as photocatalysts for industrial/wastewater treatment as well as in antimicrobial therapeutics.}, } @article {pmid35644289, year = {2022}, author = {Sanati, M and Afshari, AR and Kesharwani, P and Sukhorukov, VN and Sahebkar, A}, title = {Recent trends in the application of nanoparticles in cancer therapy: The involvement of oxidative stress.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {348}, number = {}, pages = {287-304}, doi = {10.1016/j.jconrel.2022.05.035}, pmid = {35644289}, issn = {1873-4995}, mesh = {Humans ; *Nanoparticles/chemistry ; Nanotechnology ; *Neoplasms/drug therapy/pathology ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; }, abstract = {In the biomedical area, the interdisciplinary field of nanotechnology has the potential to bring numerous unique applications, including better tactics for cancer detection, diagnosis, and therapy. Nanoparticles (NPs) have been the topic of many research and material applications throughout the last decade. Unlike small-molecule medications, NPs are defined by distinct physicochemical characteristics, such as a large surface-to-volume ratio, which allows them to permeate live cells with relative ease. The versatility of NPs as both therapeutics and diagnostics makes them ideal for a broad spectrum of illnesses, from infectious diseases to cancer. A significant amount of data has been participated in the current scientific publications, emphasizing the concept that NPs often produce reactive oxygen species (ROS) to a larger degree than micro-sized particles. It is important to note that oxidative stress governs a wide range of cell signaling cascades, many of which are responsible for cancer cell cytotoxicity. Here, we aimed to provide insight into the signaling pathways triggered by oxidative stress in cancer cells in response to several types of nanomaterials, such as metallic and polymeric NPs and quantum dots. We discuss recent advances in developing integrated anticancer medicines based on NPs targeted to destroy malignant cells by increasing their ROS setpoint.}, } @article {pmid35633899, year = {2022}, author = {Ali, C and Blackmond, DG and Burés, J}, title = {Kinetic Rationalization of Nonlinear Effects in Asymmetric Catalytic Cascade Reactions under Curtin-Hammett Conditions.}, journal = {ACS catalysis}, volume = {12}, number = {10}, pages = {5776-5785}, pmid = {35633899}, issn = {2155-5435}, abstract = {Observations of nonlinear effects of catalyst enantiopurity on product enantiomeric excess in asymmetric catalysis are often used to infer that more than one catalyst species is involved in one or more reaction steps. We demonstrate here, however, that in the case of asymmetric catalytic cascade reactions, a nonlinear effect may be observed in the absence of any higher order catalyst species or any reaction step involving two catalyst species. We illustrate this concept with an example from a recent report of an organocatalytic enantioselective [10 + 2] stepwise cyclization reaction. The disruption of pre-equilibria (Curtin-Hammett equilibrium) in reversible steps occurring prior to the final irreversible product formation step can result in an alteration of the final product ee from what would be expected based on a linear relationship with the enantiopure catalyst. The treatment accounts for either positive or negative nonlinear effects in systems over a wide range of conditions including "major-minor" kinetics or the more conventional "lock-and-key" kinetics. The mechanistic scenario proposed here may apply generally to other cascade reaction systems exhibiting similar kinetic features and should be considered as a viable alternative model whenever a nonlinear effect is observed in a cascade sequence of reactions.}, } @article {pmid35630417, year = {2022}, author = {Melekhin, M and Yakovleva, Y and Lebedeva, N and Nekrasova, I and Nikitashina, L and Castelli, M and Mayén-Estrada, R and Romanovich, AE and Petroni, G and Potekhin, A}, title = {Cryptic Diversity in Paramecium multimicronucleatum Revealed with a Polyphasic Approach.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630417}, issn = {2076-2607}, abstract = {Paramecium (Ciliophora) systematics is well studied, and about twenty morphological species have been described. The morphological species may include several genetic species. However, molecular phylogenetic analyses revealed that the species diversity within Paramecium could be even higher and has raised a problem of cryptic species whose statuses remain uncertain. In the present study, we provide the morphological and molecular characterization of two novel Paramecium species. While Paramecium lynni n. sp., although morphologically similar to P. multimicronucleatum, is phylogenetically well separated from all other Paramecium species, Paramecium fokini n. sp. appears to be a cryptic sister species to P. multimicronucleatum. The latter two species can be distinguished only by molecular methods. The number and structure of micronuclei, traditionally utilized to discriminate species in Paramecium, vary not only between but also within each of the three studied species and, thus, cannot be considered a reliable feature for species identification. The geographic distribution of the P. multimicronucleatum and P. fokini n. sp. strains do not show defined patterns, still leaving space for a role of the geographic factor in initial speciation in Paramecium. Future findings of new Paramecium species can be predicted from the molecular data, while morphological characteristics appear to be unstable and overlapping at least in some species.}, } @article {pmid35621795, year = {2022}, author = {Ivković, M and Sinclair, BJ and Wahlberg, E}, title = {The Century Old Taxonomic Confusion Surrounding Wiedemannia zetterstedti Fallén and Related Species Is Resolved (Diptera: Empididae): Revision of the W. zetterstedti Group.}, journal = {Insects}, volume = {13}, number = {5}, pages = {}, pmid = {35621795}, issn = {2075-4450}, abstract = {The Wiedemannia zetterstedti species group is revised after examination of all available type specimens and includes one new species (W. ulrichi Ivković & Sinclair sp. nov.) and four redescribed species (W. czernyi (Bezzi), W. longipennis (Mik) stat. rev., W. rufipes (Oldenberg) stat. rev. and W. zetterstedti (Fallén)). The following new synonyms are proposed: W. (Roederella) ouedorum Vaillant, 1952 = W. czernyi (Bezzi, 1905); Paramesia riparia Robert, 1836 = W. zetterstedti (Fallén, 1826). Lectotypes are designated for the following species/subspecies: Atalanta hirtiloba Speiser, Brachystoma escheri Zetterstedt, Clinocera czernyi Bezzi, Clinocera longipennis Mik, Paramesia riparia Robert, and Roederia czernyi rufipes Oldenberg. In addition to morphological evidence, molecular species concepts were investigated using a molecular phylogenetic divergence-based species delimitation (bPTP) and results confirmed the morphological conclusions. A key to species is presented and geographic distributions are mapped.}, } @article {pmid35621776, year = {2022}, author = {Liu, T and Geng, X and Tang, Y and Li, B and Zhang, H and Teng, K}, title = {First Report of the Immature Stages of the Leaf-Mining Genus Subclemensia Kozlov, 1987 (Lepidoptera: Incurvariidae), with a Re-Illustration of the Type Species and a Generic Concept Discussion Based on Immature Characters.}, journal = {Insects}, volume = {13}, number = {5}, pages = {}, pmid = {35621776}, issn = {2075-4450}, abstract = {The immature stages of primitive Lepidoptera can provide quite different but often useful morphological evidence and synapomorphies from those of adults. Incurvariidae is one of the most primitive lineages of extant Lepidoptera, which is species-poor but highly diverse, but half of the genera lack any information on immature stages. New knowledge on the immature stages of the family is expected to provide useful morphological evidence and synapomorphies to stabilize the generic nomenclature. Subclemensia Kozlov, 1987 is one of the monotypic genera in Incurvariidae. In this study, the immature stages of the type species of Subclemensia are reported for the first time. The leaf mine, host plant and its biological characteristics are also provided. DNA barcodes were generated to aid the species delimitation. The adult male and female genitalia are re-illustrated by color photography to supplement the original line drawings. The generic concepts of Subclemensia and other related genera are discussed based on immature characters.}, } @article {pmid35615129, year = {2022}, author = {Chang, JT and Chao, CT and Nakamura, K and Liu, HL and Luo, MX and Liao, PC}, title = {Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {824158}, pmid = {35615129}, issn = {1664-462X}, abstract = {The divergence process of incipient species is fascinating but elusive by incomplete lineage sorting or gene flow. Species delimitation is also challenging among those morphologically similar allopatric species, especially when lacking comprehensive data. Cycas sect. Asiorientales, comprised of C. taitungensis and C. revoluta in the Ryukyu Archipelago and Taiwan, diverged recently with continuous gene flow, resulting in a reciprocal paraphyletic relationship. Their previous evolutionary inferences are questioned from few genetic markers, incomplete sampling, and incomprehensive morphological comparison by a long-term taxonomic misconception. By whole range sampling, this study tests the geographic mode of speciation in the two species of Asiorientales by approximate Bayesian computation (ABC) using genome-wide single nucleotide polymorphisms (SNPs). The individual tree was reconstructed to delimit the species and track the gene-flow trajectory. With the comparison of diagnostic morphological traits and genetic data, the allopatric speciation was rejected. Alternatively, continuous but spatially heterogeneous gene flow driven by transoceanic vegetative dispersal and pollen flow with contrasting population sizes blurred their species boundary. On the basis of morphological, genetic, and evolutionary evidence, we synonymized these two Cycas species. This study highlights not only the importance of the Kuroshio Current to species evolution but also the disadvantage of using species with geographically structured genealogies as conservation units.}, } @article {pmid35589052, year = {2022}, author = {Ennes Silva, F and Valsecchi do Amaral, J and Roos, C and Bowler, M and Röhe, F and Sampaio, R and Cora Janiak, M and Bertuol, F and Ismar Santana, M and de Souza Silva Júnior, J and Rylands, AB and Gubili, C and Hrbek, T and McDevitt, AD and Boubli, JP}, title = {Molecular phylogeny and systematics of bald uakaris, genus Cacajao (Primates: Pitheciidae), with the description of a new species.}, journal = {Molecular phylogenetics and evolution}, volume = {173}, number = {}, pages = {107509}, doi = {10.1016/j.ympev.2022.107509}, pmid = {35589052}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genome ; Phylogeny ; *Pitheciidae ; }, abstract = {Bald uakaris, genus Cacajao, are Amazonian primates currently classified as one species and four subspecies based on the patterns of pelage coloration. In this study, we test if their current taxonomy is represented by the phylogenetic relationship of the main lineages retrieved from molecular data. We included, for the first time, all bald uakari taxa in a mitochondrial (cytochrome b) and genome-wide (ddRAD) phylogenetic analyses. We also examined the pattern of pelage colouration in specimens from zoological collections. Having determined the number of lineages using Maximum Likelihood and the species tree using coalescent analyses, we test their divergence time using a Bayesian approach. While the cytochrome b analysis only recovered two clades, the ddRAD analysis supported the reciprocal monophyly of five lineages of bald uakaris, with all clades including only individuals with distinct and exclusive diagnostic phenotypic characters. We found that species diversification in Cacajao occurred during the last 300 Kya and may have been influenced by the formation of rivers and flooded forests in western Amazonia. We propose that the four bald uakari subspecies currently recognised can be upgraded to species level and we describe the white uakaris from the basin of the Rio Tarauacá as a new species.}, } @article {pmid35575078, year = {2022}, author = {Lee, J and Willett, CS}, title = {Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids.}, journal = {The Journal of heredity}, volume = {113}, number = {2}, pages = {171-183}, doi = {10.1093/jhered/esab068}, pmid = {35575078}, issn = {1465-7333}, mesh = {Animals ; *Copepoda/genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.}, } @article {pmid35565523, year = {2022}, author = {Bugarski-Stanojević, V and Stamenković, G and Jojić, V and Ćosić, N and Ćirović, D and Stojković, O and Veličković, J and Savić, I}, title = {Cryptic Diversity of the European Blind Mole Rat Nannospalax leucodon Species Complex: Implications for Conservation.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {9}, pages = {}, pmid = {35565523}, issn = {2076-2615}, abstract = {We explored the cryptic speciation of the Nannospalax leucodon species complex, characterised by intense karyotype evolution and reduced phenotypic variability that has produced different lineages, out of which 25 are described as chromosomal forms (CFs), so many cryptic species remain unnoticed. Although some of them should be classified as threatened, they lack the official nomenclature necessary to be involved in conservation strategies. Reproductive isolation between seven CFs has previously been demonstrated. To investigate the amount and dynamics of genetic discrepancy that follows chromosomal changes, infer speciation levels, and obtain phylogenetic patterns, we analysed mitochondrial 16S rRNA and MT-CYTB nucleotide polymorphism among 17 CFs-the highest number studied so far. Phylogenetic trees delineated 11 CFs as separate clades. Evolutionary divergence values overlapped with acknowledged higher taxonomic categories, or sometimes exceeded them. The fact that CFs with higher 2n are evolutionary older corresponds to the fusion hypothesis of Nannospalax karyotype evolution. To participate in conservation strategies, N. leucodon classification should follow the biological species concept, and proposed cryptic species should be formally named, despite a lack of classical morphometric discrepancy. We draw attention towards the syrmiensis and montanosyrmiensis CFs, estimated to be endangered/critically endangered, and emphasise the need for detailed monitoring and population survey for other cryptic species.}, } @article {pmid35552760, year = {2022}, author = {DeRaad, DA and McCormack, JE and Chen, N and Peterson, AT and Moyle, RG}, title = {Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays.}, journal = {Systematic biology}, volume = {71}, number = {6}, pages = {1453-1470}, doi = {10.1093/sysbio/syac034}, pmid = {35552760}, issn = {1076-836X}, mesh = {Animals ; Gene Flow ; Genetic Speciation ; Genetics, Population ; *Passeriformes ; Phylogeny ; *Songbirds/genetics ; }, abstract = {Complex speciation, involving rapid divergence and multiple bouts of post-divergence gene flow, can obfuscate phylogenetic relationships and species limits. In North America, cases of complex speciation are common, due at least in part to the cyclical Pleistocene glacial history of the continent. Scrub-Jays in the genus Aphelocoma provide a useful case study in complex speciation because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages. Here, we show that a comprehensive approach to genomic reconstruction of evolutionary history, i.e., synthesizing results from species delimitation, species tree reconstruction, demographic model testing, and tests for gene flow, is capable of clarifying evolutionary history despite complex speciation. We find concordant evidence across all statistical approaches for the distinctiveness of an endemic southern Mexico lineage (A. w. sumichrasti), culminating in support for the species status of this lineage under any commonly applied species concept. We also find novel genomic evidence for the species status of a Texas endemic lineage A. w. texana, for which equivocal species delimitation results were clarified by demographic modeling and spatially explicit models of gene flow. Finally, we find that complex signatures of both ancient and modern gene flow between the non-sister California Scrub-Jay (Aphelocoma californica) and Woodhouse's Scrub-Jay (Aphelocoma woodhouseii) result in discordant gene trees throughout the species' genomes despite clear support for their overall isolation and species status. In sum, we find that a multi-faceted approach to genomic analysis can increase our understanding of complex speciation histories, even in well-studied groups. Given the emerging recognition that complex speciation is relatively commonplace, the comprehensive framework that we demonstrate for interrogation of species limits and evolutionary history using genomic data can provide a necessary roadmap for disentangling the impacts of gene flow and incomplete lineage sorting (ILS) to better understand the systematics of other groups with similarly complex evolutionary histories. [Gene flow; genomics; introgression; phylogenomics; population genetics; species delimitation; species trees; systematics.].}, } @article {pmid35535507, year = {2022}, author = {Cauz-Santos, LA and Dodsworth, S and Samuel, R and Christenhusz, MJM and Patel, D and Shittu, T and Jakob, A and Paun, O and Chase, MW}, title = {Genomic insights into recent species divergence in Nicotiana benthamiana and natural variation in Rdr1 gene controlling viral susceptibility.}, journal = {The Plant journal : for cell and molecular biology}, volume = {111}, number = {1}, pages = {7-18}, pmid = {35535507}, issn = {1365-313X}, mesh = {Australia ; Genomics ; Phylogeny ; *RNA-Dependent RNA Polymerase/genetics ; *Tobacco/genetics ; }, abstract = {One of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. This susceptibility is the result of an insertion and consequent loss of function in the RNA-dependent RNA polymerase 1 (Rdr1) gene. However, the origin and age of LAB and the evolution of N. benthamiana across its wide distribution in Australia remain relatively underexplored. Here, we have used multispecies coalescent methods on genome-wide single nucleotide polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. Our results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. We provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier, c. 1.1 million years ago, from their common ancestor than the other four in this clade and is morphologically the most distinctive. We also found that the Rdr1 gene insertion is variable among accessions from the northern portions of the Northern Territory. Furthermore, this long-isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development.}, } @article {pmid35524916, year = {2022}, author = {Zhang, B and Chen, H and Deng, M and Li, J and González, AL and Wang, S}, title = {High dimensionality of stoichiometric niches in soil fauna.}, journal = {Ecology}, volume = {103}, number = {9}, pages = {e3741}, doi = {10.1002/ecy.3741}, pmid = {35524916}, issn = {1939-9170}, mesh = {Animals ; Biomass ; Carbon/analysis ; Nitrogen/analysis ; *Phosphorus/analysis ; *Soil/chemistry ; }, abstract = {The ecological niche is a fundamental concept to understand species' coexistence in natural communities. The recently developed framework of the multidimensional stoichiometric niche (MSN) characterizes species' niches using chemical elements in living organisms. Despite the fact that living organisms are composed of multiple elements, stoichiometric studies have so far mostly focused on carbon (C), nitrogen (N), and phosphorus (P), and therefore a quantitative analysis of the dimensionality of the MSN in living organisms is still lacking, particularly for animals. Here we quantified 10 elements composing the biomass of nine soil animal taxa (958 individuals) from three trophic groups. We found that all 10 elements exhibited large variation among taxa, which was partially explained by their phylogeny. Overlaps of MSNs among the nine soil animal taxa were relatively smaller based on 10 elements, compared with those based on only C, N, and P. Discriminant analysis using all 10 elements successfully differentiated among the nine taxa (accuracy: 90%), whereas that using only C, N, and P resulted in a lower accuracy (60%). Our findings provide new evidence for MSN differentiation in soil fauna and demonstrate the high dimensionality of organismal stoichiometric niches beyond C, N, and P.}, } @article {pmid35498683, year = {2022}, author = {Xian, X and Zhao, H and Wang, R and Qiao, H and Guo, J and Zhang, G and Liu, W and Wan, F}, title = {Ecological Niche Shifts Affect the Potential Invasive Risk of Rapistrum rugosum (L.) All. in China.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {827497}, pmid = {35498683}, issn = {1664-462X}, abstract = {Ecological niche is a key concept that links species distributions. Ecological niche shifts are expected to affect the potential invasive risk of alien species. Rapistrum rugosum is an invasive agricultural weed in many countries. Wild populations of R. rugosum have been recorded in China, representing a great threat to the regional crops. Based on distribution records from different regions and relevant environmental variables, the present study predicted the potential distribution and estimated the invasive risk of R. rugosum in China. Ecological niche shifts strongly affected the potential invasive risk of R. rugosum in China. The two most important variables were annual temperature range (Bio7) and mean temperature of the coldest quarter (Bio11). The total suitable habitat for the species covered an area of 287.53 × 10[4]km[2] and was mainly distributed in Southwest, Southeast, and Central China. Australia, Canada, Brazil, the United States, and Argentina accounted for over 90% of the inspection records of R. rugosum from Chinese entry ports during 2015-2018. The intercepted R. rugosum was frequently mixed in Glycine max (L.) Merr., Hordeum vulgare L., linseed, Triticum aestivum L., and Sorghum bicolor (L.) Moench. Moreover, 80% interceptions were recorded from Tianjin, Guangdong, Nanjing, and Chengdu customs. Climatic conditions do not limit the establishment capability of R. rugosum in China. Our results provide a theoretical reference for the development of monitoring and control measures for this invasive weed.}, } @article {pmid35491980, year = {2022}, author = {Corrêa, LL and de Souza, DC and Adriano, EA}, title = {Relationship of the parasite Rhadinorhynchus plagioscionis (Acanthocephala) with Plagioscion squamosissimus host and its specificity of occurrence in the Brazilian Amazon.}, journal = {Annals of parasitology}, volume = {68}, number = {1}, pages = {177-183}, doi = {10.17420/ap6801.422}, pmid = {35491980}, issn = {2299-0631}, mesh = {*Acanthocephala ; Animals ; Brazil/epidemiology ; *Fish Diseases/epidemiology/parasitology ; *Parasites ; *Perciformes/parasitology ; }, abstract = {Objective was the relationship of the parasite Rhadinorhynchus plagioscionis with its host Plagioscion squamosissimus, providing morphological and morphometric data to prove the specificity of this parasite with its host, with reports occurring only in rivers in the Brazilian Amazon. Rhadinorhynchus plagioscionis infected P. squamosissimus captured in the municipal region of Santarém, in the state of Pará, in the eastern Brazilian Amazon. The specimens were analyzed by light and scanning electron microscopy. Morphological data obtained confirmed conspecificty with R. plagioscionis and supplemental information was added to the morphological concept of this species. The body of R. plagioscionis is cylindrical and milky-coloured with dorsal curvature, a long proboscis displaying ventral curvature with 12 longitudinal rows containing 22 to 24 hooks, which are larger and more prominent towards the end of the ventral curvature, and decrease in size in the posterior extremity of the proboscis. The present study describes, in addition to the morphological and morphometric characteristics of R. plagioscionis, which have host specificity for P. squamosissimus, a relationship being reported exclusively in the Brazilian Amazon.}, } @article {pmid35456404, year = {2022}, author = {Aggarwal, SK and Singh, A and Choudhary, M and Kumar, A and Rakshit, S and Kumar, P and Bohra, A and Varshney, RK}, title = {Pangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives.}, journal = {Genes}, volume = {13}, number = {4}, pages = {}, pmid = {35456404}, issn = {2073-4425}, mesh = {Chromosome Mapping ; Humans ; *Plant Breeding ; *Plants/genetics ; }, abstract = {Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host-pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems.}, } @article {pmid35450796, year = {2022}, author = {Wells, T and Carruthers, T and Scotland, RW}, title = {Heuristics, species, and the analysis of systematic data.}, journal = {Trends in plant science}, volume = {27}, number = {6}, pages = {524-527}, doi = {10.1016/j.tplants.2022.03.013}, pmid = {35450796}, issn = {1878-4372}, support = {T001445/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Heuristics ; }, abstract = {Disagreements over how to define species potentially render them incomparable, yet biologists routinely count and compare species. This 'species problem' persists despite the wealth of data and methods available to contemporary systematists. A heuristic approach to species provides a consistent yet flexible means of selecting, assessing, and integrating different biological data.}, } @article {pmid35420714, year = {2022}, author = {Wang, Z and Zhan, M and Hu, X}, title = {Pulsed Laser Excited Photoacoustic Effect for Disease Diagnosis and Therapy.}, journal = {Chemistry (Weinheim an der Bergstrasse, Germany)}, volume = {28}, number = {37}, pages = {e202200042}, doi = {10.1002/chem.202200042}, pmid = {35420714}, issn = {1521-3765}, mesh = {Lasers ; Light ; *Photoacoustic Techniques/methods ; Spectrum Analysis ; }, abstract = {Pulsed laser can excite light absorber to generate photoacoustic (PA) effect, that is, when the absorber is irradiated with pulsed laser, the absorbed light energy is converted into local heat to cause rapid thermoelastic expansion and generate acoustic wave. The generated PA signal has been widely employed for the diagnosis of many diseases with superb contrast, high penetrability and sensitivity. In addition, with the increase of pulsed laser energy, the resulting PA shockwave and cavitation can promote efficient drug release at lesion sites to potentiate the resulting therapeutic efficacy. Furthermore, the PA shockwave/cavitation can mechanically inhibit disease and produce reactive species. In this Concept article, the principle and research status of pulsed laser excited disease theranostics are briefly summarized, extra suggestions are proposed to inspire extensive PA probes and photodynamic materials as well as novel methodologies.}, } @article {pmid35398511, year = {2022}, author = {Rajaonison, A and Le Page, S and Maurin, T and Chaudet, H and Raoult, D and Baron, SA and Rolain, JM}, title = {Antilogic, a new supervised machine learning software for the automatic interpretation of antibiotic susceptibility testing in clinical microbiology: proof-of-concept on three frequently isolated bacterial species.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {28}, number = {9}, pages = {1286.e1-1286.e8}, doi = {10.1016/j.cmi.2022.03.035}, pmid = {35398511}, issn = {1469-0691}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Artificial Intelligence ; Bacteria ; Escherichia coli ; Humans ; Microbial Sensitivity Tests ; Software ; Supervised Machine Learning ; }, abstract = {OBJECTIVE: Antibiotic susceptibility testing (AST) is necessary in order to adjust empirical antibiotic treatment, but the interpretation of results requires experience and knowledge. We have developed a machine learning software that is capable of reading AST images without any human intervention and that automatically interprets the AST, based on a database of antibiograms that have been clinically validated with European Committee on Antimicrobial Susceptibility Testing rules.

METHODS: We built a database of antibiograms that were labelled by senior microbiologists for three species: Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. We then developed Antilogic, a Python software based on an original image segmentation module and supervised learning models that we trained against the database. Finally, we blind tested Antilogic against a validation set of 5100 photos of antibiograms.

RESULTS: We trained Antilogic against a database of 18072 pictures of antibiograms. Overall agreement against the validation set reached 97% (16 855/17 281) regarding phenotypes. The severity rate of errors was also evaluated: 1.66% (287/17 281) were major errors and 0.80% (136/17 281) were very major errors. After implementation of uncertainty quantifications, the rate of errors decreased to 0.80% (114/13 451) and 0.42% (51/13 451) for major and very major errors respectively.

DISCUSSION: Antilogic is the first machine learning software that has been developed for AST interpretation. It is based on a novel approach that differs from the typical diameter measurement and expert system approach. Antilogic is a proof of concept that artificial intelligence can contribute to faster and easier diagnostic methods in the field of clinical microbiology.}, } @article {pmid35396623, year = {2022}, author = {Koide, RT}, title = {On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35396623}, issn = {1432-184X}, abstract = {My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.}, } @article {pmid35391385, year = {2022}, author = {Hodda, M}, title = {Phylum Nematoda: trends in species descriptions, the documentation of diversity, systematics, and the species concept.}, journal = {Zootaxa}, volume = {5114}, number = {1}, pages = {290-317}, doi = {10.11646/zootaxa.5114.1.2}, pmid = {35391385}, issn = {1175-5334}, mesh = {Animals ; Documentation ; *Nematoda ; }, abstract = {This paper summarizes the trends in nematode species description and systematics emerging from a comparison of the latest comprehensive classification and census of Phylum Nematoda (Hodda 2022a, b) with earlier classifications (listed in Hodda 2007). It also offers some general observations on trends in nematode systematics emerging from the review of the voluminous literature used to produce the classification. The trends in nematodes can be compared with developments in the systematics of other organisms to shed light on many of the general issues confronting systematists now and into the future.}, } @article {pmid35388735, year = {2022}, author = {Davies, M and Galazzo, G and van Hattem, JM and Arcilla, MS and Melles, DC and de Jong, MD and Schultsz, C and Wolffs, P and McNally, A and Schaik, WV and Penders, J}, title = {Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2060676}, pmid = {35388735}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria ; Bacteroidaceae ; Diarrhea/drug therapy ; Enterobacteriaceae/genetics ; *Enterobacteriaceae Infections/microbiology ; Escherichia coli/genetics ; *Gastrointestinal Microbiome ; Humans ; Travel ; beta-Lactamases/genetics/pharmacology ; }, abstract = {Previous studies have shown high acquisition risks of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) among international travelers visiting antimicrobial resistance (AMR) hotspots. Although antibiotic use and travelers' diarrhea have shown to influence the ESBL-E acquisition risk, it remains largely unknown whether successful colonization of ESBL-E during travel is associated with the composition, functional capacity and resilience of the traveler's microbiome. The microbiome of pre- and post-travel fecal samples from 190 international travelers visiting Africa or Asia was profiled using whole metagenome shotgun sequencing. A metagenomics species concept approach was used to determine the microbial composition, population diversity and functional capacity before travel and how it is altered longitudinally. Eleven travelers were positive for ESBL-E before travel and removed from the analysis. Neither the microbial richness (Chao1), diversity (effective Shannon) and community structure (Bray-Curtis dissimilarity) in pretravel samples nor the longitudinal change of these metrics during travel were predictive for ESBL-E acquisition. A zero-inflated two-step beta-regression model was used to determine how the longitudinal change in both prevalence and abundance of each taxon was related to ESBL acquisition. There were detected increases in both the prevalence and abundance of Citrobacter freundii and two members of the genus Bacteroides, in association with remaining uncolonized by ESBL-E. These results highlight the potential of these individual microbes as a microbial consortium to prevent the acquisition of ESBL-E. The ability to alter a person's colonization resistance to a bacterium could be key to intervention strategies that aim to minimize the spread of MDR bacteria.}, } @article {pmid35377002, year = {2022}, author = {Marcatti, M and Fracassi, A and Montalbano, M and Natarajan, C and Krishnan, B and Kayed, R and Taglialatela, G}, title = {Aβ/tau oligomer interplay at human synapses supports shifting therapeutic targets for Alzheimer's disease.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {79}, number = {4}, pages = {222}, pmid = {35377002}, issn = {1420-9071}, support = {R01AG069433/NH/NIH HHS/United States ; R01AG060718/NH/NIH HHS/United States ; R01 AG069433/AG/NIA NIH HHS/United States ; R01 AG060718/AG/NIA NIH HHS/United States ; R56063405/NH/NIH HHS/United States ; }, mesh = {Aged ; *Alzheimer Disease/metabolism ; Amyloid beta-Peptides/metabolism ; Hippocampus/metabolism ; Humans ; Synapses/metabolism ; Synaptosomes/metabolism ; }, abstract = {BACKGROUND: Alzheimer's disease (AD) is characterized by progressive cognitive decline due to accumulating synaptic insults by toxic oligomers of amyloid beta (AβO) and tau (TauO). There is growing consensus that preventing these oligomers from interacting with synapses might be an effective approach to treat AD. However, recent clinical trial failures suggest low effectiveness of targeting Aβ in late-stage AD. Researchers have redirected their attention toward TauO as the levels of this species increase later in disease pathogenesis. Here we show that AβO and TauO differentially target synapses and affect each other's binding dynamics.

METHODS: Binding of labeled, pre-formed Aβ and tau oligomers onto synaptosomes isolated from the hippocampus and frontal cortex of mouse and postmortem cognitively intact elderly human brains was evaluated using flow-cytometry and western blot analyses. Binding of labeled, pre-formed Aβ and tau oligomers onto mouse primary neurons was assessed using immunofluorescence assay. The synaptic dysfunction was measured by fluorescence analysis of single-synapse long-term potentiation (FASS-LTP) assay.

RESULTS: We demonstrated that higher TauO concentrations effectively outcompete AβO and become the prevailing synaptic-associated species. Conversely, high concentrations of AβO facilitate synaptic TauO recruitment. Immunofluorescence analyses of mouse primary cortical neurons confirmed differential synaptic binding dynamics of AβO and TauO. Moreover, in vivo experiments using old 3xTgAD mice ICV injected with either AβO or TauO fully supported these findings. Consistent with these observations, FASS-LTP analyses demonstrated that TauO-induced suppression of chemical LTP was exacerbated by AβO. Finally, predigestion with proteinase K abolished the ability of TauO to compete off AβO without affecting the ability of high AβO levels to increase synaptic TauO recruitment. Thus, unlike AβO, TauO effects on synaptosomes are hampered by the absence of protein substrate in the membrane.

CONCLUSIONS: These results introduce the concept that TauO become the main synaptotoxic species at late AD, thus supporting the hypothesis that TauO may be the most effective therapeutic target for clinically manifest AD.}, } @article {pmid35366296, year = {2021}, author = {Holt, WV and Comizzoli, P}, title = {Genome resource banking for wildlife conservation: promises and caveats.}, journal = {Cryo letters}, volume = {42}, number = {6}, pages = {309-320}, pmid = {35366296}, issn = {0143-2044}, mesh = {Animals ; *Animals, Wild ; *Cryopreservation/methods ; Embryo Transfer ; Insemination, Artificial ; Male ; Mammals ; Spermatozoa ; }, abstract = {The value of cryopreserved germplasm in agriculture, aquaculture and medicine was recognized in the mid-twentieth century following the discovery in the late 1940s of a method for recovering viable spermatozoa after freeze-thawing. Sir Alan Parkes (a founder of cryobiology as a discipline) remarked that "time and space has been abolished for cattle breeding", a phrase that continues to summarise the potential value of the Genetic Resource Bank (GRB) concept for all species. The underlying principle behind these remarks was based on the recognition that spermatozoa could remain viable for many years, and still achieve pregnancies even long after the semen donor had died. Nowadays, live mammalian embryos, amphibian spermatozoa and cultured somatic cells can also be stored for future use in conservation breeding programmes, where the overarching aim is to mitigate the deleterious impacts of inbreeding on the fitness and survival of populations. Revolutionary advances in the cryobiology of coral spermatozoa, embryos and larvae are also helping to counter the damaging effects of climate change and toxic chemicals on coral reefs. In this article we review the ways in which GRBs can contribute to global conservation activities, noting that species-specific biological differences can limit the success of standard animal breeding technologies such as artificial insemination and embryo transfer. These limitations mean that there is still a need for the development of novel, and possibly species-specific, GRB technologies.}, } @article {pmid35353481, year = {2022}, author = {Chiera, S and Koch, VM and Bleyer, G and Walter, T and Bittner, C and Bachmann, J and Vogel, N}, title = {From Sticky to Slippery: Self-Functionalizing Lubricants for In Situ Fabrication of Liquid-Infused Surfaces.}, journal = {ACS applied materials & interfaces}, volume = {14}, number = {14}, pages = {16735-16745}, doi = {10.1021/acsami.2c02390}, pmid = {35353481}, issn = {1944-8252}, abstract = {Liquid-infused surfaces offer a versatile approach to create self-cleaning coatings. In such coatings, a thin film of a fluid lubricant homogeneously coats the substrate and thus prevents direct contact with a second, contaminating liquid. For stable repellency, the interfacial energies need to be controlled to ensure that the lubricant is not replaced by the contaminating liquid. Here, we introduce the concept of self-functionalizing lubricants. Functional molecular species that chemically match the lubricant but possess selective anchor groups are dissolved in the lubricant and self-adhere to the surface, forming the required surface chemistry in situ from within the applied lubricant layer. To add flexibility to the self-functionalizing concept, the substrate is first primed with a thin polydopamine base layer, which can be deposited to nearly any substrate material from aqueous solutions and retains reactivity toward electron-donating groups such as amines. The temporal progression of the in situ functionalization is investigated by ellipsometry and quartz crystal microbalance and correlated to macroscopic changes in contact angle and contact angle hysteresis. The flexibility of the approach is underlined by creating repellent coatings with various substrate/lubricant combinations. The prepared liquid-infused surfaces significantly reduce cement adhesion and provide easy-to-clean systems under real-world conditions on shoe soles.}, } @article {pmid35342559, year = {2022}, author = {Dissanayake, DSB and Holleley, CE and Sumner, J and Melville, J and Georges, A}, title = {Lineage diversity within a widespread endemic Australian skink to better inform conservation in response to regional-scale disturbance.}, journal = {Ecology and evolution}, volume = {12}, number = {3}, pages = {e8627}, pmid = {35342559}, issn = {2045-7758}, abstract = {Much attention is paid in conservation planning to the concept of a species, to ensure comparability across studies and regions when classifying taxa against criteria of endangerment and setting priorities for action. However, various jurisdictions now allow taxonomic ranks below the level of species and nontaxonomic intraspecific divisions to be factored into conservation planning-subspecies, key populations, evolutionarily significant units, or designatable units. Understanding patterns of genetic diversity and its distribution across the landscape is a key component in the identification of species boundaries and determination of substantial geographic structure within species. A total of 12,532 reliable polymorphic SNP loci were generated from 63 populations (286 individuals) covering the distribution of the Australian eastern three-lined skink, Bassiana duperreyi, to assess genetic population structure in the form of diagnosable lineages and their distribution across the landscape, with particular reference to the recent catastrophic bushfires of eastern Australia. Five well-supported diagnosable operational taxonomic units (OTUs) existed within B. duperreyi. Low levels of divergence of B. duperreyi between mainland Australia and Tasmania (no fixed allelic differences) support the notion of episodic exchange of alleles across Bass Strait (ca 60 m, 25 Kya) during periods of low sea level during the Upper Pleistocene rather than the much longer period of isolation (1.7 My) indicated by earlier studies using mitochondrial sequence variation. Our study provides foundational work for the detailed taxonomic re-evaluation of this species complex and the need for biodiversity assessment to include an examination of cryptic species and/or cryptic diversity below the level of species. Such information on lineage diversity within species and its distribution in the context of disturbance at a regional scale can be factored into conservation planning regardless of whether a decision is made to formally diagnose new species taxonomically and nomenclaturally.}, } @article {pmid35330218, year = {2022}, author = {Salvador-Montoya, CA and Elias, SG and Popoff, OF and Robledo, GL and Urcelay, C and Góes-Neto, A and Martínez, S and Drechsler-Santos, ER}, title = {Neotropical Studies on Hymenochaetaceae: Unveiling the Diversity and Endemicity of Phellinotus.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {3}, pages = {}, pmid = {35330218}, issn = {2309-608X}, abstract = {Phellinotus, a neotropical genus of wood-decay fungi commonly found on living members of the Fabaceae family, was initially described as containing two species, P. neoaridus and P. piptadeniae. The members of this genus, along with six other well-established genera and some unresolved lineages, are the current representatives of the 'phellinotus clade'. On the other hand, based on a two-loci phylogenetic analysis, some entities/lineages of the 'phellinotus clade' have been found in Fomitiporella s.l. In this work, we performed four-loci phylogenetic analyses and based on our results the genera of the 'phellinotus clade' are shown to be monophyletic groups. In addition to the natural groups confirmed as different genera, morphological revisions, phylogenetic relationships, and host distribution of different specimens resembling P. neoaridus and P. piptadeniae revealed three new species in the Phellinotus genus, referred to here as P. magnoporatus, P. teixeirae and P. xerophyticus. Furthermore, for P. piptadeniae a narrower species concept was adopted with redefined morphological characters and a more limited distribution range. Both P. neoaridus and P. teixeirae have a distribution range restricted to seasonally dry tropical forests in South America. Additionally, based on detailed morphological revisions Phellinus&nbsp;badius, Phellinus&nbsp;resinaceus, and Phellinus&nbsp;scaber are transferred to the Phellinotus genus. The geographic distribution and host range of the genus are then discussed.}, } @article {pmid35309395, year = {2022}, author = {Kurniawan, SB and Pambudi, DSA and Ahmad, MM and Alfanda, BD and Imron, MF and Abdullah, SRS}, title = {Ecological impacts of ballast water loading and discharge: insight into the toxicity and accumulation of disinfection by-products.}, journal = {Heliyon}, volume = {8}, number = {3}, pages = {e09107}, pmid = {35309395}, issn = {2405-8440}, abstract = {Since the implementation of the International Maritime Organization 2004 regulation, most ships have been equipped with on-dock ballast water treatment. While this method is effective in solving the invasive alien species problem, concerns are raised due to the potential release of disinfection by-products (DBPs) as the result of the chemical treatment. This review paper aims to summarize the history of ballast water management (BWM) and the currently used on-dock technology. Chlorination, oxidation, and ozonation are highlighted as the most currently applied methods to treat ballast water on-dock. This paper then focuses on the potential release of toxic DBPs as the result of the selected corresponding treatment methods. Tri-halo methane, haloacetic acid, and several acetic acid-related compounds are emphasized as toxic DBPs with concentrations reaching more than 10 μg/L. The potential toxicities of DBPs, including acute toxicity, carcinogenicity, genotoxicity, and mutagenicity, to aquatic organisms, are then discussed in detail. Future research directions related to the advanced treatment of DBPs before final discharge and analysis of DBPs in coastal sediments, which are barely studied at present, are suggested to enhance the current knowledge on the fate and the ecological impact of BWM.}, } @article {pmid35297758, year = {2022}, author = {Sharma, P and Johnson, MA and Mazloom, R and Allen, C and Heath, LS and Lowe-Power, TM and Vinatzer, BA}, title = {Meta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology.}, journal = {Microbial genomics}, volume = {8}, number = {3}, pages = {}, pmid = {35297758}, issn = {2057-5858}, mesh = {Biological Evolution ; Genome, Bacterial ; Genomics ; *Ralstonia solanacearum/genetics ; }, abstract = {Ralstonia solanacearum species complex (RSSC) strains are bacteria that colonize plant xylem tissue and cause vascular wilt diseases. However, individual strains vary in host range, optimal disease temperatures and physiological traits. To increase our understanding of the evolution, diversity and biology of the RSSC, we performed a meta-analysis of 100 representative RSSC genomes. These 100 RSSC genomes contain 4940 genes on average, and a pangenome analysis found that there are 3262 genes in the core genome (~60 % of the mean RSSC genome) with 13 128 genes in the extensive flexible genome. A core genome phylogenetic tree and a whole-genome similarity matrix aligned with the previously named species (R. solanacearum , R. pseudosolanacearum , R. syzygii) and phylotypes (I–IV). These analyses also highlighted a third unrecognized sub-clade of phylotype II. Additionally, we identified differences between phylotypes with respect to gene content and recombination rate, and we delineated population clusters based on the extent of horizontal gene transfer. Multiple analyses indicate that phylotype II is the most diverse phylotype, and it may thus represent the ancestral group of the RSSC. We also used our genome-based framework to test whether the RSSC sequence variant (sequevar) taxonomy is a robust method to define within-species relationships of strains. The sequevar taxonomy is based on alignments of a single conserved gene (egl). Although sequevars in phylotype II describe monophyletic groups, the sequevar system breaks down in the highly recombinogenic phylotype I, which highlights the need for an improved, cost-effective method for genotyping strains in phylotype I. Finally, we enabled quick and precise genome-based identification of newly sequenced RSSC strains by assigning Life Identification Numbers (LINs) to the 100 strains and by circumscribing the RSSC and its sub-groups in the LINbase Web service.}, } @article {pmid35251357, year = {2022}, author = {Dawes, JHP and Zhou, X and Moinuddin, M}, title = {System-level consequences of synergies and trade-offs between SDGs: quantitative analysis of interlinkage networks at country level.}, journal = {Sustainability science}, volume = {17}, number = {4}, pages = {1435-1457}, pmid = {35251357}, issn = {1862-4057}, abstract = {UNLABELLED: The Sustainable Development Goals (SDGs) present a complex system of 17 goals and 169 individual targets whose interactions can be described in terms of co-benefits and trade-offs between policy actions. We analyse in detail target-by-target interlinkage networks established by the Institute for Global Environmental Strategies (IGES) SDG Interlinkages Tool. We discuss two quantitative measures of network structure; the leading eigenvector of the interlinkage networks ('eigencentrality') and a notion of hierarchy within the network motivated by the concept of trophic levels for species in food webs. We use three interlinkage matrices generated by IGES: the framework matrix which provides a generic network model of the interlinkages at the target level, and two country-specific matrices for Bangladesh and Indonesia that combine SDG indicator data with the generic framework matrix. Our results echo, and are confirmed by, similar work at the level of whole SDGs that has shown that SDGs 1-3 (ending poverty, and providing food security and healthcare) are much more likely to be achieved than the environmentally- related SDGs 13-15 concerned with climate action, life on land and life below water. Our results here provide a refinement in terms of specific targets within each of these SDGs. We find that not all targets within SDGs 1-3 are equally well-supported, and not all targets within SDGs 13-15 are equally at risk of not being achieved. Finally, we point to the recurring issue of data gaps that hinders our quantitative analysis, in particular for SDGs 5 (gender equality) and 13 (climate action) where the huge gaps in indicator data that mean the true nature of the interlinkages and importance of these two SDGs are not fully recognised.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11625-022-01109-y.}, } @article {pmid35250961, year = {2022}, author = {Stengel, A and Stanke, KM and Quattrone, AC and Herr, JR}, title = {Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {847067}, pmid = {35250961}, issn = {1664-302X}, abstract = {Species concepts have long provided a source of debate among biologists. These lively debates have been important for reaching consensus on how to communicate across scientific disciplines and for advancing innovative strategies to study evolution, population biology, ecology, natural history, and disease epidemiology. Species concepts are also important for evaluating variability and diversity among communities, understanding biogeographical distributions, and identifying causal agents of disease across animal and plant hosts. While there have been many attempts to address the concept of species in the fungi, there are several concepts that have made taxonomic delimitation especially challenging. In this review we discuss these major challenges and describe methodological approaches that show promise for resolving ambiguity in fungal taxonomy by improving discrimination of genetic and functional traits. We highlight the relevance of eco-evolutionary theory used in conjunction with integrative taxonomy approaches to improve the understanding of interactions between environment, ecology, and evolution that give rise to distinct species boundaries. Beyond recent advances in genomic and phenomic methods, bioinformatics tools and modeling approaches enable researchers to test hypothesis and expand our knowledge of fungal biodiversity. Looking to the future, the pairing of integrative taxonomy approaches with multi-locus genomic sequencing and phenomic techniques, such as transcriptomics and proteomics, holds great potential to resolve many unknowns in fungal taxonomic classification.}, } @article {pmid35248764, year = {2022}, author = {Wee, NQ and Cribb, TH and Cutmore, SC}, title = {Four new monorchiids from marine teleost fishes of Moreton Bay and the Great Barrier Reef, Australia, including the proposal of a new genus.}, journal = {Parasitology international}, volume = {89}, number = {}, pages = {102566}, doi = {10.1016/j.parint.2022.102566}, pmid = {35248764}, issn = {1873-0329}, mesh = {Animals ; Australia ; Bays ; Female ; Fishes ; *Gastropoda ; Phylogeny ; Species Specificity ; *Trematoda ; }, abstract = {We report four new species of monorchiids infecting teleost fishes from Australian waters. Two new species of Paralasiotocus Wee, Cutmore, Pérez-del-Olmo & Cribb, 2020, Pa. abstrusus n. sp. and Pa. tectus n. sp., are described from haemulids of the Great Barrier Reef. The two species are morphologically cryptic and occur in sympatry but differ significantly in cox1 mtDNA and ITS2 rDNA sequence data. Paralasiotocus tectus n. sp. is found only in Plectorhinchus albovittatus (Rüppell) whereas Pa. abstrusus n. sp. infects Pl. albovittatus, Plectorhinchus flavomaculatus (Cuvier) and Plectorhinchus lineatus (Linnaeus). The two species differ from all known species of Paralasiotocus in the possession of a clear gap in the spines of the terminal organ. A new species is described from a mullid, Parupeneus spilurus (Bleeker), from off Heron Island and Moreton Bay. The new species is morphologically broadly consistent with the concept of Paralasiotocus in the possession of an unspined genital atrium, bipartite terminal organ, and lobed ovary. However, it possesses a highly lobed cirrus and is phylogenetically widely separated from the two species of Paralasiotocus characterized here, and thus we propose Lobucirruatus infloresco n. g., n. sp. Proctotrema prominens n. sp., is described from Pl. albovittatus. It is differentiated from all other species of Proctotrema in the combination of a prominent metraterm, slightly fusiform body, slightly funnel-shaped oral sucker, elongate cirrus-sac, unlobed ovary, and caeca that terminate in the post-testicular region.}, } @article {pmid35210921, year = {2022}, author = {Tochihara, Y and Hosoya, T}, title = {Examination of the generic concept and species boundaries of the genus Erioscyphella (Lachnaceae, Helotiales, Ascomycota) with the proposal of new species and new combinations based on the Japanese materials.}, journal = {MycoKeys}, volume = {87}, number = {}, pages = {1-52}, pmid = {35210921}, issn = {1314-4049}, abstract = {The genus Erioscyphella Kirschst., which was morphologically confused with Lachnum, was herein examined. Based on molecular phylogenetic analyses using a combined dataset of ITS, LSU, mtSSU, and RPB2 and morphological examinations, Erioscyphella was distinguished from Lachnum and redefined by longer ascospores and the presence of apical amorphous materials and/or resinous materials equipped on hairs. Species boundaries recognized by morphology/ecology and phylogenetic analyses were cross-checked using species delimitation analyses based on DNA barcode sequences downloaded from UNITE, resulting in that species' taxonomic problems being uncovered. Six new species (E.boninensis, E.insulae, E.otanii, E.papillaris, E.paralushanensis, and E.sasibrevispora) and two new combinations (E.hainanensis and E.sinensis) were proposed.}, } @article {pmid35205151, year = {2022}, author = {Paura, B and Di Marzio, P}, title = {Making a Virtue of Necessity: The Use of Wild Edible Plant Species (Also Toxic) in Bread Making in Times of Famine According to Giovanni Targioni Tozzetti (1766).}, journal = {Biology}, volume = {11}, number = {2}, pages = {}, pmid = {35205151}, issn = {2079-7737}, abstract = {In 1766, the agricultural scientist Giovanni Targioni Tozzetti described for the Grand Duchy of Tuscany, the wild and cultivated plant species that could be used, in times of famine, to increase the quantity of flour or vegetable mass in bread making. These wild plants can be defined as wild edible plants (WEPs) or "alimurgic species", a concept usually traced back to Giovanni Targioni Tozzetti himself. The 342 plant names mentioned in the text are in the Tuscan vernacular, so a research work was done on bibliographic sources from the 1800s in order to match them with their current nomenclature. This process led to an "alimurgic flora" repertoire based on the writing of Targioni Tozzetti; and a comparison with our AlimurgITA database of 1103 wild edible plants used in Italy. It is particularly interesting that in his short treatise, Giovanni Targioni Tozzetti identified eight toxic plants (corresponding to 14 species), indicating how to eliminate the poisonous substances from their useful roots. We treat them in detail, examining their current and past use, their geographical distribution in Italy, and their eventual toxicity. We obtained 343 matches, of which 198 were reliable (certain matches) and 145 possessed some degree of uncertainty (due to generic or collective vernacular names). Among the 198 certain identifications, 140 species are present in the AlimurgITA database (92 mentioned for Tuscany) and 58 are not; for bread-making there are only documentary traces of 53 species for Italy and 7 for Tuscany. Moreover, among the total 198 species, 84 showed some degree of hazard. Researching edible toxic spontaneous species allows: (1) investigation, from an unusual perspective, of a historical period in which the poor conditions of some social strata led to finding unusual solutions to food provision; (2) idea generation to re-enable potentially useful WEPs whose use has been lost. Making a virtue of necessity!}, } @article {pmid35183341, year = {2022}, author = {Costa, MM and Saleh, AA and Melo, MP and Guimarães, EA and Esele, JP and Zeller, KA and Summerell, BA and Pfenning, LH and Leslie, JF}, title = {Fusarium mirum sp. nov, intertwining Fusarium madaense and Fusarium andiyazi, pathogens of tropical grasses.}, journal = {Fungal biology}, volume = {126}, number = {3}, pages = {250-266}, doi = {10.1016/j.funbio.2021.12.002}, pmid = {35183341}, issn = {1878-6146}, mesh = {*Fusarium/genetics ; Phylogeny ; Poaceae ; Zea mays ; }, abstract = {Many species in the Fusarium fujikuroi Species Complex (FFSC) have an affinity for grass species, with whom they live in an endophytic association or cause disease. We recovered isolates of Fusarium from agriculturally important grasses in Africa and Brazil, and characterized them with morphological markers, mating type, and Amplified Fragment Length Polymorphisms (AFLPs). We also conducted multi-locus phylogenetic analyses based on partial DNA sequences of translation elongation factor-1α (TEF1), β-tubulin (TUB), and the second largest subunit of RNA polymerase (RPB2) gene regions. Sexual cross fertility was used to test the biological species concept and the sexual stage of F. madaense is described. A novel species within the FFSC, Fusarium mirum, that is different from the other known species in the complex, was formally described. Fusarium mirum, F. madaense, and Fusarium andiyazi are a tightly intertwined species trio that are morphologically identical, but phylogenetically distinguishable, and amongst whom interspecific genetic exchange may still occur. These three species are so close that they cannot be reliably distinguished if only sequences of the TEF1 gene are used. In pathogenicity tests, all tested isolates of F. madaense from sugarcane, sorghum, maize, millet and Brachiaria could induce stalk rot in sorghum, maize and millet, and pokkah boeng in sugarcane. This study increases our understanding of the diversity of species within the FFSC that cause disease in tropical grasses or act as endophytes, and their geographic distributions. The genetically close relationship between F. mirum, F. madaense, and F. andiyazi provides an opportunity to study and identify factors underlying their limited inter-specific cross-fertility and sympatric speciation.}, } @article {pmid35177251, year = {2022}, author = {Cannon, CH and Lerdau, M}, title = {Asking half the question in explaining tropical diversity.}, journal = {Trends in ecology & evolution}, volume = {37}, number = {5}, pages = {392-393}, doi = {10.1016/j.tree.2022.01.006}, pmid = {35177251}, issn = {1872-8383}, mesh = {*Gene Flow ; *Hybridization, Genetic ; }, } @article {pmid35145340, year = {2022}, author = {Sugita, R and Tanaka, K}, title = {Thyridium revised: Synonymisation of Phialemoniopsis under Thyridium and establishment of a new order, Thyridiales.}, journal = {MycoKeys}, volume = {86}, number = {}, pages = {147-176}, pmid = {35145340}, issn = {1314-4049}, abstract = {The genus Thyridium, previously known as a saprobic or hemibiotrophic ascomycete on various plants, was revised taxonomically and phylogenetically. Sequences of the following six regions, that is, the nuclear ribosomal internal transcribed spacer (ITS) region, the large subunit (LSU) of rDNA, the second largest RNA polymerase II subunit (rpb2) gene, translation elongation factor 1-alpha (tef1) gene, the actin (act) gene, and the beta-tubulin (tub2) gene, were generated for molecular phylogenetic analyses of species of this genus. Phialemoniopsis, a genus encompassing medically important species, is synonymised with Thyridium based on molecular evidence and morphological similarities in their asexual characters. The generic concept for Thyridium is expanded to include species possessing both coelomycetous and hyphomycetous complex asexual morphs. In addition to type species of Thyridium, T.vestitum, nine species were accepted in Thyridium upon morphological comparison and molecular phylogenetic analyses in this study. All seven species of Phialemoniopsis were treated as members of the genus Thyridium and new combinations were proposed. A bambusicolous fungus, Pleosporapunctulata, was transferred to Thyridium, and an epitype is designated for this species. A new species, T.flavostromatum, was described from Phyllostachyspubescens. The family Phialemoniopsidaceae, proposed as a familial placement for Phialemoniopsis, was regarded as a synonym of Thyridiaceae. A new order, Thyridiales, was established to accommodate Thyridiaceae; it forms a well-supported, monophyletic clade in Sordariomycetes.}, } @article {pmid35141133, year = {2022}, author = {Ingelbrecht, J and Morgan, DL and Lear, KO and Fazeldean, T and Lymbery, AJ and Norman, BM and Martin, SB}, title = {A new microbothriid monogenean Dermopristis pterophilus n. sp. from the skin of the Critically Endangered green sawfish Pristis zijsron Bleeker, 1851 (Batoidea: Pristidae) in Western Australia.}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {17}, number = {}, pages = {185-193}, pmid = {35141133}, issn = {2213-2244}, abstract = {A new microbothriid monogenean Dermopristis pterophilus n. sp. is described from the skin of the Critically Endangered green sawfish Pristis zijsron Bleeker, 1851 in the Ashburton River delta, northern Western Australia. Analyses of the 28S ribosomal DNA marker and the molecular barcoding markers Histone 3 and Elongation Factor 1 α confirmed position among the Microbothriidae, with close affinity to the only other sequenced representative of Dermopristis Kearn, Whittington and Evans-Groing, 2010. The new species is morphologically consistent with the concept of Dermopristis; it has two testes, lacks a male copulatory organ and has a simple haptor. It is smaller than its two congeners D. paradoxus Kearn, Whittington and Evans-Gowing, 2010 and D. cairae Whittington and Kearn, 2011 and is most similar to the former, distinguished only in that it lacks the strong, transverse, parallel ridges on the ventral body surface that characterise that species. It is more easily distinguished from D. cairae, differing in body shape, possession of a seminal receptacle, and relative position and size of the haptor. It may further differ from both species by fine details of the gut diverticula, although these details are difficult to ascertain. Spermatophores were observed in the new species, similar to those previously reported for D. cairae. The new species exhibits site attachment preference: infections were greatest on and immediately adjacent to the host pelvic fins (including male reproductive organs, i.e. claspers), moderate in proximity to the dorsal and pectoral fins, few on the caudal fin and peduncle, and infrequently, isolated worms occurred elsewhere on the dorsal and ventral surfaces of the body. There was no incidence of infection on the head (including rostrum). We presume D. pterophilus is restricted to P. zijsron and thus likely faces the same threat of extinction.}, } @article {pmid35140307, year = {2022}, author = {Saetang, T and Marrone, F and Vecchioni, L and Maiphae, S}, title = {Morphological and molecular diversity patterns of the genus Tropodiaptomus Kiefer, 1932 (Copepoda, Calanoida, Diaptomidae) in Thailand.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {2218}, pmid = {35140307}, issn = {2045-2322}, mesh = {Animals ; Copepoda/*anatomy & histology/classification/*genetics ; DNA, Mitochondrial ; Evolution, Molecular ; Female ; Male ; Phylogeny ; Sequence Alignment ; Thailand ; }, abstract = {Tropodiaptomus is one of the most specious genera in the family Diaptomidae, but it is often rare in terms of distribution and abundance. Moreover, Tropodiaptomus species show a noteworthy variability in some of the morphological characters considered of prime importance in diaptomid taxonomy, and the presence of cryptic or pseudocryptic species is likely. Thus, through a geographically-wide sampling in Thailand, we aimed to investigate the local diversity of the genus and to compare the morphological and molecular diversity pattern based on mitochondrial and nuclear genes sequences. DNA taxonomy was also implemented in order to check whether the Tropodiaptomus lineages were independent species according to the "evolutionary genetic species concept". Six Tropodiaptomus morphospecies were found, three of which are putative species new to Science pending a formal description. The finding of such a high incidence of undescribed species stresses the existence of a significant "Linnean shortfall" affecting Thai diaptomids. The molecular results showed that most of the studied species could be identified consistently with their morphology-based taxonomy. However, Tropodiaptomus vicinus and T. cf. lanaonus showed a high level of genetic diversity, suggesting that traditional morphological techniques might be inadequate for correctly assessing their taxonomical status.}, } @article {pmid35137405, year = {2022}, author = {Dugeny, E and de Lorgeril, J and Petton, B and Toulza, E and Gueguen, Y and Pernet, F}, title = {Seaweeds influence oyster microbiota and disease susceptibility.}, journal = {The Journal of animal ecology}, volume = {91}, number = {4}, pages = {805-818}, doi = {10.1111/1365-2656.13662}, pmid = {35137405}, issn = {1365-2656}, mesh = {Animals ; *Crassostrea/microbiology ; Disease Susceptibility ; *Microbiota ; Seawater ; *Seaweed ; }, abstract = {A growing awareness of role that microbiota can play in mediating the effects of pathogens on hosts has given rise to the concept of the pathobiome. Recently, we demonstrated that the Pacific oyster mortality syndrome affecting Crassostrea gigas oysters is caused by infection with the Ostreid herpesvirus type 1 (OsHV-1) followed by infection with multiple bacterial taxa. Here we extend the concept of this pathobiome beyond the host species and its bacterial microbiota by investigating how seaweed living in association with oysters influences their response to the disease. We hypothesized that by their mere presence in the environment, different species of seaweeds can positively or negatively influence the risk of disease in oysters by shaping their bacterial microbiota and their immune response. Although seaweed and oysters do not have direct ecological interactions, they are connected by seawater and likely share microbes. To test our hypothesis, oysters were acclimated with green, brown or red algae for 2 weeks and then challenged with OsHV-1. We monitored host survival and pathogen proliferation and performed bacterial microbiota and transcriptome analyses. We found that seaweeds can alter the bacterial microbiota of the host and its response to the disease. More particularly, green algae belonging to the genus Ulva spp. induced bacterial microbiota dysbiosis in oyster and modification of its transcriptional immune response leading to increased susceptibility to the disease. This work provides a better understanding of a marine disease and highlights the importance of considering both macrobiotic and microbiotic interactions for conservation, management and exploitation of marine ecosystems and resources.}, } @article {pmid35137286, year = {2022}, author = {Krasnov, BR and Vinarski, MV and Korallo-Vinarskaya, NP and Shenbrot, GI and Khokhlova, IS}, title = {Dark host specificity in two ectoparasite taxa: repeatability, parasite traits, and environmental effects.}, journal = {Parasitology research}, volume = {121}, number = {3}, pages = {851-866}, pmid = {35137286}, issn = {1432-1955}, mesh = {Animals ; Host Specificity ; Host-Parasite Interactions ; *Mites ; *Parasites ; Phylogeny ; *Siphonaptera ; }, abstract = {We applied the concept of dark diversity (species that may potentially inhabit a locality but are absent) to the host spectrum of a parasite and defined it as dark host specificity (DHS). We studied the trait-associated and geographic patterns of dark host specificity in fleas and gamasid mites parasitic on small mammals, asking the following questions: (a) Is dark host specificity repeatable across populations of the same species? (b) Is it associated with morphological and/or ecological species traits? (c) What are the factors associated with geographical variation in the DHS among populations of the same species? The DHS was repeatable within species with a large proportion of variance among samples, accounted for by differences between species. The average DHS of fleas, but not mites, was affected by parasite traits, with the DHS being higher in fleas with larger geographic ranges, higher characteristic abundance levels, and summer reproduction peaks. In the majority of ectoparasites, the regional DHS decreased with an increase in either structural or phylogenetic host specificity. The associations between the DHS and the environmental or host-associated characteristics of a region were revealed in a few species (eight of 22 fleas and three of 12 mites). The DHS decreased with (a) an increase in air temperature in two fleas, (b) a decrease in precipitation in two fleas, and (c) an increase in regional host species richness (in three fleas and three mites). Overall, our results suggest that dark host specificity in arthropod ectoparasites is a species-specific character associated, to a large extent, with the breadth of their host-related niches, while the influences of parasite traits and local environmental conditions are minor.}, } @article {pmid35127879, year = {2021}, author = {Lees, P and Bäumer, W and Toutain, PL}, title = {The Decline and Fall of Materia Medica and the Rise of Pharmacology and Therapeutics in Veterinary Medicine.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {777809}, pmid = {35127879}, issn = {2297-1769}, abstract = {Materia Medica is a Latin term, relating to the history of pharmacy. It describes the sources (vegetable, animal and mineral), nature, preparation, and properties of substances or mixtures of substances, which were used as remedies for the treatment of diseases. Bourgelat authored the first veterinary Materia Medica book. This review describes the evolution and ultimate downfall of Materia Medica concepts and practices. Its survival for more than two millennia reflected the impact of religion and dogmas on therapy. The consignment of Materia Medica to history was signified by publication of the first modern book of veterinary pharmacology and therapeutics by Meyer Jones in 1953. Previously, the dominance of Materia Medica was linked to an hippiatry culture, which was shared with farriers and quacks. The Pasteurian and pharmacological revolutions of the second half of the nineteenth century led to its gradual abandonment. This review explains why the existence of authentically active substances, such as opioid analgesics, cardiotonics and general anesthetics either were not used for those actions or were badly prescribed, in part because of historical precedence and in part from lack of pathophysiological knowledge to justify rational use. The modern concept of dosage, in particular inter-species differences, was not understood. There were also major dogmas, supporting false indications, such as failure to recognize pain as a symptom to be treated, whereas inflammation was only a disease symptom involving excess of activity of the blood system, which had to be vigorously addressed by bleeding and purging. This review covers a well-defined period, ranging from Bourgelat, who wrote the first book of Materia Medica for veterinary studies to the first edition of Meyer Jones textbook in 1953, which marked the end of Materia Medica and the beginning of pharmacology in veterinary medicine.}, } @article {pmid35125561, year = {2022}, author = {Monsó, S}, title = {How to Tell If Animals Can Understand Death.}, journal = {Erkenntnis}, volume = {87}, number = {1}, pages = {117-136}, pmid = {35125561}, issn = {0165-0106}, support = {M 2518/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {It is generally assumed that humans are the only animals who can possess a concept of death. However, the ubiquity of death in nature and the evolutionary advantages that would come with an understanding of death provide two prima facie reasons for doubting this assumption. In this paper, my intention is not to defend that animals of this or that nonhuman species possess a concept of death, but rather to examine how we could go about empirically determining whether animals can have a concept of death. In order to answer this question, I begin by sketching an account of concept possession that favours intensional classification rather than mere extensional discrimination. Further, I argue that the concept of death should be construed as neither binary nor universal. I then present a proposal for a set of minimal conditions that must be met to have a concept of death. I argue that having a minimal understanding of death entails first expecting a dead individual to be alive, and then grasping its non-functionality and irreversibility. Lastly, I lay out the sort of observational and experimental evidence that we should look for to determine whether animals have the capacity for a minimal comprehension of death.}, } @article {pmid35115605, year = {2022}, author = {Mortelliti, A and Brehm, AM and Evans, BE}, title = {Umbrella effect of monitoring protocols for mammals in the Northeast US.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {1893}, pmid = {35115605}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; *Environmental Monitoring ; Maine ; *Mammals ; Population Density ; Seasons ; Species Specificity ; Time Factors ; }, abstract = {Developing cost-effective monitoring protocols is a priority for wildlife conservation agencies worldwide. In particular, developing protocols that cover a wide range of species is highly desirable. Here we applied the 'umbrella species' concept to the context of ecological monitoring; specifically testing the hypothesis that protocols developed for the American marten would contextually allow detecting occupancy trends for 13 other mammalian species (i.e., an umbrella effect). We conducted a large-scale four-year camera trapping survey across a gradient of forest disturbance in Maine, USA. We sampled 197 sites using a total of 591 cameras and collected over 800,000 photographs to generate detection histories for the most common terrestrial species. By combining multi-season occupancy modelling and power analyses, we estimated the required sampling effort to detect 10%, 25% and 50% declines in the fourteen species. By conducting a spatially explicit comparison of sampling effort, we found evidence that monitoring protocols for American marten would provide an umbrella effect for up to 11 other mammal species. The capacity of the umbrella effect varied among species, with fisher, snowshoe hare, red squirrel, and black bear consistently covered under several scenarios. Our results support the application of the umbrella species concept to monitoring (here defined as 'umbrella monitoring species'), providing empirical evidence for its use by management agencies.}, } @article {pmid35115054, year = {2022}, author = {Bellais, S and Nehlich, M and Ania, M and Duquenoy, A and Mazier, W and van den Engh, G and Baijer, J and Treichel, NS and Clavel, T and Belotserkovsky, I and Thomas, V}, title = {Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {24}, pmid = {35115054}, issn = {2049-2618}, mesh = {Anaerobiosis ; Animals ; Bacteria/metabolism ; Faecalibacterium prausnitzii ; Flow Cytometry ; *Gastrointestinal Microbiome ; Rabbits ; }, abstract = {BACKGROUND: There is a growing interest in using gut commensal bacteria as "next generation" probiotics. However, this approach is still hampered by the fact that there are few or no strains available for specific species that are difficult to cultivate. Our objective was to adapt flow cytometry and cell sorting to be able to detect, separate, isolate, and cultivate new strains of commensal species from fecal material. We focused on the extremely oxygen sensitive (EOS) species Faecalibacterium prausnitzii and the under-represented, health-associated keystone species Christensenella minuta as proof-of-concept.

RESULTS: A BD Influx® cell sorter was equipped with a glovebox that covered the sorting area. This box was flushed with nitrogen to deplete oxygen in the enclosure. Anaerobic conditions were maintained during the whole process, resulting in only minor viability loss during sorting and culture of unstained F. prausnitzii strains ATCC 27766, ATCC 27768, and DSM 17677. We then generated polyclonal antibodies against target species by immunizing rabbits with heat-inactivated bacteria. Two polyclonal antibodies were directed against F. prausnitzii type strains that belong to different phylogroups, whereas one was directed against C. minuta strain DSM 22607. The specificity of the antibodies was demonstrated by sorting and sequencing the stained bacterial fractions from fecal material. In addition, staining solutions including LIVE/DEAD™ BacLight™ Bacterial Viability staining and polyclonal antibodies did not severely impact bacterial viability while allowing discrimination between groups of strains. Finally, we combined these staining strategies as well as additional criteria based on bacterial shape for C. minuta and were able to detect, isolate, and cultivate new F. prausnitzii and C. minuta strains from healthy volunteer's fecal samples.

CONCLUSIONS: Targeted cell-sorting under anaerobic conditions is a promising tool for the study of fecal microbiota. It gives the opportunity to quickly analyze microbial populations, and can be used to sort EOS and/or under-represented strains of interest using specific antibodies, thus opening new avenues for culture experiments. Video abstract.}, } @article {pmid35101981, year = {2022}, author = {Cazzolla Gatti, R and Reich, PB and Gamarra, JGP and Crowther, T and Hui, C and Morera, A and Bastin, JF and de-Miguel, S and Nabuurs, GJ and Svenning, JC and Serra-Diaz, JM and Merow, C and Enquist, B and Kamenetsky, M and Lee, J and Zhu, J and Fang, J and Jacobs, DF and Pijanowski, B and Banerjee, A and Giaquinto, RA and Alberti, G and Almeyda Zambrano, AM and Alvarez-Davila, E and Araujo-Murakami, A and Avitabile, V and Aymard, GA and Balazy, R and Baraloto, C and Barroso, JG and Bastian, ML and Birnbaum, P and Bitariho, R and Bogaert, J and Bongers, F and Bouriaud, O and Brancalion, PHS and Brearley, FQ and Broadbent, EN and Bussotti, F and Castro da Silva, W and César, RG and Češljar, G and Chama Moscoso, V and Chen, HYH and Cienciala, E and Clark, CJ and Coomes, DA and Dayanandan, S and Decuyper, M and Dee, LE and Del Aguila Pasquel, J and Derroire, G and Djuikouo, MNK and Van Do, T and Dolezal, J and Đorđević, IĐ and Engel, J and Fayle, TM and Feldpausch, TR and Fridman, JK and Harris, DJ and Hemp, A and Hengeveld, G and Herault, B and Herold, M and Ibanez, T and Jagodzinski, AM and Jaroszewicz, B and Jeffery, KJ and Johannsen, VK and Jucker, T and Kangur, A and Karminov, VN and Kartawinata, K and Kennard, DK and Kepfer-Rojas, S and Keppel, G and Khan, ML and Khare, PK and Kileen, TJ and Kim, HS and Korjus, H and Kumar, A and Kumar, A and Laarmann, D and Labrière, N and Lang, M and Lewis, SL and Lukina, N and Maitner, BS and Malhi, Y and Marshall, AR and Martynenko, OV and Monteagudo Mendoza, AL and Ontikov, PV and Ortiz-Malavasi, E and Pallqui Camacho, NC and Paquette, A and Park, M and Parthasarathy, N and Peri, PL and Petronelli, P and Pfautsch, S and Phillips, OL and Picard, N and Piotto, D and Poorter, L and Poulsen, JR and Pretzsch, H and Ramírez-Angulo, H and Restrepo Correa, Z and Rodeghiero, M and Rojas Gonzáles, RDP and Rolim, SG and Rovero, F and Rutishauser, E and Saikia, P and Salas-Eljatib, C and Schepaschenko, D and Scherer-Lorenzen, M and Šebeň, V and Silveira, M and Slik, F and Sonké, B and Souza, AF and Stereńczak, KJ and Svoboda, M and Taedoumg, H and Tchebakova, N and Terborgh, J and Tikhonova, E and Torres-Lezama, A and van der Plas, F and Vásquez, R and Viana, H and Vibrans, AC and Vilanova, E and Vos, VA and Wang, HF and Westerlund, B and White, LJT and Wiser, SK and Zawiła-Niedźwiecki, T and Zemagho, L and Zhu, ZX and Zo-Bi, IC and Liang, J}, title = {The number of tree species on Earth.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {6}, pages = {}, pmid = {35101981}, issn = {1091-6490}, support = {R13 TR002524/TR/NCATS NIH HHS/United States ; }, mesh = {*Conservation of Natural Resources ; Earth, Planet ; *Forests ; Trees/*classification/growth & development ; }, abstract = {One of the most fundamental questions in ecology is how many species inhabit the Earth. However, due to massive logistical and financial challenges and taxonomic difficulties connected to the species concept definition, the global numbers of species, including those of important and well-studied life forms such as trees, still remain largely unknown. Here, based on global ground-sourced data, we estimate the total tree species richness at global, continental, and biome levels. Our results indicate that there are ∼73,000 tree species globally, among which ∼9,000 tree species are yet to be discovered. Roughly 40% of undiscovered tree species are in South America. Moreover, almost one-third of all tree species to be discovered may be rare, with very low populations and limited spatial distribution (likely in remote tropical lowlands and mountains). These findings highlight the vulnerability of global forest biodiversity to anthropogenic changes in land use and climate, which disproportionately threaten rare species and thus, global tree richness.}, } @article {pmid35098022, year = {2021}, author = {Jarmolowicz, DP and Greer, BD and Killeen, PR and Huskinson, SL}, title = {Applied Quantitative Analysis of Behavior: What It Is, and Why We Care-Introduction to the Special Section.}, journal = {Perspectives on behavior science}, volume = {44}, number = {4}, pages = {503-516}, pmid = {35098022}, issn = {2520-8977}, support = {R01 DA045011/DA/NIDA NIH HHS/United States ; }, abstract = {Science evolves from prior approximations of its current form. Interest in changes in species over time was not a new concept when Darwin made his famous voyage to the Galapagos Islands; concern with speciation stretches back throughout the history of modern thought. Behavioral science also does and must evolve. Such change can be difficult, but it can also yield great dividends. The focus of the current special section is on a common mutation that appears to have emerged across these areas and the critical features that define an emerging research area-applied quantitative analysis of behavior (AQAB). In this introduction to the "Special Issue on Applications of Quantitative Methods," we will outline some of the common characteristics of research in this area, an exercise that will surely be outdated as the research area continues to progress. In doing so, we also describe how AQAB is relevant to theory, behavioral pharmacology, applied behavior analysis, and health behaviors. Finally, we provide a summary for the articles that appear in this special issue. The authors of these papers are all thinking outside the Skinner box, creating new tools and approaches, and testing them against relevant data. If we can keep up this evolution of methods and ideas, behavior analysis will regain its place at the head of the table!}, } @article {pmid35050093, year = {2022}, author = {Hörandl, E}, title = {Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {2}, pages = {}, pmid = {35050093}, issn = {2223-7747}, abstract = {Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as "units". Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.}, } @article {pmid35035160, year = {2022}, author = {Samanta, A and Ghosh, S and Sarkar, S}, title = {Sustained generation of peroxide from the air by carbon nano onion under visible light to combat RNA virus.}, journal = {Journal of chemical sciences (Bangalore, India)}, volume = {134}, number = {1}, pages = {9}, pmid = {35035160}, issn = {0974-3626}, abstract = {Carbon nano onion (CNO) from dried grass has been synthesized by carbonization in the size range, 20 to 100 nm. This shows catalytic property to transform aerial oxygen under visible light to generate reactive oxygen species (ROS). A concept has been presented herein to show that this CNO even under room light generates hydrogen peroxide which inhibits WSN influenza virus (H1N1). The advantage of introducing CNO, synthesized from a cheap source to cater to the global need, is to sterilize infected hospitals indoor and outdoor, aircraft carriers, air conditioner vents due to its sustained conversion of air to ROS. Thus, CNO use could prevent frequent evacuation as used by conventional sanitisers to sterilize infected places from other RNA virus and hospital pathogens under COVID-19 pandemic. Carbon nano onion (CNO) under aerial oxygen on exposure with visible light generates ROS which is capable to rupture the lipid envelope of SARS-CoV-2 followed by disintegrating its RNA.}, } @article {pmid35001485, year = {2022}, author = {Cernava, T and Berg, G}, title = {The emergence of disease-preventing bacteria within the plant microbiota.}, journal = {Environmental microbiology}, volume = {24}, number = {8}, pages = {3259-3263}, pmid = {35001485}, issn = {1462-2920}, mesh = {Bacteria/genetics ; *Disease Resistance ; *Microbiota ; Plant Roots/microbiology ; Plants/microbiology ; }, abstract = {Microbiome studies have facilitated the discovery of harmful as well as beneficial microorganisms over the last years. Recently, distinct bacteria were found within the microbiota of crop plants that confer disease resistance to their hosts. Although it is well known that the interplay between microbes and plants can result in improved plant health, the phenomenon of holistically disease-preventing bacteria is new. Here, we put the recent discoveries of disease-preventing bacteria in context with decade-long plant microbiome research that has preceded them. In addition, we provide explanations as to why disease resistance in certain plants, mediated by specific bacteria, has only recently been discovered. We argue that such findings were primarily limited by technological constraints and that analogous findings are very likely to be made with other plant species. The general concept may even be extendable to additional groups of organisms. We, therefore, suggest the introduction of the specific term soterobiont in order to facilitate an unambiguous definition of disease-preventing microorganisms within the microbiota of higher organisms.}, } @article {pmid34999241, year = {2022}, author = {Barreto Xavier-Leite, A and da Silva Cáceres, ME and Aptroot, A and Moncada, B and Lücking, R and Tomio Goto, B}, title = {Phylogenetic revision of the lichenized family Gomphillaceae (Ascomycota: Graphidales) suggests post-K-Pg boundary diversification and phylogenetic signal in asexual reproductive structures.}, journal = {Molecular phylogenetics and evolution}, volume = {168}, number = {}, pages = {107380}, doi = {10.1016/j.ympev.2021.107380}, pmid = {34999241}, issn = {1095-9513}, mesh = {*Ascomycota/genetics ; Base Sequence ; DNA, Ribosomal/genetics ; *Lichens/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {We present the first broad molecular-phylogenetic revision of the lichenized family Gomphillaceae, based on 408 newly generated sequences of the mitochondrial SSU rDNA and nuclear LSU rDNA, representing 342 OTUs. The phylogenetic analysis of 20 out of the 28 currently accepted genera resulted in 48 clades. Twelve genera were resolved as monophyletic: Actinoplaca, Arthotheliopsis, Bullatina, Caleniopsis, Corticifraga, Gomphillus, Gyalectidium, Gyalidea, Jamesiella, Rolueckia, Rubrotricha, and Taitaia. Two genera resulted paraphyletic, namely Aulaxina (including Caleniopsis) and Asterothyrium (including Linhartia). Six genera were in part highly polyphyletic: Aderkomyces, Calenia, Echinoplaca, Gyalideopsis, Psorotheciopsis, and Tricharia. While ascoma morphology and anatomy has traditionally been considered as main character complex to distinguish genera, our study supported the notion that the characteristic asexual anamorph of Gomphillaceae, the so-called hyphophores, are diagnostic for most of the newly recognized clades. As a result, we recognize 26 new genus-level clades, three of which have names available (Microxyphiomyces, Psathyromyces, Spinomyces) and 23 that will require formal description as new genera. We also tested monophyly for 53 species-level names for which two or more specimens were sequenced: 27 were supported as monophyletic and representing a single species, 13 as monophyletic but with an internal topology suggesting cryptic speciation, four as paraphyletic, and nine as polyphyletic. These data suggest that species richness in the family is higher than indicated by the number of accepted names (currently 425); they also confirm that recently refined species concepts reflect species richness better than the broad concepts applied in Santesson's monograph. A divergence time analysis revealed that foliicolous Gomphillaceae diversified after the K-Pg-boundary and largely during the Miocene, a notion supported by limited data available for other common foliicolous lineages such as Chroodiscus (Graphidaceae), Pilocarpaceae, and Porinaceae. This contradicts recent studies suggesting that only macrofoliose Lecanoromycetes exhibit increased diversification rates in the Cenozoic.}, } @article {pmid34977281, year = {2022}, author = {Benton, ML and Jimenez, VA and Newman, N and Gonzales, SW and Grant, KA and Turner, RT and Iwaniec, UT and Baker, EJ}, title = {Dose-response effects of alcohol on biochemical markers of bone turnover in non-human primates: Effects of species, sex and age of onset of drinking.}, journal = {Bone reports}, volume = {16}, number = {}, pages = {101159}, pmid = {34977281}, issn = {2352-1872}, support = {P51 OD011092/OD/NIH HHS/United States ; R24 AA019431/AA/NIAAA NIH HHS/United States ; }, abstract = {PURPOSE: Alcohol consumption suppressed bone turnover in male non-human primates; however, it is unclear the extent to which this effect depends upon biological variables. Using archived plasma samples, we investigated whether sex, age of onset of alcohol intake, and species influence the effects of graded increases in alcohol consumption on bone turnover markers.

METHODS: 91 male and female macaques (rhesus and cynomolgus), ranging in age from 4 years (adolescent) to 10 years (adult) were required to increase their consumption of ethanol in 30-day increments: 0 g/kg/day, followed by 0.5 g/kg/day, 1.0 g/kg/day, and, finally, 1.5 g/kg/day. Plasma osteocalcin (formation), plasma CTX (resorption) and osteocalcin to CTX ratio (turnover balance) were measured during these intervals to assess the dose-response effects of alcohol.

RESULTS: We detected no relationship between dose and osteocalcin when all monkeys were combined, but there was a significant effect of sex (lower levels in females) and interactions between alcohol dose and sex (osteocalcin levels increased with dose in rhesus females). In contrast, we detected a negative linear dose-response relationship for ethanol and CTX. We did not detect a relationship between dose and osteocalcin to CTX ratio overall, but there was a significant positive relationship detected in females (no change in males). Increased age predicted lower biomarker levels for both osteocalcin and CTX. Species was a significant predictor for osteocalcin and the osteocalcin to CTX ratio in these models.

CONCLUSION: These findings indicate that age, sex, and species influence bone turnover and support the concept that factors beyond quantity of alcohol affect skeletal response to alcohol consumption.}, } @article {pmid34970296, year = {2021}, author = {Peres, PHF and Luduvério, DJ and Bernegossi, AM and Galindo, DJ and Nascimento, GB and Oliveira, ML and Sandoval, EDP and Vozdova, M and Kubickova, S and Cernohorska, H and Duarte, JMB}, title = {Revalidation of Mazama rufa (Illiger 1815) (Artiodactyla: Cervidae) as a Distinct Species out of the Complex Mazama americana (Erxleben 1777).}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {742870}, pmid = {34970296}, issn = {1664-8021}, abstract = {The red brocket deer Mazama americana Erxleben, 1777 is considered a polyphyletic complex of cryptic species with wide chromosomal divergence. Evidence indicates that the observed chromosomal divergences result in reproductive isolation. The description of a neotype for M. americana allowed its genetic characterization and represented a comparative basis to resolve the taxonomic uncertainties of the group. Thus, we designated a neotype for the synonym Mazama rufa Illiger, 1815 and tested its recognition as a distinct species from the M. americana complex with the analysis of morphological, cytogenetic and molecular data. We also evaluated its distribution by sampling fecal DNA in the wild. Morphological data from craniometry and body biometry indicated an overlap of quantitative measurements between M. rufa and the entire M. americana complex. The phylogenetic hypothesis obtained through mtDNA confirmed the reciprocal monophyly relationship between M. americana and M. rufa, and both were identified as distinct molecular operational taxonomic units by the General Mixed Yule Coalescent species delimitation analysis. Finally, classic cytogenetic data and fluorescence in situ hybridization with whole chromosome painting probes showed M. rufa with a karyotype of 2n = 52, FN = 56. Comparative analysis indicate that at least fifteen rearrangements separate M. rufa and M. americana (sensu stricto) karyotypes, which confirmed their substantial chromosomal divergence. This divergence should represent an important reproductive barrier and allow its characterization as a distinct and valid species. Genetic analysis of fecal samples demonstrated a wide distribution of M. rufa in the South American continent through the Atlantic Forest, Cerrado and south region of Amazon. Thus, we conclude for the revalidation of M. rufa as a distinct species under the concept of biological isolation, with its karyotype as the main diagnostic character. The present work serves as a basis for the taxonomic review of the M. americana complex, which should be mainly based on cytogenetic characterization and directed towards a better sampling of the Amazon region, the evaluation of available names in the species synonymy and a multi-locus phylogenetic analysis.}, } @article {pmid34949226, year = {2021}, author = {Comizzoli, P and Power, ML and Bornbusch, SL and Muletz-Wolz, CR}, title = {Interactions between reproductive biology and microbiomes in wild animal species.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {87}, pmid = {34949226}, issn = {2524-4671}, abstract = {Many parts of the animal body harbor microbial communities, known as animal-associated microbiomes, that affect the regulation of physiological functions. Studies in human and animal models have demonstrated that the reproductive biology and such microbiomes also interact. However, this concept is poorly studied in wild animal species and little is known about the implications to fertility, parental/offspring health, and survival in natural habitats. The objective of this review is to (1) specify the interactions between animals' reproductive biology, including reproductive signaling, pregnancy, and offspring development, and their microbiomes, with an emphasis on wild species and (2) identify important research gaps as well as areas for further studies. While microbiomes present in the reproductive tract play the most direct role, other bodily microbiomes may also contribute to facilitating reproduction. In fish, amphibians, reptiles, birds, and mammals, endogenous processes related to the host physiology and behavior (visual and olfactory reproductive signals, copulation) can both influence and be influenced by the structure and function of microbial communities. In addition, exposures to maternal microbiomes in mammals (through vagina, skin, and milk) shape the offspring microbiomes, which, in turn, affects health later in life. Importantly, for all wild animal species, host-associated microbiomes are also influenced by environmental variations. There is still limited literature on wild animals compared to the large body of research on model species and humans. However, the few studies in wild species clearly highlight the necessity of increased research in rare and endangered animals to optimize conservation efforts in situ and ex situ. Thus, the link between microbiomes and reproduction is an emerging and critical component in wild animal conservation.}, } @article {pmid34930559, year = {2022}, author = {Hilário, S and Santos, L and Phillips, AJL and Alves, A}, title = {Caveats of the internal transcribed spacer region as a barcode to resolve species boundaries in Diaporthe.}, journal = {Fungal biology}, volume = {126}, number = {1}, pages = {54-74}, doi = {10.1016/j.funbio.2021.10.005}, pmid = {34930559}, issn = {1878-6146}, mesh = {DNA, Ribosomal ; Phylogeny ; Plants ; *Saccharomycetales ; }, abstract = {Species in Diaporthe are largely reported as important plant pathogens. Identification of species in this genus has been complemented by morphological and molecular features. However, one important factor delaying this process is the struggle to formulate robust species concepts to create adequate international phytosanitary measures. Regardless of the wide use of the internal transcribed spacer (ITS) rDNA region, established as the primary DNA barcode for fungi, the tendency for intraspecific variation has been reported, misleading interpretation of phylogenetic analyses. Therefore, the present study aimed to illustrate, using specific examples, how the ITS region may be problematic for species delimitation. We showed that the ITS region is highly variable, with strains of Diaporthe malorum and Diaporthe novem falling into more than one clade, which if analyzed on their own, would be likely recognized as distinct taxa. Divergent ITS paralogs were also proven to coexist within the genome of D. novem. We also suggest that ITS may have escaped from concerted evolution or has undergone a duplication event. Furthermore, this study reports for the first time the existence of a putative hybrid in the genus Diaporthe. Our findings offer new clues towards the intraspecific and intragenomic variation in the ITS region, raising questions about its value for barcoding, i.e., identifying species in the genus Diaporthe. Therefore, we recommend that the ITS region be analyzed cautiously and always compared for congruence prior to description of novel taxa.}, } @article {pmid34910548, year = {2021}, author = {Zhang, XJ and Ji, YX and Cheng, X and Cheng, Y and Yang, H and Wang, J and Zhao, LP and Huang, YP and Sun, D and Xiang, H and Shen, LJ and Li, PL and Ma, JP and Tian, RF and Yang, J and Yao, X and Xu, H and Liao, R and Xiao, L and Zhang, P and Zhang, X and Zhao, GN and Wang, X and Hu, ML and Tian, S and Wan, J and Cai, J and Ma, X and Xu, Q and Wang, Y and Touyz, RM and Liu, PP and Loomba, R and She, ZG and Li, H}, title = {A small molecule targeting ALOX12-ACC1 ameliorates nonalcoholic steatohepatitis in mice and macaques.}, journal = {Science translational medicine}, volume = {13}, number = {624}, pages = {eabg8116}, doi = {10.1126/scitranslmed.abg8116}, pmid = {34910548}, issn = {1946-6242}, mesh = {Acetyl-CoA Carboxylase ; Animals ; Liver/metabolism ; Macaca/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism ; }, abstract = {Nonalcoholic steatohepatitis (NASH) is a progressive liver disease and has become a leading indication for liver transplantation in the United States. The development of effective therapies for NASH is a major unmet need. Here, we identified a small molecule, IMA-1, that can treat NASH by interrupting the arachidonate 12-lipoxygenase (ALOX12)–acetyl-CoA carboxylase 1 (ACC1) interaction. IMA-1 markedly blocked diet-induced NASH progression in both male mice and Cynomolgus macaque therapeutic models. The anti-NASH efficacy of IMA-1 was comparable to ACC inhibitor in both species. Protein docking simulations and following functional experiments suggested that the anti-NASH effects of IMA-1 were largely dependent on its direct binding to a pocket in ALOX12 proximal to its ACC1-interacting surface instead of inhibiting ALOX12 lipoxygenase activity. IMA-1 treatment did not elicit hyperlipidemia, a known side effect of direct inhibition of ACC enzymatic activity, in both mice and macaques. These findings provide proof of concept across multiple species for the use of small molecule–based therapies for NASH.}, } @article {pmid34901703, year = {2021}, author = {Pronozin, AY and Bragina, MK and Salina, EA}, title = {Crop pangenomes.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {25}, number = {1}, pages = {57-63}, doi = {10.18699/VJ21.007}, pmid = {34901703}, issn = {2500-0462}, abstract = {Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants' chromosome structures, gene identification and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection. However, large structural genome changes, including gene copy number variations (CNVs) and gene presence/absence variations (PAVs), prevail in crops. These genomic variations play an important role in the functional set of genes and the gene composition in individuals of the same species and provide the genetic determination of the agronomically important crops properties. A high degree of genomic variation observed indicates that single reference genomes do not represent the diversity within a species, leading to the pangenome concept. The pangenome represents information about all genes in a taxon: those that are common to all taxon members and those that are variable and are partially or completely specific for particular individuals. Pangenome sequencing and analysis technologies provide a large-scale study of genomic variation and resources for an evolutionary research, functional genomics and crop breeding. This review provides an analysis of agricultural plants' pangenome studies. Pangenome structural features, methods and programs for bioinformatic analysis of pangenomic data are described.}, } @article {pmid34887548, year = {2022}, author = {Conrad, RE and Viver, T and Gago, JF and Hatt, JK and Venter, SN and Rossello-Mora, R and Konstantinidis, KT}, title = {Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations.}, journal = {The ISME journal}, volume = {16}, number = {5}, pages = {1222-1234}, pmid = {34887548}, issn = {1751-7370}, mesh = {Bacteria/genetics ; *Genome, Bacterial ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.}, } @article {pmid34874999, year = {2021}, author = {Tomaszewska, P and Vorontsova, MS and Renvoize, SA and Ficinski, SZ and Tohme, J and Schwarzacher, T and Castiblanco, V and de Vega, JJ and Mitchell, RAC and Heslop-Harrison, JS}, title = {Complex polyploid and hybrid species in an apomictic and sexual tropical forage grass group: genomic composition and evolution in Urochloa (Brachiaria) species.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcab147}, pmid = {34874999}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment , often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species.

METHODS: Some 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima.

KEY RESULTS: Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs​. In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids.

CONCLUSIONS: We suggest a new coherent nomenclature for the genomes present​. We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.}, } @article {pmid34866663, year = {2021}, author = {Monsó, S and Osuna-Mascaró, AJ}, title = {Death is common, so is understanding it: the concept of death in other species.}, journal = {Synthese}, volume = {199}, number = {1-2}, pages = {2251-2275}, pmid = {34866663}, issn = {0039-7857}, support = {M 2518/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Comparative thanatologists study the responses to the dead and the dying in nonhuman animals. Despite the wide variety of thanatological behaviours that have been documented in several different species, comparative thanatologists assume that the concept of death (CoD) is very difficult to acquire and will be a rare cognitive feat once we move past the human species. In this paper, we argue that this assumption is based on two forms of anthropocentrism: (1) an intellectual anthropocentrism, which leads to an over-intellectualisation of the CoD, and (2) an emotional anthropocentrism, which yields an excessive focus on grief as a reaction to death. Contrary to what these two forms of anthropocentrism suggest, we argue that the CoD requires relatively little cognitive complexity and that it can emerge independently from mourning behaviour. Moreover, if we turn towards the natural world, we can see that the minimal cognitive requirements for a CoD are in fact met by many nonhuman species and there are multiple learning pathways and opportunities for animals in the wild to develop a CoD. This allows us to conclude that the CoD will be relatively easy to acquire and, so, we can expect it to be fairly common in nature.}, } @article {pmid34865251, year = {2022}, author = {Igai, K and Kitade, O and Fu, J and Omata, K and Yonezawa, T and Ohkuma, M and Hongoh, Y}, title = {Fine-scale genetic diversity and putative ecotypes of oxymonad protists coinhabiting the hindgut of Reticulitermes speratus.}, journal = {Molecular ecology}, volume = {31}, number = {4}, pages = {1317-1331}, doi = {10.1111/mec.16309}, pmid = {34865251}, issn = {1365-294X}, mesh = {Animals ; Ecotype ; Genetic Variation/genetics ; Humans ; *Isoptera/genetics ; *Oxymonadida ; Phylogeny ; Symbiosis ; }, abstract = {The hindgut of lower termites is generally coinhabited by multiple morphologically identifiable protist species. However, it is unclear how many protist species truly coexist in this miniaturized environment, and moreover, it is difficult to define the fundamental unit of protist diversity. Species delineation of termite gut protists has therefore been guided without a theory-based concept of species. Here, we focused on the hindgut of the termite Reticulitermes speratus, where 10 or 11 morphologically distinct oxymonad cell types, that is, morphospecies, coexist. We elucidated the phylogenetic structure of all co-occurring oxymonads and addressed whether their diversity can be explained by the "ecotype" hypothesis. Oxymonad-specific 18S rRNA gene amplicon sequencing analyses of whole-gut samples, combined with single-cell 18S rRNA sequencing of the oxymonad morphospecies, identified 210 one-nucleotide-level variants. The phylogenetic analysis of these variants revealed the presence of microdiverse clusters typically within 1% sequence divergence. Each known oxymonad morphospecies comprised one to several monophyletic or paraphyletic microdiverse clusters. Using these sequence data sets, we conducted computational simulation to predict the rates of ecotype formation and periodic selection, and to demarcate putative ecotypes. Our simulations suggested that the oxymonad genetic divergence is constrained primarily by strong selection, in spite of limited population size and possible bottlenecks during intergenerational transmission. A total of 33 oxymonad ecotypes were predicted, and most of the putative ecotypes were consistently detected among different colonies and host individuals. These findings provide a possible theoretical basis for species diversity and underlying mechanisms of coexistence of termite gut protists.}, } @article {pmid34849831, year = {2022}, author = {Finger, N and Farleigh, K and Bracken, JT and Leaché, AD and François, O and Yang, Z and Flouri, T and Charran, T and Jezkova, T and Williams, DA and Blair, C}, title = {Genome-Scale Data Reveal Deep Lineage Divergence and a Complex Demographic History in the Texas Horned Lizard (Phrynosoma cornutum) throughout the Southwestern and Central United States.}, journal = {Genome biology and evolution}, volume = {14}, number = {1}, pages = {}, pmid = {34849831}, issn = {1759-6653}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Demography ; Genetic Variation ; *Lizards/genetics ; Phylogeny ; Phylogeography ; United States ; }, abstract = {The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study, we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas horned lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat type, with desert populations in AZ and NM showing the largest genetic divergence from the remaining populations. The mtDNA data also support a divergent desert population, but other relationships differ and suggest mtDNA introgression. Genotype-environment association with bioclimatic variables supports divergence along precipitation gradients more than along temperature gradients. Demographic analyses support a complex history, with introgression and gene flow playing an important role during diversification. Bayesian multispecies coalescent analyses with introgression (MSci) analyses also suggest that gene flow occurred between populations. Paleo-species distribution models support two southern refugia that geographically correspond to contemporary lineages. We find that divergence times are underestimated and population sizes are overestimated when introgression occurred and is ignored in coalescent analyses, and furthermore, inference of ancient introgression events and demographic history is sensitive to inclusion of a single recently admixed sample. Our analyses cannot refute the riverine barrier or glacial refugia hypotheses. Results also suggest that populations are continuing to diverge along habitat gradients. Finally, the strong evidence of admixture, gene flow, and mtDNA introgression among populations suggests that P. cornutum should be considered a single widespread species under the General Lineage Species Concept.}, } @article {pmid34843500, year = {2021}, author = {Keeley, BW and Keeley, ATH}, title = {Acoustic wave response to groove arrays in model ears.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0260020}, pmid = {34843500}, issn = {1932-6203}, mesh = {Acoustics ; Animals ; Biological Evolution ; Ear/*anatomy & histology/*physiology ; Hearing/*physiology ; Humans ; Models, Biological ; Sound ; }, abstract = {Many mammals and some owls have parallel grooved structures associated with auditory structures that may be exploiting acoustic products generated by groove arrays. To test the hypothesis that morphological structures in the ear can manipulate acoustic information, we expose a series of similar-sized models with and without groove arrays to different sounds in identical conditions and compare their amplitude and frequency responses. We demonstrate how two different acoustic signals are uniquely influenced by the models. Depending on multiple factors (i.e., array characteristics, acoustic signal used, and distance from source) the presence of an array can increase the signal strength of select spectral components when compared to a model with no array. With few exceptions, the models with arrays increased the total amplitude of acoustic signals over that of the smooth model at all distances we tested up to 160 centimeters. We conclude that the ability to uniquely alter the signal based on an array's characteristics is evolutionarily beneficial and supports the concept that different species have different array configurations associated with their biological needs.}, } @article {pmid34824324, year = {2021}, author = {Ojea, E and Fontán, E and Fuentes-Santos, I and Bueno-Pardo, J}, title = {Assessing countries' social-ecological resilience to shifting marine commercial species.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22926}, pmid = {34824324}, issn = {2045-2322}, abstract = {Climate change is already impacting fisheries with species moving across fishing areas, crossing institutional borders, and thus creating conflicts over fisheries management. In this scenario, scholars agree that adaptation to climate change requires that fisheries increase their social, institutional, and ecological resilience. The resilience or capacity of a fishery to be maintained without shifting to a different state (e.g., collapse) is at stake under climate change impacts and overexploitation. Despite this urgent need, applying the resilience concept in a spatially explicit and quantitative manner to inform policy remains unexplored. We take a resilience approach and operationalize the concept in industrial fisheries for two species that have been observed to significantly shift distribution in European waters: hake (Merluccius merluccius) and cod (Gadus morhua), in the context of the European Union institutional settings. With a set of resilience factors from the literature and by means of contemporary and historic data, we select indicators that are combined into an index that measures resilience on the ecologic, socioeconomic, and institutional dimensions of the fishery. We find that the resilience index varies among species and countries, with lower resilience levels in the socioeconomic dimension of the fisheries. We also see that resilience largely depends on the overexploitation status of the fishery. The results highlight the need to address social and institutional settings to enhance fisheries adaptation to climate change and allow to inform on climate resilient adaptation pathways for the fisheries.}, } @article {pmid34810959, year = {2021}, author = {Rengifo-Correa, L and Juan Luis Tllez-Rendn, JLX and Esteban, L and Huerta, H and Morrone, JJ}, title = {The Triatoma phyllosoma species group (Hemiptera: Reduviidae: Triatominae), vectors of Chagas disease: Diagnoses and a key to the species.}, journal = {Zootaxa}, volume = {5023}, number = {3}, pages = {335-365}, doi = {10.11646/zootaxa.5023.3.2}, pmid = {34810959}, issn = {1175-5334}, mesh = {Animals ; *Chagas Disease ; *Triatoma ; *Triatominae ; United States ; }, abstract = {The Triatoma phyllosoma species group includes 17 species of kissing bugs, most of them implicated in the transmission of Chagas disease in the Americas. The species of this group are T. bassolsae Alejandre-Aguilar, Nogueda-Torres, Cortz-Jmenez, Jurberg, Galvo Carcavallo, 1999, T. brailovskyi Martnez, Carcavallo Pelaez, 1984, T. dimidiata (Latreille, 1811), T. gerstaeckeri (Stl, 1859), T. gomeznunezi Martnez, Carcavallo Juberg, 1994, T. hegneri Mazzotti, 1940, T. huehuetenanguensis Lima-Cordn, Monroy, Stevens, Rodas, Rodas, Dorn Justi, 2019, T. indictiva Neiva, 1912, T. longipennis Usinger, 1939, T. mazzottii Usinger, 1941, T. mexicana (Herrich-Schaeffer, 1848), T. mopan Dorn, Justi, Dale, Stevens, Galvo, Lima-Cordn Monroy, 2018, T. pallidipennis (Stl, 1872), T. phyllosoma (Burmeister, 1835), T. picturata Usinger, 1939, T. recurva (Stl, 1868), and T. sanguisuga (LeConte, 1855). The validity of some species of the group was uncertain, because of both cryptic species and hybrid occurrence. Species exhibiting these particularities were formerly classified in the T. dimidiata and T. phyllosoma complexes. Although we recognize the historical value of these species complexes, we do not recommend their further use. Instead, we recognize the T. phyllosoma species group here reviewed, considering the current knowledge of the systematics and reproductive behavior of the group. We implement the cohesion species concept, validating the species status of T. bassolsae, T. longipennis, T. mazzottii, T. pallidipennis, T. phyllosoma, and T. picturata. We also provide diagnoses, photographs and a taxonomic key including the recently described species.}, } @article {pmid34810900, year = {2021}, author = {Huys, R and Mu, F}, title = {Johnwellsia, a new intertidal genus of Parastenheliidae (Copepoda, Harpacticoida) from the Taiwan Strait, China, including a review of the family and key to genera.}, journal = {Zootaxa}, volume = {5051}, number = {1}, pages = {236-318}, doi = {10.11646/zootaxa.5051.1.13}, pmid = {34810900}, issn = {1175-5334}, mesh = {Animals ; China ; *Copepoda ; Neoptera ; Taiwan ; }, abstract = {A new genus of Parastenheliidae, Johnwellsia gen. nov., is proposed for its type and only species, J. bipartita sp. nov., collected from Dadeji Beach in Xiamen, Taiwan Strait, China. The intricate taxonomic history of the family is reviewed with special emphasis on its type genus Parastenhelia Thompson Scott, 1903. It is concluded that P. hornelli Thompson Scott, 1903 is the type of the genus and that the widely adopted previous designation of Harpacticus spinosus Fischer, 1860 as type species of Parastenhelia is invalid. The taxonomic concept of Parastenhelia is restricted to the hornelli-group which includes four valid species: P. hornelli, P. similis Thompson Scott, 1903, P. oligochaeta Wells Rao, 1987, and P. willemvervoorti sp. nov. The currently accepted concept of Parastenhelia spinosa as a highly variable cosmopolitan species is rejected. The genus Microthalestris Sars, 1905 (type: Thalestris forficula Claus, 1863) is resurrected to accommodate most Parastenhelia species that were previously placed in the spinosa-group. Two species, Thalestris forficuloides Scott Scott, 1894 and Parastenhelia antarctica Scott, 1912, are reinstated as valid members of the genus which further includes Parastenhelia gracilis Brady, 1910, Microthalestris littoralis Sars, 1911, P. costata Pallares, 1982, P. minuta Pallares, 1982, P. bulbosa Gee, 2006 and five new species: M. campbelliensis sp. nov.; M. polaris sp. nov.; M. santacruzensis sp. nov.; M. sarsi sp. nov. and M. variabilis sp. nov. Both the type species, Thalestris forficula, and Harpacticus spinosus are considered species inquirendae in Microthalestris. Three new genera are proposed to accommodate the remaining Parastenhelia species. Porirualia gen. nov. contains P. megarostrum Wells, Hicks Coull, 1982 (type) and P. pyriformis Song, Kim Chang, 2003, and is the sistergroup of Johnwellsia gen. nov. Parastenhelia aydini Kuru Karaytu, 2015 is placed in the monotypic genus Karaytugia gen. nov. while all species with penicillate elements on the antenna and P1 are transferred to Penicillicaris gen. nov., including Thalestris pectinimana Car, 1884, which is removed from the synonyms of the Parastenhelia spinosa (Fischer, 1860) complex, and three new species: P. maldivensis sp. nov., P. penicillata sp. nov., and P. sewelli sp. nov. The genus Karllangia Noodt, 1964 (type: K. arenicola Noodt, 1964) is relegated to a junior subjective synonym of Thalestrella Monard, 1935a (type: T. ornatissima Monard, 1935a). New or updated diagnoses for each genus, and differential diagnoses for species where appropriate, are provided. A key to the ten currently recognized genera in the Parastenheliidae is presented as well as keys to species for Parastenhelia, Microthalestris, Thalestrella and Penicillicaris gen. nov.}, } @article {pmid34810802, year = {2021}, author = {Sayyadzadeh, G and Esmaeili, HR}, title = {Does the Garra population (Teleostei: Cyprinidae: Labeoninae) from the Kol River drainage, Persian Gulf basin merit formal description?.}, journal = {Zootaxa}, volume = {5048}, number = {2}, pages = {265-278}, doi = {10.11646/zootaxa.5048.2.7}, pmid = {34810802}, issn = {1175-5334}, mesh = {Animals ; *Cyprinidae/genetics ; DNA, Mitochondrial/genetics ; Female ; Indian Ocean ; Phylogeny ; *Rivers ; }, abstract = {Recognizing and defining a species has been a controversial concern for a long time. To define the variation and the limitation between different species, especially closely related taxa in a complex species group, several concepts have been proposed which may lead to different taxonomic decisions. When a taxonomist studies a specific taxon, she/he should adopt a species concept and provide a species limitation to define the studied taxa. Garra population from the Kol River drainage, Persian Gulf basin has already been considered as Garra sp., based on molecular data, and to date no taxonomic decision has been made to provide a specific name for it. The Kol population presents several morphological characters that distinguish it from congeners: fully scaled breast; 78 branched dorsal-fin rays; caudal fin with 1617 branched rays and well-developed mental disc with free lateral and posterior margins. It is also distinguished from all other congeners in the Garra rufa group in Iran, by having two fixed, diagnostic nucleotide substitutions in the mtDNA COI barcode region. Furthermore, the Kol population demonstrates some distinct osteological characteristics in comparison to its closest species G. mondica. Based on the integrative molecular phylogenetic and species delimitation analyses, and morphological, osteological and distribution range data presented here, we think that the Kol River population merits formal description and can be considered as a distinct taxonomic unit (species).}, } @article {pmid34794720, year = {2021}, author = {Jenkins, N and Gorman, R and Douglas, C and Ashall, V and Ritchie, L and Jack-Waugh, A}, title = {Multi-species dementia studies: Contours, contributions and controversies.}, journal = {Journal of aging studies}, volume = {59}, number = {}, pages = {100975}, doi = {10.1016/j.jaging.2021.100975}, pmid = {34794720}, issn = {1879-193X}, mesh = {*Dementia ; Humans ; Social Justice ; Surveys and Questionnaires ; }, abstract = {Developed via an online collaborative writing project involving members of the Multi-species Dementia International Research Network, this article seeks to refocus "the lens of the dementia debate" (Bartlett & O'Connor, 2007) by bringing dementia's complicated relations with the more-than-human world into sharper relief. Specifically, the article explores four thematic areas (contours) within contemporary dementia studies (Care & Caring; Illness Experience & Disease Pathology; Environment, Self & Sustainability; Power, Rights & Social Justice) where the application of multi-species theories and concepts has potential to foster innovation and lead to new ways of thinking and working. Whilst incorporating multi-species perspectives within dementia studies can create new ways of responding and new spaces of response-ability, the potential for conflict and controversy remains high. It is imperative, therefore, that the field of dementia studies not only becomes a site within which multi-species perspectives can flourish, but that dementia studies also becomes a vehicle through which multi-species concepts may be refined.}, } @article {pmid34775488, year = {2022}, author = {Martinez-Hernandez, F and Diop, A and Garcia-Heredia, I and Bobay, LM and Martinez-Garcia, M}, title = {Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {1025-1035}, pmid = {34775488}, issn = {1751-7370}, support = {R01 GM132137/GM/NIGMS NIH HHS/United States ; }, mesh = {*Alphaproteobacteria ; DNA Viruses/genetics ; Nucleotides ; Oceans and Seas ; Seawater/microbiology ; *Viruses/genetics ; }, abstract = {Viral genetic microdiversity drives adaptation, pathogenicity, and speciation and has critical consequences for the viral-host arms race occurring at the strain and species levels, which ultimately impact microbial community structure and biogeochemical cycles. Despite the fact that most efforts have focused on viral macrodiversity, little is known about the microdiversity of ecologically important viruses on Earth. Recently, single-virus genomics discovered the putatively most abundant ocean virus in temperate and tropical waters: the uncultured dsDNA virus vSAG 37-F6 infecting Pelagibacter, the most abundant marine bacteria. In this study, we report the cooccurrence of up to ≈1,500 different viral strains (>95% nucleotide identity) and ≈30 related species (80-95% nucleotide identity) in a single oceanic sample. Viral microdiversity was maintained over space and time, and most alleles were the result of synonymous mutations without any apparent adaptive benefits to cope with host translation codon bias and efficiency. Gene flow analysis used to delimitate species according to the biological species concept (BSC) revealed the impact of recombination in shaping vSAG 37-F6 virus and Pelagibacter speciation. Data demonstrated that this large viral microdiversity somehow mirrors the host species diversity since ≈50% of the 926 analyzed Pelagibacter genomes were found to belong to independent BSC species that do not significantly engage in gene flow with one another. The host range of this evolutionarily successful virus revealed that a single viral species can infect multiple Pelagibacter BSC species, indicating that this virus crosses not only formal BSC barriers but also biomes since viral ancestors are found in freshwater.}, } @article {pmid34753574, year = {2021}, author = {Dias, BC and Batista, AD and da Silveira Petruci, JF}, title = {μOPTO: A microfluidic paper-based optoelectronic tongue as presumptive tests for the discrimination of alkaloid drugs for forensic purposes.}, journal = {Analytica chimica acta}, volume = {1187}, number = {}, pages = {339141}, doi = {10.1016/j.aca.2021.339141}, pmid = {34753574}, issn = {1873-4324}, mesh = {*Cocaine ; Colorimetry ; Microfluidics ; *Pharmaceutical Preparations ; Tongue ; }, abstract = {Natural and synthetic alkaloids are widely used for several applications, ranging from clinical purposes to criminal activities. Presumptive color tests are considered a leading tool to reveal on-scene substance identification via rapid chemical reactions that result in visual color changes. Colorimetric tests are popular due to their inherent simplicity, low cost, promptitude and portability; however, in many cases the results of such tests may not be predictable, partly because of the interference from similar species. In this proof-of-concept study, we present a paper-based microfluidic optoelectronic tongue - the so-called μOPTO - comprised of 6 indicators in lieu of one specific test and capable of discriminating 8 different alkaloid drugs (i.e. scopolamine, atropine, cocaine, morphine, ephedrine, caffeine, dipyrone and alprazolam) used for recreational, criminal and medical purposes. The wax printing method was employed to fabricate the microfluidic analytical device with six circular spots for reagent accommodation connected to a centered spot to enable simultaneous reactions with one sample injection. Digital images were obtained using an ordinary flatbed scanner, and the RGB information from before and after sample exposure was extracted using appropriate software. The color changes related to each spot were used to build differential maps with a unique fingerprint for each drug. The chemometric tools (i.e. PCA and HCA) showed suitable discrimination of all studied alkaloids in different quantities. To demonstrate a practical application, different alcoholic beverages spiked with scopolamine - a famous substance that causes drug abuse - were analyzed using the optoelectronic tongue. The results showed that small quantities of the drug were identified in different beverages, demonstrating that our device has the potential to be used in situ to prevent ingestion of contaminated samples.}, } @article {pmid34723110, year = {2020}, author = {Hg Solomon, L and Baio, C}, title = {An Argument for an Ecosystemic AI: Articulating Connections across Prehuman and Posthuman Intelligences.}, journal = {International journal of community well-being}, volume = {3}, number = {4}, pages = {559-584}, pmid = {34723110}, issn = {2524-5309}, abstract = {As an art collective Cesar & Lois develops projects that examine sociotechnical systems, attempting to challenge anthropocentric technological pathways while linking to intelligences sourced in biological circuitry. As artists we imagine new configurations for what we understand as (social, economic, technological) networks and intelligences. With this ecosystemic approach we consider the possibility of an artificial intelligence (AI) that supports well-being in a broad sense, accommodating relationships across different layers of living worlds and involving local and global communities of all kinds. This thinking is grounded in research by theorists across disciplines, including communications and media theory, microbiology, anthropology, decolonial studies, social ecology, sociology and environmental psychology. At a time when human beings and their ecosystems face grave threats due to climate change and a global pandemic, we are rethinking the basis for our AIs, and for the resulting decision-making on behalf of societies and ecosystems. Creative projects by Cesar & Lois provide alternative conceptual models for thinking across networks, reframing the artists' and potentially viewers' understanding of what motivates and shapes societies. Referencing a series of artworks and the theories that underpin them, this article envisages a sociotechnical framework that takes into account ecosystems and challenges the philosophical orientations that guide society. Degenerative Cultures is an artwork in which the artists overlap microbiological organisms, AI and human systems as a speculative restructuring of networks across human and nonhuman entities. The push for ecosystemic technologies and intelligences is linked to the expansion of community to include planetary constituents, such as nonhuman beings and environments. The artists posit that such ecosystemic networks would be capable of taking into account the planet's human societies as well as nonhuman species and their environments, broadening the concept of community well-being and shifting the technological architecture to meet the complex needs of the planet and its constituent parts. The experimental series, [ECO]nomic Revolution, layers Physarum polycephalum, or slime mold, over the mapped demographics of human cities. The species polycephalum references multi-brains, and implies a decentralized logic, which for the non-neurological microbiological network translates to the sharing of nutrients and regulated growth across a culture. Assuming a perspective based in the arts, this proposition imagines a shift from the dominant conceptions of AI as an individual intelligence and frames it as part of a network that necessarily includes ecosystems. We envision the creation of sociotechnical systems that could be modeled on networked lifeforms that have optimized themselves across millions of years, like the organism Physarum polycephalum, which occurs globally in moist environments, or like those microbial populations within and outside of human bodies, whose percussive biological processing interacts with and alters many layers of lifeforms. We argue that an environmentally responsive intelligence based on relationships across living systems potentially serves a broad community composed of diverse human populations, nonhuman beings and ecosystems.}, } @article {pmid34720775, year = {2021}, author = {Boekhout, T and Aime, MC and Begerow, D and Gabaldón, T and Heitman, J and Kemler, M and Khayhan, K and Lachance, MA and Louis, EJ and Sun, S and Vu, D and Yurkov, A}, title = {The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks.}, journal = {Fungal diversity}, volume = {109}, number = {1}, pages = {27-55}, pmid = {34720775}, issn = {1560-2745}, support = {R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; R01 AI133654/AI/NIAID NIH HHS/United States ; R37 AI039115/AI/NIAID NIH HHS/United States ; }, abstract = {Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.}, } @article {pmid34707577, year = {2021}, author = {Li, S and Yang, S and Zhou, Y and Disoma, C and Dong, Z and Du, A and Zhang, Y and Chen, Y and Huang, W and Chen, J and Song, D and Chen, Z and Liu, P and Li, S and Zheng, R and Liu, S and Razzaq, A and Chen, X and Tao, S and Yu, C and Feng, T and Liao, W and Peng, Y and Jiang, T and Huang, J and Wu, W and Hu, L and Wang, L and Li, S and Xia, Z}, title = {Microbiome Profiling Using Shotgun Metagenomic Sequencing Identified Unique Microorganisms in COVID-19 Patients With Altered Gut Microbiota.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {712081}, pmid = {34707577}, issn = {1664-302X}, abstract = {COVID-19 is mainly associated with respiratory distress syndrome, but a subset of patients often present gastrointestinal (GI) symptoms. Imbalances of gut microbiota have been previously linked to respiratory virus infection. Understanding how the gut-lung axis affects the progression of COVID-19 can provide a novel framework for therapies and management. In this study, we examined the gut microbiota of patients with COVID-19 (n = 47) and compared it to healthy controls (n = 19). Using shotgun metagenomic sequencing, we have identified four microorganisms unique in COVID-19 patients, namely Streptococcus thermophilus, Bacteroides oleiciplenus, Fusobacterium ulcerans, and Prevotella bivia. The abundances of Bacteroides stercoris, B. vulgatus, B. massiliensis, Bifidobacterium longum, Streptococcus thermophilus, Lachnospiraceae bacterium 5163FAA, Prevotella bivia, Erysipelotrichaceae bacterium 6145, and Erysipelotrichaceae bacterium 2244A were enriched in COVID-19 patients, whereas the abundances of Clostridium nexile, Streptococcus salivarius, Coprococcus catus, Eubacterium hallii, Enterobacter aerogenes, and Adlercreutzia equolifaciens were decreased (p < 0.05). The relative abundance of butyrate-producing Roseburia inulinivorans is evidently depleted in COVID-19 patients, while the relative abundances of Paraprevotella sp. and the probiotic Streptococcus thermophilus were increased. We further identified 30 KEGG orthology (KO) modules overrepresented, with 7 increasing and 23 decreasing modules. Notably, 15 optimal microbial markers were identified using the random forest model to have strong diagnostic potential in distinguishing COVID-19. Based on Spearman's correlation, eight species were associated with eight clinical indices. Moreover, the increased abundance of Bacteroidetes and decreased abundance of Firmicutes were also found across clinical types of COVID-19. Our findings suggest that the alterations of gut microbiota in patients with COVID-19 may influence disease severity. Our COVID-19 classifier, which was cross-regionally verified, provides a proof of concept that a set of microbial species markers can distinguish the presence of COVID-19.}, } @article {pmid34687495, year = {2022}, author = {Della Terra, PP and Gonsales, FF and de Carvalho, JA and Hagen, F and Kano, R and Bonifaz, A and Camargo, ZP and Rodrigues, AM}, title = {Development and evaluation of a multiplex qPCR assay for rapid diagnostics of emerging sporotrichosis.}, journal = {Transboundary and emerging diseases}, volume = {69}, number = {4}, pages = {e704-e716}, doi = {10.1111/tbed.14350}, pmid = {34687495}, issn = {1865-1682}, mesh = {Animals ; *Cat Diseases/diagnosis/epidemiology ; Cats ; Disease Outbreaks ; Phylogeny ; Real-Time Polymerase Chain Reaction/veterinary ; Sequence Analysis, DNA/veterinary ; *Sporothrix/genetics ; *Sporotrichosis/diagnosis/epidemiology/veterinary ; }, abstract = {Sporothrix schenckii and related species are the agents of human and animal sporotrichosis. Routine diagnoses using classical mycological approaches are unspecific due to overlapping phenotypes. As the frequency and prevalence of sporotrichosis increases worldwide, developing specific, sensitive and cost-effective diagnostic tools is essential to understand the distribution patterns, map-affected areas and promote specific public health strategies to mitigate future outbreaks. Polymorphisms among the β-tubulin gene were exploited to speciate S. brasiliensis, S. schenckii and S. globosa in a one-tube multiplex probe-based qPCR assay. A panel of 84 Sporothrix revealed 100% specificity (AUC = 1.000, 95% CI = 0.971-1.000, p < .0001) without cross-reacting with other medically relevant fungi, human, feline or murine DNA. Speciation via multiplex qPCR matched phylogenetic identification (Kappa = 1.0; 95% CI = 1.0-1.0; very good agreement), supporting its use as a reliable alternative to DNA sequencing. Remarkably, the lower limit of detection was 3 copies of the target for all species. As a proof of concept, we used swabs of wound exudate of 70 cats suspected of sporotrichosis to reveal an overwhelming occurrence of S. brasiliensis in 69 specimens (sensitivity = 98.57%; 95%CI: 92.3-100.0 and specificity = 100%; 95% CI = 78.2-100). In comparison to culture, qPCR showed a larger area under the curve (AUC = 0.993±0.007; 95% CI = 0.944-1.000; p < .0001; Youden's index = 0.9857), supporting that qPCR is an essential tool for accurately detect Sporothrix DNA directly from clinical samples, thus accelerating the diagnosis of sporotrichosis. Moreover, our multiplex qPCR system has the potential to increase diagnostic capacity in Sporothrix-affected areas, helping the local animal health agent or veterinarian to quickly identify and isolate new cases, which will likely benefit thousands of patients infected every year worldwide.}, } @article {pmid34672346, year = {2022}, author = {Wells, T and Carruthers, T and Muñoz-Rodríguez, P and Sumadijaya, A and Wood, JRI and Scotland, RW}, title = {Species as a Heuristic: Reconciling Theory and Practice.}, journal = {Systematic biology}, volume = {71}, number = {5}, pages = {1233-1243}, pmid = {34672346}, issn = {1076-836X}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; T001445/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; *Heuristics ; Humans ; Phylogeny ; }, abstract = {Species are crucial to most branches of biological research, yet remain controversial in terms of definition, delimitation, and reality. The difficulty of resolving the "species problem" stems from the tension between their theoretical concept as groups of evolving and highly variable organisms and the practical need for a stable and comparable unit of biology. Here, we suggest that treating species as a heuristic can be consistent with a theoretical definition of what species are and with the practical means by which they are identified and delimited. Specifically, we suggest that theoretically species are heuristic since they comprise clusters of closely related individuals responding in a similar manner to comparable sets of evolutionary and ecological forces, whilst they are practically heuristic because they are identifiable by the congruence of contingent properties indicative of those forces. This reconciliation of the theoretical basis of species with their practical applications in biological research allows for a loose but relatively consistent definition of species based on the strategic analysis and integration of genotypic, phenotypic, and ecotypic data. [Cohesion; heuristic; homeostasis; lineage; species problem.].}, } @article {pmid34665841, year = {2021}, author = {Ellepola, G and Herath, J and Manamendra-Arachchi, K and Wijayathilaka, N and Senevirathne, G and Pethiyagoda, R and Meegaskumbura, M}, title = {Molecular species delimitation of shrub frogs of the genus Pseudophilautus (Anura, Rhacophoridae).}, journal = {PloS one}, volume = {16}, number = {10}, pages = {e0258594}, pmid = {34665841}, issn = {1932-6203}, mesh = {Amphibian Proteins/genetics ; Animals ; Anura/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; Databases, Genetic ; Homeodomain Proteins/*genetics ; India ; Phylogeny ; Phylogeography ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA-Rag-1; mt-DNA- 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island's aseasonal 'wet zone' and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges-ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.}, } @article {pmid34647136, year = {2021}, author = {Yang, MY and Wang, YX and Chang, QH and Li, LF and Liu, YF and Cao, F}, title = {Cytochalasans and azaphilones: suitable chemotaxonomic markers for the Chaetomium species.}, journal = {Applied microbiology and biotechnology}, volume = {105}, number = {21-22}, pages = {8139-8155}, pmid = {34647136}, issn = {1432-0614}, mesh = {Benzopyrans ; *Chaetomium ; Cytochalasins ; Pigments, Biological ; }, abstract = {The accurate taxonomic concept of the fungal Chaetomium species has been a hard work due to morphological similarity. Chemotaxonomy based on secondary metabolites is a powerful tool for taxonomical purposes, which could be used as an auxiliary reference to solve the problems encountered in the classification of Chaetomium. Among secondary metabolites produced by Chaetomium, cytochalasans and azaphilones exhibited a pattern of distribution and frequency of occurrence that establish them as chemotaxonomic markers for the Chaetomium species. This review attempted to elucidate the composition of the Chaetomium species and its relationship with classical taxonomy by summarizing the pattern of cytochalasans and azaphilones distribution and biosynthesis in the Chaetomium species. KEY POINTS: • Secondary metabolites from the genus Chaetomium are summarized. • Cytochalasans and azaphilones could be characteristic metabolites of the Chaetomium species. • Cytochalasans and azaphilones could be used to analyze for taxonomical purposes.}, } @article {pmid34636670, year = {2021}, author = {Tierney, BT and Szymanski, E and Henriksen, JR and Kostic, AD and Patel, CJ}, title = {Using Cartesian Doubt To Build a Sequencing-Based View of Microbiology.}, journal = {mSystems}, volume = {6}, number = {5}, pages = {e0057421}, pmid = {34636670}, issn = {2379-5077}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; }, abstract = {The technological leap of DNA sequencing generated a tension between modern metagenomics and historical microbiology. We are forcibly harmonizing the output of a modern tool with centuries of experimental knowledge derived from culture-based microbiology. As a thought experiment, we borrow the notion of Cartesian doubt from philosopher Rene Descartes, who used doubt to build a philosophical framework from his incorrigible statement that "I think therefore I am." We aim to cast away preconceived notions and conceptualize microorganisms through the lens of metagenomic sequencing alone. Specifically, we propose funding and building analysis and engineering methods that neither search for nor rely on the assumption of independent genomes bound by lipid barriers containing discrete functional roles and taxonomies. We propose that a view of microbial communities based in sequencing will engender novel insights into metagenomic structure and may capture functional biology not reflected within the current paradigm.}, } @article {pmid34626519, year = {2022}, author = {Kollár, J and Poulíčková, A and Dvořák, P}, title = {On the relativity of species, or the probabilistic solution to the species problem.}, journal = {Molecular ecology}, volume = {31}, number = {2}, pages = {411-418}, doi = {10.1111/mec.16218}, pmid = {34626519}, issn = {1365-294X}, mesh = {*Genetic Speciation ; *Genomics ; Phylogeny ; Probability ; }, abstract = {For centuries, both scientists and philosophers have discussed the nature of species resulting in c. 35 species concepts proposed to date. However, in our opinion, none of them incorporated neither recent advances in evolutionary genomics nor dimensionality of species in befitting depth. Our attempt to do so resulted in the following conclusions. Due to the continuous nature of evolution (regardless of its rate and constancy), species are inevitably undefinable as natural discontinuous units (except those originating in saltatory speciation) whenever the time dimension is taken into consideration. Therefore, the very existence of species as a natural discontinuous entity is relative to its dimensionality. A direct consequence of the relativity of species is the duality of speciators (e.g., incipient species) meaning that, in a given time, they may be perceived as both being and not being a species. Finally, the most accurate way to reflect both the relativity of species and the duality of speciators in species delimitation is probabilistic. While the novelty of these ideas may be questionable, they still deserve more extensive attention from the biological community. Here, we hope to draw such attention by outlining one of the possible pathways towards a new kind of probabilistic species delimitation methods based on the probability of irreversible divergence of evolutionary lineages. We anticipate that our probabilistic view of speciation has the potential to facilitate some of the most serious and universal issues of current taxonomy and to ensure unity of the species-level taxonomy across the tree of life.}, } @article {pmid34624875, year = {2021}, author = {Chen, H and Qi, X and Zhang, L and Li, X and Ma, J and Zhang, C and Feng, H and Yao, M}, title = {COVID-19 screening using breath-borne volatile organic compounds.}, journal = {Journal of breath research}, volume = {15}, number = {4}, pages = {}, doi = {10.1088/1752-7163/ac2e57}, pmid = {34624875}, issn = {1752-7163}, mesh = {Biomarkers ; Breath Tests ; *COVID-19 ; *Exhalation ; Humans ; Machine Learning ; SARS-CoV-2 ; *Volatile Organic Compounds ; }, abstract = {Rapid screening of COVID-19 is key to controlling the pandemic. However, current nucleic acid amplification involves lengthy procedures in addition to the discomfort of taking throat/nasal swabs. Here we describe potential breath-borne volatile organic compound (VOC) biomarkers together with machine learning that can be used for point-of-care screening of COVID-19. Using a commercial gas chromatograph-ion mobility spectrometer, higher levels of propanol were detected in the exhaled breath of COVID-19 patients (N= 74) and non-COVID-19 respiratory infections (RI) (N= 30) than those of non-COVID-19 controls (NC)/health care workers (HCW) (N= 87), and backgrounds (N= 87). In contrast, breath-borne acetone was found to be significantly lower for COVID-19 patients than other subjects. Twelve key endogenous VOC species using supervised machine learning models (support vector machines, gradient boosting machines (GBMs), and Random Forests) were shown to exhibit strong capabilities in discriminating COVID-19 from (HCW + NC) and RI with a precision ranging from 91% to 100%. GBM and Random Forests models can also discriminate RI patients from healthy subjects with a precision of 100%. In addition, the developed models using breath-borne VOCs could also detect a confirmed COVID-19 patient but with a false negative throat swab polymerase chain reaction test. It takes 10 min to allow an entire breath test to finish, including analysis of the 12 key VOC species. The developed technology provides a novel concept for non-invasive rapid point-of-care-test screening for COVID-19 in various scenarios.}, } @article {pmid34618523, year = {2021}, author = {Delamater, AR and Wasserman, EA}, title = {Comparative cognition-Conceptual and methodological advancements.}, journal = {Journal of experimental psychology. Animal learning and cognition}, volume = {47}, number = {3}, pages = {219-222}, doi = {10.1037/xan0000309}, pmid = {34618523}, issn = {2329-8464}, mesh = {Animals ; *Cognition ; *Concept Formation ; Dogs ; Mice ; Pan troglodytes ; Rats ; }, abstract = {This special issue originally placed a Call for Papers that emphasized the importance of "Conceptual and Methodological" advances in the field of Comparative Cognition. Represented here is a collection of 14 papers that helps to display some of the diversity of ideas and approaches within this flourishing research area. The first paper in this issue, by Gazes and Lazareva (2021), discusses transitive inference learning from the perspectives of: identifying the problems of contextual variables in studying different species; whether associative processes can or cannot fully account for the behavior and, if not, what alternative representational mechanisms might be at work; and, finally, how ecological considerations may support comparative research by suggesting novel theoretical and empirical questions. The next paper, by Loy et al. (2021) investigates questions related to the complexity of learning in invertebrate species, single-celled organisms, and plants. The paper by Rawlings et al. (2021) reviews the literature on cumulative cultural evolution, primarily in nonhuman primate species, and critically evaluates the importance of identifying the essential conceptual and methodological issues in what many have deemed to be a uniquely human form of behavior. The paper by Goto and Watanabe (2021) explores whether the mouse visual system is sensitive to Gestalt principles, using operant discrimination learning tasks similar to those used previously to document Gestalt processing in chimpanzees and humans. Qadri and Cook (2021) use the innovative approach of "adaptive genetic algorithms" to assess the relative importance of different features of a stimulus in controlling organisms' discrimination learning performance. Wittek et al. (2021) introduce a novel method for studying the importance of visual accumulation processes in pigeons when information is presented to a single hemisphere at a time. The paper by Cowie et al. (2021) focuses on a misallocation model of two-step sequence learning in young children and explores from a behavioranalytic viewpoint the implications of assuming that reinforcement might be misattributed to a misremembered response at the beginning of the behavioral sequence. The paper by López-Tolsa and Pellón (2021) explores whether the opportunity to display schedule-induced drinking as an early response within a behavioral sequence might alter the accuracy of temporal control in different-length fixed-interval schedule tasks with rats. Crystal (2021) reviews the literature examining episodic memory in nonhuman species and considers a variety of criteria and methods thought to be crucial for establishing empirical evidence for episodic memory in nonhumans, in general, and rats, in particular. Vila et al. (2021) discuss the use a novel 'hide-and-seek' task in preschool age children to study episodic-like memory; their work illustrates how memory dynamics can change over time in a manner not very unlike what has been demonstrated in other nonhuman research paradigms. The paper by Krichbaum et al. (2021) discusses some of the methodological difficulties one faces in studying spatial cognition in canines. The paper by Castro et al. (2021) uses a complex categorization learning task in which different sets of display features are diagnostic, or not, of category mastery depending upon context. The paper by Vernouillet et al. (2021) explores the formation of same/different concept learning in two species of corvids (pinyon jays and California scrub jays). The final paper, by Lazarowski et al. (2021) examines the possibility of abstract same/different learning in canines using a trial-unique training matching-to-sample procedure with olfactory stimuli. (PsycInfo Database Record (c) 2021 APA, all rights reserved).}, } @article {pmid34608378, year = {2021}, author = {Voigt, K and James, TY and Kirk, PM and Santiago, ALCMA and Waldman, B and Griffith, GW and Fu, M and Radek, R and Strassert, JFH and Wurzbacher, C and Jerônimo, GH and Simmons, DR and Seto, K and Gentekaki, E and Hurdeal, VG and Hyde, KD and Nguyen, TTT and Lee, HB}, title = {Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals.}, journal = {Fungal diversity}, volume = {109}, number = {1}, pages = {59-98}, pmid = {34608378}, issn = {1560-2745}, abstract = {The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa, has dramatically changed the classification system of early-diverging fungi over the past several decades. The number of phyla established for non-Dikarya fungi has increased from 2 to 17. However, to date, both the classification and phylogeny of the basal fungi are still unresolved. In this article, we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal phyla. We also provide information on the ecology and distribution in Mucoromycota and highlight the impact of chytrids on amphibian populations. Species concepts in Chytridiomycota, Aphelidiomycota, Rozellomycota, Neocallimastigomycota are discussed in this paper. To preserve the current application of the genus Nephridiophaga (Chytridiomycota: Nephridiophagales), a new type species, Nephridiophaga blattellae, is proposed.}, } @article {pmid34602861, year = {2021}, author = {Penner, S}, title = {How the in situ monitoring of bulk crystalline phases during catalyst activation results in a better understanding of heterogeneous catalysis.}, journal = {CrystEngComm}, volume = {23}, number = {37}, pages = {6470-6480}, pmid = {34602861}, issn = {1466-8033}, abstract = {The present Highlight article shows the importance of the in situ monitoring of bulk crystalline compounds for a more thorough understanding of heterogeneous catalysts at the intersection of catalysis, materials science, crystallography and inorganic chemistry. Although catalytic action is widely regarded as a purely surface-bound phenomenon, there is increasing evidence that bulk processes can detrimentally or beneficially influence the catalytic properties of various material classes. Such bulk processes include polymorphic transformations, formation of oxygen-deficient structures, transient phases and the formation of a metal-oxide composite. The monitoring of these processes and the subsequent establishment of structure-property relationships are most effective if carried out in situ under real operation conditions. By focusing on synchrotron-based in situ X-ray diffraction as the perfect tool to follow the evolution of crystalline species, we exemplify the strength of the concept with five examples from various areas of catalytic research. As catalyst activation studies are increasingly becoming a hot topic in heterogeneous catalysis, the (self-)activation of oxide- and intermetallic compound-based materials during methanol steam and methane dry reforming is highlighted. The perovskite LaNiO3 is selected as an example to show the complex structural dynamics before and during methane dry reforming, which is only revealed upon monitoring all intermediate crystalline species in the transformation from LaNiO3 into Ni/La2O3/La2O2CO3. ZrO2-based materials form the second group, indicating the in situ decomposition of the intermetallic compound Cu51Zr14 into an epitaxially stabilized Cu/tetragonal ZrO2 composite during methanol steam reforming, the stability of a ZrO0.31C0.69 oxycarbide and the gas-phase dependence of the tetragonal-to-monoclinic ZrO2 polymorphic transformation. The latter is the key parameter to the catalytic understanding of ZrO2 and is only appreciated in full detail once it is possible to follow the individual steps of the transformation between the crystalline polymorphic structures. A selected example is devoted to how the monitoring of crystalline reactive carbon during methane dry reforming operation aids in the mechanistic understanding of a Ni/MnO catalyst. The most important aspect is the strict use of in situ monitoring of the structural changes occurring during (self-)activation to establish meaningful structure-property relationships allowing conclusions beyond isolated surface chemical aspects.}, } @article {pmid34594535, year = {2021}, author = {Firneno, TJ and O'Neill, JR and Itgen, MW and Kihneman, TA and Townsend, JH and Fujita, MK}, title = {Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance.}, journal = {Ecology and evolution}, volume = {11}, number = {18}, pages = {12739-12753}, pmid = {34594535}, issn = {2045-7758}, abstract = {The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g., cryptic species), differences in criteria of species concepts, lineages being in the early stages of the speciation or divergence process, and discordance between gene topologies (e.g., mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offers the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group, we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical and integrative hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that a stable taxonomy has over conservation-related actions.}, } @article {pmid34582186, year = {2021}, author = {Pham, TC and Nguyen, VN and Choi, Y and Lee, S and Yoon, J}, title = {Recent Strategies to Develop Innovative Photosensitizers for Enhanced Photodynamic Therapy.}, journal = {Chemical reviews}, volume = {121}, number = {21}, pages = {13454-13619}, doi = {10.1021/acs.chemrev.1c00381}, pmid = {34582186}, issn = {1520-6890}, mesh = {Humans ; Nanotechnology ; *Neoplasms/drug therapy ; *Photochemotherapy/methods ; Photosensitizing Agents/pharmacology/therapeutic use ; Reactive Oxygen Species ; }, abstract = {This review presents a robust strategy to design photosensitizers (PSs) for various species. Photodynamic therapy (PDT) is a photochemical-based treatment approach that involves the use of light combined with a light-activated chemical, referred to as a PS. Attractively, PDT is one of the alternatives to conventional cancer treatment due to its noninvasive nature, high cure rates, and low side effects. PSs play an important factor in photoinduced reactive oxygen species (ROS) generation. Although the concept of photosensitizer-based photodynamic therapy has been widely adopted for clinical trials and bioimaging, until now, to our surprise, there has been no relevant review article on rational designs of organic PSs for PDT. Furthermore, most of published review articles in PDT focused on nanomaterials and nanotechnology based on traditional PSs. Therefore, this review aimed at reporting recent strategies to develop innovative organic photosensitizers for enhanced photodynamic therapy, with each example described in detail instead of providing only a general overview, as is typically done in previous reviews of PDT, to provide intuitive, vivid, and specific insights to the readers.}, } @article {pmid34575741, year = {2021}, author = {Wijayawardene, NN and Bahram, M and Sánchez-Castro, I and Dai, DQ and Ariyawansa, KGSU and Jayalal, U and Suwannarach, N and Tedersoo, L}, title = {Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {7}, number = {9}, pages = {}, pmid = {34575741}, issn = {2309-608X}, abstract = {Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual-asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.}, } @article {pmid34574328, year = {2021}, author = {Zhu, X and Wu, M and Deng, R and Rizwan Khan, M and Deng, S and Wang, X and Busquets, R and Deng, W and Luo, A}, title = {Amplification Refractory Mutation System (ARMS)-PCR for Waxy Sorghum Authentication with Single-Nucleotide Resolution.}, journal = {Foods (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {34574328}, issn = {2304-8158}, abstract = {Waxy sorghum has greater economic value than wild sorghum in relation to their use in food processing and the brewing industry. Thus, the authentication of the waxy sorghum species is an important issue. Herein, a rapid and sensitive Authentication Amplification Refractory Mutation System-PCR (aARMS-PCR) method was employed to identify sorghum species via its ability to resolve single-nucleotide in genes. As a proof of concept, we chose a species of waxy sorghum containing the wx[c] mutation which is abundantly used in liquor brewing. The aARMS-PCR can distinguish non-wx[c] sorghum from wx[c] sorghum to guarantee identification of specific waxy sorghum species. It allowed to detect as low as 1% non-wx[c] sorghum in sorghum mixtures, which ar one of the most sensitive tools for food authentication. Due to its ability for resolving genes with single-nucleotide resolution and high sensitivity, aARMS-PCR may have wider applicability in monitoring food adulteration, offering a rapid food authenticity verification in the control of adulteration.}, } @article {pmid34562419, year = {2021}, author = {Soares, FA and Martins Dos Santos, B and Rosa, SL and Loiola, SHN and Suzuki, CTN and Sabadini, E and Bresciani, KDS and Falcão, AX and Gomes, JF}, title = {Dissolved air flotation as potential new mechanism for intestinal parasite diagnosis in feces.}, journal = {Acta tropica}, volume = {224}, number = {}, pages = {106137}, doi = {10.1016/j.actatropica.2021.106137}, pmid = {34562419}, issn = {1873-6254}, mesh = {Animals ; Ascaris lumbricoides ; Feces ; Humans ; *Intestinal Diseases, Parasitic/diagnosis ; *Parasites ; *Strongyloides stercoralis ; }, abstract = {The parasitological examination of feces is recommended for the laboratory diagnosis of intestinal parasites due to its practicality, low-cost, and moderate diagnostic sensitivity. Dissolved Air Flotation (DAF) is an efficient technical principle used in other areas to separate dispersed solids. This study sought the preliminary evaluation of a proof-of-concept prototype as a tool for detecting species of parasites by adjusting DAF. Two DAF prototype units were developed to evaluate microbubbles' generation amidst fecal suspension and parasites' capture. For this evaluation, samples were screened and processed by the TF-Test technique (Control) and simultaneously by DAF device. The dimensional and attachment characteristics in the formation of the microbubbles were evaluated, and the percentage of parasitic recovery in floated and not-floated regions compared by Student's t-test. The second prototype unit proved to be more efficient in forming microbubbles with diameters between 34 and 170µm. The flotation tests showed a recovery of 73.27%, 58.12%, 37.85%, and 91.89% for Ascaris lumbricoides, Hymenolepis diminuta, Giardia duodenalis, and Strongyloides stercoralis, respectively. This study confirmed the selective interaction between microbubbles and parasite eggs and larvae during the flotation process using the DAF principle for the first time through imaging.}, } @article {pmid34561474, year = {2021}, author = {Ramos, C and Calus, M and Schokker, D}, title = {Persistence of functional microbiota composition across generations.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19007}, pmid = {34561474}, issn = {2045-2322}, mesh = {Animals ; Culicidae/microbiology ; Datasets as Topic ; *Host Microbial Interactions ; Host Specificity ; Humans ; Microbiota/*physiology ; Plants/microbiology ; Zooplankton/microbiology ; }, abstract = {Holobionts are defined as a host and its microbiota, however, only a fraction of the bacteria are inherited vertically and thus coevolve with the host. The "it's the song, not the singer" theory proposes that functional traits, instead of taxonomical microbiota composition, could be preserved across generations if interspecies interaction patterns perpetuate themselves. We tested conservation of functional composition across generations using zooplankton, mosquito, and plant datasets. Then, we tested if there is a change of functional microbiota composition over time within a generation in human datasets. Finally, we simulated microbiota communities to investigate if (pairwise) interactions can lead to multiple stable community compositions. Our results suggest that the vertically transmitted microbiota starts a predictable change of functions performed by the microbiota over time, whose robustness depends on the arrival of diverse migrants. This succession culminates in a stable functional composition state. The results suggest that the host-microbiota interaction and higher order interactions in general have an important contribution to the robustness of the final community. If the proposed mechanism proves to be valid for a diverse array of host species, this would support the concept of holobionts being used as units of selection, including animal breeding, suggesting this has a wider applicability.}, } @article {pmid34548403, year = {2021}, author = {Adkins-Jablonsky, SJ and Clark, CM and Papoulis, SE and Kuhl, MD and Morris, JJ}, title = {Market forces determine the distribution of a leaky function in a simple microbial community.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {39}, pages = {}, pmid = {34548403}, issn = {1091-6490}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Biological Evolution ; *Drug Resistance, Microbial ; Escherichia coli/drug effects/*physiology ; *Microbiota ; Models, Theoretical ; }, abstract = {Many biological functions are leaky, and organisms that perform them contribute some of their products to a community "marketplace" in which nonperforming individuals may compete for them. Leaky functions are partitioned unequally in microbial communities, and the evolutionary forces determining which species perform them and which become beneficiaries are poorly understood. Here, we demonstrate that the market principle of comparative advantage determines the distribution of a leaky antibiotic resistance gene in an environment occupied by two "species"-strains of Escherichia coli growing on mutually exclusive resources and thus occupying separate niches. Communities comprised of antibiotic-resistant cells were rapidly invaded by sensitive cells of both types. While the two phenotypes coexisted stably for 500 generations, in 15/18 replicates, antibiotic sensitivity became fixed in one species. Fixation always occurred in the same species despite both species being genetically identical except for their niche-defining mutation. In the absence of antibiotic, the fitness cost of resistance was identical in both species. However, the intrinsic resistance of the species that ultimately became the sole helper was significantly lower, and thus its reward for expressing the resistance gene was higher. Opportunity cost of resistance, not absolute cost or efficiency of antibiotic removal, determined which species became the helper, consistent with the economic theory of comparative advantage. We present a model that suggests that this market-like dynamic is a general property of Black Queen systems and, in communities dependent on multiple leaky functions, could lead to the spontaneous development of an equitable and efficient division of labor.}, } @article {pmid34526521, year = {2021}, author = {Korshunova, TA and Driessen, FMF and Picton, BE and Martynov, AV}, title = {The multilevel organismal diversity approach deciphers difficult to distinguish nudibranch species complex.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18323}, pmid = {34526521}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Biological Evolution ; Europe ; Gastropoda/anatomy & histology/*classification/genetics/ultrastructure ; Genes, Mitochondrial ; Genetic Variation ; Phenotype ; Phylogeny ; Phylogeography ; Terminology as Topic ; }, abstract = {Species identification is a key procedure for broad-scoped ecological, phylogeographic and evolutionary studies. However, to perform a taxonomic study in the molecular era is a complicated task that has many pitfalls. In the present study we use particular examples of common but difficult to distinguish European species within the genus of Polycera (Nudibranchia, Mollusca) to discuss the general issues of the "cryptic species" problem that has broad biological and interdisciplinary importance and can significantly impede ecological, evolutionary, and other biodiversity-related research. The largest dataset of molecular and morphological information for European nudibranchs ever applied encompasses a wide geographical area and shapes a robust framework in this study. Four species are recognized in the species complex, including a new one. It is shown that a lack of appropriate taxonomic analysis led recently to considerable errors in species identity assessment of this complex. Chromatic polymorphism for each species is mapped in a periodic-like framework and combined with statistical analysis of the diagnostic features that considerably facilitates identification of particular species in the complex for biologists and practitioners. The present study evidently shows that "cryptic" and "non-cryptic" components are present within the same species. Therefore, this species complex is well suited for the exploring and testing of general biological problems. One of the main conclusions of this study is that division of biological diversity into "cryptic" and "non-cryptic" components is counterproductive. We propose that the central biological phenomenon of a species can instead be universally designated as multilevel organismal diversity thereby provide a practical set of methods for its investigation.}, } @article {pmid34525609, year = {2021}, author = {Li, C and Feng, TJ and Zhang, HL and Chen, DH and Cressman, R and Liao, JB and Tao, Y}, title = {Multilayer network structure enhances the coexistence of competitive species.}, journal = {Physical review. E}, volume = {104}, number = {2-1}, pages = {024402}, doi = {10.1103/PhysRevE.104.024402}, pmid = {34525609}, issn = {2470-0053}, abstract = {The concept of a multiplex network can be used to characterize the dispersal paths and states of different species in a patch habitat system. The multiplex network is one of three types of multilayer networks. In this study, the effect of a multiplex network on the long-term stable coexistence of species is investigated using the concept of metapopulation. Based on the mean field approximation, the stability analysis of a two-species system shows that, compared to the single layer network, the multiplex network is more conducive to the stable coexistence of species when one species has a stronger colonization ability. That is, in such a patch habitat system, if the dispersal paths of the stronger species are different than those of the weaker species, then the larger the heterogeneity of the dispersal network of the stronger species is, the more likely the long-term stable coexistence of species. This result provides a different perspective for understanding the biodiversity in heterogeneous habitats.}, } @article {pmid34522346, year = {2021}, author = {Aarnio, S and Soininen, J}, title = {Taxonomic and functional diversity covary in rock pool microalgal communities despite their different drivers.}, journal = {Ecology and evolution}, volume = {11}, number = {17}, pages = {11852-11873}, pmid = {34522346}, issn = {2045-7758}, abstract = {Local biodiversity has traditionally been estimated with taxonomic diversity metrics such as species richness. Recently, the concept of biodiversity has been extended beyond species identity by ecological traits determining the functional role of a species in a community. This interspecific functional diversity typically responds more strongly to local environmental variation compared with taxonomic diversity, while taxonomic diversity may mirror more strongly dispersal processes compared with functional metrics. Several trait-based indices have been developed to measure functional diversity for various organisms and habitat types, but studies of their applicability on aquatic microbial communities have been underrepresented. We examined the drivers and covariance of taxonomic and functional diversity among diatom rock pool communities on the Baltic Sea coast. We quantified three taxonomic (species richness, Shannon's diversity, and Pielou's evenness) and three functional (functional richness, evenness, and divergence) diversity indices and determined abiotic factors best explaining variation in these indices by generalized linear mixed models. The six diversity indices were highly collinear except functional evenness, which merely correlated significantly with taxonomic evenness. All diversity indices were always explained by water conductivity and temperature-sampling month interaction. Taxonomic diversity was further consistently explained by pool distance to the sea, and functional richness and divergence by pool location. The explained variance in regression models did not markedly differ between taxonomic and functional metrics. Our findings do not clearly support the superiority of neither set of diversity indices in explaining coastal microbial diversity, but rather highlight the general overlap among the indices. However, as individual metrics may be driven by different factors, the greatest advantage in assessing biodiversity is nevertheless probably achieved with a simultaneous application of the taxonomic and functional diversity metrics.}, } @article {pmid34490139, year = {2021}, author = {Tian, XY and Xing, JW and Zheng, QQ and Gao, PF}, title = {919 Syrup Alleviates Postpartum Depression by Modulating the Structure and Metabolism of Gut Microbes and Affecting the Function of the Hippocampal GABA/Glutamate System.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {694443}, pmid = {34490139}, issn = {2235-2988}, mesh = {Animals ; Bacteria ; Bacteroidetes ; Bifidobacterium ; *Depression, Postpartum/drug therapy ; Desulfovibrio ; Female ; *Gastrointestinal Microbiome ; Glutamic Acid ; Hippocampus ; Humans ; Mice ; Mice, Inbred BALB C ; Pregnancy ; gamma-Aminobutyric Acid ; }, abstract = {Postpartum depression (PPD) is a mental disorder that affects pregnant women around the world, with serious consequences for mothers, families, and children. Its pathogenesis remains unclear, and medications for treating PPD that can be used during lactation remain to be identified. 919 syrup (919 TJ) is a Chinese herbal medicine that has been shown to be beneficial in the treatment of postpartum depression in both clinical and experimental studies. The mechanism of action of 919 TJ is unclear. 919 syrup is ingested orally, making the potential interaction between the drug and the gut microbiome impossible to ignore. We therefore hypothesized that 919 syrup could improve the symptoms of postpartum depression by affecting the structure and function of the intestinal flora, thereby altering hippocampal metabolism. We compared changes in hippocampal metabolism, fecal metabolism, and intestinal microflora of control BALB/c mice, mice with induced untreated PPD, and mice with induced PPD treated with 919 TJ, and found that 4-aminobutyric acid (GABA) in the hippocampus corresponded with PPD behaviors. Based on changes in GABA levels, multiple key gut bacterial species (Mucispirillum schaedleri, Bifidobacterium pseudolongum, Desulfovibrio piger, Alloprevotella tannerae, Bacteroides sp.2.1.33B and Prevotella sp. CAG:755) were associated with PPD. Metabolic markers that may represent the function of the intestinal microbiota in mice with PPD were identified (Met-Arg, urocanic acid, thioetheramide-PC, L-pipecolic acid, and linoleoyl ethanolamide). The relationship between these factors is not a simple one-to-one correspondence, but more likely a network of staggered functions. We therefore believe that the composition and function of the entire intestinal flora should be emphasized in research studying the gut and PPD, rather than changes in the abundance of individual bacterial species. The introduction of this concept of "GutBalance" may help clarify the relationship between gut bacteria and systemic disease.}, } @article {pmid34482441, year = {2021}, author = {Eijsackers, H and Maboeta, M}, title = {Do Endemic Soil Fauna Species Deserve Extra Protection for Adverse Heavy Metal Conditions?.}, journal = {Reviews of environmental contamination and toxicology}, volume = {258}, number = {}, pages = {55-71}, pmid = {34482441}, issn = {0179-5953}, mesh = {Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; Mining ; Soil ; *Soil Pollutants/analysis/toxicity ; }, abstract = {The concept of Ecotoxicological Species Sensitivity Distributions, as used in EU and US, to derive environmental standards for contaminants, starts from the assumption that by protecting the majority of species (95% confidence interval) all species will be protected. Nevertheless, 5% of the species outside the confidence interval might become harmed; half of it being the most sensitive for the particular compound tested. With respect to protection of rare endemic species it is not clear, however, if contamination is a driving factor for endemicity. The aim of this paper is to explore whether endemic and rare species deserve extra protection from adverse environmental conditions. To this end, a brief overview of the various forms of endemism, their relation to environmental stress factors and the distribution of endemic species is discussed. Further, the sensitivities of these species towards environmental stress factors are analysed, in order to conclude if and how endemic species could be better protected against environmental stress factors. This was achieved by specifically focusing on the potential impacts of metalliferous soils, mining, the treatment of mined soil and the storage of treated mine waste. It is concluded that at present there are some signals about specific sensitivities, but the database is much too small for a definite conclusion about adverse environmental factors as a threat to endemic species. The data gap has to be filled in with experimental tests with endemic species. This is hampered by the protection status of these endemic, rare species. Recommendations and derived activities are proposed to address this.}, } @article {pmid34481948, year = {2022}, author = {Sabbag, AF and Thomé, MTC and Lyra, ML and Brasileiro, CA and Moriarty Lemmon, E and Lemmon, A and Haddad, CFB}, title = {Sympatric and independently evolving lineages in the Thoropa miliaris - T. taophora species complex (Anura: Cycloramphidae).}, journal = {Molecular phylogenetics and evolution}, volume = {166}, number = {}, pages = {107220}, doi = {10.1016/j.ympev.2021.107220}, pmid = {34481948}, issn = {1095-9513}, mesh = {Animals ; *Anura ; Forests ; Phylogeny ; Ranidae ; *Sympatry ; }, abstract = {Species delimitation can be challenging and affected by subjectivity. Sibling lineages that occur in sympatry constitute good candidates for species delimitation regardless of the adopted species concept. The Thoropa miliaris + T. taophora species complex exhibits high genetic diversity distributed in several lineages that occur sympatrically in the southeastern Atlantic Forest of Brazil. We used 414 loci obtained by anchored hybrid enrichment to characterize genetic variation in the Thoropa miliaris species group (T. saxatilis, T megatympanum, T. miliaris, and T. taophora), combining assignment analyses with traditional and coalescent phylogeny reconstruction. We also investigated evolutionary independence in co-occurring lineages by estimating gene flow, and validated lineages under the multispecies coalescent. We recovered most previously described lineages as unique populations in assignment analyses; exceptions include two lineages within T. miliaris that are further substructured, and the merging of all T. taophora lineages. We found very low probabilities of gene flow between sympatric lineages, suggesting independent evolution. Species tree inferences and species delimitation yielded resolved relationships and indicate that all lineages constitute putative species that diverged during the Pliocene and Pleistocene, later than previously estimated.}, } @article {pmid34429913, year = {2021}, author = {van Valkenburg, JLCH and Costerus, M and Westenberg, M}, title = {Pennisetum setaceum or Pennisetum advena cultivars, what ornamental do we have in our garden.}, journal = {Ecology and evolution}, volume = {11}, number = {16}, pages = {11216-11222}, pmid = {34429913}, issn = {2045-7758}, abstract = {Pennisetum Rich. or following recent taxonomic insights Cenchrus L. is a genus with some 120 species worldwide, especially in warm areas. The genus includes some crops, some ornamentals but mostly species that are considered weedy. The name of one of the weedy species Pennisetum setaceum (Forssk.) Chiov. is also found on labels of ornamental grasses as P. setaceum "Rubrum." It has been debated to belong to a species on its own Pennisetum advena Wipff & Veldkamp or Cenchrus advena (Wipff & Veldkamp) Morrone, only known from cultivation, whereas others still adhere to a broader species concept of P. setaceum. The recent inclusion of P. setaceum on the EU List of Union concern has revitalized the discussion on this issue for commercial reasons. Based on a morphological and molecular comparison (ITS, rbcL, and the trnh-psbA intergenic spacer sequences) of the type specimen of P. advena, five of its "cultivars" in trade and collections of P. setaceum from different regions of the world we conclude that plants currently in trade in Western Europe belong to a separate species P. advena. A drooping inflorescence is consistent as is the difference in width of the leaf blade, the leaf blade being flat or involute, the central vein being swollen or not, and the length of the stipe being 0.3-1.1 mm in P. advena and 1.1-3.1 mm in P. setaceum. On the chloroplast markers rbcL and trnH-psbA, the species consistently differ in 2 and 4 base pairs, respectively. On the nuclear ITS sequence, there is only 90% overlap between the two species. This justifies these ornamentals to be excluded from the List of Union concern of EU regulation 1143/2014.}, } @article {pmid34420696, year = {2021}, author = {Kraisitudomsook, N and Healy, RA and Smith, ME}, title = {Molecular systematics and taxonomic overview of the bird's nest fungi (Nidulariaceae).}, journal = {Fungal biology}, volume = {125}, number = {9}, pages = {693-703}, doi = {10.1016/j.funbio.2021.04.003}, pmid = {34420696}, issn = {1878-6146}, mesh = {*Agaricales/classification/genetics ; Animals ; Birds ; *Cyathus ; DNA, Fungal/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {Fungi in the Nidulariaceae, otherwise known as 'bird's nest fungi', are among the least studied groups of Agaricomycetes (Basidiomycota). Bird's nest fungi are globally distributed and typically grow on woody debris or animal dung as saprotrophs. This group of fungi is morphologically diverse with ca. 200 described species. Phylogenetic relationships of bird's nest fungi were investigated with four commonly used loci (ITS, LSU, tef, and rpb2). The family was resolved as a monophyletic group with Squamanitaceae as a potential sister taxon. Cyathus and Crucibulum each formed its own independent and well-supported clade. Nidula and Nidularia formed a clade together, but each genus is polyphyletic. Two Mycocalia species included in our analyses were on their own separate branches, indicating that this genus is also polyphyletic. Misidentifications were detected in most genera, suggesting that species concepts need to be revisited and refined throughout Nidulariaceae. Several bird's nest fungi species have global geographical distributions whereas others may have more limited ranges. Basic morphological characters of bird's nest fungi have likely been lost or gained multiple times. The phylogenetic placement of Crucibulum is unclear and the sister lineage of bird's nest fungi is not conclusive. Further studies with data from rare species and additional informative genes are needed to fully resolve the topology of Nidulariaceae and identify its sister group with more certainty.}, } @article {pmid34393558, year = {2021}, author = {Pohjoismäki, J and Bergström, C}, title = {Review of the Nordic Gymnocheta Robineau-Desvoidy (Diptera, Tachinidae) with report of two species new to Europe.}, journal = {ZooKeys}, volume = {1053}, number = {}, pages = {145-184}, pmid = {34393558}, issn = {1313-2989}, abstract = {The genus Gymnocheta Robineau-Desvoidy, 1830 (Diptera, Tachinidae) has until now been represented by two species in Europe, G.viridis (Fallén, 1810) and G.magna Zimin, 1958. Two species are newly recorded from Finland and Sweden, Gymnochetalucida Zimin, 1958 and G.zhelochovtsevi Zimin, 1958, both previously known only from the Russian Far East and Japan. These four European species are redescribed and illustrated, including the first description of the female of G.zhelochovtsevi. A key is provided to seven of the eight described species of Palaearctic Gymnocheta. The holotype of G.viridis was examined and found to differ from the present concept of the species, instead matching the concept of the more recently described G.magna. In the interests of nomenclatural stability, the two names are maintained in their current usage pending a request to the International Commission on Zoological Nomenclature to replace the current holotype of G.viridis with a neotype that corresponds to the long-established concept of that species.}, } @article {pmid34370791, year = {2021}, author = {Schweininger, J and Scherer, M and Rothemund, F and Schilling, EM and Wörz, S and Stamminger, T and Muller, YA}, title = {Cytomegalovirus immediate-early 1 proteins form a structurally distinct protein class with adaptations determining cross-species barriers.}, journal = {PLoS pathogens}, volume = {17}, number = {8}, pages = {e1009863}, pmid = {34370791}, issn = {1553-7374}, mesh = {*Adaptation, Physiological ; Animals ; Cytomegalovirus/*physiology ; Cytomegalovirus Infections/metabolism/*virology ; Humans ; Immediate-Early Proteins/*chemistry/*metabolism ; Intranuclear Inclusion Bodies/*metabolism ; Primates ; Protein Folding ; Protein Structure, Tertiary ; Rats ; Species Specificity ; *Virus Replication ; }, abstract = {Restriction factors are potent antiviral proteins that constitute a first line of intracellular defense by blocking viral replication and spread. During co-evolution, however, viruses have developed antagonistic proteins to modulate or degrade the restriction factors of their host. To ensure the success of lytic replication, the herpesvirus human cytomegalovirus (HCMV) expresses the immediate-early protein IE1, which acts as an antagonist of antiviral, subnuclear structures termed PML nuclear bodies (PML-NBs). IE1 interacts directly with PML, the key protein of PML-NBs, through its core domain and disrupts the dot-like multiprotein complexes thereby abrogating the antiviral effects. Here we present the crystal structures of the human and rat cytomegalovirus core domain (IE1CORE). We found that IE1CORE domains, also including the previously characterized IE1CORE of rhesus CMV, form a distinct class of proteins that are characterized by a highly similar and unique tertiary fold and quaternary assembly. This contrasts to a marked amino acid sequence diversity suggesting that strong positive selection evolved a conserved fold, while immune selection pressure may have fostered sequence divergence of IE1. At the same time, we detected specific differences in the helix arrangements of primate versus rodent IE1CORE structures. Functional characterization revealed a conserved mechanism of PML-NB disruption, however, primate and rodent IE1 proteins were only effective in cells of the natural host species but not during cross-species infection. Remarkably, we observed that expression of HCMV IE1 allows rat cytomegalovirus replication in human cells. We conclude that cytomegaloviruses have evolved a distinct protein tertiary structure of IE1 to effectively bind and inactivate an important cellular restriction factor. Furthermore, our data show that the IE1 fold has been adapted to maximize the efficacy of PML targeting in a species-specific manner and support the concept that the PML-NBs-based intrinsic defense constitutes a barrier to cross-species transmission of HCMV.}, } @article {pmid34356731, year = {2021}, author = {Romanowski, EG and Gupta, S and Pericleous, A and Kadouri, DE and Shanks, RMQ}, title = {Clearance of Gram-Negative Bacterial Pathogens from the Ocular Surface by Predatory Bacteria.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {10}, number = {7}, pages = {}, pmid = {34356731}, issn = {2079-6382}, support = {P30 EY008098/EY/NEI NIH HHS/United States ; P30-EY08098/EY/NEI NIH HHS/United States ; }, abstract = {It was previously demonstrated that predatory bacteria are able to efficiently eliminate Gram-negative pathogens including antibiotic-resistant and biofilm-associated bacteria. In this proof-of-concept study we evaluated whether two species of predatory bacteria, Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus, were able to alter the survival of Gram-negative pathogens on the ocular surface. Clinical keratitis isolates of Pseudomonas aeruginosa (strain PAC) and Serratia marcescens (strain K904) were applied to the ocular surface of NZW rabbits followed by application of predatory bacteria. At time intervals, surviving pathogenic bacteria were enumerated. In addition, B. bacteriovorus and S. marcescens were applied to porcine organ culture corneas under contact lenses, and the ocular surface was examined by scanning electron microscopy. The ocular surface epithelial layer of porcine corneas exposed to S. marcescens, but not B. bacteriovorus was damaged. Using this model, neither pathogen could survive on the rabbit ocular surface for longer than 24 h. M. aeruginosavorus correlated with a more rapid clearance of P. aeruginosa but not S. marcescens from rabbit eyes. This study supports previous evidence that predatory bacteria are well tolerated by the cornea, but suggest that predatory bacteria do not considerably change the ability of the ocular surface to clear the tested Gram-negative bacterial pathogens from the ocular surface.}, } @article {pmid34349936, year = {2021}, author = {Sasano, Y and Tanaka, H and Haketa, Y and Kobayashi, Y and Ishibashi, Y and Morimoto, T and Sato, R and Shigeta, Y and Yasuda, N and Asahi, T and Maeda, H}, title = {Ion-pairing π-electronic systems: ordered arrangement and noncovalent interactions of negatively charged porphyrins.}, journal = {Chemical science}, volume = {12}, number = {28}, pages = {9645-9657}, pmid = {34349936}, issn = {2041-6520}, abstract = {In this study, charged π-electronic species are observed to develop stacking structures based on electrostatic and dispersion forces. [i] π- [i] π Interaction, defined herein, functions for the stacking structures consisting of charged π-electronic species and is in contrast to conventional π-π interaction, which mainly exhibits dispersion force, for electronically neutral π-electronic species. Establishing the concept of [i] π- [i] π interaction requires the evaluation of interionic interactions for π-electronic ion pairs. Free base (metal-free) and diamagnetic metal complexes of 5-hydroxy-10,15,20-tris(pentafluorophenyl)porphyrin were synthesized, producing π-electronic anions upon the deprotonation of the hydroxy unit. Coexisting cations in the ion pairs with porphyrin anions were introduced as the counter species of the hydroxy anion as a base for commercially available cations and as ion-exchanged species, via Na[+] in the intermediate ion pairs, for synthesized π-electronic cations. Solid-state ion-pairing assemblies were constructed for the porphyrin anions in combination with aliphatic tetrabutylammonium (TBA[+]) and π-electronic 4,8,12-tripropyl-4,8,12-triazatriangulenium (TATA[+]) cations. The ordered arrangements of charged species, with the contributions of the charge-by-charge and charge-segregated modes, were observed according to the constituent charged building units. The energy decomposition analysis (EDA) of single-crystal packing structures revealed that electrostatic and dispersion forces are important factors in stabilizing the stacking of π-electronic ions. Furthermore, crystal-state absorption spectra of the ion pairs were correlated with the assembling modes. Transient absorption spectroscopy of the single crystals revealed the occurrence of photoinduced electron transfer from the π-electronic anion in the charge-segregated mode.}, } @article {pmid34327789, year = {2022}, author = {Singavarapu, B and Beugnon, R and Bruelheide, H and Cesarz, S and Du, J and Eisenhauer, N and Guo, LD and Nawaz, A and Wang, Y and Xue, K and Wubet, T}, title = {Tree mycorrhizal type and tree diversity shape the forest soil microbiota.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {4236-4255}, doi = {10.1111/1462-2920.15690}, pmid = {34327789}, issn = {1462-2920}, mesh = {Bacteria/genetics ; Forests ; *Microbiota ; *Mycorrhizae ; Plants ; Soil ; Soil Microbiology ; Trees/microbiology ; }, abstract = {There is limited knowledge on how the association of trees with different mycorrhizal types shapes soil microbial communities in the context of changing tree diversity levels. We used arbuscular (AM) and ectomycorrhizal (EcM) tree species as con- and heterospecific tree species pairs (TSPs), which were established in plots of three tree diversity levels including monocultures, two-species mixtures and multi-tree species mixtures in a tree diversity experiment in subtropical China. We found that the tree mycorrhizal type had a significant effect on fungal but not bacterial alpha diversity. Furthermore, only EcM but not AM TSPs fungal alpha diversity increased with tree diversity, and the differences between AM and EcM TSPs disappeared in multi-species mixtures. Tree mycorrhizal type, tree diversity and their interaction had significant effects on fungal community composition. Neither fungi nor bacteria showed any significant compositional variation in TSPs located in multi-species mixtures. Accordingly, the most influential taxa driving the tree mycorrhizal differences at low tree diversity were not significant in multi-tree species mixtures. Collectively, our results indicate that tree mycorrhizal type is an important factor determining the diversity and community composition of soil microbes, and higher tree diversity levels promote convergence of the soil microbial communities. SIGNIFICANCE STATEMENT: More than 90% of terrestrial plants have symbiotic associations with mycorrhizal fungi which could influence the coexisting microbiota. Systematic understanding of the individual and interactive effects of tree mycorrhizal type and tree species diversity on the soil microbiota is crucial for the mechanistic comprehension of the role of microbes in forest soil ecological processes. Our tree species pair (TSP) concept coupled with random sampling within and across the plots, allowed us the unbiased assessment of tree mycorrhizal type and tree diversity effects on the tree-tree interaction zone soil microbiota. Unlike in monocultures and two-species mixtures, we identified species-rich and converging fungal and bacterial communities in multi-tree species mixtures. Consequently, we recommend planting species-rich mixtures of EcM and AM trees, for afforestation and reforestation regimes. Specifically, our findings highlight the significance of tree mycorrhizal type in studying 'tree diversity - microbial diversity - ecosystem function' relationships.}, } @article {pmid34313108, year = {2021}, author = {Liu, JL and Zhang, JQ and Zhou, Y and Xiao, DR and Zhuo, Y and Chai, YQ and Yuan, R}, title = {Crystallization-Induced Enhanced Electrochemiluminescence from Tetraphenyl Alkene Nanocrystals for Ultrasensitive Sensing.}, journal = {Analytical chemistry}, volume = {93}, number = {31}, pages = {10890-10897}, doi = {10.1021/acs.analchem.1c01258}, pmid = {34313108}, issn = {1520-6882}, mesh = {Alkenes ; *Biosensing Techniques ; Crystallization ; Electrochemical Techniques ; Luminescent Measurements ; *Nanoparticles ; }, abstract = {Organic materials with diverse structures and brilliant glowing colors have been attracting extensive attention in optical electronic devices and electrochemiluminescence (ECL) fields and are currently faced with the issue of low ECL efficiency. Herein, a series of tetraphenyl alkene nanocrystals (TPA NCs) with an ordered molecular structure were synthesized to explore regularities in the crystallization-induced enhanced (CIE) ECL emission effects by altering the number and position of vinyl on the backbone of TPA molecules. Among those TPA NCs, tetraphenyl-1,3-butadiene (TPB) NCs exhibit the brightest ECL emission via a coreactant pathway, with the relative ECL efficiency of up to 31.53% versus the standard [Ru(bpy)3][2+]/TEA system, which is thousands of times higher than that of free TPB molecules. The high ECL efficiency of TPB NCs originates from the effective electron transfer of unique J-aggregates on the a axis of the nanocrystals to notably promote radiative transition and the restriction on the free rotation of TPB molecules to further suppress the nonradiative transition, which has exhibited great potential in ultrasensitive biosensing, efficient light-emitting devices, and clear ECL imaging fields. As a proof of concept, since dopamine (DA) can form benzoquinone species by electrochemical oxidation to realize intermediate radical quenching and excited-state quenching on the TPB NCs/TEA system, the TPB NCs with the CIE ECL effect are used to construct an ultrasensitive ECL-sensing platform for the determination of DA with a lower detection limit of 3.1 nM.}, } @article {pmid34267608, year = {2021}, author = {Lushchak, VI and Storey, KB}, title = {Oxidative stress concept updated: Definitions, classifications, and regulatory pathways implicated.}, journal = {EXCLI journal}, volume = {20}, number = {}, pages = {956-967}, pmid = {34267608}, issn = {1611-2156}, abstract = {Reactive oxygen species were discovered in living organisms in the early 1950's and their action has been implicated in diverse biological processes. First formulated by H. Sies in 1985[57], the oxidative stress concept stimulated substantial interest in reactive oxygen species and it is now common that fundamental research in various biomedical fields includes mention of research on the involvement of oxidative stress. Such strong interest has resulted in the development of definitions and classifications of oxidative stress and much research progress in the field. Although we clearly understand the limitations of various definitions or classifications, such parameters may help to provide quantitative descriptions, compare related processes among different laboratories, and introduce some measurable parameters. This paper highlights recent advances in the areas of oxidative stress definitions and the classification of oxidative stresses. Such items are directly associated with our understanding of the molecular mechanisms involved in organismal responses to oxidative insults. The knowledge accumulated to date indicates that selective expression of specific genes is a central player in the adaptive response to oxidative stress and reversible oxidation of cysteine residues of sensor proteins is a key process regulating responses to oxidative stress.}, } @article {pmid34255862, year = {2022}, author = {Wang, R and Shu, P and Zhang, C and Zhang, J and Chen, Y and Zhang, Y and Du, K and Xie, Y and Li, M and Ma, T and Zhang, Y and Li, Z and Grierson, D and Pirrello, J and Chen, K and Bouzayen, M and Zhang, B and Liu, M}, title = {Integrative analyses of metabolome and genome-wide transcriptome reveal the regulatory network governing flavor formation in kiwifruit (Actinidia chinensis).}, journal = {The New phytologist}, volume = {233}, number = {1}, pages = {373-389}, doi = {10.1111/nph.17618}, pmid = {34255862}, issn = {1469-8137}, mesh = {*Actinidia/genetics/metabolism ; Fruit/genetics/metabolism ; Gene Expression Regulation, Plant ; Metabolome ; Plant Proteins/metabolism ; Transcriptome/genetics ; }, abstract = {Soluble sugars, organic acids and volatiles are important components that determine unique fruit flavor and consumer preferences. However, the metabolic dynamics and underlying regulatory networks that modulate overall flavor formation during fruit development and ripening remain largely unknown for most fruit species. In this study, by integrating flavor-associated metabolism and transcriptome data from 12 fruit developmental and ripening stages of Actinidia chinensis cv Hongyang, we generated a global map of changes in the flavor-related metabolites throughout development and ripening of kiwifruit. Using this dataset, we constructed complex regulatory networks allowing to identify key structural genes and transcription factors that regulate the metabolism of soluble sugars, organic acids and important volatiles in kiwifruit. Moreover, our study revealed the regulatory mechanism involving key transcription factors regulating flavor metabolism. The modulation of flavor metabolism by the identified key transcription factors was confirmed in different kiwifruit species providing the proof of concept that our dataset provides a suitable tool for clarification of the regulatory factors controlling flavor biosynthetic pathways that have not been previously illuminated. Overall, in addition to providing new insight into the metabolic regulation of flavor during fruit development and ripening, the outcome of our study establishes a foundation for flavor improvement in kiwifruit.}, } @article {pmid34254441, year = {2021}, author = {Liu, X and Ye, S and Lan, G and Su, P and Zhang, X and Price, CAH and Li, Y and Liu, J}, title = {Atomic Pyridinic Nitrogen Sites Promoting Levulinic Acid Hydrogenations over Double-Shelled Hollow Ru/C Nanoreactors.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {17}, number = {33}, pages = {e2101271}, doi = {10.1002/smll.202101271}, pmid = {34254441}, issn = {1613-6829}, mesh = {Hydrogenation ; *Levulinic Acids ; Nanotechnology ; *Nitrogen ; }, abstract = {Nitrogen-doped nanocarbons are widely used as supports for metal-heterogeneous catalytic conversions. When nitrogen-doped nanocarbon supports are used to disperse metallic nanoparticles (MNPs), the nitrogen dopant can enhance MNPs electron density to reach higher catalytic activity and promote MNPs stability through anchoring effects. However, the precise identification of active nitrogen species between N-dopants and reactants is rarely reported. Herein, a proof-of-concept study on the active N species for levulinic acid hydrogenation is reported. A double-shell structured carbon catalyst (DSC) is designed with selectively locating ultrafine Ru NPs only on inner carbon shell, specifically, different N species on the external carbon shell. Through the design of such a nanostructure, it is demonstrated that the alkaline pyridinic N species on the outer shell serves as an anchor point for the spontaneous binding of the acidic reactant. The pyridinic N content can be modulated from 7.4 to 29.2 mg gcat[-1] by selecting different precursors. Finally, the Ru-DSC-CTS (using chitosan as the precursor) catalyst achieves a 99% conversion of levulinic acid under 70 °C and 4 MPa hydrogen pressure for 1 h. This work sheds light on the design of nanoreactors at the atomic scale and investigates heterogeneous catalysis at the molecular level.}, } @article {pmid34215287, year = {2021}, author = {Ravazi, A and de Oliveira, J and Campos, FF and Madeira, FF and Dos Reis, YV and de Oliveira, ABB and de Azeredo-Oliveira, MTV and da Rosa, JA and Galvão, C and Alevi, KCC}, title = {Trends in evolution of the Rhodniini tribe (Hemiptera, Triatominae): experimental crosses between Psammolestes tertius Lent & Jurberg, 1965 and P. coreodes Bergroth, 1911 and analysis of the reproductive isolating mechanisms.}, journal = {Parasites & vectors}, volume = {14}, number = {1}, pages = {350}, pmid = {34215287}, issn = {1756-3305}, mesh = {Animals ; Cytogenetic Analysis ; *Evolution, Molecular ; Female ; Male ; Reproduction ; Triatominae/*genetics/*physiology ; }, abstract = {BACKGROUND: The tribe Rhodniini is a monophyletic group composed of 24 species grouped into two genera: Rhodnius and Psammolestes. The genus Psammolestes includes only three species, namely P. coreodes, P. tertius and P. arthuri. Natural hybridization events have been reported for the Rhodniini tribe (for genus Rhodnius specifically). Information obtained from hybridization studies can improve our understanding of the taxonomy and systematics of species. Here we report the results from experimental crosses performed between P. tertius and P. coreodes and from subsequent analyses of the reproductive and morphological aspects of the hybrids.

METHODS: Crossing experiments were conducted between P. tertius and P. coreodes to evaluate the pre- and post-zygotic barriers between species of the Rhodniini tribe. We also performed cytogenetic analyses of the F1 hybrids, with a focus on the degree of pairing between the homeologous chromosomes, and morphology studies of the male gonads to evaluate the presence of gonadal dysgenesis. Lastly, we analyzed the segregation of phenotypic characteristics.

RESULTS: Interspecific experimental crosses demonstrated intrageneric genomic compatibility since hybrids were produced in both directions. However, these hybrids showed a high mortality rate, suggesting a post-zygotic barrier resulting in hybrid unviability. The F1 hybrids that reached adulthood presented the dominant phenotypic segregation pattern for P. tertius in both directions. These insects were then intercrossed; the hybrids were used in the cross between P. tertius ♀ × P. coreodes ♂ died before oviposition, and the F1 hybrids of P. coreodes ♀ x P. tertius ♂ oviposited and their F2 hybrids hatched (however, all specimens died after hatching, still in first-generation nymph stage, pointing to a hybrid collapse event). Morphological analyses of male gonads from F1 hybrids showed that they did not have gonadal dysgenesis. Cytogenetic analyses of these triatomines showed that there were metaphases with 100% pairing between homeologous chromosomes and metaphases with pairing errors.

CONCLUSION: The results of this study demonstrate that Psammolestes spp. have intrageneric genomic compatibility and that post-zygotic barriers, namely unviability of hybrid and hybrid collapse, resulted in the breakdown of the hybrids of P. tertius and P. coreodes, confirming the specific status of species based on the biological concept of species.}, } @article {pmid34214001, year = {2021}, author = {Wang, J and Shao, S and Liu, C and Song, Z and Liu, S and Wu, S}, title = {The genus Paraconiothyrium: species concepts, biological functions, and secondary metabolites.}, journal = {Critical reviews in microbiology}, volume = {47}, number = {6}, pages = {781-810}, doi = {10.1080/1040841X.2021.1933898}, pmid = {34214001}, issn = {1549-7828}, mesh = {*Ascomycota ; *Biological Products ; Ecosystem ; Phylogeny ; }, abstract = {The genus Paraconiothyrium has worldwide distribution with diverse host habitats and exhibits potential utilisation as biocontrol agent, bioreactor and antibiotic producer. In this review, we firstly comprehensively summarise the current taxonomic status of Paraconiothyrium species, including their category names, morphological features, habitats, and multigene phylogenetic relationships. Some Paraconiothyrium species possess vital biological functions and potential applications in medicine, agriculture, industry, and environmental protection. A total of 147 secondary metabolites have been reported so far from Paraconiothyrium, among which 95 are novel. This paper serves to provide an overview of their diverse structures with chemical classification and biological activities. To date, 27 species of Paraconiothyrium have been documented; however, only seven have been investigated for their secondary metabolites or biological functions. Our review is expected to draw more attention to this genus for providing a taxonomic reference, discovering extensive biological functions, and searching in-depth for new bioactive natural products.}, } @article {pmid34208261, year = {2021}, author = {Wolf, M}, title = {How to Teach about What Is a Species.}, journal = {Biology}, volume = {10}, number = {6}, pages = {}, pmid = {34208261}, issn = {2079-7737}, abstract = {To ask students what a species is always has something rhetorical about it. Too quickly comes the rote answer, often learned by heart without ever thinking about it: "A species is a reproductive community of populations (reproductively isolated from others), which occupies a specific niche in nature" (Mayr 1982). However, do two people look alike because they are twins or are they twins because they look alike? "Two organisms do not belong to the same species because they mate and reproduce, but they only are able to do so because they belong to the same species" (Mahner and Bunge 1997). Unfortunately, most biology (pre-university) teachers have no opinion on whether species are real or conceptual, simply because they have never been taught the question themselves, but rather one answer they still pass on to their students today, learned by heart without ever thinking about it. Species are either real or conceptual and, in my opinion, it is this "or" that we should teach about. Only then can we discuss those fundamental questions such as who or what is selected, who or what evolves and, finally, what is biodiversity and phylogenetics all about? Individuals related to each other by the tree of life.}, } @article {pmid34197900, year = {2021}, author = {Pfingstl, T and Lienhard, A and Baumann, J and Koblmüller, S}, title = {A taxonomist's nightmare - Cryptic diversity in Caribbean intertidal arthropods (Arachnida, Acari, Oribatida).}, journal = {Molecular phylogenetics and evolution}, volume = {163}, number = {}, pages = {107240}, doi = {10.1016/j.ympev.2021.107240}, pmid = {34197900}, issn = {1095-9513}, mesh = {Animals ; *Arachnida ; Caribbean Region ; Dreams ; Humans ; *Mites ; Phylogeny ; }, abstract = {There has been a long controversy about what defines a species and how to delimitate them which resulted in the existence of more than two dozen different species concepts. Recent research on so-called "cryptic species" heated up this debate as some scientists argue that these cryptic species are only a result of incompatible species concepts. While this may be true, we should keep in mind that all concepts are nothing more than human constructs and that the phenomenon of high phenotypic similarity despite reproductive isolation is real. To investigate and understand this phenomenon it is important to classify and name cryptic species as it allows to communicate them with other fields of science that use Linnaean binomials. To provide a common framework for the description of cryptic species, we propose a possible protocol of how to formally name and describe these taxa in practice. The most important point of this protocol is to explain which species concept was used to delimitate the cryptic taxon. As a model, we present the case of the allegedly widespread Caribbean intertidal mite Thalassozetes barbara, which in fact consists of seven phenotypically very similar but genetically distinct species. All species are island or short-range endemics with poor dispersal abilities that have evolved in geographic isolation. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the morphological stasis of this cryptic species complex.}, } @article {pmid34197484, year = {2021}, author = {Tovo, A and Stivanello, S and Maritan, A and Suweis, S and Favaro, S and Formentin, M}, title = {Upscaling human activity data: A statistical ecology approach.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0253461}, pmid = {34197484}, issn = {1932-6203}, mesh = {*Big Data ; Computer Communication Networks/*statistics & numerical data ; *Datasets as Topic ; Electronic Mail/*statistics & numerical data ; Humans ; Social Media/*statistics & numerical data ; }, abstract = {Big data require new techniques to handle the information they come with. Here we consider four datasets (email communication, Twitter posts, Wikipedia articles and Gutenberg books) and propose a novel statistical framework to predict global statistics from random samples. More precisely, we infer the number of senders, hashtags and words of the whole dataset and how their abundances (i.e. the popularity of a hashtag) change through scales from a small sample of sent emails per sender, posts per hashtag and word occurrences. Our approach is grounded on statistical ecology as we map inference of human activities into the unseen species problem in biodiversity. Our findings may have applications to resource management in emails, collective attention monitoring in Twitter and language learning process in word databases.}, } @article {pmid34188827, year = {2021}, author = {Zhang, T and Domke, GM and Russell, MB and Lichstein, JW}, title = {An index for measuring functional extension and evenness in trait space.}, journal = {Ecology and evolution}, volume = {11}, number = {12}, pages = {7461-7473}, pmid = {34188827}, issn = {2045-7758}, abstract = {Most existing functional diversity indices focus on a single facet of functional diversity. Although these indices are useful for quantifying specific aspects of functional diversity, they often present some conceptual or practical limitations in estimating functional diversity. Here, we present a new functional extension and evenness (FEE) index that encompasses two important aspects of functional diversity. This new index is based on the straightforward notion that a community has high diversity when its species are distant from each other in trait space. The index quantifies functional diversity by evaluating the overall extension of species traits and the interspecific differences of a species assemblage in trait space. The concept of minimum spanning tree (MST) of points was adopted to obtain the essential distribution properties for a species assembly in trait space. We combined the total length of MST branches (extension) and the variation of branch lengths (evenness) into a raw FEE0 metric and then translated FEE0 to a species richness-independent FEE index using a null model approach. We assessed the properties of FEE and used multiple approaches to evaluate its performance. The results show that the FEE index performs well in quantifying functional diversity and presents the following desired properties: (a) It allows a fair comparison of functional diversity across different species richness levels; (b) it preserves the essence of single-facet indices while overcoming some of their limitations; (c) it standardizes comparisons among communities by taking into consideration the trait space of the shared species pool; and (d) it has the potential to distinguish among different community assembly processes. With these attributes, we suggest that the FEE index is a promising metric to inform biodiversity conservation policy and management, especially in applications at large spatial and/or temporal scales.}, } @article {pmid34186980, year = {2021}, author = {Madi-Ravazzi, L and Segala, LF and Roman, BE and Alevi, KCC and Prediger, C and Yassin, A and Hua-VAN, AL and Miller, WJ}, title = {Integrative taxonomy and a new species description in the sturtevanti subgroup of the Drosophila saltans group (Diptera: Drosophilidae).}, journal = {Zootaxa}, volume = {4980}, number = {2}, pages = {269292}, doi = {10.11646/zootaxa.4980.2.3}, pmid = {34186980}, issn = {1175-5334}, mesh = {Animals ; Drosophila/*anatomy & histology/*classification ; Female ; French Guiana ; Genes, Mitochondrial ; Phylogeny ; }, abstract = {Although the biological concept of species is well established in animals, sometimes the decision about the specific status of a new species is difficult and hence requires support of an integrative analysis of several character sets. To date, the species Drosophila sturtevanti, D. magalhaesi, D. milleri and D. dacunhai, belonging to the sturtevanti subgroup of the Neotropical saltans species group, are identified mainly by the aedeagus morphology, but also present some differences in spot coloration and patterning of the female sixth tergite and in the shape and size of the spermathecae, parallel to a pattern of reproductive isolation. In the present study, we describe a novel saltans group species from French Guiana belonging to the sturtevanti subgroup. Our species designation is based on an integrative approach covering (i) aedeagi and spermathecae morphology by scanning electron microscopy, (ii) analysis of female sixth-tergite color, (iii) morphometrical analysis of aedeagi and wings, (iv) analysis of partial sequence of the COI, COII and ND4 mitochondrial genes as well as (v) intercrosses for analysis of reproductive isolation. The comparative analysis of the results on these markers with those of D. sturtevanti, D. milleri and D. dacunhai supports that this line belongs to a new species of the sturtevanti subgroup that we name Drosophila lehrmanae sp. nov. in honor of Prof. Lee Ehrman´s 85th birthday.}, } @article {pmid34186915, year = {2021}, author = {Chen, Z and Yang, X and Menzel, F and Wu, H and Huang, J}, title = {Three Oriental species of Pseudoaerumnosa Rudzinski (Diptera, Sciaridae) <br />from China.}, journal = {Zootaxa}, volume = {4969}, number = {3}, pages = {551562}, doi = {10.11646/zootaxa.4969.3.7}, pmid = {34186915}, issn = {1175-5334}, mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; Nematocera/*classification ; Phylogeny ; }, abstract = {Three Oriental species of the genus Pseudoaerumnosa Rudzinski, 2006 from China are described and illustrated: P. regularis sp. n., P. tianmushana sp. n. and P. tkoci Vilkamaa, Halenius Ševčík, 2019. The morphological species concepts were supported by the DNA barcodes of COI sequences. The genetic distances of Pseudoaerumnosa species were analyzed and a neighbor-joining tree was constructed, based on 37 sequences of nine species.}, } @article {pmid34186817, year = {2021}, author = {Joharchi, O and Friedrich, S}, title = {Two new species of Gaeolaelaps Evans amp; Till (Acari: Laelapidae) from the Andes Mountains, Peru.}, journal = {Zootaxa}, volume = {4995}, number = {1}, pages = {56-70}, doi = {10.11646/zootaxa.4995.1.3}, pmid = {34186817}, issn = {1175-5334}, mesh = {Altitude ; Animals ; Mites/*classification ; Peru ; Soil ; }, abstract = {Two new species of mites in the genus Gaeolaelaps (Laelapidae) are described from specimens collected from soil-litter in the Peruvian Andes G. acanthopedus sp. nov. and G. andensis sp. nov.. Both species are consistent with the current concept of the genus Gaeolaelaps Evans Till. The genus Gaeolaelaps is reported for the first time from Peru.}, } @article {pmid34186736, year = {2021}, author = {Karar, YFM and Blend, CK and Dronen, NO and Adel, A}, title = {Towards resolving the problematic status of the digenean genus Astiotrema Looss, 1900: An updated concept and revision of species composition for Astiotrema (sensu stricto).}, journal = {Zootaxa}, volume = {4991}, number = {1}, pages = {36-72}, doi = {10.11646/zootaxa.4991.1.2}, pmid = {34186736}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; *Fishes/parasitology ; Host Specificity ; Species Specificity ; *Trematoda/anatomy & histology/classification/physiology ; }, abstract = {Species of Astiotrema Looss, 1900 (sensu lato) infect a wide range of fishes, amphibians and reptilians. They also possess a considerably wide spectrum of morphological features. Several species were recognized for variable, confusing, overlapping and unspecialized morphological characters rather than for unique distinguishing features, causing continuing dispute around the validity of several species. Following comprehensive review, a revised restricted concept of Astiotrema is proposed including a morphologically strict definition. Both Tremiorchis Mehra Negi, 1926 and Astioglossimetra Bilqees, Khatoon Khan, 2002 are synonymized with Astiotrema (sensu stricto). Several nominal species are synonymized, others are excluded and characters for each recognized species are presented and explained. Only eight species are recognized: Astiotrema cyclemysi Siddiqi, 1965, Astiotrema emydis Ejsmont, 1930, Astiotrema fotedari Dhar, 1977, Astiotrema impletum (Looss, 1899) Looss, 1900, Astiotrema karachiensis (Bilqees, Khatoon Khan, 2002) n. comb., Astiotrema odhneri Bhalerao, 1936, Astiotrema ranarum (Mehra Negi, 1926) Fotedar, 1971 and Astiotrema reniferum (Looss, 1898) Looss, 1900. A key to the species of Astiotrema (sensu stricto) is presented, a comprehensive list of all host-locality records is included and host-parasite specificity is elucidated.}, } @article {pmid34186610, year = {2021}, author = {Carmo-Neto, AMD and Lamas, CJE and Urso-Guimarães, MV}, title = {Review of Insulestremia Jaschhof, 2004 (Diptera; Cecidomyiidae; Lestremiinae) with description of two new species from Brazil.}, journal = {Zootaxa}, volume = {4966}, number = {3}, pages = {367375}, doi = {10.11646/zootaxa.4966.3.8}, pmid = {34186610}, issn = {1175-5334}, mesh = {Animals ; Brazil ; Diptera/*classification ; }, abstract = {This study presents the first records of the subfamily Lestremiinae and the genus Insulestremia Jaschhof in Brazil. Insulestremia, a previously monotypic genus described from the Galapagos Islands, has three species in Brazil: I. sinclairi Jaschhof, I. amorimi sp. nov. and I. amenti sp. nov. The new species are described, the generic concept is reviewed, and a key to the species of Insulestremia is provided.}, } @article {pmid34168629, year = {2021}, author = {Kubiak, AM and Bailey, TS and Dubois, LJ and Theys, J and Lambin, P}, title = {Efficient Secretion of Murine IL-2 From an Attenuated Strain of Clostridium sporogenes, a Novel Delivery Vehicle for Cancer Immunotherapy.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {669488}, pmid = {34168629}, issn = {1664-302X}, abstract = {Despite a history dating back to the 1800s, using Clostridium bacteria to treat cancer has not advanced beyond the observation that they can colonise and partially destroy solid tumours. Progress has been hampered by their inability to eradicate the viable portion of tumours, and an instinctive anxiety around injecting patients with a bacterium whose close relatives cause tetanus and botulism. However, recent advances in techniques to genetically engineer Clostridium species gives cause to revisit this concept. This paper illustrates these developments through the attenuation of C. sporogenes to enhance its clinical safety, and through the expression and secretion of an immunotherapeutic. An 8.6 kb sequence, corresponding to a haemolysin operon, was deleted from the genome and replaced with a short non-coding sequence. The resultant phenotype of this strain, named C. sporogenes-NT, showed a reduction of haemolysis to levels similar to the probiotic strain, C. butyricum M588. Comparison to the parental strain showed no change in growth or sporulation. Following injection of tumour-bearing mice with purified spores of the attenuated strain, high levels of germination were detected in all tumours. Very low levels of spores and vegetative cells were detected in the spleen and lymph nodes. The new strain was transformed with four different murine IL-2-expressing plasmids, differentiated by promoter and signal peptide sequences. Biologically active mIL-2, recovered from the extracellular fraction of bacterial cultures, was shown to stimulate proliferation of T cells. With this investigation we propose a new, safer candidate for intratumoral delivery of cancer immunotherapeutics.}, } @article {pmid34163294, year = {2021}, author = {Moser, V and Baur, H and Lehmann, AW and Lehmann, GUC}, title = {Two species? - Limits of the species concepts in the pygmy grasshoppers of the Tetrix bipunctata complex (Orthoptera, Tetrigidae).}, journal = {ZooKeys}, volume = {1043}, number = {}, pages = {33-59}, pmid = {34163294}, issn = {1313-2989}, abstract = {Today, integrative taxonomy is often considered the gold standard when it comes to species recognition and delimitation. Using the Tetrix bipunctata complex, we here present a case where even integrative taxonomy may reach its limits. The Tetrix bipunctata complex consists of two morphs, bipunctata and kraussi, which are easily distinguished by a single character, the length of the hind wing. Both morphs are widely distributed in Europe and reported to occur over a large area in sympatry, where they occasionally may live also in syntopy. The pattern has led to disparate classifications, as on the one extreme, the morphs were treated merely as forms or subspecies of a single species, on the other, as separate species. For this paper, we re-visited the morphology by using multivariate ratio analysis (MRA) of 17 distance measurements, checked the distributional data based on verified specimens and examined micro-habitat use. We were able to confirm that hind wing length is, indeed, the only morphological difference between bipunctata and kraussi. We were also able to exclude a mere allometric scaling. The morphs are, furthermore, largely sympatrically distributed, with syntopy occurring regularly. However, a microhabitat niche difference can be observed. Ecological measurements in a shared habitat confirm that kraussi prefers a drier and hotter microhabitat, which possibly also explains the generally lower altitudinal distribution. Based on these results, we can exclude classification as subspecies, but the taxonomic classification as species remains unclear. Even with different approaches to classify the Tetrix bipunctata complex, this case is, therefore, not settled. We recommend continuing to record kraussi and bipunctata separately.}, } @article {pmid34159593, year = {2021}, author = {Ng, CK and Tan, J}, title = {Cryptic species and grey zone speciation of the Barbodes binotatus complex (Teleostei, Cyprinidae) in Sundaland.}, journal = {Journal of fish biology}, volume = {99}, number = {4}, pages = {1256-1273}, doi = {10.1111/jfb.14829}, pmid = {34159593}, issn = {1095-8649}, mesh = {Animals ; *Cyprinidae/genetics ; Cytochromes b/genetics ; Fresh Water ; *Genetic Speciation ; Indonesia ; Phylogeny ; }, abstract = {Morphology-based taxonomy of freshwater fish is effective when there are representative specimens covering large regions. However, in Sundaland, where the presence of cryptic species is high, the technique has its limitations. This is compounded by uncritical descriptions of holotypes in old literature. We demonstrate the problem using Barbodes binotatus first described from an ink drawing. Several species in the Barbodes genus of Sundaland exhibit morphological similarity to B. binotatus. We applied new DNA sequences of 16S, cytochrome c oxidase subunit I (COI), cytochrome b (Cytb) and recombination-activating gene 1 (RAG1), and pigmentation markers to clarify species complex boundaries in the Malay Peninsula, namely B. aff. binotatus "Malay Peninsula", Barbodes cf. banksi and Barbodes rhombeus. Results suggest B. binotatus-like specimens in the Malay Peninsula are B. rhombeus based on a threshold of 3% COI genetic divergence. B. aff. binotatus recorded in Sumatra, Borneo and the Philippines are likely valid but undescribed species. However, if the 2% COI threshold is applied, some populations in the northern Malay Peninsula would qualify as new and undescribed species. The implications of the 2% threshold and the likelihood of "grey zone" incipient populations are discussed. We further found a rapid visual method, not reported previously, to delineate B. aff. binotatus and B. cf. banksi, but it requires further validation. Additionally, we offer fresh perspectives by discussing the roles of biological species concept, morphological species concept, genetic species concept and mate recognition concept in the B. binotatus complex. Our findings reinforce the standpoint that species delineation is not entirely a binary process, but there is a spectrum to consider, especially in biogeography intersection regions.}, } @article {pmid34149739, year = {2021}, author = {Dumas, A and Knaus, UG}, title = {Raising the 'Good' Oxidants for Immune Protection.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {698042}, pmid = {34149739}, issn = {1664-3224}, mesh = {Animals ; Humans ; Immune System Phenomena/*physiology ; Oxidants/*immunology/metabolism ; Oxidation-Reduction ; Reactive Oxygen Species/*immunology/metabolism ; }, abstract = {Redox medicine is a new therapeutic concept targeting reactive oxygen species (ROS) and secondary reaction products for health benefit. The concomitant function of ROS as intracellular second messengers and extracellular mediators governing physiological redox signaling, and as damaging radicals instigating or perpetuating various pathophysiological conditions will require selective strategies for therapeutic intervention. In addition, the reactivity and quantity of the oxidant species generated, its source and cellular location in a defined disease context need to be considered to achieve the desired outcome. In inflammatory diseases associated with oxidative damage and tissue injury, ROS source specific inhibitors may provide more benefit than generalized removal of ROS. Contemporary approaches in immunity will also include the preservation or even elevation of certain oxygen metabolites to restore or improve ROS driven physiological functions including more effective redox signaling and cell-microenvironment communication, and to induce mucosal barrier integrity, eubiosis and repair processes. Increasing oxidants by host-directed immunomodulation or by exogenous supplementation seems especially promising for improving host defense. Here, we summarize examples of beneficial ROS in immune homeostasis, infection, and acute inflammatory disease, and address emerging therapeutic strategies for ROS augmentation to induce and strengthen protective host immunity.}, } @article {pmid34117667, year = {2021}, author = {Ximendes, E and Marin, R and Shen, Y and Ruiz, D and Gómez-Cerezo, D and Rodríguez-Sevilla, P and Lifante, J and Viveros-Méndez, PX and Gámez, F and García-Soriano, D and Salas, G and Zalbidea, C and Espinosa, A and Benayas, A and García-Carrillo, N and Cussó, L and Desco, M and Teran, FJ and Juárez, BH and Jaque, D}, title = {Infrared-Emitting Multimodal Nanostructures for Controlled In Vivo Magnetic Hyperthermia.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {33}, number = {30}, pages = {e2100077}, doi = {10.1002/adma.202100077}, pmid = {34117667}, issn = {1521-4095}, mesh = {Animals ; Cell Line, Tumor ; Contrast Media/*chemistry ; Fluorescent Dyes/chemistry ; Hot Temperature ; Humans ; Hyperthermia, Induced ; Infrared Rays ; Magnetic Fields ; Magnetic Iron Oxide Nanoparticles/*chemistry ; Magnetics ; Mice ; Nanocapsules/*chemistry ; Optical Imaging ; Photothermal Therapy ; Silver Compounds/chemistry ; }, abstract = {Deliberate and local increase of the temperature within solid tumors represents an effective therapeutic approach. Thermal therapies embrace this concept leveraging the capability of some species to convert the absorbed energy into heat. To that end, magnetic hyperthermia (MHT) uses magnetic nanoparticles (MNPs) that can effectively dissipate the energy absorbed under alternating magnetic fields. However, MNPs fail to provide real-time thermal feedback with the risk of unwanted overheating and impeding on-the-fly adjustment of the therapeutic parameters. Localization of MNPs within a tissue in an accurate, rapid, and cost-effective way represents another challenge for increasing the efficacy of MHT. In this work, MNPs are combined with state-of-the-art infrared luminescent nanothermometers (LNTh; Ag2 S nanoparticles) in a nanocapsule that simultaneously overcomes these limitations. The novel optomagnetic nanocapsule acts as multimodal contrast agents for different imaging techniques (magnetic resonance, photoacoustic and near-infrared fluorescence imaging, optical and X-ray computed tomography). Most crucially, these nanocapsules provide accurate (0.2 °C resolution) and real-time subcutaneous thermal feedback during in vivo MHT, also enabling the attainment of thermal maps of the area of interest. These findings are a milestone on the road toward controlled magnetothermal therapies with minimal side effects.}, } @article {pmid34117636, year = {2021}, author = {Athreya, S and Hopkins, A}, title = {Conceptual issues in hominin taxonomy: Homo heidelbergensis and an ethnobiological reframing of species.}, journal = {American journal of physical anthropology}, volume = {175 Suppl 72}, number = {}, pages = {4-26}, doi = {10.1002/ajpa.24330}, pmid = {34117636}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical/*methods ; Fossils ; Hominidae/*classification ; Humans ; }, abstract = {Efforts to name and classify Middle Pleistocene Homo, often referred to as "Homo heidelbergensis" are hampered by confusing patterns of morphology but also by conflicting paleoanthropological ideologies that are embedded in approaches to hominin taxonomy, nomenclature, and the species concept. We deconstruct these issues to show how the field's search for a "real" species relies on strict adherence to pre-Darwinian essentialist naming rules in a post-typological world. We then examine Middle Pleistocene Homo through the framework of ethnobiology, which examines on how Indigenous societies perceive, classify, and name biological organisms. This research reminds us that across human societies, taxonomies function to (1) identify and classify organisms based on consensus pattern recognition and (2) construct a stable nomenclature for effective storage, retrieval and communication of information. Naming Middle Pleistocene Homo as a "real" species cannot be verified with the current data; and separating regional groups into distinct evolutionary lineages creates taxa that are not defined by readily perceptible or universally salient differences. Based on ethnobiological studies of this kind of patterning, referring to these hominins above the level of the species according to their generic category with modifiers (e.g., "European Middle Pleistocene Homo") is consistent with observed human capabilities for cognitive differentiation, is both necessary and sufficient given the current data, and will allow for the most clear communication across ideologies going forward.}, } @article {pmid34111824, year = {2021}, author = {Novick, A and Doolittle, WF}, title = {'Species' without species.}, journal = {Studies in history and philosophy of science}, volume = {87}, number = {}, pages = {72-80}, doi = {10.1016/j.shpsa.2021.03.006}, pmid = {34111824}, issn = {0039-3681}, mesh = {*Semantics ; }, abstract = {Biological science uses multiple species concepts. Order can be brought to this diversity if we recognize two key features. First, any given species concept is likely to have a patchwork structure, generated by repeated application of the concept to new domains. We illustrate this by showing how two species concepts (biological and ecological) have been modified from their initial eukaryotic applications to apply to prokaryotes. Second, both within and between patches, distinct species concepts may interact and hybridize. We thus defend a semantic picture of the species concept as a collection of interacting patchwork structures. Thus, although not all uses of the term pick out the same kind of unit in nature, the diversity of uses reflects something more than mere polysemy. We suggest that the emphasis on the use of species to pick out natural units is itself problematic, because that is not the term's sole function. In particular, species concepts are used to manage inquiry into processes of speciation, even when these processes do not produce clearly delimited species.}, } @article {pmid34099084, year = {2021}, author = {Wee, NQ and Cutmore, SC and Cribb, TH}, title = {Gerricola queenslandensis n. g., n. sp., a new monorchiid trematode from the eastern Australian coast and its life cycle partially elucidated.}, journal = {Journal of helminthology}, volume = {95}, number = {}, pages = {e30}, doi = {10.1017/S0022149X21000213}, pmid = {34099084}, issn = {1475-2697}, mesh = {Animals ; Australia ; Bivalvia/*parasitology ; Female ; Fish Diseases/parasitology ; Fishes/*parasitology ; Life Cycle Stages ; Male ; Phylogeny ; Queensland ; *Trematoda/anatomy & histology/classification ; }, abstract = {Of over 250 species of Monorchiidae Odhner, 1911, just four are known from gerreid fishes. Here, we report adult specimens of a new species infecting Gerres oyena (Forsskål) and Gerres subfasciatus Cuvier from off Heron Island and North Stradbroke Island, Queensland, Australia. The species is morphologically most similar to the concept of Lasiotocus Looss, 1907, which currently comprises eight species, in the possession of an unspined genital atrium, bipartite terminal organ, round oral sucker and unlobed ovary. However, phylogenetic analyses of the 28S ribosomal DNA gene region shows the species to be distantly related to the two sequenced species of Lasiotocus - Lasiotocus mulli (Stossich, 1883) Odhner, 1911 and Lasiotocus trachinoti Overstreet & Brown, 1970 - and that it clearly requires a distinct genus; thus, we propose Gerricola queenslandensis n. g., n. sp. Morphologically, G. queenslandensis n. g., n. sp. differs significantly from L. mulli and L. trachinoti only in the possession of distinctly longer caeca, which terminate in the post-testicular region, and in the absence of a distinct gap in the terminal organ spines. The remaining species of Lasiotocus possess caeca that also terminate in the post-testicular region, which might warrant their transfer to Gerricola n. g. However, doubt about their monophyly due to a combination of significant morphological variation, a lack of information on some features and infection of a wide range of hosts, lead us to retain these taxa as species of Lasiotocus until molecular sequence data are available to better inform their phylogenetic and taxonomic positions. Sporocysts and cercariae of G. queenslandensis n. g., n. sp. were found in a lucinid bivalve, Codakia paytenorum (Iredale), from Heron Island. Sexual adult and intramolluscan stages were genetically matched with the ITS2 ribosomal DNA and cox1 mitochondrial DNA regions. This is the second record of the Lucinidae as a first intermediate host for the Monorchiidae. Additionally, we report sporocysts and cercariae of another monorchiid infection in a tellinid bivalve, Jactellina clathrata (Deshayes), from Heron Island. Molecular sequence data for this species do not match any sequenced species and phylogenetic analyses do not suggest any generic position.}, } @article {pmid34081496, year = {2021}, author = {Vernouillet, A and Leonard, K and Katz, JS and Magnotti, JF and Wright, A and Kelly, DM}, title = {Abstract-concept learning in two species of new world corvids, pinyon jays (Gymnorhinus Cyanocephalus) and California scrub jays (Aphelocoma Californica).}, journal = {Journal of experimental psychology. Animal learning and cognition}, volume = {47}, number = {3}, pages = {384-392}, doi = {10.1037/xan0000283}, pmid = {34081496}, issn = {2329-8464}, mesh = {Animals ; Birds ; *Concept Formation ; *Learning ; }, abstract = {concepts require individuals to identify relationships between novel stimuli. Previous studies have reported that the ability to learn abstract concepts is found in a wide range of species. In regard to a same/different concept, Clark's nutcrackers (Nucifraga columbiana) and black-billed magpies (Pica hudsonia), two corvid species, were shown to outperform other avian and primate species (Wright et al., 2017). Two additional corvid species, pinyon jays (Gymnorhinus cyanocephalus) and California scrub jays (Aphelocoma californica) chosen as they belong to a different clade than nutcrackers and magpies, were examined using the same set-size expansion procedure of the same/different task (the task used with nutcrackers and magpies) to evaluate whether this trait is common across the Corvidae lineage. During this task, concept learning is assessed with novel images after training. Results from the current study showed that when presented with novel stimuli after training with an 8-image set, discrimination accuracy did not differ significantly from chance for pinyon jays and California scrub jays, unlike the magpies and nutcrackers from previous studies that showed partial transfer at that stage. However, concept learning improved with each set-size expansion, and the jays reached full concept learning with a 128-image set. This performance is similar to the other corvids and monkeys tested, all of which outperform pigeons. Results from the current study show a qualitative similarity in full abstract-concept learning in all species tested with a quantitative difference in the set-size functions, highlighting the shared survival importance of mechanisms supporting abstract-concept learning for corvids and primates. (PsycInfo Database Record (c) 2021 APA, all rights reserved).}, } @article {pmid34077240, year = {2021}, author = {Munkvold, GP and Proctor, RH and Moretti, A}, title = {Mycotoxin Production in Fusarium According to Contemporary Species Concepts.}, journal = {Annual review of phytopathology}, volume = {59}, number = {}, pages = {373-402}, doi = {10.1146/annurev-phyto-020620-102825}, pmid = {34077240}, issn = {1545-2107}, mesh = {Animals ; Food Contamination/analysis ; *Fusarium ; *Mycotoxins/analysis ; Phylogeny ; Plant Diseases ; *Trichothecenes/analysis ; }, abstract = {Fusarium is one of the most important genera of plant-pathogenic fungi in the world and arguably the world's most important mycotoxin-producing genus. Fusarium species produce a staggering array of toxic metabolites that contribute to plant disease and mycotoxicoses in humans and other animals. A thorough understanding of the mycotoxin potential of individual species is crucial for assessing the toxicological risks associated with Fusarium diseases. There are thousands of reports of mycotoxin production by various species, and there have been numerous attempts to summarize them. These efforts have been complicated by competing classification systems based on morphology, sexual compatibility, and phylogenetic relationships. The current depth of knowledge of Fusarium genomes and mycotoxin biosynthetic pathways provides insights into how mycotoxin production is distributedamong species and multispecies lineages (species complexes) in the genus as well as opportunities to clarify and predict mycotoxin risks connected with known and newly described species. Here, we summarize mycotoxin production in the genus Fusarium and how mycotoxin risk aligns with current phylogenetic species concepts.}, } @article {pmid34065552, year = {2021}, author = {Kartavtsev, YP}, title = {Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {5}, pages = {}, pmid = {34065552}, issn = {2076-2615}, abstract = {Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.}, } @article {pmid35935892, year = {2021}, author = {Andreasen, M and Skrede, I and Jaklitsch, WM and Voglmayr, H and Nordén, B}, title = {Multi-locus phylogenetic analysis of lophiostomatoid fungi motivates a broad concept of Lophiostoma and reveals nine new species.}, journal = {Persoonia}, volume = {46}, number = {}, pages = {240-271}, pmid = {35935892}, issn = {0031-5850}, abstract = {Recent studies on the fungal families Lophiostomataceae and Lophiotremataceae (Pleosporales) have provided varying phylogenetic and taxonomic results concerning constituent genera and species. By adding DNA sequences of 24 new strains of Lophiostomataceae and nine new strains of Lophiotremataceae to a sequence data matrix from international databases, we provide a new understanding of the relationships within these families. Multigene analysis of the four molecular markers ITS, LSU, TEF1-α, and RPB2 reveals that the genera within Lophio-tremataceae are phylogenetically well supported. Lophiostoma myriocarpum is recognised as a species of Lophiotrema in contrast to earlier concepts. In Lophiostomataceae, we resurrect a broad generic concept of the genus Lophiostoma and reduce 14 genera to synonymy: Alpestrisphaeria, Biappendiculispora, Capulatispora, Coelodictyosporium, Guttulispora, Lophiohelichrysum, Lophiopoacea, Neopaucispora, Neotrematosphaeria, Platystomum, Pseudocapulatispora, Pseudolophiostoma, Pseudoplatystomum, and Sigarispora. Nine new species are described based on molecular data and in most cases supported by morphological characters: Antealophiotrema populicola, Atrocalyx nordicus, Lophiostoma carpini, Lophiostoma dictyosporium, Lophiostoma erumpens, Lophiostoma fusisporum, Lophiostoma jotunheimenense, Lophiostoma plantaginis, and Lophiostoma submuriforme. Lophiostoma caespitosum and Lophiotrema myriocarpum are lecto- and epitypified to stabilise their species concepts. High intraspecific variability of several morphological traits is common within Lophiostomataceae. Citation: Andreasen M, Skrede I, Jaklitsch WM, et al. 2021. Multi-locus phylogenetic analysis of lophiostomatoid fungi motivates a broad concept of Lophiostoma and reveals nine new species. Persoonia 46: 240-271. https://doi.org/10.3767/persoonia.2021.46.09.}, } @article {pmid34026029, year = {2021}, author = {Lei, Y and Liu, Q}, title = {Tolerance niche expansion and potential distribution prediction during Asian openbill bird range expansion.}, journal = {Ecology and evolution}, volume = {11}, number = {10}, pages = {5562-5574}, pmid = {34026029}, issn = {2045-7758}, abstract = {It is prevalent to use ecological niche models in the analysis of species expansion and niche changes. However, it is difficult to estimate the niche when alien species fail to establish in exotic areas. Here, we applied the tolerance niche concept, which means that niche of species can live and grow but preclude a species from establishing self-sustaining populations, in such fail-to-establish events. Taking the rapidly expanded bird, Asian openbill (Anastomus oscitans), as a model species, we investigated niche dynamics and its potential effects on the population by Niche A and ecospat, predicted potential distribution by biomod2. Results showed that niche expansion has occurred in two non-native populations caused by the tolerance of colder and wetter environments, and potential distribution mainly concentrated on equatorial islands. Our study suggested that the expanded niche belongs to tolerance niche concept according to the populations' dynamics and GPS tracking evidence. It is essential to consider source populations when we analyze the alien species. We recommended more consideration to the application of tolerance niche in alien species research, and there is still a need for standard measurement frameworks for analyzing the tolerance niche.}, } @article {pmid33981506, year = {2021}, author = {Garibian, PG and Karabanov, DP and Neretina, AN and Taylor, DJ and Kotov, AA}, title = {Bosminopsis deitersi (Crustacea: Cladocera) as an ancient species group: a revision.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11310}, pmid = {33981506}, issn = {2167-8359}, abstract = {Water fleas (Crustacea: Cladocera) of the Family Bosminidae have been studied since the founding of paleolimnology and freshwater ecology. However, one species, Bosminopsis deitersi, stands out for its exceptional multicontinental range and broad ecological requirements. Here we use an integrated morphological and multilocus genetic approach to address the species problem in B. deitersi. We analyzed 32 populations of B. deitersi s. lat. Two nuclear and two mitochondrial loci were used to carry out the bGMYC, mPTP and STACEY algorithms for species delimitation. Detailed morphological study was also carried out across continents. The evidence indicated a widely distributed cryptic species in the Old World (Bosminopsis zernowi) that is genetically divergent from B. deitersi s.str. We revised the taxonomy and redescribed the species in this complex. Our sampling indicated that B. zernowi had weak genetic differentiation across its range. A molecular clock and biogeographic analysis with fossil calibrations suggested a Mesozoic origin for the Bosminopsis deitersi group. Our evidence rejects the single species hypothesis for B. deitersi and is consistent with an ancient species group (potentially Mesozoic) that shows marked morphological conservation. The family Bosminidae, then, has examples of both rapid morphological evolution (Holocene Bosmina), and morphological stasis (Bosminopsis).}, } @article {pmid33974865, year = {2021}, author = {Stankowski, S and Ravinet, M}, title = {Quantifying the use of species concepts.}, journal = {Current biology : CB}, volume = {31}, number = {9}, pages = {R428-R429}, doi = {10.1016/j.cub.2021.03.060}, pmid = {33974865}, issn = {1879-0445}, mesh = {Classification/*methods ; *Dissent and Disputes ; Reproducibility of Results ; *Research Personnel ; Species Specificity ; *Surveys and Questionnaires ; }, abstract = {Humans conceptualize the diversity of life by classifying individuals into types we call 'species'[1]. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin[2]. So much energy has been devoted to the so-called 'species problem' that no amount of discourse will ever likely solve it[2][,][3]. Dozens of species concepts are currently recognized[3], but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently[1][,][2]. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.}, } @article {pmid33927547, year = {2021}, author = {Kmetova-Biro, E and Stoynov, E and Ivanov, I and Peshev, H and Marin, S and Bonchev, L and Stoev, IP and Stoyanov, G and Nikolova, Z and Vangelova, N and Parvanov, D and Grozdanov, A}, title = {Re-introduction of Griffon Vulture (Gyps fulvus) in the Eastern Balkan Mountains, Bulgaria - completion of the establishment phase 2010-2020.}, journal = {Biodiversity data journal}, volume = {9}, number = {}, pages = {e66363}, pmid = {33927547}, issn = {1314-2828}, abstract = {The current study presents and analyses the results from the recently completed 11-year-establishment phase, following the start of the local re-introduction of the Griffon Vulture (Gyps fulvus) in Kotlenska Planina SPA and Sinite Kamani Nature Park in the Eastern Balkan Mountains of Bulgaria in the period 2010-2020. As a result of the re-introduction efforts and release of 153 individuals, the Griffon Vulture has been successfully reproducing again in the Eastern Balkan Mountains since 2016, after more than 40-50 years of absence. At 2020, the local population consists of some 80 local and up to 80-115 birds, together with sojourn individuals. Amongst them, 23-25 breeding pairs, located in five different colonies and two more frequently used roosting sites. The current average productivity remains relatively low: 0.41 fledglings/territorial pair and fledging success of 0.61 fledglings/breeding pair between 2016 and 2020, but shows a trend to increase with time and the growing experience of the young locally re-introduced population. The mortality confirmed between 2010-2021 accounts for 33%, mostly due to electrocution as a post-release effect in the first six months following their release. Our data show that the newly established population in the Eastern Balkan Mountains mostly forages on feeding sites, having a comparatively small 95% home range: 281.88 ± 91 km[2] and 50% core area: 6.6 ± 2.28 km[2] (range 4.7-8.5 km[2]). We, therefore, consider the establishment phase of the re-introduction of Griffon Vulture in this particular site as successfully completed, but management should continue. Furthermore, the area of the Eastern Balkan Mountains can currently be regarded as a "source" for the species within the source-sink population regulation concept in the national and Balkan context.}, } @article {pmid33915697, year = {2021}, author = {Matzek, D and Baldauf, HM and Schieweck, R and Popper, B}, title = {Evaluation of a Configurable, Mobile and Modular Floor-Pen System for Group-Housing of Laboratory Rabbits.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {4}, pages = {}, pmid = {33915697}, issn = {2076-2615}, abstract = {The major responsibility of researchers and laboratory animal facilities is to ensure animal well-being during the time of acclimatization, experiments, and recovery. In this context, animal housing conditions are of utmost importance. Here, we implemented a mobile and modular floor-pen housing system for laboratory rabbits that combines rabbits' natural behavioral requirements and the high hygiene standards needed in biomedical science. Twelve female New Zealand White (NZW) rabbits were single- or group-housed for 12 months in mobile and modular floor-pens. Their general health status was evaluated at the end of the experimental setup. Further, we performed behavioral analysis of six additional NZW females group-housed for eight weeks in pens of two different sizes. We show that our improved housing concept supported species-specific behavioral patterns. Taken together, our housing system provides an optimal setup for rabbits in animal facilities that combines strict requirements for animal experiments with animal welfare.}, } @article {pmid33891700, year = {2021}, author = {Piarroux, R and Gabriel, F and Grenouillet, F and Collombon, P and Louasse, P and Piarroux, M and Normand, AC}, title = {Using MALDI-ToF mass spectrometry to identify mushroom species: Proof of concept analysis of Amanita genus specimens.}, journal = {Medical mycology}, volume = {59}, number = {9}, pages = {890-900}, doi = {10.1093/mmy/myab018}, pmid = {33891700}, issn = {1460-2709}, mesh = {Amanita/*classification/*genetics ; France ; Mushroom Poisoning/*microbiology ; Sequence Analysis, DNA/*methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; }, abstract = {UNLABELLED: Food poisoning caused by toxic mushrooms, such as species in the Amanita genus, occurs frequently around the world. To properly treat these patients, it is important to rapidly and accurately identify the causal species. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry is a rapid technique that has been used in medical laboratories for the past three decades to identify bacteria, yeasts, and filamentous fungi.Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-Tof MS) is a rapid method used for the past three decades to identify microorganisms. In this study, we created and internally validated a MALDI-Tof MS reference database comprising 15 Amanita species frequently encountered in France, and we challenged this database with 38 Amanita specimens from four French locations, using a free online application for MALDI-ToF spectra identifications.Assessment of the database showed that mass spectra can be obtained by analyzing any portion of a carpophore and that all portions enabled identification of the carpophore at the species level. Most carpophores were correctly identified using our database, with the exception of specimens from the Vaginatae section. Decay tests also demonstrated that decayed portions (like those found in the kitchen garbage can) of Amanita phalloides mushrooms could be properly identified using MALDI-ToF MS.Our findings provide important insight for toxicology laboratories that often rely on DNA sequencing to identify meal leftovers implicated in food poisoning. In future developments, this technique could also be used to detect counterfeit mushrooms by including other genera in the reference database.

LAY SUMMARY: MALDI-ToF MS is a powerful identification tool for microorganisms. We demonstrate that the technique can be applied to Amanita specimens. This will prevent food intoxications as a rapid and definite identification can be obtained, and it can also be used for food remnants.}, } @article {pmid33891394, year = {2021}, author = {Picchetti, P and Moreno-Alcántar, G and Talamini, L and Mourgout, A and Aliprandi, A and De Cola, L}, title = {Smart Nanocages as a Tool for Controlling Supramolecular Aggregation.}, journal = {Journal of the American Chemical Society}, volume = {143}, number = {20}, pages = {7681-7687}, doi = {10.1021/jacs.1c00444}, pmid = {33891394}, issn = {1520-5126}, abstract = {An important aspect in the field of supramolecular chemistry is the control of the composition and aggregation state of supramolecular polymers and the possibility of stabilizing out-of-equilibrium states. The ability to freeze metastable systems and release them on demand, under spatiotemporal control, to allow their thermodynamic evolution toward the most stable species is a very attractive concept. Such temporal blockage could be realized using stimuli-responsive "boxes" able to trap and redirect supramolecular polymers. In this work, we report the use of a redox responsive nanocontainer, an organosilica nanocage (OSCs), for controlling the dynamic self-assembly pathway of supramolecular aggregates of a luminescent platinum compound (PtAC). The aggregation of the complexes leads to different photoluminescent properties that allow visualization of the different assemblies and their evolution. We discovered that the nanocontainers can encapsulate kinetically trapped species characterized by an orange emission, preventing their evolution into the thermodynamically stable aggregation state characterized by blue-emitting fibers. Interestingly, the out-of-equilibrium trapped Pt species (PtAC@OSCs) can be released on demand by the redox-triggered degradation of OSCs, re-establishing their self-assembly toward the thermodynamically stable state. To demonstrate that control of the self-assembly pathway occurs also in complex media, we followed the evolution of the supramolecular aggregates inside living cells, where the destruction of the cages allows the intracellular release of PtAC aggregates, followed by the formation of microscopic blue emitting fibers. Our approach highlights the importance of "ondemand" confinement as a tool to temporally stabilize transient species which modulate complex self-assembly pathways in supramolecular polymerization.}, } @article {pmid33877247, year = {2021}, author = {Oalđe, M and Kolarević, S and Živković, J and Alimpić Aradski, A and Jovanović Marić, J and Kračun Kolarević, M and Đorđević, J and Marin, PD and Šavikin, K and Vuković-Gačić, B and Duletić-Laušević, S}, title = {A comprehensive assessment of the chemical composition, antioxidant, genoprotective and antigenotoxic activities of Lamiaceae species using different experimental models in vitro.}, journal = {Food & function}, volume = {12}, number = {7}, pages = {3233-3245}, doi = {10.1039/d1fo00447f}, pmid = {33877247}, issn = {2042-650X}, mesh = {Antimutagenic Agents/*pharmacology ; Antioxidants/*pharmacology ; DNA Damage/drug effects ; DNA Repair ; Fibroblasts/drug effects ; Flavonoids/analysis ; Humans ; Lamiaceae/*chemistry ; Mutagenicity Tests ; Oxidative Stress/drug effects ; Plant Extracts/*chemistry ; Polyphenols/analysis ; Salmonella typhimurium/metabolism ; }, abstract = {This research was aimed to assess the potential of Glechoma hederacea, Hyssopus officinalis, Lavandula angustifolia, Leonurus cardiaca, Marrubium vulgare and Sideritis scardica (Lamiaceae) methanolic, ethanolic and aqueous extracts against the damaging effects of oxidative stress using different experimental models. The chemical characterization was done spectrophotometrically by quantifying total phenolics, phenolic acids, flavonoids and flavonols in the extracts, as well as by employing HPLC-DAD technique. Moreover, DPPH assay was used to assess the extracts' radical scavenging potential. Genoprotective properties of the extracts were evaluated using plasmid pUC19 Escherichia coli XL1-Blue, whereas their antigenotoxic potential was determined using Salmonella typhimurium TA1535/pSK1002 and normal human lung fibroblasts. All of the extracts showed antioxidant activity in DPPH assay. Furthermore, the results have shown that aqueous extracts provided the best protection for plasmid DNA, while alcoholic extracts most effectively contributed to the preservation of prokaryotic DNA. Additionally, each of the tested samples significantly protected the eukaryotic cells against genomic damages. Finally, despite not showing exceptional results in DPPH assay, S. scardica extracts are regarded as the most favorable in maintaining the integrity of DNA, which might be due to high quantities of phenolics such as quercetin (up to 17.95 mg g[-1]), naringin (up to 5.07 mg g[-1]) and luteolin-7-O-glucoside (up to 3.54 mg g[-1]). Overall, this comprehensive concept highlights the ability of these Lamiaceae species to safeguard the DNA from reactive oxygen species, to curtail the inflicted damage and also improve the efficiency of the DNA repair mechanisms, while emphasizing the importance of polyphenols as their active principles.}, } @article {pmid33875585, year = {2021}, author = {Holding, ML and Strickland, JL and Rautsaw, RM and Hofmann, EP and Mason, AJ and Hogan, MP and Nystrom, GS and Ellsworth, SA and Colston, TJ and Borja, M and Castañeda-Gaytán, G and Grünwald, CI and Jones, JM and Freitas-de-Sousa, LA and Viala, VL and Margres, MJ and Hingst-Zaher, E and Junqueira-de-Azevedo, ILM and Moura-da-Silva, AM and Grazziotin, FG and Gibbs, HL and Rokyta, DR and Parkinson, CL}, title = {Phylogenetically diverse diets favor more complex venoms in North American pitvipers.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {17}, pages = {}, pmid = {33875585}, issn = {1091-6490}, support = {P20 GM109094/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Animals ; Crotalinae/*genetics/metabolism ; Diet/*trends/veterinary ; Gene Expression/genetics ; North America ; Phylogeny ; Predatory Behavior/physiology ; Proteomics/methods ; Selection, Genetic/genetics ; Snake Venoms/*genetics/metabolism ; Tooth/metabolism ; Transcriptome/genetics ; }, abstract = {The role of natural selection in the evolution of trait complexity can be characterized by testing hypothesized links between complex forms and their functions across species. Predatory venoms are composed of multiple proteins that collectively function to incapacitate prey. Venom complexity fluctuates over evolutionary timescales, with apparent increases and decreases in complexity, and yet the causes of this variation are unclear. We tested alternative hypotheses linking venom complexity and ecological sources of selection from diet in the largest clade of front-fanged venomous snakes in North America: the rattlesnakes, copperheads, cantils, and cottonmouths. We generated independent transcriptomic and proteomic measures of venom complexity and collated several natural history studies to quantify dietary variation. We then constructed genome-scale phylogenies for these snakes for comparative analyses. Strikingly, prey phylogenetic diversity was more strongly correlated to venom complexity than was overall prey species diversity, specifically implicating prey species' divergence, rather than the number of lineages alone, in the evolution of complexity. Prey phylogenetic diversity further predicted transcriptomic complexity of three of the four largest gene families in viper venom, showing that complexity evolution is a concerted response among many independent gene families. We suggest that the phylogenetic diversity of prey measures functionally relevant divergence in the targets of venom, a claim supported by sequence diversity in the coagulation cascade targets of venom. Our results support the general concept that the diversity of species in an ecological community is more important than their overall number in determining evolutionary patterns in predator trait complexity.}, } @article {pmid33853671, year = {2021}, author = {Shen, S and Liu, SL and Jiang, JH and Zhou, LW}, title = {Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences.}, journal = {IMA fungus}, volume = {12}, number = {1}, pages = {10}, pmid = {33853671}, issn = {2210-6340}, abstract = {"Sanghuang" refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of "Sanghuang" in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to "Sanghuang" in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.}, } @article {pmid33848300, year = {2021}, author = {Wang, H and Jiang, B and Gu, J and Wei, T and Lin, L and Huang, Y and Liang, D and Huang, J}, title = {Molecular phylogeny and species delimitation of the genus Tonkinacris (Orthoptera, Acrididae, Melanoplinae) from China.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249431}, pmid = {33848300}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; China ; Genetic Variation ; Grasshoppers/*genetics ; *Phylogeny ; }, abstract = {Tonkinacris is a small group in Acrididae. While a few species were occasionally sampled in some previous molecular studies, there is no revisionary research devoted to the genus. In this study, we explored the phylogeny of and the relationships among Chinese species of the genus Tonkinacris using the mitochondrial COI barcode and the complete sequences of ITS1 and ITS2 of the nuclear ribosomal DNA. The phylogeny was reconstructed in maximum likelihood and Bayesian inference frameworks, respectively. The overlap range between intraspecific variation and interspecific divergence was assessed via K2P distances. Species boundaries were delimitated using phylogenetic species concept, NJ tree, K2P distance, the statistical parsimony network as well as the GMYC model. The results demonstrate that the Chinese Tonkinacris species is a monophyletic group and the phylogenetic relationship among them is (T. sinensis, (T. meridionalis, (T. decoratus, T. damingshanus))). While T. sinensis, T. meridionalis and T. decoratus were confirmed being good independent species strongly supported by both morphological and molecular evidences, the validity of T. damingshanus was not perfectly supported by molecular evidence in this study.}, } @article {pmid33848285, year = {2021}, author = {Pearson, PN and Penny, L}, title = {Coiling directions in the planktonic foraminifer Pulleniatina: A complex eco-evolutionary dynamic spanning millions of years.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249113}, pmid = {33848285}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; Foraminifera/cytology/*genetics ; Zooplankton/cytology/genetics ; }, abstract = {Planktonic foraminifera are heterotrophic sexually reproducing marine protists with an exceptionally complete fossil record that provides unique insights into long-term patterns and processes of evolution. Populations often exhibit strong biases towards either right (dextral) or left (sinistral) shells. Deep-sea sediment cores spanning millions of years reveal that some species show large and often rapid fluctuations in their dominant coiling direction through time. This is useful for biostratigraphic correlation but further work is required to understand the population dynamical processes that drive these fluctuations. Here we address the case of coiling fluctuations in the planktonic foraminifer genus Pulleniatina based on new high-resolution counts from two recently recovered sediment cores from either side of the Indonesian through-flow in the tropical west Pacific and Indian Oceans (International Ocean Discovery Program Sites U1486 and U1483). We use single-specimen stable isotope analyses to show that dextral and sinistral shells from the same sediment samples can show significant differences in both carbon and oxygen isotopes, implying a degree of ecological separation between populations. In one case we detect a significant difference in size between dextral and sinistral specimens. We suggest that major fluctuations in coiling ratio are caused by cryptic populations replacing one another in competitive sweeps, a mode of evolution that is more often associated with asexual organisms than with the classical 'biological species concept'.}, } @article {pmid33844023, year = {2021}, author = {Farah, IT and Islam, M and Zinat, KT and Rahman, AH and Bayzid, S}, title = {Species Tree Estimation from Gene Trees by Minimizing Deep Coalescence and Maximizing Quartet Consistency: A Comparative Study and the Presence of Pseudo Species Tree Terraces.}, journal = {Systematic biology}, volume = {70}, number = {6}, pages = {1213-1231}, doi = {10.1093/sysbio/syab026}, pmid = {33844023}, issn = {1076-836X}, mesh = {Computer Simulation ; *Genetic Speciation ; *Genome ; Models, Genetic ; Phylogeny ; }, abstract = {Species tree estimation from multilocus data sets is extremely challenging, especially in the presence of gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Summary methods have been developed which estimate gene trees and then combine the gene trees to estimate a species tree by optimizing various optimization scores. In this study, we have extended and adapted the concept of phylogenetic terraces to species tree estimation by "summarizing" a set of gene trees, where multiple species trees with distinct topologies may have exactly the same optimality score (i.e., quartet score, extra lineage score, etc.). We particularly investigated the presence and impacts of equally optimal trees in species tree estimation from multilocus data using summary methods by taking ILS into account. We analyzed two of the most popular ILS-aware optimization criteria: maximize quartet consistency (MQC) and minimize deep coalescence (MDC). Methods based on MQC are provably statistically consistent, whereas MDC is not a consistent criterion for species tree estimation. We present a comprehensive comparative study of these two optimality criteria. Our experiments, on a collection of data sets simulated under ILS, indicate that MDC may result in competitive or identical quartet consistency score as MQC, but could be significantly worse than MQC in terms of tree accuracy-demonstrating the presence and impacts of equally optimal species trees. This is the first known study that provides the conditions for the data sets to have equally optimal trees in the context of phylogenomic inference using summary methods. [Gene tree; incomplete lineage sorting; phylogenomic analysis, species tree; summary method.].}, } @article {pmid33830905, year = {2021}, author = {Li, Y and O'Donnell, AC and Ochman, H}, title = {Discriminating arboviral species.}, journal = {The Journal of general virology}, volume = {102}, number = {4}, pages = {}, pmid = {33830905}, issn = {1465-2099}, support = {R35 GM118038/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Arbovirus Infections/*virology ; *Arboviruses/classification/genetics ; Culicidae/*virology ; Databases, Genetic ; *Flavivirus/classification/genetics ; Mosquito Vectors/*virology ; }, abstract = {Mosquito-borne arboviruses, including a diverse array of alphaviruses and flaviviruses, lead to hundreds of millions of human infections each year. Current methods for species-level classification of arboviruses adhere to guidelines prescribed by the International Committee on Taxonomy of Viruses (ICTV), and generally apply a polyphasic approach that might include information about viral vectors, hosts, geographical distribution, antigenicity, levels of DNA similarity, disease association and/or ecological characteristics. However, there is substantial variation in the criteria used to define viral species, which can lead to the establishment of artificial boundaries between species and inconsistencies when inferring their relatedness, variation and evolutionary history. In this study, we apply a single, uniform principle - that underlying the Biological Species Concept (BSC) - to define biological species of arboviruses based on recombination between genomes. Given that few recombination events have been documented in arboviruses, we investigate the incidence of recombination within and among major arboviral groups using an approach based on the ratio of homoplastic sites (recombinant alleles) to non-homoplastic sites (vertically transmitted alleles). This approach supports many ICTV-designations but also recognizes several cases in which a named species comprises multiple biological species. These findings demonstrate that this metric may be applied to all lifeforms, including viruses, and lead to more consistent and accurate delineation of viral species.}, } @article {pmid33812359, year = {2021}, author = {Ikenaga, J and Kajihara, H and Yoshida, M}, title = {Kulikovia alborostrata and Kulikovia fulva comb. nov. (Nemertea: Heteronemertea) are Sister Species with Prezygotic Isolating Barriers.}, journal = {Zoological science}, volume = {38}, number = {2}, pages = {193-202}, doi = {10.2108/zs200112}, pmid = {33812359}, issn = {0289-0003}, mesh = {Animals ; Germ Cells ; Invertebrates/*classification/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {The heteronemertean Kulikovia alborostrata (Takakura, 1898) was originally described as Lineus alborostratus based on material from Misaki, Japan. Although this species was regarded as consisting of two color variants, purple and brown-yellow, the identity of these variants has never been examined based on topotypes. In this study, we performed a multi-locus phylogeny reconstruction, species delimitation analyses, and cross-fertilization experiments to examine the species status of Takakura's original taxon concept consisting of these color variants. Our results suggest that the purple type is identical to Lineus alborostratus Takakura, 1898 auct. (currently Kulikovia alborostrata), whereas the brown-yellow type is conspecific with Lineus fulvus Iwata, 1954, originally established from Hokkaido. These two species appear to have a sister-taxon relationship and are reproductively isolated from each other by prezygotic mechanisms involving gamete incompatibility, minimally separated with 2.8% (16S rRNA) and 14.4% (COI) uncorrected p-distances. We propose that the purple type be considered as representing the true identity of the nominal species Lineus alborostratus (currently assigned to the genus Kulikovia) to maintain the common usage of the name. Although Takakura's type material is not extant, we consider that neotypification is unnecessary in this case because no taxonomic/nomenclatural confusion persists. We also propose to transfer Lineus fulvus to yield Kulikovia fulva comb. nov.}, } @article {pmid33805967, year = {2021}, author = {Cequier, A and Sanz, C and Rodellar, C and Barrachina, L}, title = {The Usefulness of Mesenchymal Stem Cells beyond the Musculoskeletal System in Horses.}, journal = {Animals : an open access journal from MDPI}, volume = {11}, number = {4}, pages = {}, pmid = {33805967}, issn = {2076-2615}, abstract = {The differentiation ability of mesenchymal stem cells (MSCs) initially raised interest for treating musculoskeletal injuries in horses, but MSC paracrine activity has widened their scope for inflammatory and immune-mediated pathologies in both equine and human medicine. Furthermore, the similar etiopathogenesis of some diseases in both species has advanced the concept of "One Medicine, One Health". This article reviews the current knowledge on the use of MSCs for equine pathologies beyond the locomotor system, highlighting the value of the horse as translational model. Ophthalmologic and reproductive disorders are among the most studied for MSC application. Equine asthma, equine metabolic syndrome, and endotoxemia have been less explored but offer an interesting scenario for human translation. The use of MSCs in wounds also provides a potential model for humans because of the healing particularities in both species. High-burden equine-specific pathologies such as laminitis have been suggested to benefit from MSC-therapy, and MSC application in challenging disorders such as neurologic conditions has been proposed. The available data are preliminary, however, and require further development to translate results into the clinic. Nevertheless, current evidence indicates a significant potential of equine MSCs to enlarge their range of application, with particular interest in pathologies analogous to human conditions.}, } @article {pmid33805574, year = {2021}, author = {Réblová, M and Kolařík, M and Nekvindová, J and Miller, AN and Hernández-Restrepo, M}, title = {Phylogeny, Global Biogeography and Pleomorphism of Zanclospora.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33805574}, issn = {2076-2607}, abstract = {Zanclospora (Chaetosphaeriaceae) is a neglected, phialidic dematiaceous hyphomycete with striking phenotypic heterogeneity among its species. Little is known about its global biogeography due to its extreme scarcity and lack of records verified by molecular data. Phylogenetic analyses of six nuclear loci, supported by phenotypic data, revealed Zanclospora as highly polyphyletic, with species distributed among three distantly related lineages in Sordariomycetes. Zanclospora is a pleomorphic genus with multiple anamorphic stages, of which phaeostalagmus-like and stanjehughesia-like are newly discovered. The associated teleomorphs were previously classified in Chaetosphaeria. The generic concept is emended, and 17 species are accepted, 12 of which have been verified with DNA sequence data. Zanclospora thrives on decaying plant matter, but it also occurs in soil or as root endophytes. Its global diversity is inferred from metabarcoding data and published records based on field observations. Phylogenies of the environmental ITS1 and ITS2 sequences derived from soil, dead wood and root samples revealed seven and 15 phylotypes. The field records verified by DNA data indicate two main diversity centres in Australasia and Caribbean/Central America. In addition, environmental ITS data have shown that Southeast Asia represents a third hotspot of Zanclospora diversity. Our data confirm that Zanclospora is a rare genus.}, } @article {pmid33794366, year = {2021}, author = {Hertaeg, J and Sauer, C and Bertelsen, MF and Hammer, S and Lund, P and Weisbjerg, MR and Clauss, M}, title = {Physical characteristics of forestomach contents from two nondomestic small ruminants, the blackbuck (Antilope cervicapra) and the Arabian sand gazelle (Gazella subgutturosa marica).}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {257}, number = {}, pages = {110941}, doi = {10.1016/j.cbpa.2021.110941}, pmid = {33794366}, issn = {1531-4332}, mesh = {Animal Feed ; Animals ; Antelopes/*physiology ; Cattle ; Deer/*physiology ; Diet ; Female ; Gastrointestinal Tract/physiology ; Male ; Phylogeny ; Rumen/metabolism/physiology ; Ruminants/physiology ; Species Specificity ; Stomach/*metabolism ; }, abstract = {Rumen content stratification and the degree of dissociation of particle and fluid retention in the reticulorumen differ between 'moose-type' and 'cattle-type' ruminant species. These differences are not strictly linked to diet, except for a seeming limitation of 'moose-type' ruminants to a browsing niche. Nevertheless, these differences can be plausibly linked to other observed differences in ruminants, such as the intraruminal papillation pattern, or the size of the omasum. However, many of the corresponding measures are still only available for a restricted number of species. Here, we investigated the dry matter (i.e., the inverse of the moisture) concentration in forestomach contents of 10 blackbuck (Antilope cervicapra) and 7 Arabian sand gazelle (Gazella subgutturosa marica), and quantified the rumen papillation pattern. The blackbucks had distinct rumen contents stratification, with more moisture in ventral than in dorsal contents (difference 3.6% units, P < 0.001), whereas this difference was much less pronounced in the sand gazelles (0.6% units, P = 0.227). While reticulum contents were particularly moist in both species, omasum contents were particularly dry in sand gazelles, but did not differ in moisture from rumen contents in the blackbuck. This species is an outlier among ruminants due to its extremely small omasum. The intraruminal papillation pattern did not differ between blackbucks and sand gazelles and showed a surface enlargement factor (SEF) in the dorsal rumen of 27-28% of the SEF in the Atrium ruminis. Compared to data on digesta retention in the same species, the findings are in line with the overall concept of a high fluid throughput causing a distinct stratification of rumen contents and intraruminal papillation, and necessitating a large omasum for fluid re-absorption. However, the data also show that individual species may not correspond to all the assumptions of the concept, suggesting taxon-specific differences between species. Reasons for these differences cannot be linked to a dietary grass-browse spectrum, but may lie in evolutionary contingency.}, } @article {pmid33757059, year = {2021}, author = {DE Aguiar Brotto, TR and Tavares, MT}, title = {Review of the leucotela species-group of Conura (Hymenoptera: Chalcididae) from Amazon rainforest.}, journal = {Zootaxa}, volume = {4942}, number = {3}, pages = {zootaxa.4942.3.5}, doi = {10.11646/zootaxa.4942.3.5}, pmid = {33757059}, issn = {1175-5334}, mesh = {Animals ; Female ; *Hymenoptera ; Male ; Rainforest ; }, abstract = {The leucotela species-group of Conura Spinola (Hymenoptera: Chalcididae) was initially proposed to include C. leucotela (Walker 1862) within the subgenus Spilochalcis Thomson. Despite this treatment, the accurate identification of C. leucotela is not possible based on the literature. In this paper, C. leucotela is redescribed and two new species, C. paraleucotela sp. nov. and C. pseudoleucotela sp. nov., are described within the leucotela group, with all the species based on female singletons. Additionally, diagnoses and illustrations are presented for two other unnamed species based on males. The taxonomic concept of the species group is discussed, and new diagnostic characters are proposed. An identification key and illustration of species are provided. The morphology of the coupling mechanism of the propodeum and gaster of some species of the leucotela group and its relation with possible hosts is discussed. A short discussion of rarity of the leucotela group is presented.}, } @article {pmid33754340, year = {2021}, author = {Stankowski, S and Ravinet, M}, title = {Defining the speciation continuum.}, journal = {Evolution; international journal of organic evolution}, volume = {75}, number = {6}, pages = {1256-1273}, doi = {10.1111/evo.14215}, pmid = {33754340}, issn = {1558-5646}, mesh = {*Genetic Speciation ; Models, Biological ; Reproductive Isolation ; *Terminology as Topic ; }, abstract = {A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present-day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.}, } @article {pmid33747031, year = {2021}, author = {Zhu, L and Marjani, SL and Jiang, Z}, title = {The Epigenetics of Gametes and Early Embryos and Potential Long-Range Consequences in Livestock Species-Filling in the Picture With Epigenomic Analyses.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {557934}, pmid = {33747031}, issn = {1664-8021}, support = {R01 HD102533/HD/NICHD NIH HHS/United States ; }, abstract = {The epigenome is dynamic and forged by epigenetic mechanisms, such as DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA species. Increasing lines of evidence support the concept that certain acquired traits are derived from environmental exposure during early embryonic and fetal development, i.e., fetal programming, and can even be "memorized" in the germline as epigenetic information and transmitted to future generations. Advances in technology are now driving the global profiling and precise editing of germline and embryonic epigenomes, thereby improving our understanding of epigenetic regulation and inheritance. These achievements open new avenues for the development of technologies or potential management interventions to counteract adverse conditions or improve performance in livestock species. In this article, we review the epigenetic analyses (DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs) of germ cells and embryos in mammalian livestock species (cattle, sheep, goats, and pigs) and the epigenetic determinants of gamete and embryo viability. We also discuss the effects of parental environmental exposures on the epigenetics of gametes and the early embryo, and evidence for transgenerational inheritance in livestock.}, } @article {pmid33723272, year = {2021}, author = {Pröschold, T and Rieser, D and Darienko, T and Nachbaur, L and Kammerlander, B and Qian, K and Pitsch, G and Bruni, EP and Qu, Z and Forster, D and Rad-Menendez, C and Posch, T and Stoeck, T and Sonntag, B}, title = {An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5916}, pmid = {33723272}, issn = {2045-2322}, support = {I 2238/FWF_/Austrian Science Fund FWF/Austria ; P 28333/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Biodiversity ; Biological Variation, Population ; Ciliophora/*classification/cytology/*genetics ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Ecology ; Ecosystem ; Lakes ; Nucleic Acid Conformation ; Phenotype ; Phylogeny ; Seasons ; Symbiosis ; Water/*parasitology ; }, abstract = {Species of the genus Coleps are one of the most common planktonic ciliates in lake ecosystems. The study aimed to identify the phenotypic plasticity and genetic variability of different Coleps isolates from various water bodies and from culture collections. We used an integrative approach to study the strains by (i) cultivation in a suitable culture medium, (ii) screening of the morphological variability including the presence/absence of algal endosymbionts of living cells by light microscopy, (iii) sequencing of the SSU and ITS rDNA including secondary structures, (iv) assessment of their seasonal and spatial occurrence in two lakes over a one-year cycle both from morphospecies counts and high-throughput sequencing (HTS), and, (v) proof of the co-occurrence of Coleps and their endosymbiotic algae from HTS-based network analyses in the two lakes. The Coleps strains showed a high phenotypic plasticity and low genetic variability. The algal endosymbiont in all studied strains was Micractinium conductrix and the mutualistic relationship turned out as facultative. Coleps is common in both lakes over the whole year in different depths and HTS has revealed that only one genotype respectively one species, C. viridis, was present in both lakes despite the different lifestyles (mixotrophic with green algal endosymbionts or heterotrophic without algae). Our results suggest a future revision of the species concept of the genus Coleps.}, } @article {pmid33715442, year = {2021}, author = {Curveira-Santos, G and Sutherland, C and Tenan, S and Fernández-Chacón, A and Mann, GKH and Pitman, RT and Swanepoel, LH}, title = {Mesocarnivore community structuring in the presence of Africa's apex predator.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1946}, pages = {20202379}, pmid = {33715442}, issn = {1471-2954}, mesh = {Africa ; Animals ; *Carnivora ; Ecosystem ; Geography ; Humans ; *Lions ; }, abstract = {Apex predator reintroductions have proliferated across southern Africa, yet their ecological effects and proposed umbrella benefits of associated management lack empirical evaluations. Despite a rich theory on top-down ecosystem regulation via mesopredator suppression, a knowledge gap exists relating to the influence of lions (Panthera leo) over Africa's diverse mesocarnivore (less than 20 kg) communities. We investigate how geographical variation in mesocarnivore community richness and occupancy across South African reserves is associated with the presence of lions. An interesting duality emerged: lion reserves held more mesocarnivore-rich communities, yet mesocarnivore occupancy rates and evenness-weighted diversity were lower in the presence of lions. Human population density in the reserve surroundings had a similarly ubiquitous negative effect on mesocarnivore occupancy. The positive association between species richness and lion presence corroborated the umbrella species concept but translated into small differences in community size. Distributional contractions of mesocarnivore species within lion reserves, and potentially corresponding numerical reductions, suggest within-community mesopredator suppression by lions, probably as a result of lethal encounters and responses to a landscape of fear. Our findings offer empirical support for the theoretical understanding of processes underpinning carnivore community assembly and are of conservation relevance under current large-predator orientated management and conservation paradigms.}, } @article {pmid33679677, year = {2021}, author = {On, SLW and Zhang, Y and Gehring, A and Patsekin, V and Chelikani, V and Flint, S and Wang, H and Billington, C and Fletcher, GC and Lindsay, J and Robinson, JP}, title = {Elastic Light Scatter Pattern Analysis for the Expedited Detection of Yersinia Species in Pork Mince: Proof of Concept.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {641801}, pmid = {33679677}, issn = {1664-302X}, abstract = {Isolation of the pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis from foods typically rely on slow (10-21 day) "cold enrichment" protocols before confirmed results are obtained. We describe an approach that yields results in 39 h that combines an alternative enrichment method with culture on a non-selective medium, and subsequent identification of suspect colonies using elastic light scatter (ELS) analysis. A prototype database of ELS profiles from five Yersinia species and six other bacterial genera found in pork mince was established, and used to compare similar profiles of colonies obtained from enrichment cultures from pork mince samples seeded with representative strains of Y. enterocolitica and Y. pseudotuberculosis. The presumptive identification by ELS using computerised or visual analyses of 83/90 colonies in these experiments as the target species was confirmed by partial 16S rDNA sequencing. In addition to seeded cultures, our method recovered two naturally occurring Yersinia strains. Our results indicate that modified enrichment combined with ELS is a promising new approach for expedited detection of foodborne pathogenic yersiniae.}, } @article {pmid33671365, year = {2021}, author = {Jia, TZ and Caudan, M and Mamajanov, I}, title = {Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {2}, pages = {}, pmid = {33671365}, issn = {2075-1729}, abstract = {Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.}, } @article {pmid33668927, year = {2021}, author = {Nave, M and Taş, M and Raupp, J and Tiwari, VK and Ozkan, H and Poland, J and Hale, I and Komatsuda, T and Distelfeld, A}, title = {The Independent Domestication of Timopheev's Wheat: Insights from Haplotype Analysis of the Brittle rachis 1 (BTR1-A) Gene.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33668927}, issn = {2073-4425}, mesh = {Domestication ; Evolution, Molecular ; Haplotypes ; Loss of Function Mutation ; Phylogeny ; Plant Proteins/*genetics ; Sequence Analysis, DNA/*methods ; Tetraploidy ; Triticum/classification/genetics/*growth & development ; }, abstract = {Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes BTR1-A and BTR1-B in the A and B subgenomes, respectively, that are responsible for this most visible domestication trait in T. turgidum. Resequencing of a large panel of wild and domesticated T. turgidum accessions subsequently led to the identification of the two progenitor haplotypes of the btr1-A and btr1-B domesticated alleles. Here, we extended the haplotype analysis to other T. turgidum subspecies and to the BTR1 homologues in the related T. timopheevii species. Our results showed that all the domesticated wheat subspecies within T. turgidum share common BTR1-A and BTR1-B haplotypes, confirming their common origin. In T. timopheevii, however, we identified a novel loss-of-function btr1-A allele underlying a partially brittle spike phenotype. This novel recessive allele appeared fixed within the pool of domesticated Timopheev's wheat but was also carried by one wild timopheevii accession exhibiting partial brittleness. The promoter region for BTR1-B could not be amplified in any T. timopheevii accessions with any T. turgidum primer combination, exemplifying the gene-level distance between the two species. Altogether, our results support the concept of independent domestication processes for the two polyploid, wheat-related species.}, } @article {pmid33617989, year = {2021}, author = {Schenková, J and Kment, P and Malenovský, I and Tóthová, A}, title = {Myxobdella socotrensis sp. nov., a new parasitic leech from Socotra Island, with comments on the phylogeny of Praobdellidae (Hirudinida: Arhynchobdellida).}, journal = {Parasitology international}, volume = {82}, number = {}, pages = {102310}, doi = {10.1016/j.parint.2021.102310}, pmid = {33617989}, issn = {1873-0329}, mesh = {Animals ; Brachyura/*physiology ; Female ; Indian Ocean Islands ; Leeches/anatomy & histology/*classification/genetics/*physiology ; Male ; Phylogeny ; Yemen ; }, abstract = {The Socotra Archipelago (Yemen) is remarkable for unique ecosystems and high endemism, for which it is often referred to as the "Galápagos of the Indian Ocean". Here we describe a new parasitic leech Myxobdella socotrensis sp. nov. from Socotra, the largest island of the archipelago. The new species was found in a freshwater spring attached to the endemic crab Socotrapotamon socotrensis (Hilgendorf, 1883) (Crustacea: Potamidae). Based on its morphology, ecology and a phylogenetic analysis of DNA sequence data (12S, 18S, 28S and COI gene markers), the new leech species is classified into the highly diversified family Praobdellidae (Hirudinida: Arhynchobdellida), distributed in tropical regions of Africa, Asia and Central and South America. The praobdellid leeches are known to infest mammalian mucous membranes, however, some taxa are associated with other hosts, namely crabs, amphibians and birds. By its morphology, the new species fits quite well in the current concept of the genus Myxobdella Oka, 1917. However, the monophyly of Myxobdella was not supported here by molecular data, pointing at the need of a more comprehensive systematic revision of the genus and family. As far as known, Myxobdella socotrensis sp. nov. is endemic to the Socotra Island, but more data are needed to understand its evolutionary origin, biology and distribution.}, } @article {pmid33611116, year = {2021}, author = {Hales, JE and Aoudjane, S and Aeppli, G and Dalby, PA}, title = {Proof-of-concept analytical instrument for label-free optical deconvolution of protein species in a mixture.}, journal = {Journal of chromatography. A}, volume = {1641}, number = {}, pages = {461968}, doi = {10.1016/j.chroma.2021.461968}, pmid = {33611116}, issn = {1873-3778}, support = {BB/E005942/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Chromatography/*instrumentation ; Fluorescence ; *Optical Phenomena ; Ovalbumin/analysis ; *Proof of Concept Study ; Proteins/*analysis ; Serum Albumin, Bovine/analysis ; }, abstract = {The adoption of process analytical technologies by the biopharmaceutical industry can reduce the cost of therapeutic drugs and facilitate investigation of new bioprocesses. Control of critical process parameters to retain critical product quality attributes within strict bounds is important for ensuring a consistently high product quality, but developing the sophisticated analytical technologies required has proven to be a major challenge. Here, we demonstrate a new optical technique for continuous monitoring of protein species as they are eluted from a chromatographic column, even when they fully co-elute with other protein species, without making any assumption about or peak-fitting to the elution profile. To achieve this, we designed and constructed a time-resolved intrinsic fluorescence lifetime chromatograph, and established an analytical framework for deconvolving and quantifying distinct but co-eluting protein species in real time. This proof-of-concept technology has potentially useful applications as a process analytical technology and more generally as an analytical technique for label-free quantification of proteins in mixtures.}, } @article {pmid33595417, year = {2021}, author = {Réblová, M and Nekvindová, J and Kolařík, M and Hernández-Restrepo, M}, title = {Delimitation and phylogeny of Dictyochaeta, and introduction of Achrochaeta and Tubulicolla, genera nova.}, journal = {Mycologia}, volume = {113}, number = {2}, pages = {390-433}, doi = {10.1080/00275514.2020.1822095}, pmid = {33595417}, issn = {1557-2536}, mesh = {Ascomycota/*classification/*genetics ; Cluster Analysis ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/genetics ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; }, abstract = {Dictyochaeta (Chaetosphaeriaceae) is a phialidic dematiaceous hyphomycete with teleomorphs classified in Chaetosphaeria. It is associated with significant variability of asexual morphological traits, which led to its broad delimitation. In the present study, six loci: nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), nuc 18S rDNA (18S), nuc 28S rDNA (28S), DNA-directed RNA polymerase II second largest subunit gene (RPB2), translation elongation factor 1-α (TEF1-α), and β-tubulin (TUB2), along with comparative morphological and cultivation studies, are used to reevaluate the concept of Dictyochaeta and establish species boundaries. Based on revised species, morphological characteristics of conidia (shape, septation, absence or presence of setulae), collarettes (shape), and setae (presence or absence) and an extension of the conidiogenous cell proved to be important at the generic level. The dual DNA barcoding using ITS and TEF1-α, together with TUB2, facilitated accurate identification of Dictyochaeta species. Thirteen species are accepted, of which seven are characterized in this study; an identification key is provided. It was revealed that D. fuegiana, the type species, is a complex of three distinct species including D. querna and the newly described D. stratosa. Besides, a new species, D. detriticola, and two new combinations, D. callimorpha and D. montana, are proposed. An epitype of D. montana is selected. Dictyochaeta includes saprobes on decaying wood, bark, woody fruits, and fallen leaves. Dictyochaeta is shown to be distantly related to the morphologically similar Codinaea, which is resolved as paraphyletic. Chaetosphaeria talbotii with a Dictyochaeta anamorph represents a novel lineage in the Chaetosphaeriaceae; it is segregated from Dictyochaeta, and a new genus Achrochaeta is proposed. Multigene phylogenetic analysis revealed that D. cylindrospora belongs to the Vermiculariopsiellales, and a new genus Tubulicolla is introduced.}, } @article {pmid33569656, year = {2021}, author = {Portera, M and Mandrioli, M}, title = {Who's afraid of epigenetics? Habits, instincts, and Charles Darwin's evolutionary theory.}, journal = {History and philosophy of the life sciences}, volume = {43}, number = {1}, pages = {20}, pmid = {33569656}, issn = {1742-6316}, mesh = {*Biological Evolution ; *Epigenesis, Genetic ; Epigenomics/*history ; *Habits ; *Heredity ; History, 19th Century ; *Selection, Genetic ; }, abstract = {Our paper aims at bringing to the fore the crucial role that habits play in Charles Darwin's theory of evolution by means of natural selection. We have organized the paper in two steps: first, we analyse value and functions of the concept of habit in Darwin's early works, notably in his Notebooks, and compare these views to his mature understanding of the concept in the Origin of Species and later works; second, we discuss Darwin's ideas on habits in the light of today's theories of epigenetic inheritance, which describe the way in which the functioning and expression of genes is modified by the environment, and how these modifications are transmitted over generations. We argue that Darwin's lasting and multifaceted interest in the notion of habit, throughout his intellectual life, is both conceptually and methodologically relevant. From a conceptual point of view, intriguing similarities can be found between Darwin's (early) conception of habit and contemporary views on epigenetic inheritance. From a methodological point of view, we suggest that Darwin's plastic approach to habits, from his early writings up to the mature works, can provide today's evolutionary scientists with a viable methodological model to address the challenging task of extending and expanding evolutionary theory, with particular reference to the integration of epigenetic mechanisms into existing models of evolutionary change. Over his entire life Darwin has modified and reassessed his views on habits as many times as required by evidence: his work on this notion may represent the paradigm of a habit of good scientific research methodology.}, } @article {pmid33566450, year = {2021}, author = {Martin, BT and Chafin, TK and Douglas, MR and Placyk, JS and Birkhead, RD and Phillips, CA and Douglas, ME}, title = {The choices we make and the impacts they have: Machine learning and species delimitation in North American box turtles (Terrapene spp.).}, journal = {Molecular ecology resources}, volume = {21}, number = {8}, pages = {2801-2817}, doi = {10.1111/1755-0998.13350}, pmid = {33566450}, issn = {1755-0998}, mesh = {Animals ; Gene Flow ; Machine Learning ; North America ; Phylogeny ; *Turtles/genetics ; }, abstract = {Model-based approaches that attempt to delimit species are hampered by computational limitations as well as the unfortunate tendency by users to disregard algorithmic assumptions. Alternatives are clearly needed, and machine-learning (M-L) is attractive in this regard as it functions without the need to explicitly define a species concept. Unfortunately, its performance will vary according to which (of several) bioinformatic parameters are invoked. Herein, we gauge the effectiveness of M-L-based species-delimitation algorithms by parsing 64 variably-filtered versions of a ddRAD-derived SNP data set collected from North American box turtles (Terrapene spp.). Our filtering strategies included: (i) minor allele frequencies (MAF) of 5%, 3%, 1%, and 0% (= none), and (ii) maximum missing data per-individual/per-population at 25%, 50%, 75%, and 100% (= no filtering). We found that species-delimitation via unsupervised M-L impacted the signal-to-noise ratio in our data, as well as the discordance among resolved clades. The latter may also reflect biogeographic history, gene flow, incomplete lineage sorting, or combinations thereof (as corroborated from previously observed patterns of differential introgression). Our results substantiate M-L as a viable species-delimitation method, but also demonstrate how commonly observed patterns of phylogenetic discordance can seriously impact M-L-classification.}, } @article {pmid33565164, year = {2022}, author = {Bouzid, NM and Archie, JW and Anderson, RA and Grummer, JA and Leaché, AD}, title = {Evidence for ephemeral ring species formation during the diversification history of western fence lizards (Sceloporus occidentalis).}, journal = {Molecular ecology}, volume = {31}, number = {2}, pages = {620-631}, doi = {10.1111/mec.15836}, pmid = {33565164}, issn = {1365-294X}, mesh = {Animals ; Biological Evolution ; Gene Flow ; Geography ; *Lizards/genetics ; Phylogeny ; }, abstract = {Divergence is often ephemeral, and populations that diverge in response to regional topographic and climatic factors may not remain reproductively isolated when they come into secondary contact. We investigated the geographical structure and evolutionary history of population divergence within Sceloporus occidentalis (western fence lizard), a habitat generalist with a broad distribution that spans the major biogeographical regions of Western North America. We used double digest RAD sequencing to infer population structure, phylogeny and demography. Population genetic structure is hierarchical and geographically structured with evidence for gene flow between biogeographical regions. Consistent with the isolation-expansion model of divergence during Quaternary glacial-interglacial cycles, gene flow and secondary contact are supported as important processes explaining the demographic histories of populations. Although populations may have diverged as they spread northward in a ring-like manner around the Sierra Nevada and southern Cascade Ranges, there is strong evidence for gene flow among populations at the northern terminus of the ring. We propose the concept of an "ephemeral ring species" and contrast S. occidentalis with the classic North American ring species, Ensatina eschscholtzii. Contrary to expectations of lower genetic diversity at northern latitudes following post-Quaternary-glaciation expansion, the ephemeral nature of divergence in S. occidentalis has produced centres of high genetic diversity for different reasons in the south (long-term stability) vs. the north (secondary contact).}, } @article {pmid33560551, year = {2021}, author = {Zhao, L and Sakornwimon, W and Lin, W and Zhang, P and Chantra, R and Dai, Y and Aierken, R and Wu, F and Li, S and Kittiwattanawong, K and Wang, X}, title = {Early divergence and differential population histories of the Indo-Pacific humpback dolphin in the Pacific and Indian Oceans.}, journal = {Integrative zoology}, volume = {16}, number = {4}, pages = {612-625}, doi = {10.1111/1749-4877.12527}, pmid = {33560551}, issn = {1749-4877}, mesh = {Animals ; DNA, Mitochondrial ; Dolphins/*classification/*genetics ; Gene Flow ; Indian Ocean ; Pacific Ocean ; *Phylogeography ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The currently recognized Indo-Pacific humpback dolphin occurs in estuaries and surrounding shallow waters from the South China Sea to the Asian coast of the Indian Ocean. However, a recent study suggested that the humpback dolphin from the Bay of Bengal may represent a distinct phylogenetic species. In this study, we sequenced 915-bp mtDNA segments from five geographic populations in both Chinese and Thai waters; together with previously published sequences, these data revealed that the ancestral Indo-Pacific humpback dolphin might have split during the transition from the Oligocene to Miocene (23.45 Mya, 95% HPD: 16.65-26.55 Mya), and then dispersed along the Pacific and Indian Ocean coasts of Asia. Genetic differentiation was detected between most of the examined populations, except for only a few pairwise populations in the northern South China Sea. Genetic differentiation/distance between the humpback dolphins from the northern and southern South China Sea met the sub-species threshold value proposed for marine mammals, whereas that between the humpback dolphins in the Pacific and the Indian Ocean was above the species threshold. Bayesian inference of historic gene flow indicated low but constant northward gene flow along the Indian Ocean coast; however, there was a recent abrupt increase in gene flow in the Pacific region, likely due to the shortening coastline at the low stand of sea level. Our results revealed that the current taxonomic classification of Indo-Pacific humpback dolphins may not reflect their phylogeography.}, } @article {pmid33546461, year = {2021}, author = {Kaasalainen, U and Tuovinen, V and Kirika, PM and Mollel, NP and Hemp, A and Rikkinen, J}, title = {Diversity of Leptogium (Collemataceae, Ascomycota) in East African Montane Ecosystems.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33546461}, issn = {2076-2607}, abstract = {Tropical mountains and especially their forests are hot spots of biodiversity threatened by human population pressure and climate change. The diversity of lichens in tropical Africa is especially poorly known. Here we use the mtSSU and nuITS molecular markers together with morphology and ecology to assess Leptogium (Peltigerales, Ascomycota) diversity in the tropical mountains of Taita Hills and Mt. Kasigau in Kenya and Mt. Kilimanjaro in Tanzania. The sampled habitats cover a wide range of ecosystems from savanna to alpine heath vegetation and from relatively natural forests to agricultural environments and plantation forests. We demonstrate that Leptogium diversity in Africa is much higher than previously known and provide preliminary data on over 70 putative species, including nine established species previously known from the area and over 60 phylogenetically, morphologically, and/or ecologically defined Operational Taxonomic Units (OTUs). Many traditional species concepts are shown to represent morphotypes comprised of several taxa. Many of the species were only found from specific ecosystems and/or restricted habitats and are thus threatened by ongoing habitat fragmentation and degradation of the natural environment. Our results emphasize the importance of molecular markers in species inventories of highly diverse organism groups and geographical areas.}, } @article {pmid33542589, year = {2020}, author = {Fawley, MW and Fawley, KP}, title = {Identification of Eukaryotic Microalgal Strains.}, journal = {Journal of applied phycology}, volume = {32}, number = {5}, pages = {2699-2709}, pmid = {33542589}, issn = {0921-8971}, support = {P20 GM103429/GM/NIGMS NIH HHS/United States ; }, abstract = {Proper identification and documentation of microalgae is often lacking in publications of applied phycology, algal physiology and biochemistry. Identification of many eukaryotic microalgae can be very daunting to the non-specialist. We present a systematic process for identifying eukaryotic microalgae using morphological evidence and DNA sequence analysis. Our intent was to provide an identification method that could be used by non-taxonomists, but which is grounded in the current techniques used by algal taxonomists. Central to the identification is database searches with DNA sequences of appropriate loci. We provide usable criteria for identification at the genus or species level, depending on the availability of sequence data in curated databases and repositories. Particular attention is paid to dealing with possible misidentifications in DNA databases and utilizing current taxonomy.}, } @article {pmid33539375, year = {2021}, author = {Lee, Y and Thieme, T and Kim, H}, title = {Complex evolution in Aphis gossypii group (Hemiptera: Aphididae), evidence of primary host shift and hybridization between sympatric species.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0245604}, pmid = {33539375}, issn = {1932-6203}, mesh = {Animals ; Aphids/*genetics ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genetic Loci ; Genetic Variation ; Haplotypes ; Host-Pathogen Interactions/*genetics ; *Hybridization, Genetic ; Microsatellite Repeats/genetics ; Rhamnus/genetics ; *Sympatry ; }, abstract = {Aphids provide a good model system to understand the ecological speciation concept, since the majority of the species are host-specific, and they spend their entire lifecycle on certain groups of host plants. Aphid species that apparently have wide host plant ranges have often turned out to be complexes of host-specialized biotypes. Here we investigated the various host-associated populations of the two recently diverged species, Aphis gossypii and A. rhamnicola, having multiple primary hosts, to understand the complex evolution with host-associated speciation. Using mitochondrial DNA marker and nine microsatellite loci, we reconstructed the haplotype network, and analyzed the genetic structure and relationships. Approximate Bayesian computation was also used to infer the ancestral primary host and host-associated divergence, which resulted in Rhamnus being the most ancestral host for A. gossypii and A. rhamnicola. As a result, Aphis gossypii and A. rhamnicola do not randomly use their primary and secondary host plants; rather, certain biotypes use only some secondary and specific primary hosts. Some biotypes are possibly in a diverging state through specialization to specific primary hosts. Our results also indicate that a new heteroecious race can commonly be derived from the heteroecious ancestor, showing strong evidence of ecological specialization through a primary host shift in both A. gossypii and A. rhamnicola. Interestingly, A. gossypii and A. rhamnicola shared COI haplotypes with each other, thus there is a possibility of introgression by hybridization between them by cross-sharing same primary hosts. Our results contribute to a new perspective in the study of aphid evolution by identifying complex evolutionary trends in the gossypii sensu lato complex.}, } @article {pmid33534662, year = {2021}, author = {Bradshaw, M and Braun, U and Meeboon, J and Tobin, P}, title = {Phylogeny and taxonomy of powdery mildew caused by Erysiphe species on Corylus hosts.}, journal = {Mycologia}, volume = {113}, number = {2}, pages = {459-475}, doi = {10.1080/00275514.2020.1837568}, pmid = {33534662}, issn = {1557-2536}, mesh = {Asia ; Corylus/*microbiology ; DNA, Fungal/*genetics ; DNA, Ribosomal Spacer/genetics ; Erysiphe/*classification/*genetics/pathogenicity ; North America ; *Phylogeny ; Plant Diseases/*microbiology ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; }, abstract = {Erysiphe species (powdery mildews) on Corylus and Ostrya hosts (Betulaceae subfam. Coryloideae) in Asia and North America are widespread pathogens on these economically and ecologically valuable nut crops. An improved understanding of their phylogeny and taxonomy is of ecological and applied importance. Phylogenetic analyses and morphological reexaminations conducted in this study revealed a higher degree of diversity and cryptic speciation than reflected in earlier species concepts. North American collections on C. cornuta, which were previously assigned to E. corylacearum, proved to constitute a species of its own and are herein introduced as E. cornutae, sp. nov. Two additional North American species, E. coryli-americanae, sp. nov. and E. ostryae, sp. nov., have been detected on C. americana and O. virginiana and are described. They are morphologically similar to E. cornutae, but genetically distinct. Based on phylogenetic analyses, E. corylacearum is an Asian species confined to various Asian Corylus species. Sequence data retrieved from Japanese type material of E. corylicola revealed that this species clusters with sequences from E. elevata on Catalpa species, distant from all other Erysiphe species on Corylus. Morphologically similar, yet distinct, specimens on C. sieboldiana, which were previously assigned to E. corylicola, form a distinct, distant clade. The species involved is described herein as E. pseudocorylacearum, sp. nov. Additionally, an unusual infection of C. sieboldiana in Japan by E. syringae has been shown by means of sequence data. The phylogeny and taxonomy of Erysiphe species belonging to the Corylioideae are discussed in detail, and a key to the species concerned is provided.}, } @article {pmid33532072, year = {2021}, author = {Génier, CSV and Guglielmo, CG and Mitchell, GW and Falconer, M and Hobson, KA}, title = {Nutritional consequences of breeding away from riparian habitats in Bank Swallows: new evidence from multiple endogenous markers.}, journal = {Conservation physiology}, volume = {9}, number = {1}, pages = {coaa140}, pmid = {33532072}, issn = {2051-1434}, abstract = {The Bank Swallow (Riparia riparia), a threatened species in Canada, breeds primarily in banks at lakeshores and rivers and in artificial (typically inland) aggregate mining pits. Inland pits may be ecological traps for this species, but relative dietary trade-offs between these two nesting habitats have not been investigated. The availability of aquatic emergent insects at lakeshores may have associated nutritional benefits for growing nestlings due to increased omega-3 fatty acids (FAs) in prey. We compared the diets of juvenile swallows from lakeshore and inland pit sites using assays of stable isotope values (δ[13]C, δ[15]N, δ[2]H) of feathers, faecal DNA metabarcoding and blood plasma FAs. Colony proximity to Lake Erie influenced the use of aquatic versus terrestrial insects by Bank Swallow adults and juveniles. Feather δ[2]H was particularly useful as a tracer of aquatic emergent versus terrestrial prey, and inland juveniles had feathers enriched in [2]H, reflective of diets composed of fewer aquatic emergent insects. DNA metabarcoding of juvenile and adult faecal material indicated that lakeshore birds consumed more aquatic-emergent chironomids than inland birds. Lakeshore juveniles had elevated plasma omega-3 eicosapentaenoic acid levels compared with inland pit-breeding birds. We discuss the need to consider 'nutritional landscapes' and the importance of this concept in conservation of declining species and populations.}, } @article {pmid33502509, year = {2021}, author = {Cong, Q and Shen, J and Zhang, J and Li, W and Kinch, LN and Calhoun, JV and Warren, AD and Grishin, NV}, title = {Genomics Reveals the Origins of Historical Specimens.}, journal = {Molecular biology and evolution}, volume = {38}, number = {5}, pages = {2166-2176}, pmid = {33502509}, issn = {1537-1719}, support = {R35 GM127390/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Altitude ; Animals ; Butterflies/*genetics ; DNA, Ancient/*analysis ; Genomics/*methods ; Pigmentation/genetics ; }, abstract = {Centuries of zoological studies have amassed billions of specimens in collections worldwide. Genomics of these specimens promises to reinvigorate biodiversity research. However, because DNA degrades with age in historical specimens, it is a challenge to obtain genomic data for them and analyze degraded genomes. We developed experimental and computational protocols to overcome these challenges and applied our methods to resolve a series of long-standing controversies involving a group of butterflies. We deduced the geographical origins of several historical specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old specimens that serve as irreplaceable embodiments of species concepts cannot be confidently assigned to extant species or population due to the lack of diagnostic morphological features and clear documentation of the collection locality. The ability to determine where they were collected will resolve many on-going disputes. More broadly, we show the utility of applying genomics to historical museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.}, } @article {pmid33495621, year = {2021}, author = {Nowinski, B and Moran, MA}, title = {Niche dimensions of a marine bacterium are identified using invasion studies in coastal seawater.}, journal = {Nature microbiology}, volume = {6}, number = {4}, pages = {524-532}, pmid = {33495621}, issn = {2058-5276}, mesh = {California ; Dinoflagellida/physiology ; *Ecosystem ; Eutrophication ; Gene Expression ; Heterotrophic Processes ; *Models, Biological ; Phytoplankton/physiology ; Rhodobacteraceae/genetics/*physiology ; Seawater/chemistry/*microbiology ; Stress, Physiological ; }, abstract = {Niche theory is a foundational ecological concept that explains the distribution of species in natural environments. Identifying the dimensions of any organism's niche is challenging because numerous environmental factors can affect organism viability. We used serial invasion experiments to introduce Ruegeria pomeroyi DSS-3, a heterotrophic marine bacterium, into a coastal phytoplankton bloom on 14 dates. RNA-sequencing analysis of R. pomeroyi was conducted after 90 min to assess its niche dimensions in this dynamic ecosystem. We identified ~100 external conditions eliciting transcriptional responses, which included substrates, nutrients, metals and biotic interactions such as antagonism, resistance and cofactor synthesis. The peak bloom was characterized by favourable states for most of the substrate dimensions, but low inferred growth rates of R. pomeroyi at this stage indicated that its niche was narrowed by factors other than substrate availability, most probably negative biotic interactions with the bloom dinoflagellate. Our findings indicate chemical and biological features of the ocean environment that can constrain where heterotrophic bacteria survive.}, } @article {pmid33482977, year = {2021}, author = {Tibayrenc, M and Ayala, FJ}, title = {Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria.}, journal = {Advances in parasitology}, volume = {111}, number = {}, pages = {75-117}, doi = {10.1016/bs.apar.2020.12.001}, pmid = {33482977}, issn = {2163-6079}, mesh = {Animals ; *Bacteria/genetics/pathogenicity ; Biological Evolution ; Humans ; Infections/*microbiology ; *Parasites/genetics/pathogenicity ; *Yeasts/genetics/pathogenicity ; }, abstract = {The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).}, } @article {pmid33479828, year = {2021}, author = {Nittu, G and Bhavana, PM and Shameer, TT and Ramakrishnan, B and Archana, R and Kaushal, KK and Khedkar, GD and Mohan, G and Jyothi, M and Sanil, R}, title = {Simple Nested Allele-Specific approach with penultimate mismatch for precise species and sex identification of tiger and leopard.}, journal = {Molecular biology reports}, volume = {48}, number = {2}, pages = {1667-1676}, pmid = {33479828}, issn = {1573-4978}, mesh = {Alleles ; Animals ; Biomarkers ; DNA Primers ; Endangered Species ; Female ; Forensic Genetics/*methods ; Gender Identity ; India ; Male ; Panthera/blood/*genetics/metabolism ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Species Specificity ; Tigers/blood/*genetics/metabolism ; X Chromosome/genetics ; Y Chromosome/genetics ; }, abstract = {Accurate species and sex identification of non-invasive and forensic samples of the tiger and leopard is still confusing when using the allele-specific methods. We designed allele-specific methods with penultimate nucleotide mismatch in a nested manner for the exact identification and double-checking of forensic samples. The mismatch design is a novel concept in species and sex identification, making the allele-specific targeting precise. We developed three sets of markers, a 365 bp outer and a 98 bp inner marker for nested tiger species identification assay, 136 bp leopard specific marker, and carnivore sex identification markers. We validated the method with tissue/blood forensic samples of various felids and herbivorous available in our lab and on known fecal samples from Vandalur Zoo. We also collected 37 scat samples at diverse stages of deterioration from the Mudumalai Tiger Reserve, Tamil Nadu, India. The 365 bp targeted markers resulted in 70.2% (n = 22; 22/37) amplification success, while the 98 bp FAM-labelled marker amplified 89% (n = 33; 33/37) scat samples independently. The 136 bp leopard markers answered four scat samples (11%) unrequited by the tiger specific markers. We evaluated species and the sex identification with these markers in another 190 non-invasive samples provided by the Mudumalai Tiger Reserve authorities. Among which 56.3% (n = 107) of samples were recognized as tiger (64 male and 43 female) and 38.9% (n = 74) as leopard (41 male and 33 female). The method supersedes any other previous methods in this regard by its high accuracy and simplicity.}, } @article {pmid33469721, year = {2021}, author = {Kim, MS and Kim, KH and Hwang, SJ and Lee, TK}, title = {Role of Algal Community Stability in Harmful Algal Blooms in River-Connected Lakes.}, journal = {Microbial ecology}, volume = {82}, number = {2}, pages = {309-318}, pmid = {33469721}, issn = {1432-184X}, mesh = {Ecosystem ; *Harmful Algal Bloom ; Lakes ; *Microcystis ; Rivers ; }, abstract = {Harmful algal blooms (HABs) in freshwater produce toxins that pose a threat to public health and aquatic ecosystems. Although algal communities have been studied globally to understand the characteristics of HABs, the occurrence of toxic cyanobacteria in freshwater ecosystems is rarely understood. Unlike abiotic factors, the effects of biotic factors (e.g., interaction, dominance, and variability) on the occurrence of toxic cyanobacteria were overlooked due to the intricate interaction of microorganisms under different environmental conditions. To address this problem, a comprehensive ecological concept stability, which encompasses variations in species or communities due to changing biological interactions or environmental fluctuations, was applied in this study. The algal communities in six river-connected lakes in the North Han River, South Korea, were classified into high and low stability groups. The algal species belonging to diatoms and green algae groups played a major role in the interaction within the algal community in highly stable lakes, but the frequency of Microcystis led the interaction within the algal community at the center of the network in low-stability lakes. These results indicate that the interaction within the cluster is easily changed by Microcystis, where the abundance explosively increases in lakes with low algal community stability. Water quality is more strongly associated with the occurrence of toxic cyanobacteria (Microcystis and Dolichospermum). In low-stability lakes, more diverse water quality indicators are correlated with the development of toxic algae than in high-stability lakes. This paper is the first report on the importance of algal community stability in freshwater in the occurrence of toxic cyanobacteria and offers a new perspective on Microcystis monitoring and management.}, } @article {pmid33437443, year = {2021}, author = {Steibl, S and Laforsch, C}, title = {Compartmentalized organization of ecological niche occupation in insular invertebrate communities.}, journal = {Ecology and evolution}, volume = {11}, number = {1}, pages = {471-480}, pmid = {33437443}, issn = {2045-7758}, abstract = {Understanding the mechanisms of species distribution within ecosystems is a fundamental question of ecological research. The current worldwide changes and loss of habitats associated with a decline in species richness render this topic a key element for developing mitigation strategies. Ecological niche theory is a widely accepted concept to describe species distribution along environmental gradients where each taxon occupies its own distinct set of environmental parameters, that is, its niche. Niche occupation has been described in empirical studies for different closely related taxa, like ant, ungulate, or skink species, just to name a few. However, how species assemblages of whole ecosystems across multiple taxa are structured and organized has not been investigated thoroughly, although considering all taxa of a community would be essential when analyzing realized niches. Here, we investigated the organization of niche occupation and species distribution for the whole ground-associated invertebrate community of small tropical insular ecosystems. By correlating environmental conditions with species occurrences using partial canonical correspondence analysis (pCCA), we demonstrated that the ground-associated invertebrate community does not spread evenly across the overall niche space, but instead is compartmentalized in four distinct clusters: crustacean and gastropod taxa occurred in one cluster, attributable to the beach habitat, whereas hexapods and spider taxa occurred in three distinct inland clusters, attributable to distinct inland habitats, that is, grassland, open forest, and dense forest. Within the clusters, co-occurrence pattern analysis suggested only a few negative interactions between the different taxa. By studying ground-associated insular invertebrate communities, we have shown that species distribution and niche occupation can be, similar to food webs, organized in a compartmentalized way. The compartmentalization of the niche space might thereby be a mechanism to increase ecosystem resilience, as disturbances cascade more slowly throughout the ecosystem.}, } @article {pmid33437429, year = {2021}, author = {Liu, M and Shoukouhi, P and Bisson, KR and Wyka, SA and Broders, KD and Menzies, JG}, title = {Sympatric divergence of the ergot fungus, Claviceps purpurea, populations infecting agricultural and nonagricultural grasses in North America.}, journal = {Ecology and evolution}, volume = {11}, number = {1}, pages = {273-293}, pmid = {33437429}, issn = {2045-7758}, abstract = {The ergot diseases of agricultural and nonagricultural grasses are caused by the infection of Claviceps spp. (Hypocreales, Ascomycota) on florets, producing dark spur-like sclerotia on spikes that are toxic to humans and animals, leading to detrimental impacts on agriculture and economy due to the downgrading of cereal grains, import-export barriers, reduced yield, and ecological concerns. At least seven phylogenetic lineages (phylogenetic species) were identified within the premolecular concept of C. purpurea s.l. (sensu lato) in agricultural areas and vicinities in Canada and the Western United States. Claviceps purpurea s.s (sensu stricto) remained as the most prevalent species with a wide host range, including cereal crops, native, invasive, and weedy grasses. The knowledge on genetic diversity and distribution of C. purpurea s.s. in North America is lacking. The objective of the present study was to shed light on genetic differentiation and evolution of the natural populations of C. purpurea s.s. Multilocus DNA sequences of samples from Canada and the Western USA were analyzed using a phylogenetic network approach, and population demographic parameters were investigated. Results showed that three distinct genetically subdivided populations exist, and the subdivision is not correlated with geographic or host differentiations. Potential intrinsic mechanisms that might play roles in leading to the cessation of gene flows among the subpopulations, that is, mating and/or vegetative incompatibility, genomic adaptation, were discussed. The neutrality of two house-keeping genes that are widely used for DNA barcoding, that is, translation elongation factor 1-α (TEF1-α) and RNA polymerase II second largest subunit (RPB2), was challenged and discussed.}, } @article {pmid33410172, year = {2021}, author = {Ng, E and Tay, JRH and Balan, P and Ong, MMA and Bostanci, N and Belibasakis, GN and Seneviratne, CJ}, title = {Metagenomic sequencing provides new insights into the subgingival bacteriome and aetiopathology of periodontitis.}, journal = {Journal of periodontal research}, volume = {56}, number = {2}, pages = {205-218}, doi = {10.1111/jre.12811}, pmid = {33410172}, issn = {1600-0765}, mesh = {*Dental Plaque ; Dysbiosis ; Humans ; *Microbiota/genetics ; *Periodontitis/genetics/therapy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {"Open-ended" molecular techniques such as 16S rRNA sequencing have revealed that the oral bacteriome of subgingival plaque is more diverse than originally thought. 16S rRNA analysis has demonstrated that constituents of the overall bacterial community are qualitatively similar in health and disease, differing mainly in their relative proportions with respect to each other. Species in low abundance can also act as critical species, leading to the concept of global community dysbiosis which relates to shifts in community structure, rather than shifts in membership. Correlation analysis suggests that coordinated interactions in the community are essential for incipient dysbiosis and disease pathogenesis. The subgingival bacteriome also provides biomarkers that are useful for disease detection and management. Combined with clinical and biological parameters, these may assist clinicians in developing and implementing effective treatment strategies to restore microbial homeostasis and monitor disease. Identification of higher risk groups or poor responders to treatment using unique subgingival bacteriome signatures may also lead to early intervention.}, } @article {pmid33396008, year = {2021}, author = {Arpaia, S}, title = {Environmental risk assessment in agro-ecosystems: Revisiting the concept of receiving environment after the EFSA guidance document.}, journal = {Ecotoxicology and environmental safety}, volume = {208}, number = {}, pages = {111676}, doi = {10.1016/j.ecoenv.2020.111676}, pmid = {33396008}, issn = {1090-2414}, mesh = {Crops, Agricultural/genetics/*growth & development ; Ecosystem ; Environmental Monitoring/legislation & jurisprudence/*methods ; Food Safety/*methods ; Government Publications as Topic ; Guidelines as Topic ; Pesticides/toxicity ; Plants, Genetically Modified/*growth & development ; Risk Assessment/methods ; }, abstract = {The environmental risk assessment (ERA) for genetically modified plants (GMPs) is a prerequisite for commercial approval of these new varieties according to regulatory systems worldwide. The first country to regulate GM crops was the USA and the issue of possible environmental impacts was based on the principles used in risk assessment of pesticides. Two main pillars of this approach are the use of surrogate species for testing effects on non-target organisms using a tiered assessment with clear thresholds to indicate the need to move between tiers. The latest EFSA guidance document on ERA of Genetically Modified Organisms considers specifically the receiving environment in preparation of ERA for commercial cultivation of GMPs. According to existing guidelines in the EU, the receiving environment is defined by three mutually interacting components: the characteristics of the environmental stressor (i.e. the GM plant), the bio-geographical regions where the commercial release of the crop is expected and the agricultural systems therein. Difference in agronomic and ecological conditions (e.g. use of different varieties, vegetation of adjacent areas, non-target species assemblages, sensitivity of local species to the stressors) suggests that explicit considerations of the receiving environments are necessary. Results from field experiments indicate that differences in cultivation practices, e.g. the herbicide regime used on herbicide-tolerant GM crops, may induce direct and indirect effects on wild plant distribution and abundance, with consequent repercussions on food webs based on these plants. Moreover, ecological literature indicates that the concept of surrogate species has clear limitations if applied broadly to any ERA. Starting from case studies regarding GMPs, this paper discusses some ecological and agronomic characteristics of agro-ecosystems, which have implications in the elaboration of both hazard and exposure analyses during ERA. The species selection approach indicated in the EFSA Guidance Document and the consideration of the area(s) of the expected release of the new variety may provide the basis to an ecologically sound ERA for a range of environmental stressors. The quality of the data that become available for risk managers with this approach may support a more transparent and dependable ERA and risk management for GMPs as well as for other potential environmental stressors in agro-ecosystems.}, } @article {pmid33368983, year = {2021}, author = {Padial, JM and De la Riva, I}, title = {A paradigm shift in our view of species drives current trends in biological classification.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {96}, number = {2}, pages = {731-751}, doi = {10.1111/brv.12676}, pmid = {33368983}, issn = {1469-185X}, mesh = {*Ecosystem ; *Genetics, Population ; Geography ; Phylogeny ; }, abstract = {Discontent about changes in species classifications has grown in recent years. Many of these changes are seen as arbitrary, stemming from unjustified conceptual and methodological grounds, or leading to species that are less distinct than those recognised in the past. We argue that current trends in species classification are the result of a paradigm shift toward which systematics and population genetics have converged and that regards species as the phylogenetic lineages that form the branches of the Tree of Life. Species delimitation now consists of determining which populations belong to which individual phylogenetic lineage. This requires inferences on the process of lineage splitting and divergence, a process to which we have only partial access through incidental evidence and assumptions that are themselves subject to refutation. This approach is not free of problems, as horizontal gene transfer, introgression, hybridisation, incorrect assumptions, sampling and methodological biases can mislead inferences of phylogenetic lineages. Increasing precision is demanded through the identification of both sister relationships and processes blurring or mimicking phylogeny, which has triggered, on the one hand, the development of methods that explicitly address such processes and, on the other hand, an increase in geographical and character data sampling necessary to infer/test such processes. Although our resolving power has increased, our knowledge of sister relationships - what we designate as species resolution - remains poor for many taxa and areas, which biases species limits and perceptions about how divergent species are or ought to be. We attribute to this conceptual shift the demise of trinominal nomenclature we are witnessing with the rise of subspecies to species or their rejection altogether; subspecies are raised to species if they are found to correspond to phylogenetic lineages, while they are rejected as fabricated taxa if they reflect arbitrary partitions of continuous or non-hereditary variation. Conservation strategies, if based on taxa, should emphasise species and reduce the use of subspecies to avoid preserving arbitrary partitions of continuous variation; local variation is best preserved by focusing on biological processes generating ecosystem resilience and diversity rather than by formally naming diagnosable units of any kind. Since many binomials still designate complexes of species rather than individual species, many species have been discovered but not named, geographical sampling is sparse, gene lineages have been mistaken for species, plenty of species limits remain untested, and many groups and areas lack adequate species resolution, we cannot avoid frequent changes to classifications as we address these problems. Changes will not only affect neglected taxa or areas, but also popular ones and regions where taxonomic research remained dormant for decades and old classifications were taken for granted.}, } @article {pmid33354143, year = {2020}, author = {Toledo, CAP and Souza, VC and Lucas, EJ}, title = {Nomenclatural and taxonomic updates in Rourea subgen. Rourea sect. Multifoliolatae (Connaraceae).}, journal = {PhytoKeys}, volume = {169}, number = {}, pages = {137-175}, pmid = {33354143}, issn = {1314-2011}, abstract = {The pantropical genus Rourea Aubl. (Connaraceae) is composed of ca. 70 species, most of which occur in the Neotropics. Rourea is currently subdivided into three subgenera, with the American taxa included in Rourea subgen. Rourea. Forero (1976) recognised six sections for the species of the New World, with Rourea subgen. R. sect. Multifoliolatae being exclusive to Brazil, characterised by multifoliolate leaves, relatively small leaflets and the staminal tube (0.8-)1-1.5 mm long. Following Forero's (1976) treatment, additional botanical collections have become available in Brazilian herbaria, allowing re-evaluation of species concepts. This work recognises and revises 12 species in this section, mainly restricted to southeastern Brazil and southern Bahia. A nomenclatural and taxonomic study of these species is here presented, including an identification key, morphological descriptions, illustrations and geographic distribution maps. A new species is also described.}, } @article {pmid35019612, year = {2020}, author = {Darpentigny, C and Sillard, C and Menneteau, M and Martinez, E and Marcoux, PR and Bras, J and Jean, B and Nonglaton, G}, title = {Antibacterial Cellulose Nanopapers via Aminosilane Grafting in Supercritical Carbon Dioxide.}, journal = {ACS applied bio materials}, volume = {3}, number = {12}, pages = {8402-8413}, doi = {10.1021/acsabm.0c00688}, pmid = {35019612}, issn = {2576-6422}, abstract = {In this work, we present an innovative strategy for the grafting of an antibacterial agent onto nanocellulose materials in supercritical carbon dioxide (scCO2). Dense cellulose nanofibril (CNF) nanopapers were prepared and subsequently functionalized in supercritical carbon dioxide with an aminosilane, N-(6-aminohexyl)aminopropyltrimethoxysilane (AHA-P-TMS). Surface characterization (X-ray photoelectron spectroscopy, contact angle, ζ-potential analysis) evidenced the presence of the aminosilane. The results show that the silane conformation depends on the curing process: a nonpolycondensed conformation of grafted silane with the amino groups facing outwards was favored by curing in an oven, while the curing step performed in scCO2 yielded CNF structures with the alkyl chain facing outwards. The grafted nanopapers exhibited antibacterial activity, and no antibacterial agent was released into the media. Furthermore, these materials proved to benefit from low cytotoxicity. This study offers a proof of concept for the covalent grafting of active species on nanocellulose structures and the control of aminosilane orientation using a green and controlled approach. These newly designed materials could be used for their antibacterial activity in the biomedical field. Thus, perspectives for topical administration and design of wound dressing could be envisaged.}, } @article {pmid33321948, year = {2020}, author = {Skuza, L and Filip, E and Szućko, I and Bocianowski, J}, title = {SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species.}, journal = {International journal of molecular sciences}, volume = {21}, number = {24}, pages = {}, pmid = {33321948}, issn = {1422-0067}, mesh = {DNA Barcoding, Taxonomic/methods ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; *INDEL Mutation ; Secale/classification/*genetics ; Untranslated Regions ; }, abstract = {Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3-8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.}, } @article {pmid33311254, year = {2020}, author = {Baker, AJ and Heraty, JM}, title = {The New World ant parasitoid genus Orasema (Hymenoptera: Eucharitidae).}, journal = {Zootaxa}, volume = {4888}, number = {1}, pages = {zootaxa.4888.1.1}, doi = {10.11646/zootaxa.4888.1.1}, pmid = {33311254}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; *Ants ; *Hymenoptera ; }, abstract = {A key is provided to 16 recognized species groups, plus several species not assigned to species group, of Orasema Cameron (Eucharitidae), a widespread New World genus of myrmicine ant (Formicidae: Myrmicinae) parasitoids ranging from northern Argentina to southern Canada. Eight of the species groups are revised, of which five are newly established; keys are given to the species of each treated group, 22 species are newly described, and detailed life histories of several well-documented species are discussed. Revised are the Orasema coloradensis group (four species: O. coloradensis Wheeler, O. iridescens n. sp., O. scaura n. sp., and O. violacea Ashmead), the Orasema bakeri group (six species: O. bablyi n. sp., O. bakeri Gahan, O. dubitata n. sp., O. polymyrmex n. sp., O. taii Chien Heraty, and O. texana Gahan), the Orasema tolteca group (two species: O. castilloae n. sp. and O. tolteca Mann), the Orasema sixaolae group (newly established, with four species: O. brachycephala n. sp., O. nebula n. sp., O. sixaolae Wheeler Wheeler, and O. tinalandia n. sp.), the Orasema acuminata group (newly established, with two species: O. acuminata n. sp. and O. cerulea n. sp.), the Orasema peraltai group (newly established, with two species: O. chrysozona n. sp. and O. peraltai n. sp.), the Orasema johnsoni group (newly established, with two species: O. johnsoni n. sp. and O. spyrogaster n. sp.), and the Orasema heacoxi group (newly established, with two species: O. heacoxi n. sp. and O. masonicki n. sp.). Newly described or treated species not placed to species group are O. brasiliensis (Bréthes), O. cirrhocnemis n. sp., O. monstrosa n. sp., O. mutata n. sp., O. psarops n. sp., and O. roppai n. sp. Species concepts and relationships are based on morphology and a recently published molecular phylogeny.}, } @article {pmid33304032, year = {2020}, author = {Jarrett, S}, title = {Consciousness reduced: The role of the 'idiot' in early evolutionary psychology.}, journal = {History of the human sciences}, volume = {33}, number = {5}, pages = {110-137}, pmid = {33304032}, issn = {0952-6951}, abstract = {A conception of the idiotic mind was used to substantiate late 19th-century theories of mental evolution. A new school of animal/comparative psychologists attempted from the 1870s to demonstrate that evolution was a mental as well as a physical process. This intellectual enterprise necessitated the closure, or narrowing, of the 'consciousness gap' between human and animal species. A concept of a quasi-non-conscious human mind, set against conscious intention and ability in higher animals, provided an explanatory framework for the human-animal continuum and the evolution of consciousness. The article addresses a significant lacuna in the historiographies of intellectual disability, animal science, and evolutionary psychology, where the application of a conception of human idiocy to advance theories of consciousness evolution has not hitherto been explored. These ideas retain contemporary resonance in ethology and cognitive psychology, and in the theory of 'speciesism', outlined by Peter Singer in Animal Liberation (1975), which claims that equal consideration of interests is not arbitrarily restricted to members of the human species, and advocates euthanasia of intellectually disabled human infants. Speciesism remains at the core of animal rights activism today. The article also explores the influence of the idea of the semi-evolved idiot mind in late-Victorian anthropology and neuroscience. These ideas operated in a separate intellectual sphere to eugenic thought. They were (and remain) deeply influential, and were at the heart of the idea of the moral idiot or imbecile, targeted in the 1913 Mental Deficiency Act, as well as in 20th-century animal and human consciousness theory.}, } @article {pmid33299185, year = {2020}, author = {Hoyal Cuthill, JF and Guttenberg, N and Budd, GE}, title = {Impacts of speciation and extinction measured by an evolutionary decay clock.}, journal = {Nature}, volume = {588}, number = {7839}, pages = {636-641}, pmid = {33299185}, issn = {1476-4687}, mesh = {Animals ; *Extinction, Biological ; *Fossils ; *Genetic Speciation ; History, Ancient ; *Machine Learning ; Plants ; Time Factors ; }, abstract = {The hypothesis that destructive mass extinctions enable creative evolutionary radiations (creative destruction) is central to classic concepts of macroevolution[1,2]. However, the relative impacts of extinction and radiation on the co-occurrence of species have not been directly quantitatively compared across the Phanerozoic eon. Here we apply machine learning to generate a spatial embedding (multidimensional ordination) of the temporal co-occurrence structure of the Phanerozoic fossil record, covering 1,273,254 occurrences in the Paleobiology Database for 171,231 embedded species. This facilitates the simultaneous comparison of macroevolutionary disruptions, using measures independent of secular diversity trends. Among the 5% most significant periods of disruption, we identify the 'big five' mass extinction events[2], seven additional mass extinctions, two combined mass extinction-radiation events and 15 mass radiations. In contrast to narratives that emphasize post-extinction radiations[1,3], we find that the proportionally most comparable mass radiations and extinctions (such as the Cambrian explosion and the end-Permian mass extinction) are typically decoupled in time, refuting any direct causal relationship between them. Moreover, in addition to extinctions[4], evolutionary radiations themselves cause evolutionary decay (modelled co-occurrence probability and shared fraction of species between times approaching zero), a concept that we describe as destructive creation. A direct test of the time to over-threshold macroevolutionary decay[4] (shared fraction of species between two times ≤ 0.1), counted by the decay clock, reveals saw-toothed fluctuations around a Phanerozoic mean of 18.6 million years. As the Quaternary period began at a below-average decay-clock time of 11 million years, modern extinctions further increase life's decay-clock debt.}, } @article {pmid33242175, year = {2020}, author = {Friedman, WE and Endress, PK}, title = {Alexander Moritzi, a Swiss Pre-Darwinian Evolutionist: Insights into the Creationist-Transmutationist Debates of the 1830s and 1840s.}, journal = {Journal of the history of biology}, volume = {53}, number = {4}, pages = {549-585}, doi = {10.1007/s10739-020-09619-0}, pmid = {33242175}, issn = {1573-0387}, abstract = {Alexander Moritzi (1806-1850) is one of the most obscure figures in the early history of evolutionary thought. Best known for authoring a flora of Switzerland, Moritzi also published Réflexions sur l'espèce en histoire naturelle (1842), a remarkable book about evolution with an overtly materialist viewpoint. In this work, Moritzi argues that the (then) generally accepted line between species and varieties is artificial, that varieties can over time give rise to new species, and that deep time and turnover of species in the fossil record clearly support an evolutionary interpretation of biological diversity. Moritzi was also a gradualist and viewed relationships between taxa as best represented by a ramifying tree. Although Réflexions was the first full book to be written on the topic of evolution following Lamarck's Philosophie zoologique (1809), Moritzi's evolutionist contribution was stillborn, read by almost no one in his lifetime and ultimately absent from the many historiographies of evolutionary thought. This is unfortunate since many of the arguments Moritzi marshaled on behalf of an evolutionary explanation of life can be found in subsequent transmutationist writings by Frédéric Gérard, Robert Chambers, Henri Lecoq, Baden Powell, Charles Naudin, Herbert Spencer, Alfred Russel Wallace, and Charles Darwin-none of whom is likely to have ever known of the existence of Réflexions. Finally, Moritzi's arguments, along with those found in Darwin's private essay on evolution of the same year, provide an excellent window into the state of evolutionary thought and debate over the nature of species at the beginning of the 1840s.}, } @article {pmid33237299, year = {2021}, author = {Valentin, G and Abdel, T and Gaëtan, D and Jean-François, D and Matthieu, C and Mathieu, R}, title = {GreenPhylDB v5: a comparative pangenomic database for plant genomes.}, journal = {Nucleic acids research}, volume = {49}, number = {D1}, pages = {D1464-D1471}, pmid = {33237299}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Crops, Agricultural ; *Databases, Genetic ; *Gene Expression Regulation, Plant ; Gene Ontology ; *Genome, Plant ; Genomics/*methods ; Internet ; Molecular Sequence Annotation ; Multigene Family ; Oryza/genetics/metabolism ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plants/classification/*genetics/metabolism ; Protein Interaction Mapping ; Sequence Alignment ; Sequence Homology, Amino Acid ; Software ; }, abstract = {Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.}, } @article {pmid33236750, year = {2020}, author = {Takeya, S and Muromachi, S and Hachikubo, A and Ohmura, R and Hyodo, K and Yoneyama, A}, title = {X-Ray attenuation and image contrast in the X-ray computed tomography of clathrate hydrates depending on guest species.}, journal = {Physical chemistry chemical physics : PCCP}, volume = {22}, number = {47}, pages = {27658-27665}, doi = {10.1039/d0cp05466f}, pmid = {33236750}, issn = {1463-9084}, abstract = {In this study, X-ray imaging of inclusion compounds encapsulating various guest species was investigated based on the calculation of X-ray attenuation coefficients. The optimal photon energies of clathrate hydrates were simulated for high-contrast X-ray imaging based on the type of guest species. The proof of concept was provided by observations of Kr hydrate and tetra-n-butylammonium bromide (TBAB) semi-clathrate hydrate using absorption-contrast X-ray computed tomography (CT) and radiography with monochromated synchrotron X-rays. The radiographic image of the Kr hydrate also revealed a sudden change in its attenuation coefficient owing to the K-absorption edge of Kr as the guest element. With a photon energy of 35 keV, X-ray CT provided sufficient segmentation for the TBAB semi-clathrate hydrate coexisting with ice. In contrast, the simulation did not achieve the sufficient segmentation of the CH4 and CO2 hydrates coexisting with water or ice, but it revealed the capability of absorption-contrast X-ray CT to model the physical properties of clathrate hydrates, such as Ar and Cl2 hydrates. These results demonstrate that the proposed method can be used to investigate the spatial distribution of specific elements within inclusion compounds or porous materials.}, } @article {pmid33233345, year = {2020}, author = {Corsini, M and Moroni, E and Ravelli, C and Grillo, E and Presta, M and Mitola, S}, title = {In Situ DNA/Protein Interaction Assay to Visualize Transcriptional Factor Activation.}, journal = {Methods and protocols}, volume = {3}, number = {4}, pages = {}, pmid = {33233345}, issn = {2409-9279}, abstract = {The chick embryo chorioallantoic membrane (CAM) represents a powerful in vivo model to study several physiological and pathological processes including inflammation and tumor progression. Nevertheless, the possibility of deepening the molecular processes in the CAM system is biased by the absence/scarcity of chemical and biological reagents, designed explicitly for avian species. This is particularly true for transcriptional factors, proteinaceous molecules that regulate various cellular responses, including proliferation, survival, and differentiation. Here, we propose a detailed antibody-independent protocol to visualize the activation and nuclear translocation of transcriptional factors in cells or in tissues of different animal species. As a proof of concept, DNA/cAMP response element-binding protein (CREB) interaction was characterized on the CAM tissue using oligonucleotides containing the palindromic binding sequence of CREB. Scrambled oligonucleotides were used as controls. In situ DNA/protein interaction protocol is a versatile method that is useful for the study of transcription factors in the cell and tissue of different origins.}, } @article {pmid33200960, year = {2021}, author = {Geiser, DM and Al-Hatmi, AMS and Aoki, T and Arie, T and Balmas, V and Barnes, I and Bergstrom, GC and Bhattacharyya, MK and Blomquist, CL and Bowden, RL and Brankovics, B and Brown, DW and Burgess, LW and Bushley, K and Busman, M and Cano-Lira, JF and Carrillo, JD and Chang, HX and Chen, CY and Chen, W and Chilvers, M and Chulze, S and Coleman, JJ and Cuomo, CA and de Beer, ZW and de Hoog, GS and Del Castillo-Múnera, J and Del Ponte, EM and Diéguez-Uribeondo, J and Di Pietro, A and Edel-Hermann, V and Elmer, WH and Epstein, L and Eskalen, A and Esposto, MC and Everts, KL and Fernández-Pavía, SP and da Silva, GF and Foroud, NA and Fourie, G and Frandsen, RJN and Freeman, S and Freitag, M and Frenkel, O and Fuller, KK and Gagkaeva, T and Gardiner, DM and Glenn, AE and Gold, SE and Gordon, TR and Gregory, NF and Gryzenhout, M and Guarro, J and Gugino, BK and Gutierrez, S and Hammond-Kosack, KE and Harris, LJ and Homa, M and Hong, CF and Hornok, L and Huang, JW and Ilkit, M and Jacobs, A and Jacobs, K and Jiang, C and Jiménez-Gasco, MDM and Kang, S and Kasson, MT and Kazan, K and Kennell, JC and Kim, HS and Kistler, HC and Kuldau, GA and Kulik, T and Kurzai, O and Laraba, I and Laurence, MH and Lee, T and Lee, YW and Lee, YH and Leslie, JF and Liew, ECY and Lofton, LW and Logrieco, AF and López-Berges, MS and Luque, AG and Lysøe, E and Ma, LJ and Marra, RE and Martin, FN and May, SR and McCormick, SP and McGee, C and Meis, JF and Migheli, Q and Mohamed Nor, NMI and Monod, M and Moretti, A and Mostert, D and Mulè, G and Munaut, F and Munkvold, GP and Nicholson, P and Nucci, M and O'Donnell, K and Pasquali, M and Pfenning, LH and Prigitano, A and Proctor, RH and Ranque, S and Rehner, SA and Rep, M and Rodríguez-Alvarado, G and Rose, LJ and Roth, MG and Ruiz-Roldán, C and Saleh, AA and Salleh, B and Sang, H and Scandiani, MM and Scauflaire, J and Schmale, DG and Short, DPG and Šišić, A and Smith, JA and Smyth, CW and Son, H and Spahr, E and Stajich, JE and Steenkamp, E and Steinberg, C and Subramaniam, R and Suga, H and Summerell, BA and Susca, A and Swett, CL and Toomajian, C and Torres-Cruz, TJ and Tortorano, AM and Urban, M and Vaillancourt, LJ and Vallad, GE and van der Lee, TAJ and Vanderpool, D and van Diepeningen, AD and Vaughan, MM and Venter, E and Vermeulen, M and Verweij, PE and Viljoen, A and Waalwijk, C and Wallace, EC and Walther, G and Wang, J and Ward, TJ and Wickes, BL and Wiederhold, NP and Wingfield, MJ and Wood, AKM and Xu, JR and Yang, XB and Yli-Mattila, T and Yun, SH and Zakaria, L and Zhang, H and Zhang, N and Zhang, SX and Zhang, X}, title = {Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex.}, journal = {Phytopathology}, volume = {111}, number = {7}, pages = {1064-1079}, doi = {10.1094/PHYTO-08-20-0330-LE}, pmid = {33200960}, issn = {0031-949X}, support = {R01 EY030150/EY/NEI NIH HHS/United States ; }, mesh = {*Fusarium/genetics ; Phylogeny ; Plant Diseases ; Plants ; }, abstract = {Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.}, } @article {pmid33189990, year = {2021}, author = {Antoniadis, V and Shaheen, SM and Stärk, HJ and Wennrich, R and Levizou, E and Merbach, I and Rinklebe, J}, title = {Phytoremediation potential of twelve wild plant species for toxic elements in a contaminated soil.}, journal = {Environment international}, volume = {146}, number = {}, pages = {106233}, doi = {10.1016/j.envint.2020.106233}, pmid = {33189990}, issn = {1873-6750}, mesh = {Biodegradation, Environmental ; *Metals, Heavy/analysis ; Plants ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Green remediation of soils highly contaminated with potentially toxic elements (PTEs) can be achieved using suitable plants. Such phytoremediation procedure often takes into consideration PTE concentrations in plants only, but not produced biomass. Phytoremediation potential of certain species of wild plants for PTEs in contaminated floodplain soils has not been assessed yet. Therefore, in this work 12 native species were tested, 3 of which (Poa angustifolia, Galium mollugo, and Stellaria holostea) to our knowledge have never been used before, in a two-year pot experiment and assessed their potential as phytoremediation species. The results showed that plant PTE concentrations were dramatically elevated for Cd and Zn in Alopecurus pratensis, Arrhenatherum elatius, Bromus inermis, Artemisia vulgaris, Achillea millefolium, Galium mollugo, Stellaria holostea, and Silene vulgaris. A. vulgaris was by far the most highly PTE absorbing plant among the 12 tested in this work, especially concerning Zn, Cd, and to a lesser degree Cu and Ni. Also, among species non-studied-before, G. mollugo and S. holostea were characterized by high Zn and Cd uptake, while P. angustifolia did not. Assessing the number of harvests necessary to decrease soil PTE to half of the initial concentrations, it was found that for Cd plants would achieve site phytoremediation within 8 (A. vulgaris) to 28 (S. holostea) and 51 (G. mollugo) harvests, while for Zn, harvests ranged from 104 (A. vulgaris) to 209 (S. holostea), and 251 (A. millefolium). A clear grouping of the tested species according to their functional type was evident. Herbaceous species were collectively more efficient than grasses in PTE uptake combined by high biomass accumulation; thus, they may act as key-species in a phytoremediation-related concept. Our approach puts phytoremediation into a practical perspective as to whether the process can be achieved within a measureable amount of time. In conclusion, A. vulgaris behaved as a hyperaccumulator plant species in our heavily contaminated soil, while never-studied-before G. mollugo and S. holostea also had a hyperaccumulator behavior, especially for Cd and Zn. Although more research is necessary for conclusive results, our study is pivotal in that it would help in assessing plant species as potential phytoremediation species in heavily contaminated soils.}, } @article {pmid33171548, year = {2020}, author = {Roos, C and Helgen, KM and Miguez, RP and Thant, NML and Lwin, N and Lin, AK and Lin, A and Yi, KM and Soe, P and Hein, ZM and Myint, MNN and Ahmed, T and Chetry, D and Urh, M and Veatch, EG and Duncan, N and Kamminga, P and Chua, MAH and Yao, L and Matauschek, C and Meyer, D and Liu, ZJ and Li, M and Nadler, T and Fan, PF and Quyet, LK and Hofreiter, M and Zinner, D and Momberg, F}, title = {Mitogenomic phylogeny of the Asian colobine genus Trachypithecus with special focus on Trachypithecus phayrei (Blyth, 1847) and description of a new species.}, journal = {Zoological research}, volume = {41}, number = {6}, pages = {656-669}, pmid = {33171548}, issn = {2095-8137}, mesh = {Animal Distribution ; Animals ; Asia, Southeastern ; *Genome, Mitochondrial ; Phylogeny ; Presbytini/classification/*genetics/physiology ; Species Specificity ; }, abstract = {Trachypithecus, which currently contains 20 species divided into four groups, is the most speciose and geographically dispersed genus among Asian colobines. Despite several morphological and molecular studies, however, its evolutionary history and phylogeography remain poorly understood. Phayre's langur (Trachypithecus phayrei) is one of the most widespread members of the genus, but details on its actual distribution and intraspecific taxonomy are limited and controversial. Thus, to elucidate the evolutionary history of Trachypithecus and to clarify the intraspecific taxonomy and distribution of T. phayrei, we sequenced 41 mitochondrial genomes from georeferenced fecal samples and museum specimens, including two holotypes. Phylogenetic analyses revealed a robustly supported phylogeny of Trachypithecus, suggesting that the T. pileatus group branched first, followed by the T. francoisi group, and the T. cristatus and T. obscurus groups most recently. The four species groups diverged from each other 4.5-3.1 million years ago (Ma), while speciation events within these groups occurred much more recently (1.6-0.3 Ma). Within T. phayrei, we found three clades that diverged 1.0-0.9 Ma, indicating the existence of three rather than two taxa. Following the phylogenetic species concept and based on genetic, morphological, and ecological differences, we elevate the T. phayrei subspecies to species level, describe a new species from central Myanmar, and refine the distribution of the three taxa. Overall, our study highlights the importance of museum specimens and provides new insights not only into the evolutionary history of T. phayrei but the entire Trachypithecus genus as well.}, } @article {pmid33169788, year = {2021}, author = {Ionescu, D and Zoccarato, L and Zaduryan, A and Schorn, S and Bizic, M and Pinnow, S and Cypionka, H and Grossart, HP}, title = {Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems.}, journal = {Molecular biology and evolution}, volume = {38}, number = {3}, pages = {1040-1059}, pmid = {33169788}, issn = {1537-1719}, mesh = {*Biological Evolution ; Ecosystem ; *Genome, Bacterial ; Geologic Sediments/*microbiology ; Gram-Negative Aerobic Bacteria/*genetics/metabolism ; Heterozygote ; Phylogeny ; Polyploidy ; *Water Microbiology ; }, abstract = {Achromatium is large, hyperpolyploid and the only known heterozygous bacterium. Single cells contain approximately 300 different chromosomes with allelic diversity far exceeding that typically harbored by single bacteria genera. Surveying all publicly available sediment sequence archives, we show that Achromatium is common worldwide, spanning temperature, salinity, pH, and depth ranges normally resulting in bacterial speciation. Although saline and freshwater Achromatium spp. appear phylogenetically separated, the genus Achromatium contains a globally identical, complete functional inventory regardless of habitat. Achromatium spp. cells from differing ecosystems (e.g., from freshwater to saline) are, unexpectedly, equally functionally equipped but differ in gene expression patterns by transcribing only relevant genes. We suggest that environmental adaptation occurs by increasing the copy number of relevant genes across the cell's hundreds of chromosomes, without losing irrelevant ones, thus maintaining the ability to survive in any ecosystem type. The functional versatility of Achromatium and its genomic features reveal alternative genetic and evolutionary mechanisms, expanding our understanding of the role and evolution of polyploidy in bacteria while challenging the bacterial species concept and drivers of bacterial speciation.}, } @article {pmid33168817, year = {2020}, author = {Zhuo, C and Hou, W and Tian, H and Wang, L and Li, R}, title = {Lipidomics of the brain, retina, and biofluids: from the biological landscape to potential clinical application in schizophrenia.}, journal = {Translational psychiatry}, volume = {10}, number = {1}, pages = {391}, pmid = {33168817}, issn = {2158-3188}, support = {81871052 to C.Z.//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/International ; }, mesh = {Animals ; *Brain/metabolism ; Humans ; *Lipidomics ; Phospholipids ; *Retina/metabolism ; *Schizophrenia ; }, abstract = {Schizophrenia is a serious neuropsychiatric disorder, yet a clear pathophysiology has not been identified. To date, neither the objective biomarkers for diagnosis nor specific medications for the treatment of schizophrenia are clinically satisfactory. It is well accepted that lipids are essential to maintain the normal structure and function of neurons in the brain and that abnormalities in neuronal lipids are associated with abnormal neurodevelopment in schizophrenia. However, lipids and lipid-like molecules have been largely unexplored in contrast to proteins and their genes in schizophrenia. Compared with the gene- and protein-centric approaches, lipidomics is a recently emerged and rapidly evolving research field with particular importance for the study of neuropsychiatric disorders such as schizophrenia, in which even subtle aberrant alterations in the lipid composition and concentration of the neurons may disrupt brain functioning. In this review, we aimed to highlight the lipidomics of the brain, retina, and biofluids in both human and animal studies, discuss aberrant lipid alterations in correlation with schizophrenia, and propose future directions from the biological landscape towards potential clinical applications in schizophrenia. Recent studies are in support of the concept that aberrations in some lipid species [e.g. phospholipids, polyunsaturated fatty acids (PUFAs)] lead to structural alterations and, in turn, impairments in the biological function of membrane-bound proteins, the disruption of cell signaling molecule accessibility, and the dysfunction of neurotransmitter systems. In addition, abnormal lipidome alterations in biofluids are linked to schizophrenia, and thus they hold promise in the discovery of biomarkers for the diagnosis of schizophrenia.}, } @article {pmid33164287, year = {2020}, author = {Hosegood, J and Humble, E and Ogden, R and de Bruyn, M and Creer, S and Stevens, GMW and Abudaya, M and Bassos-Hull, K and Bonfil, R and Fernando, D and Foote, AD and Hipperson, H and Jabado, RW and Kaden, J and Moazzam, M and Peel, LR and Pollett, S and Ponzo, A and Poortvliet, M and Salah, J and Senn, H and Stewart, JD and Wintner, S and Carvalho, G}, title = {Phylogenomics and species delimitation for effective conservation of manta and devil rays.}, journal = {Molecular ecology}, volume = {29}, number = {24}, pages = {4783-4796}, doi = {10.1111/mec.15683}, pmid = {33164287}, issn = {1365-294X}, mesh = {*Biodiversity ; *Genome ; Gulf of Mexico ; Phylogeny ; }, abstract = {Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.}, } @article {pmid33160244, year = {2020}, author = {Galli, J and Calò, L and Posteraro, B and Rossi, G and Sterbini, FP and Paludetti, G and Sanguinetti, M}, title = {Pediatric oropharyngeal microbiome: Mapping in chronic tonsillitis and tonsillar hypertrophy.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {139}, number = {}, pages = {110478}, doi = {10.1016/j.ijporl.2020.110478}, pmid = {33160244}, issn = {1872-8464}, mesh = {Child ; Humans ; Hypertrophy ; *Microbiota ; Palatine Tonsil ; Recurrence ; *Tonsillitis ; }, abstract = {OBJECTIVES: Aim of our study was to map the adenotonsillar lymphoid tissues' microbiome identifying its potential etiopathogenetic role in children affected by chronic tonsillitis or tonsillar hypertrophy with Obstructive Sleep Apnea Syndrome (OSAS).

METHODS: In our study, we examined tonsillar swabs from healthy children and children affected by chronic tonsillitis or by tonsillar hypertrophy with Obstructive Sleep Apnea Syndrome (OSAS). Microbiome's analysis was performed and bacterial 16Sr RNA gene was sequenced according to metagenomic principles. Variability was described according to the biodiversity concept, indicating species found in a certain environment and changes they undergo adapting to different environmental conditions.

RESULTS: The most significant differences concern variation of microbes in a single sample (alpha diversity) of some phyla in children affected by chronic tonsillitis compared with alpha diversity in healthy children and in children affected by OSAS with tonsillar hyperplasia. Proteobacteria are prevalent in chronic tonsillitis group, Fusobacteria and Spirochete in OSAS and Firmicutes, Actinobacteria, and Bacteroidetes were found in healthy children. Finally, comparison between the groups showed that children with OSAS with tonsillar hypertrophy had a higher presence of the Fusobacterium genus.

CONCLUSION: Recurrent upper airway inflammatory and/or infectious processes are polymicrobial; chronicity of such processes appear to be related to variations in microbiome's composition and interaction among various taxonomic units. Knowledge of the microbiomes' composition together with traditional clinical biomarkers can also determine relationships between oropharyngeal microbiome and systemic pathologies to determine preventive changes in lifestyle, eating habits, environmental exposure and use of probiotics.}, } @article {pmid33158054, year = {2020}, author = {Gonzalez, JM and Puerta-Fernández, E and Santana, MM and Rekadwad, B}, title = {On a Non-Discrete Concept of Prokaryotic Species.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33158054}, issn = {2076-2607}, abstract = {The taxonomic concept of species has received continuous attention. A microbial species as a discrete box contains a limited number of highly similar microorganisms assigned to that taxon, following a polyphasic approach. In the 21st Century, with the advancements of sequencing technologies and genomics, the existence of a huge prokaryotic diversity has become well known. At present, the prokaryotic species might no longer have to be understood as discrete values (such as 1 or 2, by homology to Natural numbers); rather, it is expected that some microorganisms could be potentially distributed (according to their genome features and phenotypes) in between others (such as decimal numbers between 1 and 2; real numbers). We propose a continuous species concept for microorganisms, which adapts to the current knowledge on the huge diversity, variability and heterogeneity existing among bacteria and archaea. Likely, this concept could be extended to eukaryotic microorganisms. The continuous species concept considers a species to be delimited by the distance between a range of variable features following a Gaussian-type distribution around a reference organism (i.e., its type strain). Some potential pros and cons of a continuous concept are commented on, offering novel perspectives on our understanding of the highly diversified prokaryotic world, thus promoting discussion and further investigation in the field.}, } @article {pmid33130371, year = {2021}, author = {Harneti, D and Supratman, U}, title = {Phytochemistry and biological activities of Aglaia species.}, journal = {Phytochemistry}, volume = {181}, number = {}, pages = {112540}, doi = {10.1016/j.phytochem.2020.112540}, pmid = {33130371}, issn = {1873-3700}, mesh = {*Aglaia ; Australia ; *Biological Products ; Indonesia ; Molecular Structure ; }, abstract = {Aglaia is the largest genus in the Meliaceae family (also known as Mahagoni in Indonesia), consisting of over 150 species, of which 65 are indigenous to Indonesia. These species spread through the tropical regions, especially Southeast Asia as well as the Nothern part of Australia, and have been used in traditional medicine for the treatment of several diseases. However, preliminary chemical researches commenced in 1965, where dammarane-type triterpenoids, aglaiol was isolated, and the structure was determined by chemical reaction and spectroscopic methods. Several studies have been carried out on the stembark, bark, leaves, seeds and leaves in the last fifty five years, and about 291 metabolites have been isolated from the sesquiterpenoid, diterpenoid, triterpenoid, limonoid, steroid, lignan, and alkaloid groups, as well as flavagline, which known to be the largest. This specifically amounts to 34% of Aglaia species, reported to show cytotoxic and insecticidal potentials, and also the tendency for use as chemical markers for this species. The extracts and compounds obtained from Aglaia species are evaluated for potential biological activities, including cytotoxicity, insecticidal, anti-inflammatory, antifungal, molluscicidal, antituberculosis and antiviral effects. In addition, flavagline (rocaglamide) derivatives have been confirmed to exhibit exceptional cytotoxicity, and are, thus, considered lead compounds for further development. Therefore, the results support the concept of utilizing Aglaia species as a potential source for the production of biologically active compounds.}, } @article {pmid33118146, year = {2021}, author = {Guo, Y and Nong, Y and Li, Q and Tomlin, A and Kahlon, A and Gumpert, A and Slezak, J and Zhu, X and Bolli, R}, title = {Comparison of One and Three Intraventricular Injections of Cardiac Progenitor Cells in a Murine Model of Chronic Ischemic Cardiomyopathy.}, journal = {Stem cell reviews and reports}, volume = {17}, number = {2}, pages = {604-615}, pmid = {33118146}, issn = {2629-3277}, support = {P01 HL078825/HL/NHLBI NIH HHS/United States ; R01 HL068088/HL/NHLBI NIH HHS/United States ; UM1 HL113530/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Cardiomyopathies/therapy ; Disease Models, Animal ; *Injections, Intraventricular ; Mice ; *Myocardial Infarction/therapy ; Myocardium/*cytology ; *Stem Cells ; }, abstract = {Repeated doses of c-kit[+] cardiac progenitor cells (CPCs) are superior to a single dose in improving LV function in rats with old myocardial infarction (MI). However, this concept needs testing in different species to determine whether it is generalizable. We used a new murine model of chronic ischemic cardiomyopathy whose unique feature is that cell therapy was started late (3 months) after MI. Mice received three echo-guided intraventricular infusions, 5 weeks apart, of vehicle, CPCs × 1, or CPCs × 3. Echocardiography demonstrated that the single-dose group exhibited improved LV ejection fraction (EF) after the 1st infusion (CPCs), but not after the 2nd and 3rd (vehicle). In contrast, in the multiple-dose group LVEF continued to improve, so that the final value was greater than in vehicle or single-dose groups (P < 0.05). Hemodynamic studies showed that compared with vehicle, both preload-dependent and preload-independent functional parameters were significantly increased in the multiple-dose group but not in the single-dose group. Thus, two independent methods of functional assessment (echocardiography and hemodynamic studies) consistently demonstrated the superiority of three doses of CPCs vs. one dose. Compared with the single-dose group, the multiple-dose group exhibited less LV hypertrophy, as evidenced by a greater reduction in LV/body weight ratio and cardiomyocyte cross-sectional area. Furthermore, unlike the single dose, three CPC doses reduced myocardial inflammatory cells in the risk region. This is the first study of echo-guided intraventricular infusion of CPCs in mice with chronic ischemic cardiomyopathy. The results demonstrate that the beneficial effects of three CPC doses are greater than those of one dose, supporting the concept that multiple treatments are necessary to properly evaluate cell therapy. Our findings indicate that this concept applies not only to rat models but also to murine models. The generalizability of this strategy greatly enhances its importance and provides a rationale for large animal studies. Graphical abstract.}, } @article {pmid33116336, year = {2020}, author = {Wagner, L and Stielow, JB and de Hoog, GS and Bensch, K and Schwartze, VU and Voigt, K and Alastruey-Izquierdo, A and Kurzai, O and Walther, G}, title = {A new species concept for the clinically relevant Mucor circinelloides complex.}, journal = {Persoonia}, volume = {44}, number = {}, pages = {67-97}, pmid = {33116336}, issn = {0031-5850}, abstract = {Mucor species are common soil fungi but also known as agents of human infections (mucormycosis) and used in food production and biotechnology. Mucor circinelloides is the Mucor species that is most frequently isolated from clinical sources. The taxonomy of Mucor circinelloides and its close relatives (Mucor circinelloides complex - MCC) is still based on morphology and mating behaviour. The aim of the present study was a revised taxonomy of the MCC using a polyphasic approach. Using a set of 100 strains molecular phylogenetic analysis of five markers (ITS, rpb1, tsr1, mcm7, and cfs, introduced here) were performed, combined with phenotypic studies, mating tests and the determination of the maximum growth temperatures. The multi-locus analyses revealed 16 phylogenetic species of which 14 showed distinct phenotypical traits and were recognised as discrete species. Five of these species are introduced as novel taxa: M. amethystinus sp. nov., M. atramentarius sp. nov., M. variicolumellatus sp. nov., M. pseudocircinelloides sp. nov., and M. pseudolusitanicus sp. nov. The former formae of M. circinelloides represent one or two separate species. In the MCC, the simple presence of well-shaped zygospores only indicates a close relation of both strains, but not necessarily conspecificity. Seven species of the MCC have been implemented in human infection: M. circinelloides, M. griseocyanus, M. janssenii, M. lusitanicus, M. ramosissimus, M. variicolumellatus, and M. velutinosus.}, } @article {pmid33114441, year = {2020}, author = {Gostinčar, C}, title = {Towards Genomic Criteria for Delineating Fungal Species.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {6}, number = {4}, pages = {}, pmid = {33114441}, issn = {2309-608X}, abstract = {The discussion of fungal species delineation has yet to reach a consensus, despite the advancements in technology, which helped modernise traditional approaches. In particular, the phylogenetic species concept was one of the tools that has been used with considerable success across the fungal kingdom. The fast rise of fungal genomics provides an unprecedented opportunity to expand measuring the relatedness of fungal strains to the level of whole genomes. However, the use of genomic information in taxonomy has only just begun, and few methodological guidelines have been suggested so far. Here, a simple approach of computationally measuring genomic distances and their use as a standard for species delineation is investigated. A fixed threshold genomic distance calculated by the quick and easy-to-use tools Mash and Dashing proved to be an unexpectedly widely applicable and robust criterion for determining whether two genomes belong to the same or to different species. The accuracy of species delineation in an uncurated dataset of GenBank fungal genomes was close to 90%-and exceeded 90% with minimal curation. As expected, the discriminative power of this approach was lower at higher taxonomic ranks, but still significantly larger than zero. Simple instructions for calculation of a genomic distance between two genomes and species similarity thresholds at different k-mer sizes are suggested. The calculation of genomic distance is identified as a powerful approach for delineating fungal species and is proposed-not as the only criterion-but as an additional tool in the versatile toolbox of fungal taxonomy.}, } @article {pmid33096155, year = {2021}, author = {Suresh, S and Abozaid, A and Tsang, B and Gerlai, R}, title = {Exposure of parents to alcohol alters behavior of offspring in zebrafish.}, journal = {Progress in neuro-psychopharmacology & biological psychiatry}, volume = {111}, number = {}, pages = {110143}, doi = {10.1016/j.pnpbp.2020.110143}, pmid = {33096155}, issn = {1878-4216}, mesh = {Animals ; *Behavior, Animal ; *Child of Impaired Parents ; *Epigenomics ; Ethanol/*administration & dosage ; Female ; Male ; Pregnancy ; Prenatal Exposure Delayed Effects ; Swimming ; Zebrafish/*physiology ; }, abstract = {Alcoholism and alcohol abuse represent a significant medical and societal problem, and have been thoroughly investigated in humans as well as using animal models. A less well understood aspect of alcohol related disorders is the possible effect of this drug on offspring whose parents were exposed prior to conception. The zebrafish has been successfully employed in alcohol research, however, the effect of exposing the parents to alcohol before fertilization of the eggs on offspring has not been demonstrated in this species. In this proof of concept study, we attempt to address this hiatus. We exposed both adult male and female zebrafish to 0.0% (control) or 0.5% (vol/vol) alcohol chronically for 7 days, subsequently bred the fish within their respective treatment group, collected the fertilized eggs, allowed them to develop, and tested the behavior of free-swimming offspring at their age of 7-9 days post-fertilization. We conducted the analysis in two genetically distinct quasi-inbred strains of zebrafish, AB and TL. Although gross morphology and general activity of the fish appeared unaffected, we found significant behavioral alterations in offspring of alcohol exposed parents compared to offspring of control parents in both strains. These alterations included robustly increased duration and reduced frequency of immobility, increased turn angle, and increased intra-individual variance of turn angle in offspring of alcohol exposed parents in both strains. The mechanisms underlying these behavioral effects or whether the effects are due to exposure of the father, the mother, or both to alcohol are unknown. Nevertheless, our results now set the stage for future studies with zebrafish that will address these questions.}, } @article {pmid33091155, year = {2021}, author = {Catano, CP and Grman, E and Behrens, E and Brudvig, LA}, title = {Species pool size alters species-area relationships during experimental community assembly.}, journal = {Ecology}, volume = {102}, number = {1}, pages = {e03231}, doi = {10.1002/ecy.3231}, pmid = {33091155}, issn = {1939-9170}, mesh = {*Biodiversity ; *Soil ; }, abstract = {The species pool concept has advanced our understanding for how biodiversity is coupled at local and regional scales. However, it remains unclear how species pool size, the number of species available to disperse to a site, influences community assembly across spatial scales. We provide one of the first studies that assesses diversity across scales after experimentally assembling grassland communities from species pools of different sizes. We show that species pool size causes scale-dependent effects on diversity in grasslands undergoing restoration by altering the shape of the species-area relationship (SAR). Specifically, larger species pools increased the slope of the SAR, but not the intercept, suggesting that dispersal from a larger pool causes species to be more spatially aggregated. This increased aggregation appears to be caused by sampling effects due to fewer individuals arriving per species, rather than stronger species sorting across variation in soil moisture. These scale-dependent effects suggest that studies evaluating species pools at a single, small scale may underestimate their effects, thereby contributing to uncertainty about the importance of regional processes for community assembly and their consequences for ecological restoration.}, } @article {pmid33083831, year = {2020}, author = {Zhang, L and Li, D and Zhang, J and Yan, P and Liu, X and Wang, L and Khan, A and Liu, Z and Mu, J and Xu, J and Niu, B and Xie, J}, title = {Excessive apoptosis and ROS induced by ethionine affect neural cell viability and differentiation.}, journal = {Acta biochimica et biophysica Sinica}, volume = {52}, number = {10}, pages = {1156-1165}, pmid = {33083831}, issn = {1745-7270}, mesh = {Animals ; Apoptosis/*drug effects ; Astrocytes/metabolism ; Caspase 3/metabolism ; Cell Cycle/drug effects ; Cell Differentiation/*drug effects ; Cell Proliferation/drug effects ; Cell Survival/*drug effects ; Cells, Cultured ; Central Nervous System Diseases/etiology/metabolism ; Cyclin D1/metabolism ; Dose-Response Relationship, Drug ; Ethionine/*pharmacology ; Mice ; Neural Stem Cells/cytology/*drug effects/metabolism ; Neurons/metabolism ; Reactive Oxygen Species/*metabolism ; bcl-2-Associated X Protein/metabolism ; }, abstract = {The central nervous system (CNS) diseases are still a major cause of morbidity and mortality throughout the world, which imposes heavy burden on the development of society. Ethionine is a non-proteinogenic amino acid having similar chemical structure and activity to that of methionine, with which it competes. Previous studies have confirmed that ethionine affects various cellular functions by inhibiting the biosynthesis of proteins, RNA, DNA, and phospholipids, or all of them. The relationship of ethionine with some CNS diseases, including neural tube defects, has been investigated recently. However, the detailed effects of ethionine on the nerve cell bioactivities and the underlying mechanisms have not been fully explored. Herein, we systematically investigated the influences of ethionine on the proliferation, differentiation, and apoptosis of neural stem cells (NSCs) and post-mitotic nerve cells. We demonstrated that ethionine inhibited cell viability by disrupting the balance between proliferation and apoptosis, prevented NSCs from differentiating into neurons and astrocytes, and blocked cell progression from G1 to S phase via reducing cyclin D1 function in nerve cells including NSCs, a mouse hippocampal neuron cell line (HT-22), and a mouse brain neuroma cell line (Neuro-2a). We speculated that the inhibitory effect of ethionine on cell viability and differentiation are associated with increased reactive oxygen species production. Our results also supported the concept that ethionine may be an underlying cause of abnormal folate metabolism-induced CNS diseases. Our findings may provide important direction for the application of abnormal folate metabolism-induced CNS diseases in future NSC-based therapies.}, } @article {pmid33083106, year = {2020}, author = {Okanishi, M and Kohtsuka, H and Fujita, T}, title = {A taxonomic review of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) from Japanese coastal waters.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9836}, pmid = {33083106}, issn = {2167-8359}, abstract = {Japanese species of the genus Astrocladus (Echinodermata, Ophiuroidea, Euryalida, Gorgonocephalidae) are reviewed. Astrocladus coniferus recently has two junior synonyms, A. dofleini Döderlein and A. pardalis Döderlein, however, status of these species has long been questioned. These species concepts have not been reviewed in recent years and no molecular phylogenetic analyses have been performed. Observations of the lectotype of A. coniferus, as well as the lectotype and four paralectotypes of A. dofleini and the holotype of A. pardalis have revealed that A. coniferus and A. pardalis are conspecific and morphologically distinguishable from A. dofleini. Astrocladus coniferus and A. dofleini are supported as distinct species by our molecular data. Additionally, we re-describe A. exiguus and A. annulatus, based on recently collected specimens and the holotype. We conclude that four species, A. annulatus, A. coniferus, A. dofleini, and A. exiguus are present in Japanese waters.}, } @article {pmid33060138, year = {2020}, author = {Han, Z and Lo, WS and Lightfoot, JW and Witte, H and Sun, S and Sommer, RJ}, title = {Improving Transgenesis Efficiency and CRISPR-Associated Tools Through Codon Optimization and Native Intron Addition in Pristionchus Nematodes.}, journal = {Genetics}, volume = {216}, number = {4}, pages = {947-956}, pmid = {33060138}, issn = {1943-2631}, mesh = {Animals ; *CRISPR-Cas Systems ; *Codon Usage ; Gene Editing/*methods/standards ; Introns ; Rhabditida/*genetics ; *Transgenes ; }, abstract = {A lack of appropriate molecular tools is one obstacle that prevents in-depth mechanistic studies in many organisms. Transgenesis, clustered regularly interspaced short palindromic repeats (CRISPR)-associated engineering, and related tools are fundamental in the modern life sciences, but their applications are still limited to a few model organisms. In the phylum Nematoda, transgenesis can only be performed in a handful of species other than Caenorhabditis elegans, and additionally, other species suffer from significantly lower transgenesis efficiencies. We hypothesized that this may in part be due to incompatibilities of transgenes in the recipient organisms. Therefore, we investigated the genomic features of 10 nematode species from three of the major clades representing all different lifestyles. We found that these species show drastically different codon usage bias and intron composition. With these findings, we used the species Pristionchus pacificus as a proof of concept for codon optimization and native intron addition. Indeed, we were able to significantly improve transgenesis efficiency, a principle that may be usable in other nematode species. In addition, with the improved transgenes, we developed a fluorescent co-injection marker in P. pacificus for the detection of CRISPR-edited individuals, which helps considerably to reduce associated time and costs.}, } @article {pmid33056286, year = {2020}, author = {Miranda, GFG and Skevington, JH and Marshall, SA}, title = {New generic concepts for orphaned lineages formerly treated as part of the genus Ocyptamus Macquart, 1834 (Diptera, Syrphidae).}, journal = {Zootaxa}, volume = {4822}, number = {2}, pages = {zootaxa.4822.2.1}, doi = {10.11646/zootaxa.4822.2.1}, pmid = {33056286}, issn = {1175-5334}, mesh = {Animals ; Biological Evolution ; *Diptera ; Phylogeny ; }, abstract = {The large syrphid genus Ocyptamus Macquart has been subject to scrutiny in recent years, resulting in a more narrowly defined monophyletic Ocyptamus sensu stricto. Some of the species excluded from this narrower concept of the genus are in evolutionary lineages for which generic names are available, but other species are in lineages for which generic names do not exist. The current paper presents five new genera to correct this: Fragosa gen. nov. (former Ocyptamus stenogaster group), Hypocritanus gen. nov. (former Ocyptamus fascipennis group), Maiana gen. nov. (former Ocyptamus callidus group), Nuntianus gen. nov. (former Ocyptamus lepidus group) and Victoriana gen. nov. (former Ocyptamus melanorrhinus group). In addition to the new combinations related to these new genera, Argentinomyia aenea (Williston) comb. nov., Hybobathus pola (Curran) comb. nov., H. subchalybeus (Walker) comb. nov., H. wilhelmina (Doesburg) comb. nov., and Leucopodella nasuta (Williston) comb. nov. are moved out of Ocyptamus. Ocyptamus isthmus Thompson is a jun. syn. of Callostigma panamensis Curran stat. rev. Relevant morphological characters and their taxonomic and evolutionary implications are discussed.}, } @article {pmid33056261, year = {2020}, author = {Jaschhof, M and Jaschhof, C}, title = {Reevaluation of species richness in Winnertzia (Diptera, Cecidomyiidae, Winnertziinae), with descriptions of 37 new species from Sweden, Peru and Australia.}, journal = {Zootaxa}, volume = {4829}, number = {1}, pages = {zootaxa.4829.1.1}, doi = {10.11646/zootaxa.4829.1.1}, pmid = {33056261}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures ; Animals ; Australia ; *Biodiversity ; Body Size ; *Diptera ; Male ; Organ Size ; Peru ; Sweden ; }, abstract = {Tentative studies of Malaise trap samples from different geographic regions and habitats indicate unanimously that Winnertzia, a genus of mycophagous gall midges (Cecidomyiidae), is exceptionally speciose, but hard data in proof of that were previously unavailable. A taxonomic inventory of mycophagous cecidomyiids in Sweden has now revealed that, of 751 species found in total, 93 are Winnertzia. A preliminary census in 2013 had identified only 26 different Winnertzia in Sweden. Two factors are responsible for this increment: the inclusion of large amounts of fresh material to study and the application of a narrower species concept. The latter results from the reevaluation of male morphological characters in the light of COI sequence (DNA barcoding) data. With the inclusion of 37 new Winnertzia described here, the genus now contains 136 extant species. New Winnertzia discovered in Sweden are described here under the following names: W. acutistylus sp. nov., W. angustistylus sp. nov., W. arctostylus sp. nov., W. bicolor sp. nov., W. brachytarsus sp. nov., W. dentata sp. nov., W. egregia sp. nov., W. ekdalensis sp. nov., W. fraxinophila sp. nov., W. grytsjoenensis sp. nov., W. hamatula sp. nov., W. hemisphaerica sp. nov., W. imbecilla sp. nov., W. incisa sp. nov., W. inornata sp. nov., W. lapponica sp. nov., W. lobata sp. nov., W. longicoxa sp. nov., W. normalis sp. nov., W. oelandica sp. nov., W. ombergensis sp. nov., W. parvidens sp. nov., W. pilosistylus sp. nov., W. pratensis sp. nov., W. pustulatula sp. nov., W. quercinophila sp. nov., W. rickebasta sp. nov., W. ruliki sp. nov., W. serri sp. nov., W. setosa sp. nov., W. silvestris sp. nov., W. smalandensis sp. nov., W. sundini sp. nov., W. tumidoides sp. nov., and W. upplandensis sp. nov. Additionally, W. panguana sp. nov. is the first Winnertzia described from the Neotropical region (Peru), and W. warraensis sp. nov. is the first member of the genus described from the Australasian region (Tasmania). Parwinnertzia Felt, 1920 syn. nov. is revealed to be a junior synonym of Winnertzia Rondani, 1860, implying the recombinations of Winnertzia notmani (Felt) comb. nov. and Winnertzia italiana (Mamaev Zaitzev) comb. nov. The intrageneric classification of Winnertzia is reviewed and developed further, with the W. setosa group introduced for species whose gonostylar claw is conspicuously long and exposed, and whose gonocoxal emargination is bordered by dense, large setae. Winnertzia feralis Mamaev, revived here from synonymy with W. tridens Panelius, and W. fusca Kieffer are new faunistic records in Sweden. Swedish records published in the past of W. brachypalpa Mamaev and W. pravdini Mamaeva Mamaev rest on misidentifications, and both species are deleted from the Swedish checklist.}, } @article {pmid33056089, year = {2020}, author = {Cruz, PV and GonÇalves, IC and Mariano, R and Hamada, N}, title = {One less monotypic genus in Leptophlebiidae (Ephemeroptera): A new species of Bessierus Thomas amp; Orth and new record from Brazil.}, journal = {Zootaxa}, volume = {4820}, number = {1}, pages = {zootaxa.4820.1.11}, doi = {10.11646/zootaxa.4820.1.11}, pmid = {33056089}, issn = {1175-5334}, mesh = {Animals ; Brazil ; *Ephemeroptera ; Male ; Nymph ; Pigmentation ; }, abstract = {A new species of Bessierus Thomas Orth, formerly a monotypic genus, is described from Amapá State, Brazil. The type species of the genus, B. doloris Thomas Orth, had only its nymphs described until recently, when its male imago was associated to nymphs mainly based on pigmentation pattern. Bessierus riobranco sp. n. here described has no significant difference on pigmentation pattern from B. doloris, thus the new species could be the male imago of B. doloris, and the putative imago of B. doloris a new species, or even both described imagoes could be new species. Still, a new male imago existence cannot be neglected and we opted to provide a properly description, diagnosis and illustration, hence contributing to the knowledge of mayfly neotropical diversity and future research on the genus. The generic concept of Bessierus and its type species diagnoses are altered to accommodate the new species, and a new record of B. doloris is provided.}, } @article {pmid33055626, year = {2020}, author = {Polhemus, DA}, title = {Nine new species of Enithares (Heteroptera: Notonectidae) from New Guinea, with distributional notes on other species and an updated world checklist.}, journal = {Zootaxa}, volume = {4772}, number = {1}, pages = {zootaxa.4772.1.5}, doi = {10.11646/zootaxa.4772.1.5}, pmid = {33055626}, issn = {1175-5334}, mesh = {Animals ; *Heteroptera ; New Guinea ; }, abstract = {Nine new species of Enithares are described from New Guinea and immediately adjacent islands: E. peninsularis from the Owen Stanley Mountains of the Papuan Peninsula, E. bosavi and E. papua from southern Papua New Guinea, E. orsaki from northern Papua New Guinea, E. insularis from the D'Entrecasteaux Islands, E. tagula from the Louisiade Archipelago, E. ziwa from the central mountains of western New Guinea, E. arfak from the Arfak Mountains of the eastern Vogelkop Peninsula, and E. kasim from the western Vogelkop Peninsula. Enithares bakeri is newly recorded from New Guinea, and in combination with the new species described above brings the total number of species of Enithares in New Guinea to 16, and the regional total to 19 when including nearby islands of Waigeo, Biak, the D'Entrecasteaux group, and the Louisiade Archipelago. The species concept of E. atra is clarified and geographically restricted to southeastern New Guinea; specimens previously recorded under this name from northern New Guinea are shown to represent the new species E. orsaki. Additional distribution records for 15 previously described Enithares species are provided for many localities in the Malay Archipelago and mainland Southeast Asia, including the first records of E. bakeri from Lombok, Flores, Timor, Halmahera, and Obi; the first record of E. paramegalops from Ambon; the first records of E. gibbera from Kolombangara and Malaita in the Solomon Islands; the first record of E. intricata from Bali; the first records of E. lombokensis from Flores and Sumba; the first records of E. ripleyana from Halmahera, Ternate and Tidore; and the first record of E. ciliata from Borneo. Photomicrographs of key characters and distribution maps are provided for all new species described, accompanied by an updated world checklist for the genus with distributional notes and associated references.}, } @article {pmid33055624, year = {2020}, author = {Moore, MR and Harrison, SM and Cave, RD and Branham, MA}, title = {Mitochondrial sequence data clarify species concepts in the Cyclocephala mafaffa species complex (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini).}, journal = {Zootaxa}, volume = {4772}, number = {1}, pages = {zootaxa.4772.1.3}, doi = {10.11646/zootaxa.4772.1.3}, pmid = {33055624}, issn = {1175-5334}, mesh = {Animals ; *Coleoptera ; Phylogeny ; }, abstract = {The speciose genus Cyclocephala Dejean (Coleoptera: Scarabaeidae: Dynastinae: Cyclocephalini) has attracted research attention due to their diversity, agroeconomic importance, and floral visitation habits. Uniquely among Cyclocephala species, C. mafaffa Burmeister and C. deceptor (Casey), two nearly identical species, are diagnosed by a pronotal character: beaded or not beaded basal pronotal margin. We evaluated these morphological species hypotheses with a phylogenetic analysis of 12S and COI, neighbor-joining analysis, and several single-locus species delimitation procedures (automatic barcode gap analysis and three Poisson tree processes analyses). Together, these analyses supported the species concepts for C. deceptor and C. mafaffa. Delimitation procedures supported several distinct molecular operational taxonomic units among these taxa. We consider the separation of C. deceptor and C. mafaffa to be valid. We conservatively synonymize the West Indian subspecies C. mafaffa grandis Burmeister under C. mafaffa and offer a discussion on subspecific concepts in Cyclocephalini. We designate the lectotype of Stigmalia deficiens Casey. Implications of this study for other geographically widespread cyclocephalines or species with variable pronotal morphology are discussed.}, } @article {pmid33053414, year = {2020}, author = {Dos Reis, YV and Alevi, KCC}, title = {Hybridization in Phlebotominae (Diptera: Psychodidae): A mini-review.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {86}, number = {}, pages = {104593}, doi = {10.1016/j.meegid.2020.104593}, pmid = {33053414}, issn = {1567-7257}, mesh = {Animals ; Crosses, Genetic ; Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; *Hybridization, Genetic ; Psychodidae/*classification/*genetics ; Reproductive Isolation ; }, abstract = {Taxonomy based only on morphology, although extremely important for the classification of sandflies, has been shown to be insufficient for the delimitation of some taxa. Thus, integrative taxonomy could play a fundamental role in clarifying these and other taxonomic issues, since data from different areas are used to aggregate greater reliability in species classification. Experimental crosses are important taxonomic tools, since the presence of reproductive barriers when associated with divergence between two evolutionary lineages, confirms the specific status of taxa based on the biological species concept. In the subfamily Phlebotominae, experimental crosses were mostly focused on the study of the Lutzomyia longipalpis complex, which helped to identify different evolutionary lineages for that group of vectors. Considering the difficulty of classifying some Phlebotominae species and the importance of hybridization studies for taxonomy, we grouped all the information associated with experimental crosses in sandflies in a mini-review. In view of the results grouped in this review, it is evident that i) experimental crossings are important tools to aggregate studies of integrative taxonomy in the Phlebotominae subfamily; ii) these analyses should be applied in the taxonomic studies of cryptic species; iii) Lu longipalpis populations have pre and/or post-zygotic reproductive barriers; iv) Lu. longipalpis represents more than one species and efforts must be applied to differentiate the taxa of the Lu. longipalpis complex; v) Phlebotomus populations do not present intraspecific reproductive barriers; vi) the absence of reproductive barriers between Ph. sergenti from Israel and Turkey (representing populations of the same evolutionary lineage) does not rule out the possible existence of cryptic species, it being necessary to perform experimental crosses between the different strains indicated by the molecular markers; and finally, vii) different species of Phlebotomus have post-zygotic barriers, confirming the specific status of Ph. duboscqi, Ph. papatasi, and Ph. bergeroti.}, } @article {pmid33046857, year = {2021}, author = {Lun, Z and Ouyang, B and Kwon, DH and Ha, Y and Foley, EE and Huang, TY and Cai, Z and Kim, H and Balasubramanian, M and Sun, Y and Huang, J and Tian, Y and Kim, H and McCloskey, BD and Yang, W and Clément, RJ and Ji, H and Ceder, G}, title = {Cation-disordered rocksalt-type high-entropy cathodes for Li-ion batteries.}, journal = {Nature materials}, volume = {20}, number = {2}, pages = {214-221}, doi = {10.1038/s41563-020-00816-0}, pmid = {33046857}, issn = {1476-4660}, abstract = {High-entropy (HE) ceramics, by analogy with HE metallic alloys, are an emerging class of solid solutions composed of a large number of species. These materials offer the benefit of large compositional flexibility and can be used in a wide variety of applications, including thermoelectrics, catalysts, superionic conductors and battery electrodes. We show here that the HE concept can lead to very substantial improvements in performance in battery cathodes. Among lithium-ion cathodes, cation-disordered rocksalt (DRX)-type materials are an ideal platform within which to design HE materials because of their demonstrated chemical flexibility. By comparing a group of DRX cathodes containing two, four or six transition metal (TM) species, we show that short-range order systematically decreases, whereas energy density and rate capability systematically increase, as more TM cation species are mixed together, despite the total metal content remaining fixed. A DRX cathode with six TM species achieves 307 mAh g[-1] (955 Wh kg[-1]) at a low rate (20 mA g[-1]), and retains more than 170 mAh g[-1] when cycling at a high rate of 2,000 mA g[-1]. To facilitate further design in this HE DRX space, we also present a compatibility analysis of 23 different TM ions, and successfully synthesize a phase-pure HE DRX compound containing 12 TM species as a proof of concept.}, } @article {pmid33046719, year = {2020}, author = {Forsman, ZH and Ritson-Williams, R and Tisthammer, KH and Knapp, ISS and Toonen, RJ}, title = {Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16995}, pmid = {33046719}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*physiology ; Biological Evolution ; Coral Reefs ; Hawaii ; Host Adaptation ; Metagenomics/*methods ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {The 'species' is a key concept for conservation and evolutionary biology, yet the lines between population and species-level variation are often blurred, especially for corals. The 'Porites lobata species complex' consists of branching and mounding corals that form reefs across the Pacific. We used reduced representation meta-genomic sequencing to examine genetic relationships within this species complex and to identify candidate loci associated with colony morphology, cryptic genetic structure, and apparent bleaching susceptibility. We compared existing Porites data with bleached and unbleached colonies of the branching coral P. compressa collected in Kāne'ohe Bay Hawai'i during the 2015 coral bleaching event. Loci that mapped to coral, symbiont, and microbial references revealed genetic structure consistent with recent host-symbiont co-evolution. Cryptic genetic clades were resolved that previous work has associated with distance from shore, but no genetic structure was associated with bleaching. We identified many candidate loci associated with morphospecies, including candidate host and symbiont loci with fixed differences between branching and mounding corals. We also found many loci associated with cryptic genetic structure, yet relatively few loci associated with bleaching. Recent host-symbiont co-evolution and rapid diversification suggests that variation and therefore the capacity of these corals to adapt may be underappreciated.}, } @article {pmid33044006, year = {2021}, author = {Sandstedt, GD and Wu, CA and Sweigart, AL}, title = {Evolution of multiple postzygotic barriers between species of the Mimulus tilingii complex.}, journal = {Evolution; international journal of organic evolution}, volume = {75}, number = {3}, pages = {600-613}, pmid = {33044006}, issn = {1558-5646}, support = {T32 GM007103/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Crosses, Genetic ; *Genetic Speciation ; Hybridization, Genetic ; Mimulus/classification/*genetics ; *Reproductive Isolation ; }, abstract = {Species are often defined by their ability to interbreed (i.e., Biological Species Concept), but determining how and why reproductive isolation arises between new species can be challenging. In the Mimulus tilingii species complex, three species (M. caespitosa, M. minor, and M. tilingii) are largely allopatric and grow exclusively at high elevations (>2000 m). The extent to which geographic separation has shaped patterns of divergence among the species is not well understood. In this study, we determined that the three species are morphologically and genetically distinct, yet recently diverged. Additionally, we performed reciprocal crosses within and between the species and identified several strong postzygotic reproductive barriers, including hybrid seed inviability, F1 hybrid necrosis, and F1 hybrid male and female sterility. In this study, such postzygotic barriers are so strong that a cross between any species pair in the M. tilingii complex would cause nearly complete reproductive isolation. We consider how geographical and topographical patterns may have facilitated the evolution of several postzygotic barriers and contributed to speciation of closely related members within the M. tilingii species complex.}, } @article {pmid33025195, year = {2020}, author = {Van Regenmortel, MHV}, title = {A brief history of the species concept in virology and an opinion on the proposal to introduce Linnaean binomial virus species names.}, journal = {Archives of virology}, volume = {165}, number = {12}, pages = {3073-3077}, doi = {10.1007/s00705-020-04795-0}, pmid = {33025195}, issn = {1432-8798}, mesh = {Data Management ; Databases as Topic ; Genome, Viral ; History, 20th Century ; History, 21st Century ; Virology/*history ; Viruses/*classification ; }, abstract = {The species concept used in virology is based on the logic of the Linnaean hierarchy, which views a species class as the lowest abstract category that is included in all the higher categories in the classification, such as genera and families. As a result of this class inclusion, the members of a species class are always less numerous than the members of higher classes, which become more numerous as one moves up in the hierarchy. Because species classes always have fewer members than any of the higher classes, logic requires that they need more qualifications for establishing membership than any of the higher classes. This invalidates the claim that a species could be defined by a single property present in all its members. Species were only accepted in virus classification in 1991, because virologists assumed that it would lead to the use of Latin species names, which they rejected. Anglicized binomial species names have been used by virologists for more the 40 years and are popular because they consist of a virus name followed by a genus name that most virologists are familiar with. The ICTV has proposed to introduce a new Latinized virus species binomial nomenclature using the genus name followed by a hard-to-remember Latinized species epithet that bears little resemblance to the name of the virus itself. However, the proposal did not clarify what the advantage is of having to learn hundreds of new unfamiliar virus species names. In 2013, the ICTV changed the definition of a virus species as an abstract class and defined it as a group of physical objects, which induced virologists to believe that a virus species could be defined by a few characteristics of the viral genome. In recent years, thousands of viral sequences have been discovered in metagenomic databases, and the ICTV has suggested that it should be possible to incorporate these sequences in the current ICTV virus classification. Unfortunately, the relational properties of these hypothetical viruses that result from their biological interactions with hosts and vectors remain in the vast majority of cases totally unknown. The absence of this information makes it in fact impossible to incorporate these metagenomic sequences in the current classification of virus species.}, } @article {pmid33013519, year = {2020}, author = {Bauer, GB and Cook, PF and Harley, HE}, title = {The Relevance of Ecological Transitions to Intelligence in Marine Mammals.}, journal = {Frontiers in psychology}, volume = {11}, number = {}, pages = {2053}, pmid = {33013519}, issn = {1664-1078}, abstract = {Macphail's comparative approach to intelligence focused on associative processes, an orientation inconsistent with more multifaceted lay and scientific understandings of the term. His ultimate emphasis on associative processes indicated few differences in intelligence among vertebrates. We explore options more attuned to common definitions by considering intelligence in terms of richness of representations of the world, the interconnectivity of those representations, the ability to flexibly change those connections, and knowledge. We focus on marine mammals, represented by the amphibious pinnipeds and the aquatic cetaceans and sirenians, as animals that transitioned from a terrestrial existence to an aquatic one, experiencing major changes in ecological pressures. They adapted with morphological transformations related to streamlining the body, physiological changes in respiration and thermoregulation, and sensory/perceptual changes, including echolocation capabilities and diminished olfaction in many cetaceans, both in-air and underwater visual focus, and enhanced senses of touch in pinnipeds and sirenians. Having a terrestrial foundation on which aquatic capacities were overlaid likely affected their cognitive abilities, especially as a new reliance on sound and touch, and the need to surface to breath changed their interactions with the world. Vocal and behavioral observational learning capabilities in the wild and in laboratory experiments suggest versatility in group coordination. Empirical reports on aspects of intelligent behavior like problem-solving, spatial learning, and concept learning by various species of cetaceans and pinnipeds suggest rich cognitive abilities. The high energy demands of the brain suggest that brain-intelligence relationships might be fruitful areas for study when specific hypotheses are considered, e.g., brain mapping indicates hypertrophy of specific sensory areas in marine mammals. Modern neuroimaging techniques provide ways to study neural connectivity, and the patterns of connections between sensory, motor, and other cortical regions provide a biological framework for exploring how animals represent and flexibly use information in navigating and learning about their environment. At this stage of marine mammal research, it would still be prudent to follow Macphail's caution that it is premature to make strong comparative statements without more empirical evidence, but an approach that includes learning more about how animals flexibly link information across multiple representations could be a productive way of comparing species by allowing them to use their specific strengths within comparative tasks.}, } @article {pmid33013168, year = {2020}, author = {Mehrotra, R and Gutiérrez, MC and Scott, CM and Arnold, S and Monchanin, C and Chavanich, S}, title = {On the Plakobranchidae (Gastropoda, Sacoglossa) from soft sediment habitats of Koh Tao, Gulf of Thailand, with descriptions of two new species.}, journal = {ZooKeys}, volume = {969}, number = {}, pages = {85-121}, pmid = {33013168}, issn = {1313-2989}, abstract = {Research in recent years have provided rapid advances in biogeographic and taxonomic documentation of sea slugs around the world. However, efforts are lacking in surveying most coastlines and habitats in South-East Asia. Recent studies from the Gulf of Thailand have indicated that a wealth of unexplored sea slug diversity and ecology may be gained from an investigation of soft sediment habitats beyond the reef slopes. Additionally, the waters of Koh Tao have been found to host regionally high levels of sea slug diversity with several species awaiting taxonomic clarification. In this work the initial findings of an expanded survey effort from the waters around Koh Tao are provided, with the identity of two soft sediment-associated sacoglossan species in the family Plakobranchidae being investigated. By integrating morphological and molecular analyses, the species Plakobranchus noctisstellatus sp. nov. and Elysia aowthai sp. nov. are described and species complexes surrounding Plakobranchus ocellatus van Hasselt, 1824 and Elysia japonica Eliot, 1913 are discussed. The topics of morphological variability and the cryptic species problem are also discussed.}, } @article {pmid32997388, year = {2021}, author = {Malabarba, LR and Chuctaya, J and Hirschmann, A and de Oliveira, EB and Thomaz, AT}, title = {Hidden or unnoticed? Multiple lines of evidence support the recognition of a new species of Pseudocorynopoma (Characidae: Corynopomini).}, journal = {Journal of fish biology}, volume = {98}, number = {1}, pages = {219-236}, doi = {10.1111/jfb.14572}, pmid = {32997388}, issn = {1095-8649}, mesh = {Animals ; Characidae/*anatomy & histology/*classification ; Female ; Male ; *Phylogeny ; Rivers ; Sex Characteristics ; Species Specificity ; }, abstract = {Species delimitation is a permanent issue in systematics. The increasing recognition of geographically isolated populations as independent lineages allowed by new methods of analysis has inflated the species-populations dilemma, which involves deciding whether to consider separate lineages as different species or structured genetic populations. This is commonly observed between fishes of adjacent river basins, with some lineages being considered allopatric sister species and others considered isolated populations or variants of the same species. Pseudocorynopoma doriae is a characid diagnosed from its single congener by the number of anal-fin rays and sexually dimorphic characters of males, including distinct fin colouration. The authors found variation in the colour pattern between isolated populations previously identified as P. doriae but no variation in scale or fin-ray counts. They analysed molecular evidence at the population level and morphological differences related to life history (e.g., colour dimorphism related to inseminating behaviour). The results provide compelling evidence for the recognition of a new species of Pseudocorynopoma despite the lack of discrete differences in meristic data. The recognition of the new species is consistent with biogeographical evidence for the long-term isolation of the respective river drainages and with differences between the ichthyofaunal communities of these rivers.}, } @article {pmid32976058, year = {2021}, author = {Garfinkel, AR}, title = {The History of Botrytis Taxonomy, the Rise of Phylogenetics, and Implications for Species Recognition.}, journal = {Phytopathology}, volume = {111}, number = {3}, pages = {437-454}, doi = {10.1094/PHYTO-06-20-0211-IA}, pmid = {32976058}, issn = {0031-949X}, mesh = {*Botrytis/genetics ; Phylogeny ; *Plant Diseases ; }, abstract = {Botrytis is one of the oldest, most well studied, and most economically important fungal taxa. Nonetheless, many species in this genus have remained obscured for nearly 300 years because of the difficulty in distinguishing these species by conventional mycological methods. Aided by the use of phylogenetic tools, the genus is currently undergoing a taxonomic revolution. The number of putative species in the genus has nearly doubled over the last 10 years and more species are likely to be discovered in the future. The implementation of phylogenetic species recognition concepts in Botrytis is providing for more resolution on the relatedness among species than ever before, and this has helped to overcome issues in historical species recognition using morphology, sexual crosses, and pathogenicity tests. Meanwhile, the use of genetic tools is helping to reveal surprising insight into this archetypal necrotroph's behavior, making these approaches increasingly important in species recognition and identification. As Botrytis taxonomy continues to evolve at a rapid pace, researchers should be encouraged to continue to employ the powerful tool of phylogenetics while considering how it fits into a larger framework of classical Botrytis species recognition. Starting points for discussion on how to move forward with Botrytis species recognition are included herein, with an emphasis on the implications and utility of new species descriptions.}, } @article {pmid32944422, year = {2020}, author = {Sterling, KA and Warren, ML}, title = {Description of a new species of cryptic snubnose darter (Percidae: Etheostomatinae) endemic to north-central Mississippi.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9807}, pmid = {32944422}, issn = {2167-8359}, abstract = {Many subclades within the large North American freshwater fish genus Etheostoma (Percidae) show brilliant male nuptial coloration during the spring spawning season. Traditionally, perceived differences in color were often used to diagnose closely related species. More recently, perceived differences in male nuptial color have prompted further investigation of potential biodiversity using genetic tools. However, cryptic diversity among Etheostoma darters renders male nuptial color as unreliable for detecting and describing diversity, which is foundational for research and conservation efforts of this group of stream fishes. Etheostoma raneyi (Yazoo Darter) is an imperiled, range-limited fish endemic to north-central Mississippi. Existing genetic evidence indicates cryptic diversity between disjunctly distributed E. raneyi from the Little Tallahatchie and Yocona river watersheds despite no obvious differences in male color between the two drainages. Analysis of morphological truss and geometric measurements and meristic and male color characters yielded quantitative differences in E. raneyi from the two drainages consistent with genetic evidence. Morphological divergence is best explained by differences in stream gradients between the two drainages. Etheostoma faulkneri, the Yoknapatawpha Darter, is described as a species under the unified species concept. The discovery of cryptic diversity within E. raneyi would likely not have occurred without genetic tools. Cryptic diversity among Etheostoma darters and other stream fishes is common, but an overreliance on traditional methods of species delimitation (e.g., identification of a readily observable physical character to diagnose a species) impedes a full accounting of the diversity in freshwater fishes in the southeastern United States.}, } @article {pmid32904489, year = {2020}, author = {Frank, JL and Siegel, N and Schwarz, CF and Araki, B and Vellinga, EC}, title = {Xerocomellus (Boletaceae) in western North America.}, journal = {Fungal systematics and evolution}, volume = {6}, number = {}, pages = {265-288}, pmid = {32904489}, issn = {2589-3831}, abstract = {Understanding diversity in the genus Xerocomellus in western North America has been obscured by morphological variability, widespread use of species epithets typified by specimens from Europe and eastern North America, misunderstood phylogenetic relationships, and species complexes. We collected extensively and used genetic and morphological data to establish the occurrence of ten Xerocomellus species in western North America. We generated ITS sequences from five type collections and from vouchered representative collections to clarify our understanding of existing species concepts. We describe three new species (Xerocomellus atropurpureus, X. diffractus, and X. salicicola) and propose two new combinations (X. amylosporus and X. mendocinensis), transfer Boletus coccyginus to Hortiboletus, and provide a dichotomous key to species of Xerocomellus in western North America.}, } @article {pmid32904100, year = {2020}, author = {Marincowitz, S and Barnes, I and de Beer, ZW and Wingfield, MJ}, title = {Epitypification of Ceratocystis fimbriata.}, journal = {Fungal systematics and evolution}, volume = {6}, number = {}, pages = {289-298}, pmid = {32904100}, issn = {2589-3831}, abstract = {Ceratocystis accommodates many important pathogens of agricultural crops and woody plants. Ceratocystis fimbriata, the type species of the genus is based on a type that is unsuitable for a precise application and interpretation of the species. This is because no culture or DNA data exist for the type specimen. The aim of this study was to select a reference specimen that can serve to stabilize the name of this important fungus. We selected a strain, CBS 114723, isolated from sweet potato in North Carolina, USA, in 1998 for this purpose. The strain was selected based on the availability of a living culture in a public depository. A draft genome sequence is also available for this strain. Its morphological characteristics were studied and compared with the existing and unsuitable type specimen as well as with the original descriptions of C. fimbriata. The selected strain fits the existing concept of the species fully and we have consequently designated it as an epitype to serve as a reference specimen for C. fimbriata.}, } @article {pmid32887406, year = {2020}, author = {Milesi, F and Giacometti, M and Coppadoro, LP and Ferrari, G and Fiore, GB and Bertacco, R}, title = {On-Chip Selective Capture and Detection of Magnetic Fingerprints of Malaria.}, journal = {Sensors (Basel, Switzerland)}, volume = {20}, number = {17}, pages = {}, pmid = {32887406}, issn = {1424-8220}, mesh = {Animals ; Cattle ; Erythrocytes ; *Hemeproteins ; Magnetic Phenomena ; *Magnetics ; *Malaria/diagnosis ; Physical Phenomena ; }, abstract = {The development of innovative diagnostic tests is fundamental in the route towards malaria eradication. Here, we discuss the sorting capabilities of an innovative test for malaria which allows the quantitative and rapid detection of all malaria species. The physical concept of the test exploits the paramagnetic property of infected erythrocytes and hemozoin crystals, the magnetic fingerprints of malaria common to all species, which allows them to undergo a selective magnetophoretic separation driven by a magnetic field gradient in competition with gravity. Upon separation, corpuscles concentrate at the surface of a silicon microchip where interdigitated electrodes are placed in close proximity to magnetic concentrators. The impedance variation proportional to the amount of attracted particles is then measured. The capability of our test to perform the selective detection of infected erythrocytes and hemozoin crystals has been tested by means of capture experiments on treated bovine red blood cells, mimicking the behavior of malaria-infected ones, and suspensions of synthetic hemozoin crystals. Different configuration angles of the chip with respect to gravity force and different thicknesses of the microfluidic chamber containing the blood sample have been investigated experimentally and by multiphysics simulations. In the paper, we describe the optimum conditions leading to maximum sensitivity and specificity of the test.}, } @article {pmid32880855, year = {2021}, author = {Zhang, W and Sun, Y and Liu, J and Xu, C and Zou, X and Chen, X and Liu, Y and Wu, P and Yang, X and Zhou, S}, title = {DNA barcoding of Oryza: conventional, specific, and super barcodes.}, journal = {Plant molecular biology}, volume = {105}, number = {3}, pages = {215-228}, pmid = {32880855}, issn = {1573-5028}, mesh = {*DNA Barcoding, Taxonomic ; Likelihood Functions ; Oryza/*classification/*genetics ; Phylogeny ; Seeds/genetics ; Species Specificity ; Tissue Banks ; }, abstract = {We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world's population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.}, } @article {pmid32874124, year = {2019}, author = {Nagai, T}, title = {Sensitivity differences among seven algal species to 12 herbicides with various modes of action.}, journal = {Journal of pesticide science}, volume = {44}, number = {4}, pages = {225-232}, pmid = {32874124}, issn = {1348-589X}, abstract = {Seven algal species were used to conduct toxicity assays with 12 herbicides to determine differences in species sensitivity. A fluorescence microplate toxicity assay was used as an efficient and economical high-throughput assay. The obtained toxicity data were standardized based on the species sensitivity distribution concept. The most-sensitive individual species differed among herbicides: Desmodesmus subspicatus was most sensitive to chloronitrofen and pendimethalin; Achnanthidium minutissimum was most sensitive to chlorpropham; Nitzschia palea was most sensitive to diquat, glyphosate, and dichlobenil; Navicula pelliculosa was most sensitive to trifluralin; and Pseudanabaena foetida was most sensitive to glufosinate, asulam, and 2,4-D. Surprisingly, Raphidocelis (formerly Pseudokirchneriella) subcapitata, a standard green alga, was not the most sensitive to any of the herbicides. The results clearly showed that a single algal species cannot represent the algal assemblage in terms of sensitivity. Therefore, multispecies algal toxicity data sets are essential for assessing the ecological effect of herbicides.}, } @article {pmid32858759, year = {2020}, author = {Brassard, F and Francoeur, A and Lessard, JP}, title = {Temperature drives caste-specific morphological clines in ants.}, journal = {The Journal of animal ecology}, volume = {89}, number = {11}, pages = {2517-2530}, doi = {10.1111/1365-2656.13330}, pmid = {32858759}, issn = {1365-2656}, mesh = {Animals ; Male ; *Ants ; Body Size ; Climate ; Temperature ; }, abstract = {The morphology of organisms relates to most aspects of their life history and autecology. As such, elucidating the drivers of morphological variation along environmental gradients might give insight into processes limiting species distributions. In eusocial organisms, the concept of morphology is more complex than in solitary organisms. Eusocial insects such as ants exhibit drastic morphological differences between reproductive and worker castes. How environmental selection operates on the morphology of each caste, and whether caste-specific selection has fitness consequences is largely unknown, but is potentially crucial to understand what limits ant species' distributions. Here we aimed to examine whether ant shape and body size covaries with climate at the scale of an entire continent, and whether such relationship might be caste specific. We used 26,472 georeferenced morphometric measurements from 2,206 individual ants belonging to 32 closely related North American species in the genus Formica to assess how ant morphology relates to geographic variation in the abiotic environment. Although precipitation and seasonality explained some of the geographic variation in morphology, temperature was the best predictor. Specifically, geographic variation in body size was positively related to temperature, meaning that ants are smaller in cold than in warm environments. Moreover, the strength of the relationship between size and temperature was stronger for the reproductive castes (i.e. queens and males) than for the worker caste. The shape of workers and males also varied along these large-scale abiotic gradients. Specifically, the relative length of workers' legs, thoraxes and antennae positively related to temperature, meaning that they had shorter appendages in cold environments. In contrast, males had smaller heads, but larger thoraxes in more seasonal environments. Overall, our results suggest that geographic variation in ambient temperature influences the morphology of ants, but that the strength of this effect is caste specific. In conclusion, whereas ant ecology has traditionally focused on workers, our study shows that considering the ecology of the reproductive castes is imperative to move forward in this field.}, } @article {pmid32845927, year = {2020}, author = {Gu, J and Jiang, B and Wang, H and Wei, T and Lin, L and Huang, Y and Huang, J}, title = {Phylogeny and species delimitation of the genus Longgenacris and Fruhstorferiola viridifemorata species group (Orthoptera: Acrididae: Melanoplinae) based on molecular evidence.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0237882}, pmid = {32845927}, issn = {1932-6203}, mesh = {Animals ; Electron Transport Complex IV/genetics ; Genetic Variation ; Grasshoppers/anatomy & histology/*classification/*genetics ; Haplotypes/genetics ; Likelihood Functions ; Male ; Models, Theoretical ; *Phylogeny ; Species Specificity ; Tooth/anatomy & histology ; }, abstract = {Phylogenetic positions of the genus Longgenacris and one of its members, i.e. L. rufiantennus are controversial. The species boundaries within both of L. rufiantennus+Fruhstorferiola tonkinensis and F. viridifemorata species groups are unclear. In this study, we explored the phylogenetic positions of the genus Longgenacris and the species L. rufiantennus and the relationships among F. viridifemorata group based on the 658-base fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) barcode and the complete sequences of the internal transcribed spacer regions (ITS1 and ITS2) of the nuclear ribosomal DNA. The phylogenies were reconstructed in maximum likelihood framework using IQ-TREE. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. Phylogenetic species concept and NJ tree, K2P distance, the statistical parsimony network as well as the generalized mixed Yule coalescent model (GMYC) were employed to delimitate the species boundaries in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups. The results demonstrated that the genus Longgenacris should be placed in the subfamily Melanoplinae but not Catantopinae, and L. rufiantennus should be a member of the genus Fruhstorferiola but not Longgenacris. Species boundary delimitation confirmed the presence of oversplitting in L. rufiantennus+F. tonkinensis and F. viridifemorata species groups and suggested that each group should be treated as a single species.}, } @article {pmid32826216, year = {2020}, author = {Díaz-Garrido, N and Lozano, CP and Kreth, J and Giacaman, RA}, title = {Competition and Caries on Enamel of a Dual-Species Biofilm Model with Streptococcus mutans and Streptococcus sanguinis.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {21}, pages = {}, pmid = {32826216}, issn = {1098-5336}, support = {R01 DE021726/DE/NIDCR NIH HHS/United States ; R01 DE029492/DE/NIDCR NIH HHS/United States ; }, mesh = {*Biofilms ; Dental Caries/*microbiology ; Dental Enamel/*microbiology ; *Microbial Interactions ; Streptococcus mutans/*physiology ; Streptococcus sanguis/*physiology ; }, abstract = {Imbalances within the dental biofilm trigger dental caries, currently considered a dysbiosis and the most prevalent noncommunicable disease. There is still a gap in knowledge about the dynamics of enamel colonization by bacteria from the dental biofilm in caries. The aim, therefore, was to test whether the sequence of enamel colonization by a typically commensal and a cariogenic species modifies biofilm's cariogenicity. Dual-species biofilms of Streptococcus mutans and Streptococcus sanguinis on saliva-coated enamel slabs were inoculated in different sequences: S. mutans followed by S. sanguinis (Sm-Ss), S. sanguinis followed by S. mutans (Ss-Sm), S. mutans and S. sanguinis inoculated at the same time (Sm=Ss), and the single-species controls S. mutans followed by S. mutans (Sm-Sm) and S. sanguinis followed by S. sanguinis (Ss-Ss). Biofilms were exposed to 10% sucrose 3 times per day for 5 days, and the slabs/biofilms were retrieved to assess demineralization, viable cells, biomass, proteins, polysaccharides, and H2O2 production. Compared with Sm-Sm, primary inoculation with S. sanguinis reduced demineralization (P < 0.05). Both Ss-Sm and Sm=Ss sequences showed reduction in biomass, protein, and polysaccharide content (P < 0.05). The highest S. sanguinis viable count and H2O2 production level and the lowest acidogenicity were observed when S. sanguinis colonized enamel before S. mutans (P < 0.05). Initial enamel adherence with commensal biofilms seems to induce more intense competition against more typically cariogenic species, reducing cariogenicity.IMPORTANCE The concept of caries as an ecological disease implies the understanding of the intricate relationships among the populating microorganisms. Under frequent sugar exposure, some bacteria from the dental biofilm develop pathogenic traits that lead to imbalances (dysbiosis). Depending on which microorganism colonizes the dental surface first, different competition strategies may be developed. Studying the interactions in the entire dental biofilm is not an easy task. In this study, therefore, we modeled the interplay among these microorganisms using a caries-inducing species (S. mutans) and a health-associated species (S. sanguinis). Initial enamel adherence with S. sanguinis seems to induce more intense competition against typically caries-inducing species. Besides continuous exposure with sugars, early colonization of the enamel by highly cariogenic species like S. mutans appears to be needed to develop caries lesions as well. Promoting early colonization by health-associated bacteria such as S. sanguinis could help to maintain oral health, delaying dysbiosis.}, } @article {pmid32821528, year = {2020}, author = {Campbell, DL and Thessen, AE and Ries, L}, title = {A novel curation system to facilitate data integration across regional citizen science survey programs.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9219}, pmid = {32821528}, issn = {2167-8359}, abstract = {Integrative modeling methods can now enable macrosystem-level understandings of biodiversity patterns, such as range changes resulting from shifts in climate or land use, by aggregating species-level data across multiple monitoring sources. This requires ensuring that taxon interpretations match up across different sources. While encouraging checklist standardization is certainly an option, coercing programs to change species lists they have used consistently for decades is rarely successful. Here we demonstrate a novel approach for tracking equivalent names and concepts, applied to a network of 10 regional programs that use the same protocols (so-called "Pollard walks") to monitor butterflies across America north of Mexico. Our system involves, for each monitoring program, associating the taxonomic authority (in this case one of three North American butterfly fauna treatments: Pelham, 2014; North American Butterfly Association, Inc., 2016; Opler & Warren, 2003) that shares the most similar overall taxonomic interpretation to the program's working species list. This allows us to define each term on each program's list in the context of the appropriate authority's species concept and curate the term alongside its authoritative concept. We then aligned the names representing equivalent taxonomic concepts among the three authorities. These stepping stones allow us to bridge a species concept from one program's species list to the name of the equivalent in any other program, through the intermediary scaffolding of aligned authoritative taxon concepts. Using a software tool we developed to access our curation system, a user can link equivalent species concepts between data collecting agencies with no specialized knowledge of taxonomic complexities.}, } @article {pmid32758675, year = {2020}, author = {Porto, PS and Anjos, D and Dábilla, N and da Fonseca, SG and Souza, M}, title = {Immunoinformatic construction of an adenovirus-based modular vaccine platform and its application in the design of a SARS-CoV-2 vaccine.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {85}, number = {}, pages = {104489}, pmid = {32758675}, issn = {1567-7257}, mesh = {Antigen Presentation ; Capsid Proteins/*chemistry/genetics/immunology ; Computational Biology/*methods ; Computer Simulation ; Dependovirus/immunology ; Drug Design ; Epitopes, B-Lymphocyte/genetics/*immunology ; Humans ; Immunity, Humoral ; Interferon-gamma/metabolism ; SARS-CoV-2/drug effects/genetics/immunology ; Viral Vaccines/genetics/*immunology ; }, abstract = {The current SARS-CoV-2 pandemic has imposed new challenges and demands for health systems, especially in the development of new vaccine strategies. Vaccines for many pathogens were developed based on the display of foreign epitopes in the variable regions of the human adenovirus (HAdV) major capsid proteins (hexon, penton and fiber). The humoral immune response against the HAdV major capsid proteins was demonstrated to play a role in the development of an immune response against the epitopes in display. Through the immunoinformatic profiling of the major capsid proteins of HAdVs from different species, we developed a modular concept that can be used in the development of vaccines based on HAdV vectors. Our data suggests that different immunomodulatory potentials can be observed in the conserved regions, present in the hexon and penton proteins, from different species. Using this modular approach, we developed a HAdV-5 based vaccine strategy for SARS-CoV-2, constructed through the display of SARS-CoV-2 epitopes indicated by our prediction analysis as immunologically relevant. The sequences of the HAdV vector major capsid proteins were also edited to enhance the IFN-gamma induction and antigen presenting cells activation. This is the first study proposing a modular HAdV platform developed to aid the design of new vaccines by inducing an immune response more suited for the epitopes in display.}, } @article {pmid32737666, year = {2020}, author = {Wee, NQ and Crouch, K and Cutmore, SC and Cribb, TH}, title = {Pseudohurleytrema yolandae n. sp., the first monorchiid trematode reported from the Triacanthidae (Tetraodontiformes).}, journal = {Systematic parasitology}, volume = {97}, number = {5}, pages = {491-500}, doi = {10.1007/s11230-020-09924-6}, pmid = {32737666}, issn = {1573-5192}, mesh = {Animals ; Bays ; DNA, Helminth/genetics ; Phylogeny ; Queensland ; RNA, Ribosomal, 28S/genetics ; Species Specificity ; Tetraodontiformes/*parasitology ; Trematoda/anatomy & histology/*classification/genetics ; }, abstract = {Prior to the present study, species of the trematode family Monorchiidae Odhner, 1911 had been reported from four of the ten families of tetraodontiform fishes: the Balistidae, Monacanthidae, Ostraciidae and Tetraodontidae. Here we report the first monorchiid from the family Triacanthidae, Pseudohurleytrema yolandae n. sp. infecting Tripodichthys angustifrons (Hollard), from Moreton Bay, Queensland, Australia. The species conforms well to the morphological concept of the subfamily Hurleytrematinae Yamaguti, 1958, and the genus Pseudohurleytrema Yamaguti, 1954, in the possession of filamented eggs, a bipartite terminal organ, and a unipartite seminal vesicle. Relative to the other three recognised species of Pseudohurleytrema, the present species is distinctive in the size of the testis and eggs, position of the ovary, and the form of the vitellarium and excretory vesicle. We consider Pseudohurleytrema magnum Kaikabad & Bilqees in Bilqees, 1991 as a species inquirenda. Sequence data for the 28S ribosomal RNA gene and cox1 mitochondrial gene were generated for P. yolandae, providing the first molecular data for the genus. Phylogenetic analysis showed that P. yolandae does not form a clade with the other three hurleytrematine genera for which there are molecular data (Helicometroides Yamaguti, 1934, Hurleytrematoides Yamaguti, 1953 and Provitellus Dove & Cribb, 1998), forming a poorly-supported clade with Proctotrema addisoni Searle, Cutmore & Cribb, 2014 within the clade of the subfamily Monorchiinae Odhner, 1911. The four hurleytrematine genera resolved as four distinct clades, indicating that the current subfamilial classification requires comprehensive revision.}, } @article {pmid34692170, year = {2020}, author = {Wu, CI and Wang, X and He, Z and Shi, S}, title = {Replies to the commentaries on the question of 'Is it time to abandon the biological species concept?'.}, journal = {National science review}, volume = {7}, number = {8}, pages = {1407-1409}, pmid = {34692170}, issn = {2053-714X}, } @article {pmid34692168, year = {2020}, author = {Butlin, RK and Stankowski, S}, title = {Is it time to abandon the biological species concept? No.}, journal = {National science review}, volume = {7}, number = {8}, pages = {1400-1401}, pmid = {34692168}, issn = {2053-714X}, } @article {pmid34692167, year = {2020}, author = {Gao, L and Rieseberg, LH}, title = {While neither universally applicable nor practical operationally, the biological species concept continues to offer a compelling framework for studying species and speciation.}, journal = {National science review}, volume = {7}, number = {8}, pages = {1398-1400}, pmid = {34692167}, issn = {2053-714X}, } @article {pmid34692166, year = {2020}, author = {Wang, X and He, Z and Shi, S and Wu, CI}, title = {Genes and speciation: is it time to abandon the biological species concept?.}, journal = {National science review}, volume = {7}, number = {8}, pages = {1387-1397}, pmid = {34692166}, issn = {2053-714X}, abstract = {The biological species concept (BSC) is the cornerstone of neo-Darwinian thinking. In BSC, species do not exchange genes either during or after speciation. However, as gene flow during speciation is increasingly being reported in a substantial literature, it seems time to reassess the revered, but often doubted, BSC. Contrary to the common perception, BSC should expect substantial gene flow at the onset of speciation, not least because geographical isolation develops gradually. Although BSC does not stipulate how speciation begins, it does require a sustained period of isolation for speciation to complete its course. Evidence against BSC must demonstrate that the observed gene flow does not merely occur at the onset of speciation but continues until its completion. Importantly, recent genomic analyses cannot reject this more realistic version of BSC, although future analyses may still prove it wrong. The ultimate acceptance or rejection of BSC is not merely about a historical debate; rather, it is about the fundamental nature of species - are species (and, hence, divergent adaptations) driven by a relatively small number of genes, or by thousands of them? Many levels of biology, ranging from taxonomy to biodiversity, depend on this resolution.}, } @article {pmid32726874, year = {2020}, author = {McCoy, SJ and Krueger-Hadfield, SA and Mieszkowska, N}, title = {Evolutionary Phycology: Toward a Macroalgal Species Conceptual Framework.}, journal = {Journal of phycology}, volume = {56}, number = {6}, pages = {1404-1413}, pmid = {32726874}, issn = {1529-8817}, mesh = {*Biological Evolution ; Hybridization, Genetic ; Phylogeny ; *Seaweed ; }, abstract = {Species concepts formalize evolutionary and ecological processes, but often conflict with one another when considering the mechanisms that ultimately lead to species delimitation. Evolutionary biologists are, however, recognizing that the conceptualization of a species is separate and distinct from the delimitation of species. Indeed, if species are generally defined as separately evolving metapopulation lineages, then characteristics, such as reproductive isolation or monophyly, can be used as evidence of lineage separation and no longer conflict with the conceptualization of a species. However, little of this discussion has addressed the formalization of this evolutionary conceptual framework for macroalgal species. This may be due to the complexity and variation found in macroalgal life cycles. While macroalgal mating system variation and patterns of hybridization and introgression have been identified, complex algal life cycles generate unique eco-evolutionary consequences. Moreover, the discovery of frequent macroalgal cryptic speciation has not been accompanied by the study of the evolutionary ecology of those lineages, and, thus, an understanding of the mechanisms underlying such rampant speciation remain elusive. In this perspective, we aim to further the discussion and interest in species concepts and speciation processes in macroalgae. We propose a conceptual framework to enable phycological researchers and students alike to portray these processes in a manner consistent with dialogue at the forefront of evolutionary biology. We define a macroalgal species as an independently evolving metapopulation lineage, whereby we can test for reproductive isolation or the occupation of distinct adaptive zones, among other mechanisms, as secondary lines of supporting evidence.}, } @article {pmid32724527, year = {2020}, author = {Bangs, MR and Douglas, MR and Chafin, TK and Douglas, ME}, title = {Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus).}, journal = {Ecology and evolution}, volume = {10}, number = {13}, pages = {6477-6493}, pmid = {32724527}, issn = {2045-7758}, abstract = {The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction site-associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.}, } @article {pmid32717495, year = {2020}, author = {Sathasivan, A and Kastl, G and Korotta-Gamage, S and Gunasekera, V}, title = {Trihalomethane species model for drinking water supply systems.}, journal = {Water research}, volume = {184}, number = {}, pages = {116189}, doi = {10.1016/j.watres.2020.116189}, pmid = {32717495}, issn = {1879-2448}, mesh = {Australia ; Chlorine ; *Drinking Water ; Trihalomethanes/analysis ; *Water Pollutants, Chemical/analysis ; *Water Purification ; Water Supply ; }, abstract = {Despite the existence of significant knowedge on complex mechanisms of THM formation, a simple kinetic model to predict THM species concentration is not available, hindering application of knowlwdge for regulatory, monitoring and operational control. The parallel second order reaction (2R) model containing fast and slow reactants has been well established to describe the chlorine decay kinetics under distribution conditions. The proposed THM species model expands the 2R model by systematically incorporating the initial unproductive (not forming THM) chlorine consumption and assuming each THM species is formed at a fixed yield (µg-THM species/mg- productive chlorine consumption). The model concept is tested on 15 water samples that contain a wide range of dissolved organic carbon, specific UV absorbence, and bromide concentrations collected from Australia and US. In all samples, the model describes the THM species concentrations well (error < 3 µg/L in 84% of model estimates) as long as the chlorine profile is described accurately (R[2] > 0.984). The model formulated from the minimum data (initial and two other data points of Cl2 and THM species) predicts the rest of concentrations of THM species from only chlorine measurements. To fully optimise the system or adopt in regulatory monitoring, the effect of changes due to bulk water quality, operational conditions and wall (and biofilm) effects on THM formation kinetics should be established. A similar concept could be extended to other DBP, but rigorous testing is needed.}, } @article {pmid32714773, year = {2020}, author = {Lücking, R and Aime, MC and Robbertse, B and Miller, AN and Ariyawansa, HA and Aoki, T and Cardinali, G and Crous, PW and Druzhinina, IS and Geiser, DM and Hawksworth, DL and Hyde, KD and Irinyi, L and Jeewon, R and Johnston, PR and Kirk, PM and Malosso, E and May, TW and Meyer, W and Öpik, M and Robert, V and Stadler, M and Thines, M and Vu, D and Yurkov, AM and Zhang, N and Schoch, CL}, title = {Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?.}, journal = {IMA fungus}, volume = {11}, number = {}, pages = {14}, pmid = {32714773}, issn = {2210-6340}, abstract = {True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.}, } @article {pmid32694629, year = {2020}, author = {Quilodrán, CS and Montoya-Burgos, JI and Currat, M}, title = {Harmonizing hybridization dissonance in conservation.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {391}, pmid = {32694629}, issn = {2399-3642}, support = {310030_185327/1/SNSF_/Swiss National Science Foundation/Switzerland ; 31003A_182577/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Adaptation, Physiological/*genetics ; Biodiversity ; *Biological Evolution ; *Conservation of Natural Resources ; Human Activities/trends ; Humans ; Hybridization, Genetic/*genetics ; Reproductive Isolation ; }, abstract = {A dramatic increase in the hybridization between historically allopatric species has been induced by human activities. However, the notion of hybridization seems to lack consistency in two respects. On the one hand, it is inconsistent with the biological species concept, which does not allow for interbreeding between species, and on the other hand, it is considered either as an evolutionary process leading to the emergence of new biodiversity or as a cause of biodiversity loss, with conservation implications. In the first case, we argue that conservation biology should avoid the discussion around the species concept and delimit priorities of conservation units based on the impact on biodiversity if taxa are lost. In the second case, we show that this is not a paradox but an intrinsic property of hybridization, which should be considered in conservation programmes. We propose a novel view of conservation guidelines, in which human-induced hybridization may also be a tool to enhance the likelihood of adaptation to changing environmental conditions or to increase the genetic diversity of taxa affected by inbreeding depression. The conservation guidelines presented here represent a guide for the development of programmes aimed at protecting biodiversity as a dynamic evolutionary system.}, } @article {pmid32689915, year = {2020}, author = {Ono, J and Greig, D and Boynton, PJ}, title = {Defining and Disrupting Species Boundaries in Saccharomyces.}, journal = {Annual review of microbiology}, volume = {74}, number = {}, pages = {477-495}, doi = {10.1146/annurev-micro-021320-014036}, pmid = {32689915}, issn = {1545-3251}, mesh = {Adaptation, Physiological ; Ecosystem ; *Evolution, Molecular ; Humans ; Hybridization, Genetic ; Phylogeny ; Saccharomyces/*classification/*genetics/physiology ; }, abstract = {The genus Saccharomyces is an evolutionary paradox. On the one hand, it is composed of at least eight clearly phylogenetically delineated species; these species are reproductively isolated from each other, and hybrids usually cannot complete their sexual life cycles. On the other hand, Saccharomyces species have a long evolutionary history of hybridization, which has phenotypic consequences for adaptation and domestication. A variety of cellular, ecological, and evolutionary mechanisms are responsible for this partial reproductive isolation among Saccharomyces species. These mechanisms have caused the evolution of diverse Saccharomyces species and hybrids, which occupy a variety of wild and domesticated habitats. In this article, we introduce readers to the mechanisms isolating Saccharomyces species, the circumstances in which reproductive isolation mechanisms are effective and ineffective, and the evolutionary consequences of partial reproductive isolation. We discuss both the evolutionary history of the genus Saccharomyces and the human history of taxonomists and biologists struggling with species concepts in this fascinating genus.}, } @article {pmid32647609, year = {2020}, author = {Ahmad, SK and Hossain, F}, title = {Realizing ecosystem-safe hydropower from dams.}, journal = {Renewables: wind, water, and solar}, volume = {7}, number = {1}, pages = {2}, pmid = {32647609}, issn = {2198-994X}, abstract = {For clean hydropower generation while sustaining ecosystems, minimizing harmful impacts and balancing multiple water needs is an integral component. One particularly harmful effect not managed explicitly by hydropower operations is thermal destabilization of downstream waters. To demonstrate that the thermal destabilization by hydropower dams can be managed while maximizing energy production, we modelled thermal change in downstream waters as a function of decision variables for hydropower operation (reservoir level, powered/spillway release, storage), forecast reservoir inflow and air temperature for a dam site with in situ thermal measurements. For data-limited regions, remote sensing-based temperature estimation algorithm was established using thermal infrared band of Landsat ETM+ over multiple dams. The model for water temperature change was used to impose additional constraints of tolerable downstream cooling or warming (1-6 °C of change) on multi-objective optimization to maximize hydropower. A reservoir release policy adaptive to thermally optimum levels for aquatic species was derived. The novel concept was implemented for Detroit dam in Oregon (USA). Resulting benefits to hydropower generation strongly correlated with allowable flexibility in temperature constraints. Wet years were able to satisfy stringent temperature constraints and produce substantial hydropower benefits, while dry years, in contrast, were challenging to adhere to the upstream thermal regime.}, } @article {pmid32634138, year = {2020}, author = {Garnett, ST and Christidis, L and Conix, S and Costello, MJ and Zachos, FE and Bánki, OS and Bao, Y and Barik, SK and Buckeridge, JS and Hobern, D and Lien, A and Montgomery, N and Nikolaeva, S and Pyle, RL and Thomson, SA and van Dijk, PP and Whalen, A and Zhang, ZQ and Thiele, KR}, title = {Principles for creating a single authoritative list of the world's species.}, journal = {PLoS biology}, volume = {18}, number = {7}, pages = {e3000736}, pmid = {32634138}, issn = {1545-7885}, mesh = {Biodiversity ; *Classification ; Decision Making ; Knowledge ; Reproducibility of Results ; Species Specificity ; }, abstract = {Lists of species underpin many fields of human endeavour, but there are currently no universally accepted principles for deciding which biological species should be accepted when there are alternative taxonomic treatments (and, by extension, which scientific names should be applied to those species). As improvements in information technology make it easier to communicate, access, and aggregate biodiversity information, there is a need for a framework that helps taxonomists and the users of taxonomy decide which taxa and names should be used by society whilst continuing to encourage taxonomic research that leads to new species discoveries, new knowledge of species relationships, and the refinement of existing species concepts. Here, we present 10 principles that can underpin such a governance framework, namely (i) the species list must be based on science and free from nontaxonomic considerations and interference, (ii) governance of the species list must aim for community support and use, (iii) all decisions about list composition must be transparent, (iv) the governance of validated lists of species is separate from the governance of the names of taxa, (v) governance of lists of accepted species must not constrain academic freedom, (vi) the set of criteria considered sufficient to recognise species boundaries may appropriately vary between different taxonomic groups but should be consistent when possible, (vii) a global list must balance conflicting needs for currency and stability by having archived versions, (viii) contributors need appropriate recognition, (ix) list content should be traceable, and (x) a global listing process needs both to encompass global diversity and to accommodate local knowledge of that diversity. We conclude by outlining issues that must be resolved if such a system of taxonomic list governance and a unified list of accepted scientific names generated are to be universally adopted.}, } @article {pmid32628633, year = {2020}, author = {Zhang, F and Smith, LP and Blinov, ML and Faeder, J and Hlavacek, WS and Juan Tapia, J and Keating, SM and Rodriguez, N and Dräger, A and Harris, LA and Finney, A and Hu, B and Hucka, M and Meier-Schellersheim, M}, title = {Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.}, journal = {Journal of integrative bioinformatics}, volume = {17}, number = {2-3}, pages = {}, doi = {10.1515/jib-2020-0015}, pmid = {32628633}, issn = {1613-4516}, support = {R01 GM070923/GM/NIGMS NIH HHS/United States ; R24 GM134211/GM/NIGMS NIH HHS/United States ; R01 GM111510/GM/NIGMS NIH HHS/United States ; P41 GM103313/GM/NIGMS NIH HHS/United States ; P41 GM103712/GM/NIGMS NIH HHS/United States ; }, mesh = {Documentation ; Language ; Models, Biological ; *Programming Languages ; Software ; *Systems Biology ; }, abstract = {Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations can also be provided. Through "wildcards" representing component states, entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states, and multiple compartments. The systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the "type" concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.}, } @article {pmid32617579, year = {2021}, author = {Jiao, X and Yang, Z}, title = {Defining Species When There is Gene Flow.}, journal = {Systematic biology}, volume = {70}, number = {1}, pages = {108-119}, doi = {10.1093/sysbio/syaa052}, pmid = {32617579}, issn = {1076-836X}, support = {BB/P006493/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R01356X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Gene Flow ; Humans ; *Hybridization, Genetic ; Phylogeny ; Population Density ; }, abstract = {Whatever one's definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.[Gene flow; introgression; migration; multispecies coalescent; species concept; species delimitation.].}, } @article {pmid32582185, year = {2020}, author = {Byrne, KA and Loving, CL and McGill, JL}, title = {Innate Immunomodulation in Food Animals: Evidence for Trained Immunity?.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1099}, pmid = {32582185}, issn = {1664-3224}, mesh = {Animals ; Disease Resistance/*immunology ; Fishes/*immunology ; Immune System ; Immunomodulation/*immunology ; Livestock/*immunology ; Poultry/*immunology ; }, abstract = {Antimicrobial resistance (AMR) is a significant problem in health care, animal health, and food safety. To limit AMR, there is a need for alternatives to antibiotics to enhance disease resistance and support judicious antibiotic usage in animals and humans. Immunomodulation is a promising strategy to enhance disease resistance without antibiotics in food animals. One rapidly evolving field of immunomodulation is innate memory in which innate immune cells undergo epigenetic changes of chromatin remodeling and metabolic reprogramming upon a priming event that results in either enhanced or suppressed responsiveness to secondary stimuli (training or tolerance, respectively). Exposure to live agents such as bacille Calmette-Guerin (BCG) or microbe-derived products such as LPS or yeast cell wall ß-glucans can reprogram or "train" the innate immune system. Over the last decade, significant advancements increased our understanding of innate training in humans and rodent models, and strategies are being developed to specifically target or regulate innate memory. In veterinary species, the concept of enhancing the innate immune system is not new; however, there are few available studies which have purposefully investigated innate training as it has been defined in human literature. The development of targeted approaches to engage innate training in food animals, with the practical goal of enhancing the capacity to limit disease without the use of antibiotics, is an area which deserves attention. In this review, we provide an overview of innate immunomodulation and memory, and the mechanisms which regulate this long-term functional reprogramming in other animals (e.g., humans, rodents). We focus on studies describing innate training, or similar phenomenon (often referred to as heterologous or non-specific protection), in cattle, sheep, goats, swine, poultry, and fish species; and discuss the potential benefits and shortcomings of engaging innate training for enhancing disease resistance.}, } @article {pmid32540545, year = {2020}, author = {Miles, SM and Asiedu, E and Balaberda, AL and Ulrich, AC}, title = {Oil sands process affected water sourced Trichoderma harzianum demonstrates capacity for mycoremediation of naphthenic acid fraction compounds.}, journal = {Chemosphere}, volume = {258}, number = {}, pages = {127281}, doi = {10.1016/j.chemosphere.2020.127281}, pmid = {32540545}, issn = {1879-1298}, mesh = {Adamantane/chemistry/metabolism ; Alberta ; Biodegradation, Environmental ; Carboxylic Acids/chemistry/*metabolism ; Cyclohexanes/chemistry/metabolism ; Environmental Restoration and Remediation/*methods ; *Oil and Gas Fields ; Trichoderma/*metabolism ; Waste Water/*microbiology ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Development of Alberta's oil sands requires large volumes of water, leading to the abundance of oil sands process affected water (OSPW) that must be remediated prior to discharge or reuse. OSPW contains a variety of dissolved organic compounds, however naphthenic acids (NAs) have been found to contribute significantly to the toxicity of OSPW. A fungus, Trichoderma harzianum, isolated directly from OSPW, has previously demonstrated a high tolerance and capacity for growth in the presence of commercial NAs. This study conducted microcosm experiments to elucidate and characterize the capacity of T. harzianum to degrade labile commercial NAs (Merichem), and OSPW-sourced naphthenic acid fraction compounds (NAFCs). Additionally, two model NA compounds, the simple single ring cyclohexane carboxylic acid (CHCA) and complex diamondoid 1-adamanatane carboxylic acid (ADA), were utilized to determine the influence of NA structure on degradation. T. harzianum degraded 14% of CHCA, 13% of ADA, and 23-47% of Merichem NAs. Additionally, Orbitrap mass spectrometry revealed a large change in Z-series within NAFCs. This removal and shift in composition correlated to a 59% and 52% drop in toxicity as per Microtox, for Merichem NAs and NAFCs respectively. This proof of concept experiment confirms that the fungal species T. harzianum can contribute to the biodegradation of complex dissolved organics found in OSPW, including cyclic and diamondoid structures.}, } @article {pmid32531173, year = {2020}, author = {Xu, J}, title = {Fungal species concepts in the genomics era.}, journal = {Genome}, volume = {63}, number = {9}, pages = {459-468}, doi = {10.1139/gen-2020-0022}, pmid = {32531173}, issn = {1480-3321}, mesh = {Base Sequence ; Fungi/*classification/*genetics ; *Genome, Fungal ; *Genomics ; Phylogeny ; Reproduction ; Species Specificity ; }, abstract = {The 140 000 or so fungal species reported so far are heterogeneously defined based on varying criteria such as morphological, physiological, mating, and (or) molecular features. Incongruences are common among traits used to separating closely related species and it is often difficult to compare fungal taxonomic groups defined based on different species recognition criteria. Though DNA sequence-based classification and identification have been made, a consensus has not been reached, primarily due to intrinsic limitations in the proposed one or a few genes. Here, I argue that the fundamental reason for the observed inconsistencies is that speciation is a stochastic process with the emergence and fixation of different traits influenced differently by many non-deterministic factors such as population size, random mutation, mode(s) of reproduction, selection imposed by interacting biotic and abiotic factors, and chance events. Each species concept attempts to capture one or a few traits emerged in the continuous process of speciation. I propose that a genome sequence-based classification and identification system could unify and stabilize fungal taxonomy and help integrate taxonomy with other fields of fungal biology. The genomic species concept could be similarly argued for other groups of eukaryotic microbes as well as for plants and animals.}, } @article {pmid32529317, year = {2020}, author = {Fokkema, W and van der Jeugd, HP and Lameris, TK and Dokter, AM and Ebbinge, BS and de Roos, AM and Nolet, BA and Piersma, T and Olff, H}, title = {Ontogenetic niche shifts as a driver of seasonal migration.}, journal = {Oecologia}, volume = {193}, number = {2}, pages = {285-297}, pmid = {32529317}, issn = {1432-1939}, mesh = {*Animal Migration ; Animals ; Population Dynamics ; Reproduction ; *Salmon ; Seasons ; }, abstract = {Ontogenetic niche shifts have helped to understand population dynamics. Here we show that ontogenetic niche shifts also offer an explanation, complementary to traditional concepts, as to why certain species show seasonal migration. We describe how demographic processes (survival, reproduction and migration) and associated ecological requirements of species may change with ontogenetic stage (juvenile, adult) and across the migratory range (breeding, non-breeding). We apply this concept to widely different species (dark-bellied brent geese (Branta b. bernicla), humpback whales (Megaptera novaeangliae) and migratory Pacific salmon (Oncorhynchus gorbuscha) to check the generality of this hypothesis. Consistent with the idea that ontogenetic niche shifts are an important driver of seasonal migration, we find that growth and survival of juvenile life stages profit most from ecological conditions that are specific to breeding areas. We suggest that matrix population modelling techniques are promising to detect the importance of the ontogenetic niche shifts in maintaining migratory strategies. As a proof of concept, we applied a first analysis to resident, partial migratory and fully migratory populations of barnacle geese (Branta leucopsis). We argue that recognition of the costs and benefits of migration, and how these vary with life stages, is important to understand and conserve migration under global environmental change.}, } @article {pmid34542524, year = {2020}, author = {Toti, E and Massaro, L and Kais, A and Aiello, P and Palmery, M and Peluso, I}, title = {Entomophagy: A Narrative Review on Nutritional Value, Safety, Cultural Acceptance and A Focus on the Role of Food Neophobia in Italy.}, journal = {European journal of investigation in health, psychology and education}, volume = {10}, number = {2}, pages = {628-643}, pmid = {34542524}, issn = {2254-9625}, abstract = {In recent years, the consumption of insects, or entomophagy, has produced an increasing interest amongst scientists and ecologists as a potential source of animal protein. Eating insects is also interesting in terms of low greenhouse gas emissions and low land use. In contrast to tropical countries, where most of the 2000 edible insect species are traditionally consumed, the concept of eating insects is still new to Western culture and diet. Culture and eating habits exert a great influence on what is considered edible in the Mediterranean area, especially in Italy, where the preservation of culinary traditions is a predominant factor affecting dietary behaviour. The purpose of this narrative paper is to provide an overview of the main topics related to entomophagy. The introduction presents some information about the nutrient content and safety aspects, the second part summarises the cultural acceptance of insect in the world, while the role of food neophobia on the intention to consume insects in Italy is focused on in part three. The discussion displays important viewpoints of previously published studies and based on these perspectives it can be concluded that the Italian diet is still clearly influenced by local tradition. In conclusion, in order to introduce insects into the Italian diet, psychological motivation has to be enhanced.}, } @article {pmid32467912, year = {2020}, author = {Visagie, CM and Yilmaz, N and Vanderwolf, K and Renaud, JB and Sumarah, MW and Houbraken, J and Assebgui, R and Seifert, KA and Malloch, D}, title = {Penicillium diversity in Canadian bat caves, including a new species, P. speluncae.}, journal = {Fungal systematics and evolution}, volume = {5}, number = {}, pages = {1-15}, pmid = {32467912}, issn = {2589-3831}, abstract = {Penicillium species were commonly isolated during a fungal survey of bat hibernacula in New Brunswick and Quebec, Canada. Strains were isolated from arthropods, bats, rodents (i.e. the deer mouse Peromyscus maniculatus), their dung, and cave walls. Hundreds of fungal strains were recovered, of which Penicillium represented a major component of the community. Penicillium strains were grouped by colony characters on Blakeslee's malt extract agar. DNA sequencing of the secondary identification marker, beta-tubulin, was done for representative strains from each group. In some cases, ITS and calmodulin were sequenced to confirm identifications. In total, 13 species were identified, while eight strains consistently resolved into a unique clade with P. discolor, P. echinulatum and P. solitum as its closest relatives. Penicillium speluncae is described using macroand micromorphological characters, multigene phylogenies (including ITS, beta-tubulin, calmodulin and RNA polymerase II second largest subunit) and extrolite profiles. Major extrolites produced by the new species include cyclopenins, viridicatins, chaetoglobosins, and a microheterogenous series of cyclic and linear tetrapeptides.}, } @article {pmid32455214, year = {2020}, author = {Foster, RI and Oh, M and Lee, K and Kim, KW}, title = {Pilot-Scale Treatment of a Spent Uranium Catalyst Formally Used in the SOHIO Process: Pilot Plant Verification of the SENSEI Process.}, journal = {ACS omega}, volume = {5}, number = {19}, pages = {10939-10947}, pmid = {32455214}, issn = {2470-1343}, abstract = {Approximately 7000 drums of waste uranium catalyst are currently present in Korea and require an appropriate treatment and waste management strategy. Recently, one such process has been developed and has proven successful at both laboratory and bench scales. The success of the process has culminated in its verification at a pilot plant scale. The purpose of this paper is to describe the catalyst treatment process and present results obtained from the pilot plant study that may be applicable to other such wastes. The individual unit technologies have been tested and verified, enabling process scale-up to be successfully proven. The final volume reduction of up to 80% has been confirmed with the successful separation, encapsulation, and immobilization of residue wastes, representing a potential cost saving of US$70 million compared to the direct disposal. The inactive silica component of the waste catalyst was purified and confirmed to be free of uranium. All effluents generated during the process were treated and satisfy the appropriate Korean release criteria. The process employs the concept of Selective Extraction of Nonradioactive Species, Encapsulation, and Immobilization, and is therefore introduced as the SENSEI process.}, } @article {pmid32452095, year = {2020}, author = {Newton, LG and Starrett, J and Hendrixson, BE and Derkarabetian, S and Bond, JE}, title = {Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex.}, journal = {Molecular ecology}, volume = {29}, number = {12}, pages = {2269-2287}, doi = {10.1111/mec.15483}, pmid = {32452095}, issn = {1365-294X}, mesh = {Animals ; Biodiversity ; *Genes, Mitochondrial ; *Phylogeny ; Southeastern United States ; Species Specificity ; *Spiders/classification/genetics ; Sympatry ; }, abstract = {Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and use multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include structure, principal components analysis and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large-scale ecological data for niche-based distribution modelling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic-scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.}, } @article {pmid32445974, year = {2020}, author = {Hopkins, M and Boesch, C and Lansdall, M and Mullen, C and Mighell, A and Pavitt, S and Sarkar, A}, title = {Salivary lubricity (ex vivo) enhances upon moderate exercise: A pilot study.}, journal = {Archives of oral biology}, volume = {116}, number = {}, pages = {104743}, pmid = {32445974}, issn = {1879-1506}, mesh = {Adult ; *Exercise/physiology ; Female ; Humans ; Pilot Projects ; *Saliva ; Salivary Proteins and Peptides ; Young Adult ; alpha-Amylases ; }, abstract = {OBJECTIVE: This study sought to examine the effects of moderate intensity exercise on lubrication performance of saliva. We hypothesized that exercise would result in enhanced salivary lubricity by direct sympathetic stimulation of the salivary proteins.

STUDY DESIGN: In total, 11 healthy young pre-menopausal female participants (mean age: 24.4 ± 1.8 years, BMI: 22.1 ± 1.9 kg/m[2]) were included in a within-subjects repeated measures experimental design. Unstimulated whole saliva was collected at rest (S0), immediately after 45 min of moderate intensity cycling at ∼70 % maximum heart rate (mean: 133.4 ± 0.8 bpm) or time-match quiet rest (S1), and after a 60 min of recovery period (S2). Ex vivo salivary lubricity were measured using soft tribology. Total protein content, mucin (MUC5B) concentration, and α-amylase activity were determined.

RESULTS: Tribology results revealed that moderate intensity exercise resulted in enhanced lubricity of saliva with an order-of-magnitude lower friction coefficients in the boundary regime at S1 and S2, with frictional forces being significantly lower at S1 (p < 0.001) and S2 (p < 0.001) as compared to the Control procedure. Total protein and α-amylase secretion also increased in the Exercise procedure at S1 (p < 0.05), but concentrations returned to baseline levels at S2.

CONCLUSIONS: Moderate intensity exercise leads to an increase in α-amylase and total protein secretion resulting in enhanced lubrication performance of the saliva. However, the lubrication performance was not related to MUC5B content, suggesting the role of other proteinaceous species acting as lubricants. This proof-of-concept study serves as the first step to design exercise interventions in populations with dry mouth conditions.}, } @article {pmid32412203, year = {2019}, author = {Mosier, SL}, title = {Policies as species Viewing and classifying policy from an evolutionary biology perspective.}, journal = {Politics and the life sciences : the journal of the Association for Politics and the Life Sciences}, volume = {38}, number = {2}, pages = {117-131}, doi = {10.1017/pls.2019.10}, pmid = {32412203}, issn = {1471-5457}, mesh = {*Biological Evolution ; Ecosystem ; Genotype ; Humans ; *Policy Making ; *Politics ; *Public Policy ; Time Factors ; }, abstract = {This article proposes equating policies as species to develop a better understanding of how policies emerge, change, and diffuse across policymaking environments. Scholars have long shown an interest in understanding policy change and reinvention, whether incremental or nonincremental. The two subfields of public policy that can answer how and why policies change are not unified, leading to difficulty in comprehensively assessing policy emergence and change. The policy species concept bridges knowledge of the policy process and knowledge in the policy process by creating an operationalized definition of public policy and suggesting a process for classifying policies to observe subsequent behavior. Drawing from the field of biology, the policy species framework outlines how policies possess genotypes and phenotypes, which dictate what a policy is and how it can change. In tracing genotypic and phenetic change over time, policy evolution and change is more easily discernible. In turn, a more precise picture of how policies function is painted.}, } @article {pmid32411520, year = {2020}, author = {Sterling, KA and Nielsen, SV and Brown, AJ and Warren, ML and Noonan, BP}, title = {Cryptic diversity among Yazoo Darters (Percidae: Etheostoma raneyi) in disjunct watersheds of northern Mississippi.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e9014}, pmid = {32411520}, issn = {2167-8359}, abstract = {The Yazoo Darter, Etheostoma raneyi (Percidae), is an imperiled freshwater fish species endemic to tributaries of the Yocona and Little Tallahatchie rivers of the upper Yazoo River basin, in northern Mississippi, USA. The two populations are allopatric, isolated by unsuitable lowland habitat between the two river drainages. Relevant literature suggests that populations in the Yocona River represent an undescribed species, but a lack of data prevents a thorough evaluation of possible diversity throughout the range of the species. Our goals were to estimate phylogenetic relationships of the Yazoo Darter across its distribution and identify cryptic diversity for conservation management purposes. Maximum likelihood (ML) phylogenetic analyses of the mitochondrial cytochrome b (cytb) gene returned two reciprocally monophyletic clades representing the two river drainages with high support. Bayesian analysis of cytb was consistent with the ML analysis but with low support for the Yocona River clade. Analyses of the nuclear S7 gene yielded unresolved relationships among individuals in the Little Tallahatchie River drainage with mostly low support, but returned a monophyletic clade for individuals from the Yocona River drainage with high support. No haplotypes were shared between the drainages for either gene. Additional cryptic diversity within the two drainages was not indicated. Estimated divergence between Yazoo Darters in the two drainages occurred during the Pleistocene (<1 million years ago) and was likely linked to repeated spatial shifts in suitable habitat and changes in watershed configurations during glacial cycles. Individuals from the Yocona River drainage had lower genetic diversity consistent with the literature. Our results indicate that Yazoo Darters in the Yocona River drainage are genetically distinct and that there is support for recognizing Yazoo Darter populations in the Yocona River drainage as a new species under the unified species concept.}, } @article {pmid32408859, year = {2020}, author = {Kanzi, AM and Trollip, C and Wingfield, MJ and Barnes, I and Van der Nest, MA and Wingfield, BD}, title = {Phylogenomic incongruence in Ceratocystis: a clue to speciation?.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {362}, pmid = {32408859}, issn = {1471-2164}, mesh = {Ceratocystis/*classification/genetics ; Evolution, Molecular ; Genes, Fungal/genetics ; *Genetic Speciation ; Genome, Fungal/genetics ; Hybridization, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate. This is due to many of the commonly used species recognition concepts (e.g., morphological and biological species concepts) providing different bases for interpretation of taxonomic boundaries. Species delineation in Ceratocystis primarily relied on genealogical concordance phylogenetic species recognition (GCPSR) using multiple standard molecular markers.

RESULTS: Questions have arisen regarding the utility of these markers e.g., ITS, BT and TEF1-α due to evidence of intragenomic variation in the ITS, as well as genealogical incongruence, especially for isolates residing in a group referred to as the Latin-American clade (LAC) of the species. This study applied a phylogenomics approach to investigate the extent of phylogenetic incongruence in Ceratocystis. Phylogenomic analyses of a total of 1121 shared BUSCO genes revealed widespread incongruence within Ceratocystis, particularly within the LAC, which was typified by three equally represented topologies. Comparative analyses of the individual gene trees revealed evolutionary patterns indicative of hybridization. The maximum likelihood phylogenetic tree generated from the concatenated dataset comprised of 1069 shared BUSCO genes provided improved phylogenetic resolution suggesting the need for multiple gene markers in the phylogeny of Ceratocystis.

CONCLUSION: The incongruence observed among single gene phylogenies in this study call into question the utility of single or a few molecular markers for species delineation. Although this study provides evidence of interspecific hybridization, the role of hybridization as the source of discordance will require further research because the results could also be explained by high levels of shared ancestral polymorphism in this recently diverged lineage. This study also highlights the utility of BUSCO genes as a set of multiple orthologous genes for phylogenomic studies.}, } @article {pmid32389122, year = {2020}, author = {Guariento, E and Strutzenberger, P and Truxa, C and Fiedler, K}, title = {The trinity of ecological contrasts: a case study on rich insect assemblages by means of species, functional and phylogenetic diversity measures.}, journal = {BMC ecology}, volume = {20}, number = {1}, pages = {29}, pmid = {32389122}, issn = {1472-6785}, mesh = {Animals ; *Biodiversity ; *Forests ; Insecta ; Phylogeny ; Rivers ; }, abstract = {BACKGROUND: The 'classical' concept of species diversity was extended in the last decades into other dimensions focusing on the functional and phylogenetic diversity of communities. These measures are often argued to allow a deeper understanding of the mechanisms shaping community assembly along environmental gradients. Because of practical impediments, thus far only very few studies evaluated the performance of these diversity measures on large empirical data sets. Here, data on species-rich riparian moth communities under different flood regimes and from three different rivers has been used to compare the power of various diversity measures to uncover ecological contrasts.

RESULTS: Contrary to the expectation, classical metrics of species diversity (Hill numbers N1, N2 and Ninf) and evenness (Buzas-Gibson's E and Pielous's J) turned out to be the most powerful measures in unravelling the two gradients investigated in this study (e.g. flood regime and region). Several measures of functional and phylogenetic diversity tended to depict either only one or none of these contrasts. Rao's Q behaved similarly as species diversity and evenness. NTI and NRI showed a similar pattern among each other but, were different to all the other measures. Functional Divergence also behaved idiosyncratically across the 28 moth communities. The community weighted means of nearly all individual functional traits showed significant ecological patterns, supporting the relevance of the selected traits in shaping assemblage compositions.

CONCLUSIONS: Species diversity and evenness measures turned out to be the most powerful metrics and clearly reflected both investigated environmental contrasts. This poses the question when it is useful to compile the additional data necessary for the calculation of additional diversity measures, since assembling trait bases and community phylogenies often requires a high work load. Apart from these methodological issues, most of the diversity measures related to communities of terrestrial insects like moths increased in forests that still are subject to flooding dynamics. This emphasizes the high conservation value of riparian forests and the importance of keeping and restoring river dynamics as a means of fostering also terrestrial biodiversity in floodplain areas.}, } @article {pmid32386827, year = {2020}, author = {Phillips, RD and Peakall, R and van der Niet, T and Johnson, SD}, title = {Niche Perspectives on Plant-Pollinator Interactions.}, journal = {Trends in plant science}, volume = {25}, number = {8}, pages = {779-793}, doi = {10.1016/j.tplants.2020.03.009}, pmid = {32386827}, issn = {1878-4372}, mesh = {Ecosystem ; *Flowers ; Phenotype ; Plants ; *Pollination ; }, abstract = {Ecological niches are crucial for species coexistence and diversification, but the niche concept has been underutilized in studying the roles of pollinators in plant evolution and reproduction. Pollination niches can be objectively characterized using pollinator traits, abundance, and distributions, as well as network topology. We review evidence that floral traits represent adaptations to pollination niches, where tradeoffs in trait deployment reinforce niche specialization. In turn, specialized pollination niches potentially increase speciation rates, foster species coexistence, and constrain species range limits. By linking studies of adaptation with those on speciation and coexistence, the pollination niche provides an organizing principle for research on plant reproduction, and conceptually unites these studies with fields of biology where the niche perspective is already firmly established.}, } @article {pmid32379020, year = {2020}, author = {Gonçalves, OS and Campos, KF and de Assis, JCS and Fernandes, AS and Souza, TS and do Carmo Rodrigues, LG and Queiroz, MV and Santana, MF}, title = {Transposable elements contribute to the genome plasticity of Ralstonia solanacearum species complex.}, journal = {Microbial genomics}, volume = {6}, number = {5}, pages = {}, pmid = {32379020}, issn = {2057-5858}, mesh = {Bacterial Proteins/genetics ; Cell Plasticity ; Chromosome Mapping/*methods ; *DNA Transposable Elements ; Drug Resistance, Bacterial ; Evolution, Molecular ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Bacterial ; Genome, Bacterial ; Phylogeny ; Plant Diseases/microbiology ; Ralstonia/*genetics/pathogenicity ; Soil Microbiology ; Virulence Factors/genetics ; }, abstract = {The extensive genetic diversity of Ralstonia solanacearum, a serious soil-borne phytopathogen, has led to the concept that R. solanacearum encompasses a species complex [R. solanacearum species complex (RSSC)]. Insertion sequences (ISs) are suggested to play an important role in the genome evolution of this pathogen. Here, we identified and analysed transposable elements (TEs), ISs and transposons, in 106 RSSC genomes and 15 Ralstonia spp. We mapped 10 259 IS elements in the complete genome of 62 representative RSSC strains and closely related Ralstonia spp. A unique set of 20 IS families was widespread across the strains, IS5 and IS3 being the most abundant. Our results showed six novel transposon sequences belonging to the Tn3 family carrying passenger genes encoding antibiotic resistance and avirulence proteins. In addition, internal rearrangement events associated with ISs were demonstrated in Ralstonia pseudosolanacearum strains. We also mapped IS elements interrupting avirulence genes, which provided evidence that ISs plays an important role in virulence evolution of RSSC. Additionally, the activity of ISs was demonstrated by transcriptome analysis and DNA hybridization in R. solanacearum isolates. Altogether, we have provided collective data of TEs in RSSC genomes, opening a new path for understanding their evolutionary impact on the genome evolution and diversity of this important plant pathogen.}, } @article {pmid32337464, year = {2020}, author = {Mukherjee, M and Gangopadhyay, K and Das, R and Purkayastha, P}, title = {Development of Non-ionic Surfactant and Protein-Coated Ultrasmall Silver Nanoparticles: Increased Viscoelasticity Enables Potency in Biological Applications.}, journal = {ACS omega}, volume = {5}, number = {15}, pages = {8999-9006}, pmid = {32337464}, issn = {2470-1343}, abstract = {To enhance the interactivity with biological cells, we developed ultrasmall (5 nm in diameter) Ag NPs coated with a mixture of Tween-20 (Tw-20) surfactant and human serum albumin (HSA) or hemoglobin (Hb) proteins. These were tested with cancerous and healthy cell lines to investigate the therapeutic applicability. Using the established concept of generation of reactive oxygen species (ROS) and the ROS-induced oxidative stress in carcinogenic cells by Ag NPs, we found that the presently synthesized Ag NPs selectively destroyed the cancerous cells. A mixture of Tw-20 with protein, where the surfactant was in large excess, created a coating over the Ag NPs resulting weaker protein-protein interactions and facilitating interfacial protein-surfactant interactions, which leads to an increase in the film viscoelasticity to enhance the stability of the Ag NPs and cell viability. Moreover, this concept has been applied to drug delivery using a model fluorophore (fluorescein) on Ag NPs to explore the prospects in photodynamic therapy. The results are encouraging and deserve further investigation.}, } @article {pmid32323350, year = {2020}, author = {Fordham, G and Shanee, S and Peck, M}, title = {Effect of river size on Amazonian primate community structure: A biogeographic analysis using updated taxonomic assessments.}, journal = {American journal of primatology}, volume = {82}, number = {7}, pages = {e23136}, doi = {10.1002/ajp.23136}, pmid = {32323350}, issn = {1098-2345}, mesh = {*Animal Distribution ; Animals ; Geographic Information Systems ; Models, Theoretical ; Phylogeography/*methods ; Primates/*classification ; *Rivers ; South America ; }, abstract = {The mechanisms that underlie the diversification of Neotropical primates remain contested. One mechanism that has found support is the riverine barrier hypothesis (RBH), which postulates that large rivers impede gene flow between populations on opposite riverbanks and promote allopatric speciation. Ayres and Clutton-Brock (1992) demonstrated that larger Amazonian rivers acted as barriers, delineating the distribution limits of primate species. However, profound changes in taxonomy and species concepts have led to the proliferation of Neotropical primate taxa, which may have reduced support for their results. Using the most recent taxonomic assessments and distribution maps, we tested the effect of increasing river size on the similarity of opposite riverbank primate communities in the Amazon. First, we conducted a literature review of primate taxonomy and developed a comprehensive spatial database, then applied geographical information system to query mapped primate ranges against the riverine geography of the Amazon watershed to produce a similarity index for opposite riverbank communities. Finally, we ran models to test how measures of river size predicted levels of similarity. We found that, almost without exception, similarity scores were lower than scores from Ayres and Clutton-Brock (1992) for the same rivers. Our model showed a significant negative relationship between streamflow and similarity in all tests, and found river width significant for the segmented Amazon, but not for multiple Amazon watershed rivers. Our results support the RBH insofar as they provide evidence for the prediction that rivers with higher streamflow act as more substantial barriers to dispersal, and accordingly exhibit greater variation in community composition between riverbanks.}, } @article {pmid32317392, year = {2020}, author = {Chu, H and Gao, GF and Ma, Y and Fan, K and Delgado-Baquerizo, M}, title = {Soil Microbial Biogeography in a Changing World: Recent Advances and Future Perspectives.}, journal = {mSystems}, volume = {5}, number = {2}, pages = {}, pmid = {32317392}, issn = {2379-5077}, abstract = {Soil microbial communities are fundamental to maintaining key soil processes associated with litter decomposition, nutrient cycling, and plant productivity and are thus integral to human well-being. Recent technological advances have exponentially increased our knowledge concerning the global ecological distributions of microbial communities across space and time and have provided evidence for their contribution to ecosystem functions. However, major knowledge gaps in soil biogeography remain to be addressed over the coming years as technology and research questions continue to evolve. In this minireview, we state recent advances and future directions in the study of soil microbial biogeography and discuss the need for a clearer concept of microbial species, projections of soil microbial distributions toward future global change scenarios, and the importance of embracing culture and isolation approaches to determine microbial functional profiles. This knowledge will be critical to better predict ecosystem functions in a changing world.}, } @article {pmid32307069, year = {2020}, author = {Karasiewicz, S and Chapelle, A and Bacher, C and Soudant, D}, title = {Harmful algae niche responses to environmental and community variation along the French coast.}, journal = {Harmful algae}, volume = {93}, number = {}, pages = {101785}, doi = {10.1016/j.hal.2020.101785}, pmid = {32307069}, issn = {1878-1470}, mesh = {*Dinoflagellida ; Harmful Algal Bloom ; Humans ; Phytoplankton ; Satellite Imagery ; *Shellfish Poisoning ; }, abstract = {Distribution, frequency and intensity of harmful phytoplanktonic species are impacted by changes in environmental conditions. In the Bay of Brest, Alexandrium minutum has been responsible for several harmful algal blooms (HABs) associated with toxin production causing paralytic shellfish poisoning (PSP). Additionally, Lepidodinium chlorophorum causes green water and hypoxia locally in the Bay of Biscay. Previous studies revealed that L. chlorophorum's success was related to possible competitive exclusion. Therefore, the phytoplankton composition and the environmental conditions should be taken into account. This study aims to assess the combined effect of changes in habitat conditions and community structure with the occurrence of HAB species, on a spatial-temporal scale. For the investigation we first used the Hutchinson's niche concept by means of the Outlying Mean Index (OMI) analysis. The OMI analysis enable us to observe the environmental variables defining the ecological niche of the harmful species among the community. Secondly, we used the subniche theory to highlight the environmental variables defining the subniches in cases of high and low abundance of HABs with an estimation of the biological constraint restricting the species' subniche. This was undertaken using the Within Outlying Mean indexes (WitOMI) calculated under environmental conditions promoting high (H) and low (L) abundance bloom. Thirdly, we used the Indicator Species Concept from the Indicator Species Analysis (ISA) to link the biological restriction with potential competing or indicator species. We combined a data set from the French National Phytoplankton and Phycotoxin Monitoring Network (REPHY), the Velyger network (oyster monitoring program) and satellite imagery. A total of 44 stations, over the period of 1998-2017 using 50 taxonomic units. 36 taxa had significant niche and were mostly distributed along nutrient and salinity gradients. The two species of interest L. chlorophorum and A. minutum seemed to have similar affinity for summer-like environmental conditions and both used a marginal habitat compared to the rest of the community. A. minutum had a larger niche due to a greater affinity to the estuarine-like conditions. The subniche of the two species had a similar response to the environmental variation; their respective abundance was partly caused by greater environmental restrains. Their success in abundance appeared to be linked to local hydrodynamics which increases or reduces resources. On the other hand, the biotic pressure exerted upon A. minutum and L. chlorophorum were antagonistic. A possible competitor assemblage was exposed but the analysis was inconclusive. The methodological limitations were discussed as well as a perspective for future similar studies.}, } @article {pmid32298447, year = {2020}, author = {Seifert, B}, title = {The Gene and Gene Expression (GAGE) Species Concept: An Universal Approach for All Eukaryotic Organisms.}, journal = {Systematic biology}, volume = {69}, number = {5}, pages = {1033-1038}, doi = {10.1093/sysbio/syaa032}, pmid = {32298447}, issn = {1076-836X}, mesh = {Classification/*methods ; Eukaryota/*classification/*genetics ; *Gene Expression ; Genes/*genetics ; *Genetic Speciation ; }, abstract = {The Gene and Gene Expression (GAGE) species concept, a new version of the Pragmatic Species Concept of Seifert (2014), is proposed as a concept applicable to any described recent or fossil eukaryotic organism independent from its mode of reproduction or evolutionary history. In addition to presenting the concept as such, the article also provides practical recommendations for taxonomists when delimiting species and describing taxa. The wording of the new concept contains a heading core sentence plus five attached sentences addressing essential conditions for its translation into a sound taxonomic practice: "Species are separable clusters that have passed a threshold of evolutionary divergence and are exclusively defined by nuclear DNA sequences and/or their expression products. Nuclear DNA sequences and their expression products are different character systems but have a highly correlated indicative function. Character systems with the least risk of epigenetic or ontogenetic modification have superior indicative value when conflicts between character systems of integrative studies arise. All character systems have to be described by an adequate numerics allowing cluster formation and determination of thresholds. Thresholds for each character system should be fixed by consensus among the experts under the principle of avoiding oversplitting or lumping. Clusters must not be the expression of intraspecific polymorphism." Recognizing the distortions and conflicts caused to taxonomy through barcoding or through assessment on the basis of association with other organisms, the GAGE species concept strongly downgrades the use of cytoplasmic DNA of endosymbiotic origin (mtDNA, cpDNA) or DNA of closely associated microbes (e.g., Wolbachia bacteria) for final taxonomic decision-making. Recognizing the distortion of phylogenies by the high frequency of reticulate evolution, it is argued that delimiting and naming species has to be separated from constructing bifurcating phylogenetic trees. [Cytoplasmic DNA; lumping; nuclear DNA; numeric taxonomy; oversplitting; reticulate evolution.].}, } @article {pmid32283092, year = {2020}, author = {Namgay, R and Pemo, D and Wangdi, T and Phanitchakun, T and Harbach, RE and Somboon, P}, title = {Molecular and morphological evidence for sibling species within Anopheles (Anopheles) lindesayi Giles (Diptera: Culicidae) in Bhutan.}, journal = {Acta tropica}, volume = {207}, number = {}, pages = {105455}, doi = {10.1016/j.actatropica.2020.105455}, pmid = {32283092}, issn = {1873-6254}, mesh = {Animals ; Anopheles/*anatomy & histology/classification/*genetics ; Bhutan ; Female ; Male ; Phylogeny ; }, abstract = {This paper reports the results of a comparative molecular and morphological study of An. lindesayi collected from various districts of Bhutan and An. l. cameronensis from Thailand, compared with GenBank accessions and publications for An. l. japonicus from Japan, South Korea and China, An. l. pleccau from Taiwan, and An. lindesayi from India. Phylogenetic analyses based on ribosomal (ITS2) and mitochondrial (COI) DNA sequences using the Maximum Likelihood method revealed five genetically distinct clades (A, B, C, D and E) in Bhutan. Specimens in Clade A correspond to the original description of An. lindesayi, particularly in wing markings, the pattern of basal pale scales on the hindfemur and the single seta 4-C of larvae, and their COI sequences were closely related to one Indian sequence. Larvae of Clades B, C, D and E are similar in having seta 4-C branched rather than single. The adults of Clades C, D and E (B not available) are distinguishable from those of Clade A and other subspecies. Specimens of Clade C are unique in having a long pale spot on wing vein R and the subcosta, scattered pale scales on several veins and a dark spot at the tip of vein R2. The adults of Clades D and E are similar in having a dark spot at the tip of vein R2 and no scattered pale scales on all other veins. We provisionally recognize mosquitoes of Clades A, B, C, D and E as species A, B, C, D and E, respectively, of the Lindesayi Complex. Species A is An. lindesayi sensu stricto and the others are unnamed species. Concomitantly, the previous concept of the "Lindesayi Complex", which included An. lindesayi, An. menglangensis, An. nilgiricus and An. wellingtonianus, is now recognized as the Lindesayi Subgroup of the Lindesayi Group (Anopheles Series, subgenus Anopheles) with the five sibling species of An. lindesayi comprising a more apposite Lindesayi Complex within the subgroup.}, } @article {pmid32245520, year = {2020}, author = {Corduneanu, A and Ursache, TD and Taulescu, M and Sevastre, B and Modrý, D and Mihalca, AD}, title = {Detection of DNA of Babesia canis in tissues of laboratory rodents following oral inoculation with infected ticks.}, journal = {Parasites & vectors}, volume = {13}, number = {1}, pages = {166}, pmid = {32245520}, issn = {1756-3305}, mesh = {Administration, Oral ; Animals ; Babesia/*genetics ; Babesiosis/blood/*parasitology ; DNA, Protozoan/*analysis ; Dermacentor/*parasitology ; Female ; Gerbillinae ; Male ; Mice ; RNA, Ribosomal, 18S/genetics ; Rodentia/*parasitology ; Tick Infestations/*parasitology ; }, abstract = {BACKGROUND: Babesia spp. are apicomplexan parasites which infect a wide range of mammalian hosts. Historically, most Babesia species were described based on the assumed host specificity and morphological features of the intraerythrocytic stages. New DNA-based approaches challenge the traditional species concept and host specificity in Babesia. Using such tools, the presence of Babesia DNA was reported in non-specific mammalian hosts, including B. canis in feces and tissues of insectivorous bats, opening questions on alternative transmission routes. The aim of the present study was to evaluate if B. canis DNA can be detected in tissues of laboratory rodents following oral inoculation with infected ticks.

METHODS: Seventy-five questing adult Dermacentor reticulatus ticks were longitudinally cut in two halves and pooled. Each pool consisted of halves of 5 ticks, resulting in two analogous sets. One pool set (n = 15) served for DNA extraction, while the other set (n = 15) was used for oral inoculation of experimental animals (Mus musculus, line CD-1 and Meriones unguiculatus). Blood was collected three times during the experiment (before the inoculation, at 14 days post-inoculation and at 30 days post-inoculation). All animals were euthanized 30 days post-inoculation. At necropsy, half of the heart, lung, liver, spleen and kidneys were collected from each animal. The presence of Babesia DNA targeting the 18S rRNA gene was evaluated from blood and tissues samples. For histopathology, the other halves of the tissues were used. Stained blood smears were used for the light microscopy detection of Babesia.

RESULTS: From the 15 pools of D. reticulatus used for the oral inoculation, six were PCR-positive for B. canis. DNA of B. canis was detected in blood and tissues of 33.3% of the animals (4 out of 12) inoculated with a B. canis-positive pool. No Babesia DNA was detected in the other 18 animals which received B. canis-negative tick pools. No Babesia was detected during the histological examination and all blood smears were microscopically negative.

CONCLUSIONS: Our findings demonstrate that B. canis DNA can be detected in tissues of mammalian hosts following ingestion of infected ticks and opens the question of alternative transmission routes for piroplasms.}, } @article {pmid32242998, year = {2021}, author = {Tatarenkov, A and Earley, RL and Taylor, DS and Davis, WP and Avise, JC}, title = {Extensive hybridization and past introgression between divergent lineages in a quasi-clonal hermaphroditic fish: Ramifications for species concepts and taxonomy.}, journal = {Journal of evolutionary biology}, volume = {34}, number = {1}, pages = {49-59}, doi = {10.1111/jeb.13624}, pmid = {32242998}, issn = {1420-9101}, mesh = {Animals ; Bahamas ; Female ; Fundulidae/classification/*genetics ; *Genetic Introgression ; Hermaphroditic Organisms ; Male ; Phylogeography ; *Self-Fertilization ; *Sympatry ; }, abstract = {Extreme inbreeding is expected to reduce the incidence of hybridization, serving as a prezygotic barrier. Mangrove rivulus is a small killifish that reproduces predominantly by self-fertilization, producing highly homozygous lines throughout its geographic range. The Bahamas and Caribbean are inhabited by two highly diverged phylogeographic lineages of mangrove rivulus, Kryptolebias marmoratus and a 'Central clade' closely related to K. hermaphroditus from Brazil. The two lineages are largely allopatric, but recently were found in syntopy on San Salvador, Bahamas, where a single hybrid was reported. To better characterize the degree of hybridization and the possibility of secondary introgression, here we conducted a detailed genetic analysis of the contact zone on San Salvador. Two mixed populations were identified, one of which contained sexually mature hybrids. The distribution of heterozygosity at diagnostic microsatellite loci in hybrids showed that one of these hybrids was an immediate offspring from the K. marmoratus x Central clade cross, whereas the remaining five hybrids were products of reproduction by self-fertilization for 1-3 generations following the initial cross. Two hybrids had mitochondrial haplotypes of K. marmoratus and the remaining four hybrids had a haplotype of the Central clade, indicating that crosses go in both directions. In hybrids, alleles of parental lineages were represented in equal proportions suggesting lack of recent backcrossing to either of the parental lineages. However, sympatric populations of two lineages were less diverged than allopatric populations, consistent with introgression. Results are discussed in terms of applicability of the biological species concept for isogenic, effectively clonal, organisms.}, } @article {pmid32230691, year = {2019}, author = {Cumming, JM and Cumming, HJ}, title = {Additional DNA barcodes confirm recent morphological species concepts and synonymies in Callomyia Meigen (Diptera: Platypezidae).}, journal = {Zootaxa}, volume = {4712}, number = {2}, pages = {zootaxa.4712.2.9}, doi = {10.11646/zootaxa.4712.2.9}, pmid = {32230691}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Diptera/genetics ; Female ; }, abstract = {Cumming Wheeler (2016) revised the Nearctic species of the sexually dimorphic flat-footed fly genus Callomyia Meigen (Callomyiinae) recognizing 10 Nearctic species, including three newly described taxa, namely C. argentea Cumming, C. arnaudi Cumming, and C. browni Cumming. They also described the unknown female of C. velutina Johnson and proposed three new synonymies associating species previously described from one sex only with others described from the opposite sex (Kessel 1948; Kessel Buegler 1972). Callomyia cleta Kessel was considered a junior synonym of C. calla Kessel, C. clara Kessel was considered a junior synonym of C. corvina Kessel, and C. liardia Kessel Buegler was synonymized with C. proxima Johnson.}, } @article {pmid32220807, year = {2020}, author = {Vallot, A and Tachibana, K}, title = {The emergence of genome architecture and zygotic genome activation.}, journal = {Current opinion in cell biology}, volume = {64}, number = {}, pages = {50-57}, pmid = {32220807}, issn = {1879-0410}, mesh = {Animals ; Chromatin/metabolism ; Embryonic Development/genetics ; *Gene Expression Regulation, Developmental ; *Genome ; Transcription Factors/metabolism ; Zygote/*metabolism ; }, abstract = {The fusion of two transcriptionally silent gametes, egg and sperm, generates a totipotent zygote that activates zygotic transcription to support further development. Although the molecular details of zygotic genome activation (ZGA) are not well understood in most species, an emerging concept is that one or more pioneer transcription factors trigger zygotic transcription. Concomitantly, extensive changes in 3D chromatin organization occur during development. In this review, we discuss recent advances in understanding when and how genome architecture emerges in early metazoan embryos, how the zygotic genome is activated, and how these events might be coordinated. We also highlight some of the unknowns that may be critical to address in the future.}, } @article {pmid32206016, year = {2020}, author = {Korshunova, T and Malmberg, K and Prkić, J and Petani, A and Fletcher, K and Lundin, K and Martynov, A}, title = {Fine-scale species delimitation: speciation in process and periodic patterns in nudibranch diversity.}, journal = {ZooKeys}, volume = {917}, number = {}, pages = {15-50}, pmid = {32206016}, issn = {1313-2989}, abstract = {Using the nudibranch genus Amphorina as a model, ongoing speciation is demonstrated, as well as how periodic-like patterns in colouration can be included in an integrated method of fine-scale species delimitation. By combining several methods, including BPP analysis and the study of molecular, morphological, and ecological data from a large number of specimens within a broad geographic range from northern Europe to the Mediterranean, five species are recognised within the genus Amphorina, reviewed here for the first time. Two new species from the southwestern coast of Sweden are described, A. viriola sp. nov. and A. andra sp. nov. Evidence is provided of a recent speciation process between the two closely related, yet separate, species which inhabit the same geographic localities but demonstrate strict water depth differentiation, with one species inhabiting the shallow brackish top layer above the halocline and the other species inhabiting the underlying saltier water. The results presented here are of relevance for currently debated issues such as conservation in relation to speciation, fine species delimitation, and integration of molecular, morphological and ecological information in biodiversity studies. The periodic approach to biological taxonomy has considerable practical potential for various organismal groups.}, } @article {pmid32205089, year = {2020}, author = {Widmer, G and Köster, PC and Carmena, D}, title = {Cryptosporidium hominis infections in non-human animal species: revisiting the concept of host specificity.}, journal = {International journal for parasitology}, volume = {50}, number = {4}, pages = {253-262}, doi = {10.1016/j.ijpara.2020.01.005}, pmid = {32205089}, issn = {1879-0135}, support = {R21 AI125891/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Animals, Wild/parasitology ; *Cryptosporidiosis/parasitology/transmission ; *Cryptosporidium/classification/genetics/isolation & purification ; Cryptosporidium parvum/classification/genetics/isolation & purification ; DNA, Protozoan/analysis ; Disease Reservoirs ; Genes, Protozoan ; Host Specificity/*genetics ; Humans ; Livestock/parasitology ; Phylogeny ; Zoonoses ; }, abstract = {Parasites in the genus Cryptosporidium, phylum Apicomplexa, are found worldwide in the intestinal tract of many vertebrate species and in the environment. Driven by sensitive PCR methods, and the availability of abundant sequence data and reference genomes, the taxonomic complexity of the genus has steadily increased; 38 species have been named to date. Due to its public health importance, Cryptosporidium hominis has long attracted the interest of the research community. This species was initially described as infectious to humans only. This perception has persisted in spite of an increasing number of observations of natural and experimental infections of animals with this species. Here we summarize and discuss this literature published since 2000 and conclude that the host range of C. hominis is broader than originally described. The evolving definition of the C. hominis host range raises interesting questions about host specificity and the evolution of Cryptosporidium parasites.}, } @article {pmid32163338, year = {2020}, author = {Benny, GL and Smith, ME}, title = {Taxonomic notes on eight species of obligate mycoparasites in the genus Syncephalis isolated from soil and dung.}, journal = {Mycologia}, volume = {112}, number = {3}, pages = {552-569}, doi = {10.1080/00275514.2019.1705126}, pmid = {32163338}, issn = {1557-2536}, mesh = {Absidia/*pathogenicity ; Animals ; Feces/*microbiology ; Fungi/*classification/*cytology/*pathogenicity ; Parasites/*classification/*cytology ; *Soil Microbiology ; }, abstract = {Species of Syncephalis (Zoopagomycotina, Piptocephalidaceae) are obligate mycoparasites that grow on common saprobic species of Mortierellomycotina and Mucoromycotina in soil and dung. Despite their ubiquitous occurrence across the globe, fungi in the genus Syncephalis are understudied, and there are few modern taxonomic treatments of these fungi. In order to clarify species concepts in the genus, we provide morphological data and discuss seven classical Syncephalis species: S. basibulbosa, S. cordata, S. depressa, S. hypogena, S. intermedia, S. nodosa, and S. sphaerica. Three of these species are only known as herbarium specimens (S. basibulbosa, S. cordata, S. intermedia). We have isolated co-cultures of the remaining parasites (S. depressa, S. nodosa, and S. sphaerica) on their host fungi both from nature and from culture collections. The remaining taxon (S. hypogena) was revived from a lyophilized culture. We provide photos and updated descriptions for all of these species as well as new geographic data and references to documented herbarium specimens for each taxon. In addition, we also describe the new species S. latigena.}, } @article {pmid32162107, year = {2020}, author = {Li, ZZ and Ngarega, BK and Lehtonen, S and Gichira, AW and Karichu, MJ and Wang, QF and Chen, JM}, title = {Cryptic diversity within the African aquatic plant Ottelia ulvifolia (Hydrocharitaceae) revealed by population genetic and phylogenetic analyses.}, journal = {Journal of plant research}, volume = {133}, number = {3}, pages = {373-381}, doi = {10.1007/s10265-020-01175-2}, pmid = {32162107}, issn = {1618-0860}, mesh = {Africa ; Genetic Variation ; *Genetics, Population ; Hydrocharitaceae/*classification/genetics ; *Phylogeny ; }, abstract = {Revealing cryptic diversity is of great importance for effective conservation and understanding macroevolution and ecology of plants. Ottelia, a typical example of aquatic plants, possesses extremely variable morphology and the presence of cryptic diversity makes its classification problematic. Previous studies have revealed cryptic Ottelia species in Asia, but very little is known about the molecular systematics of this genus in Africa, a center of species diversity of Ottelia. In this study, we sampled Ottelia ulvifolia, an endemic species of tropical Africa, from Zambia and Cameroon. We used six chloroplast DNA regions, nrITS and six polymorphic microsatellite markers to estimate the molecular diversity and population genetic structure in O. ulvifolia. The phylogenetic inference, STACEY and STRUCTURE analyses supported at least three clusters within O. ulvifolia, each representing unique flower types (i.e., bisexual yellow flower, unisexual yellow flower and bisexual white flower types). Although abundant genetic variation (> 50%) was observed within the populations, excessive anthropogenic activities may result in genetic drift and bottlenecks. Here, three cryptic species of O. ulvifolia complex are defined, and insights are provided into the taxonomy of Ottelia using the phylogenetic species concept.}, } @article {pmid32161618, year = {2020}, author = {Wang, P and Chen, B and Zheng, J and Cheng, W and Zhang, H and Wang, J and Su, Y and Xu, P and Mao, Y}, title = {Fine-Scale Population Genetic Structure and Parapatric Cryptic Species of Kuruma Shrimp (Marsupenaeus japonicus), Along the Northwestern Pacific Coast of China.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {118}, pmid = {32161618}, issn = {1664-8021}, abstract = {The kuruma shrimp (Marsupenaeus japonicus) includes two cryptic species, which are distributed mostly allopatrically but co-occur in the northern South China Sea (from Huilai to Beihai). To obtain a better understanding of the fine-scale genetic structure and parapatric diversification of these two varieties in the northwestern Pacific region, we used a genotyping-by-sequencing (GBS) and comparative transcriptomics approach to establish their phylogenetic relationships. Using the GBS technique, we genotyped 28891 SNPs in 160 individuals in the Northwest Pacific. The results supported two highly diverged evolutionary lineages of kuruma shrimp (var. I and II). The ND and XM populations showed complex genetic patterns, which might be affected by the complex environment of the Taiwan Strait. In addition, the migration rates and inbreeding coefficients of XM and BH were much lower than those of the other populations, which might be related to the land-sea changes and complex ocean currents in the Taiwan Strait and Qiongzhou Strait. Based on the synonymous substitution rates (ds) of 2,491 candidate orthologs, we estimated that the divergence time between the two varieties was 0.26~0.69 Mya. Choice and no-choice interbreeding experiments provided support for the biological species concept, by showing the existence of reproductive isolation or incompatibility. In view of these differences between the two Marsupenaeus species, we believe that it is essential and urgent to establish a genetic database for each and reevaluate their ecological suitable conditions in order to improve species-specific culturing techniques. Moreover, this research can serve as a case study for future research on speciation and hybridization.}, } @article {pmid32139685, year = {2020}, author = {Chanut, N and Ghoufi, A and Coulet, MV and Bourrelly, S and Kuchta, B and Maurin, G and Llewellyn, PL}, title = {Tailoring the separation properties of flexible metal-organic frameworks using mechanical pressure.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1216}, pmid = {32139685}, issn = {2041-1723}, abstract = {Metal-organic frameworks are widely considered for the separation of chemical mixtures due to their adjustable physical and chemical properties. However, while much effort is currently devoted to developing new adsorbents for a given separation, an ideal scenario would involve a single adsorbent for multiple separations. Porous materials exhibiting framework flexibility offer unique opportunities to tune these properties since the pore size and shape can be controlled by the application of external stimuli. Here, we establish a proof-of-concept for the molecular sieving separation of species with similar sizes (CO2/N2 and CO2/CH4), via precise mechanical control of the pore size aperture in a flexible metal-organic framework. Besides its infinite selectivity for the considered gas mixtures, this material shows excellent regeneration capability when releasing the external mechanical constraint. This strategy, combining an external stimulus applied to a structurally compliant adsorbent, offers a promising avenue for addressing some of the most challenging gas separations.}, } @article {pmid32108467, year = {2020}, author = {Yu, Y and Pauli, GF and Huang, L and Gan, LS and van Breemen, RB and Li, D and McAlpine, JB and Lankin, DC and Chen, SN}, title = {Classification of Flavonoid Metabolomes via Data Mining and Quantification of Hydroxyl NMR Signals.}, journal = {Analytical chemistry}, volume = {92}, number = {7}, pages = {4954-4962}, pmid = {32108467}, issn = {1520-6882}, support = {P41 GM068944/GM/NIGMS NIH HHS/United States ; P50 AT000155/AT/NCCIH NIH HHS/United States ; }, mesh = {*Data Mining ; Flavonoids/*analysis/*metabolism ; Hydroxides/*chemistry ; Magnetic Resonance Spectroscopy ; Molecular Structure ; }, abstract = {Utilizing the distinct HMBC cross-peak patterns of lower-field range (LFR; 11.80-14.20 ppm) hydroxyl singlets, presented NMR methodology characterizes flavonoid metabolomes both qualitatively and quantitatively. It enables simultaneous classification of the structural types of 5-OH flavonoids and biogenetically related 2'-OH chalcones, as well as quantification of individual metabolites from [1]H NMR spectra, even in complex mixtures. Initially, metabolite-specific LFR 1D [1]H and 2D HMBC patterns were established via literature mining and experimental data interpretation, demonstrating that LFR HMBC patterns encode the different structural types of 5-OH flavonoids/2'-OH chalcones. Taking advantage of the simplistic multiplicity of the H,H-uncoupled LFR 5-/2'-OH singlets, individual metabolites could subsequently be quantified by peak fitting quantitative [1]H NMR (PF-qHNMR). Metabolomic analysis of enriched fractions from three medicinal licorice (Glycyrrhiza) species established proof-of-concept for distinguishing three major structural types and eight subtypes in biomedical applications. The method identified 15 G. uralensis (GU) phenols from the six possible subtypes of 5,7-diOH (iso)flav(an)ones with 6-, 8-, and nonprenyl substitution, including the new 6-prenyl-licoisoflavanone (1) and two previously unknown compounds (4 and 7). Relative (100%) qNMR established quantitative metabolome patterns suitable for species discrimination and plant metabolite studies. Absolute qNMR with combined external and internal (solvent) calibration (ECIC) identified and quantified 158 GU metabolites. HMBC-supported qHNMR analysis of flavonoid metabolomes ("flavonomics") empowers the exploration of structure-abundance-activity relationships of designated bioactivity. Its ability to identify and quantify numerous metabolites simultaneously and without identical reference materials opens new avenues for natural product discovery and botanical quality control and can be adopted to other flavonoid- and chalcone-containing taxa.}, } @article {pmid32054108, year = {2020}, author = {Iovinella, M and Carbone, DA and Cioppa, D and Davis, SJ and Innangi, M and Esposito, S and Ciniglia, C}, title = {Prevalent pH Controls the Capacity of Galdieria maxima to Use Ammonia and Nitrate as a Nitrogen Source.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, pmid = {32054108}, issn = {2223-7747}, abstract = {Galdieria maxima is a polyextremophilic alga capable of diverse metabolic processes. Ammonia is widely used in culture media typical of laboratory growth. Recent reports that this species can grow on wastes promote the concept that G. maxima might have biotechnological utility. Accordingly, there is a need to know the range of pH levels that can support G. maxima growth in a given nitrogen source. Here, we examined the combined effect of pH and nitrate/ammonium source on the growth and long-term response of the photochemical process to a pH gradient in different G. maxima strains. All were able to use differing nitrogen sources, despite both the growth rate and photochemical activity were significantly affected by the combination with the pH. All strains acidified the NH4[+]-medium (pH < 3) except G. maxima IPPAS P507. Under nitrate at pH ≥ 6.5, no strain was able to acidify the medium; noteworthy, G. maxima ACUF551 showed a good growth performance under nitrate at pH 5, despite the alkalization of the medium.}, } @article {pmid32042252, year = {2020}, author = {Skvarla, M and Kramer, M and Owen, CL and Miller, GL}, title = {Reexamination of Rhopalosiphum (Hemiptera: Aphididae) using linear discriminant analysis to determine the validity of synonymized species, with some new synonymies and distribution data.}, journal = {Biodiversity data journal}, volume = {8}, number = {}, pages = {e49102}, pmid = {32042252}, issn = {1314-2828}, abstract = {Although 17 species of Rhopalosiphum (Hemiptera: Aphididae) are currently recognized, 85 taxonomic names have been proposed historically. Some species are morphologically similar, especially alate individuals and most synonymies were proposed in catalogues without evidence. This has led to both confusion and difficulty in making accurate species-level identifications. In an attempt to address these issues, we developed a new approach to resolve synonymies based on linear discriminant analysis (LDA) and suggest that this approach may be useful for other taxonomic groups to reassess previously proposed synonymies. We compared 34 valid and synonymized species using 49 measurements and 20 ratios from 1,030 individual aphids. LDA was repeatedly applied to subsets of the data after removing clearly separated groups found in a previous iteration. We found our characters and technique worked well to distinguish among apterae. However, it separated well only those alatae with some distinctive traits, while those apterate which were morphologically similar were not well separated using LDA. Based on our morphological investigation, we transfer R. arundinariae (Tissot, 1933) to Melanaphis supported by details of the wing veination and other morphological traits and propose Melanaphis takahashii Skvarla and Miller as a replacement name for M. arundinariae (Takahashi, 1937); we also synonymize R. momo (Shinji, 1922) with R. nymphaeae (Linnaeus, 1761). Our analyses confirmed many of the proposed synonymies, which will help to stabilize the nomenclature and species concepts within Rhopalosiphum.}, } @article {pmid32035667, year = {2021}, author = {Pozio, E}, title = {Scientific achievements of the last 60 years: From a single to a multispecies concept of the genus Trichinella.}, journal = {Veterinary parasitology}, volume = {297}, number = {}, pages = {109042}, doi = {10.1016/j.vetpar.2020.109042}, pmid = {32035667}, issn = {1873-2550}, mesh = {Animals ; Birds ; Phylogeny ; *Trichinella/genetics ; *Trichinella spiralis ; *Trichinellosis/epidemiology/veterinary ; }, abstract = {The scientific basis that led to the development of a multispecies concept within the Trichinella genus originated in the 1950s, when scientists began reporting an increasing number of host-specific peculiarities among different geographic isolates. This led to speculation that important geographic variability existed within Trichinella spiralis, the only species in the genus at that time. Comparative infection results sparked great interest among investigators and led to similar studies using various geographic isolates of the parasite. In 1972, the Russian scientists V.A. Britov, S.N. Boev and B.L. Garkavi, described three new species: Trichinella nativa, Trichinella nelsoni and Trichinella pseudospiralis. This shattered the concept that the genus Trichinella was monospecific and widened the host range to include birds. The description of these new species generated an intense debate over their taxonomic validity because there were no clear morphological differences among them and because the concept of sibling species had not yet been accepted by parasitologists. The resolution of the taxonomic issues was facilitated by the adoption of new biochemical and molecular techniques for systematics research. In 1992, the first study comparing 152 isolates from various host species and geographical regions identified eight distinct taxa, coded T1 through T8; four of these represented the previously proposed species and included one new species, Trichinella britovi (T3). During the past 27 years, an increasing number of investigations in different geographical regions and hosts coupled with the availability of new and highly sensitive molecular techniques have allowed the description of four new species; Trichinella murrelli (T5), Trichinella papuae (T10), Trichinella zimbabwensis (T11) and Trichinella patagoniensis (T12), and two new genotypes Trichinella T9 and T13. Thus, the taxonomic status of Trichinella T6, T8, T9 and T13 remain unresolved. These new technologies have also advanced a more complete phylogenetic, zoogeographical and epidemiological knowledge base for future work.}, } @article {pmid32024546, year = {2020}, author = {Hanks, E and Todd, H and Palarea-Albaladejo, J and McNeilly, TN and Britton, C and Ballingall, KT}, title = {A novel technique for retrospective genetic analysis of the response to vaccination or infection using cell-free DNA from archived sheep serum and plasma.}, journal = {Veterinary research}, volume = {51}, number = {1}, pages = {9}, pmid = {32024546}, issn = {1297-9716}, mesh = {Animals ; Australia ; Genetic Variation/*immunology ; Haemonchiasis/parasitology/prevention & control/*veterinary ; Haemonchus/immunology ; Plasma/immunology ; Retrospective Studies ; Serum/immunology ; Sheep ; Sheep Diseases/parasitology/*prevention & control ; Vaccination/*veterinary ; Vaccines/administration & dosage/*immunology ; }, abstract = {Genetic variation is associated with differences in disease resistance and susceptibility among individuals within a population. To date, molecular genetic analyses of host responses have relied on extraction of genomic DNA from whole blood or tissue samples. However, such samples are not routinely collected during large-scale field studies. We demonstrate that cell-free genomic DNA (cfDNA) may be extracted and amplified from archived plasma samples, allowing retrospective analysis of host genetic diversity. This technique was also applicable to archived serum samples up to 35 years old and to different ruminant species. As proof of concept, we used this cfDNA approach to genotype the major histocompatibility complex (MHC) class II DRB1 locus of 224 Merino sheep which had participated in field trials of a commercial Haemonchus contortus vaccine, Barbervax[®], in Australia. This identified a total of 51 different DRB1 alleles and their relative frequencies. This is the first study to examine host MHC diversity using DNA extracted from archived plasma samples, an approach that may be applied to retrospective analyses of genetic diversity and responses to vaccination or infection across different species and populations.}, } @article {pmid32020195, year = {2020}, author = {Wallace, EWJ and Maufrais, C and Sales-Lee, J and Tuck, LR and de Oliveira, L and Feuerbach, F and Moyrand, F and Natarajan, P and Madhani, HD and Janbon, G}, title = {Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom.}, journal = {Nucleic acids research}, volume = {48}, number = {5}, pages = {2312-2331}, pmid = {32020195}, issn = {1362-4962}, support = {R01 AI100272/AI/NIAID NIH HHS/United States ; R01 GM071801/GM/NIGMS NIH HHS/United States ; R01 AI120464/AI/NIAID NIH HHS/United States ; 208779/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acyl-tRNA Synthetases/genetics/metabolism ; Candida albicans/genetics/metabolism ; Chromosome Mapping ; Codon, Initiator/*chemistry/metabolism ; Cryptococcus/*genetics/metabolism ; *Gene Expression Regulation, Fungal ; *Genome, Fungal ; Neurospora crassa/genetics/metabolism ; Open Reading Frames ; *Peptide Chain Initiation, Translational ; Saccharomyces cerevisiae/genetics/metabolism ; Schizosaccharomyces/genetics/metabolism ; Species Specificity ; }, abstract = {Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5' and 3' ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-mediated mRNA decay. Transcript leaders in Cryptococcus and other fungi are substantially longer and more AUG-dense than in Saccharomyces. Numerous Cryptococcus mRNAs encode predicted dual-localized proteins, including many aminoacyl-tRNA synthetases, in which a leaky AUG start codon is followed by a strong Kozak context in-frame AUG, separated by mitochondrial-targeting sequence. Analysis of other fungal species shows that such dual-localization is also predicted to be common in the ascomycete mould, Neurospora crassa. Kozak-controlled regulation is correlated with insertions in translational initiation factors in fidelity-determining regions that contact the initiator tRNA. Thus, start codon context is a signal that quantitatively programs both the expression and the structures of proteins in diverse fungi.}, } @article {pmid32010080, year = {2019}, author = {Hardy, BL and Bansal, G and Hewlett, KH and Arora, A and Schaffer, SD and Kamau, E and Bennett, JW and Merrell, DS}, title = {Antimicrobial Activity of Clinically Isolated Bacterial Species Against Staphylococcus aureus.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2977}, pmid = {32010080}, issn = {1664-302X}, abstract = {Bacteria often exist in polymicrobial communities where they compete for limited resources. Intrinsic to this competition is the ability of some species to inhibit or kill their competitors. This phenomenon is pervasive throughout the human body where commensal bacteria block the colonization of incoming microorganisms. In this regard, molecular epidemiological and microbiota-based studies suggest that species-specific interactions play a critical role in the prevention of nasal colonization of the opportunistic pathogen Staphylococcus aureus. Despite this, S. aureus exists as part of the microbiota of ∼25% of the population, suggesting that the interplay between S. aureus and commensals can be complex. Microbiota studies indicate that several bacterial genera are negatively correlated with S. aureus colonization. While these studies paint a broad overview of bacterial presence, they often fail to identify individual species-specific interactions; a greater insight in this area could aid the development of novel antimicrobials. As a proof of concept study designed to identify individual bacterial species that possess anti-S. aureus activity, we screened a small collection of clinical isolates from the Walter Reed National Military Medical Center for the ability to inhibit multiple S. aureus strains. We found that the majority of the isolates (82%) inhibited at least one S. aureus strain; 23% inhibited all S. aureus strains tested. In total, seven isolates mediated inhibitory activity that was independent of physical contact with S. aureus, and seven isolates mediated bactericidal activity. 16S rRNA based-sequencing revealed that the inhibitory isolates belonged to the Acinetobacter, Agromyces, Corynebacterium, Microbacteria, Mycobacterium, and Staphylococcus genera. Unexpectedly, these included seven distinct Acinetobacter baumannii isolates, all of which showed heterogeneous degrees of anti-S. aureus activity. Defined mechanistic studies on specific isolates revealed that the inhibitory activity was retained in conditioned cell free medium (CCFM) derived from the isolates. Furthermore, CCFM obtained from S. saprophyticus significantly decreased mortality of S. aureus-infected Galleria mellonella caterpillars. While future studies will seek to define the molecular mechanisms of the inhibitory activities, our current findings support the study of polymicrobial interactions as a strategy to understand bacterial competition and to identify novel therapeutics against S. aureus and other pathogens.}, } @article {pmid31982806, year = {2020}, author = {Malavin, S and Shmakova, L}, title = {Isolates from ancient permafrost help to elucidate species boundaries in Acanthamoeba castellanii complex (Amoebozoa: Discosea).}, journal = {European journal of protistology}, volume = {73}, number = {}, pages = {125671}, doi = {10.1016/j.ejop.2020.125671}, pmid = {31982806}, issn = {1618-0429}, mesh = {Acanthamoeba castellanii/*classification/cytology/genetics ; Genes, rRNA/genetics ; Genetic Variation ; *Permafrost ; *Phylogeny ; Species Specificity ; }, abstract = {Acanthamoeba castellanii species complex (genotype T4) comprises of more than ten species with unclear synonymy. Its molecular phylogeny has several conflicts with published morphological data. In this paper, we analyze morphometric traits and temperature preferences in six new strains belonging to A. castellanii complex isolated from Arctic permafrost in the framework of molecular phylogeny. This integrative approach allows us to cross-link genotypic and phenotypic variability and identify species-level boundaries inside the complex. We also analyze previously known and newly found discrepancies between the nuclear and mitochondrial gene-based phylogenies. We hypothesize that one reason for these discrepancies may be the intragenomic polymorphism of ribosomal RNA genes.}, } @article {pmid31975168, year = {2020}, author = {Cheng, JY and Mailund, T}, title = {Ancestral Population Genomics with Jocx, a Coalescent Hidden Markov Model.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2090}, number = {}, pages = {167-189}, pmid = {31975168}, issn = {1940-6029}, mesh = {Algorithms ; DNA, Ancient/*analysis ; Evolution, Molecular ; Genetic Variation ; Genetics, Population/*methods ; Genomics/*methods ; Humans ; Markov Chains ; Models, Genetic ; Sequence Alignment ; }, abstract = {Coalescence theory lets us probe the past demographics of present-day genetic samples and much information about the past can be gleaned from variation in rates of coalescence event as we trace genetic lineages back in time. Fewer and fewer lineages will remain, however, so there is a limit to how far back we can explore. Without recombination, we would not be able to explore ancient speciation events because of this-any meaningful species concept would require that individuals of one species are closer related than they are to individuals of another species, once speciation is complete. Recombination, however, opens a window to the deeper past. By scanning along a genomic alignment, we get a sequential variant of the coalescence process as it looked at the time of the speciation. This pattern of coalescence times is fixed at speciation time and does not erode with time; although accumulated mutations and genomic rearrangements will eventually hide the signal, it enables us to glance at events in the past that would not be observable without recombination. So-called coalescence hidden Markov models allow us to exploit this, and in this chapter, we present the tool Jocx that uses a framework of these models to infer demographic parameters in ancient speciation events.}, } @article {pmid31971565, year = {2020}, author = {Xing, H and Kembel, SW and Makarenkov, V}, title = {Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {9}, pages = {2740-2749}, doi = {10.1093/bioinformatics/btaa043}, pmid = {31971565}, issn = {1367-4811}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Phylogeny ; *Software ; }, abstract = {MOTIVATION: Phylogenetic trees and the methods for their analysis have played a key role in many evolutionary, ecological and bioinformatics studies. Alternatively, phylogenetic networks have been widely used to analyze and represent complex reticulate evolutionary processes which cannot be adequately studied using traditional phylogenetic methods. These processes include, among others, hybridization, horizontal gene transfer, and genetic recombination. Nowadays, sequence similarity and genome similarity networks have become an efficient tool for community analysis of large molecular datasets in comparative studies. These networks can be used for tackling a variety of complex evolutionary problems such as the identification of horizontal gene transfer events, the recovery of mosaic genes and genomes, and the study of holobionts.

RESULTS: The shortest path in a phylogenetic tree is used to estimate evolutionary distances between species. We show how the shortest path concept can be extended to sequence similarity networks by defining five new distances, NetUniFrac, Spp, Spep, Spelp and Spinp, and the Transfer index, between species communities present in the network. These new distances can be seen as network analogs of the traditional UniFrac distance used to assess dissimilarity between species communities in a phylogenetic tree, whereas the Transfer index is intended for estimating the rate and direction of gene transfers, or species dispersal, between different phylogenetic, or ecological, species communities. Moreover, NetUniFrac and the Transfer index can be computed in linear time with respect to the number of edges in the network. We show how these new measures can be used to analyze microbiota and antibiotic resistance gene similarity networks.

Our NetFrac program, implemented in R and C, along with its source code, is freely available on Github at the following URL address: https://github.com/XPHenry/Netfrac.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31967996, year = {2020}, author = {Martin, D and Gil, J and Zanol, J and Meca, MA and Pérez Portela, R}, title = {Digging the diversity of Iberian bait worms Marphysa (Annelida, Eunicidae).}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0226749}, pmid = {31967996}, issn = {1932-6203}, mesh = {Animals ; Annelida/*classification/*genetics ; *Biodiversity ; DNA, Ribosomal/*genetics ; *Genes, Mitochondrial ; Phylogeny ; Spain ; }, abstract = {During a visit to polychaete-rearing facilities in the vicinity of Bay of Cádiz (SW Iberian Peninsula, Atlantic Ocean), we sampled two populations of Marphysa (Annelida, Eunicidae) originally occurring at nearby intertidal soft bottoms, one being more than twice as long as the other at the same age. We analysed them using partial sequences of two mitochondrial genes, 16S rDNA and Cytochrome Oxidase I, and classical morphological observations. Our molecular results confirmed that the two populations corresponded to two different species, with PTP species delimitation values ranging from 0.973 (long-bodied species) to 0.999 (short-bodied species). Morphologically, the short-bodied species resembles the recently redescribed M. sanguinea (Montagu, 1813), but differs mainly in having some parapodia with two subacicular hooks (one bidentate and one unidentate) and three types of pectinate chaetae, Two isodont present all along the body, and one particularly large anodont asymmetric appearing only from mid-posterior parapodia. The long-bodied species resembles Marphysa aegypti Elgetany, El-Ghobashy, Ghoneim and Struck, 2018 both in size and in having very robust, unidentate subacicular hooks (single in most parapodia, two-both similar in size and form-in some posterior parapodia), but differs, among other features, in the maxillary formula, the number of acicula per parapodia and the number and shape of pectinate chaetae. Accordingly, we are here fully illustrating and formally describing the two Iberian populations as Marphysa gaditana sp. nov. (short-bodied) and Marphysa chirigota sp. nov. (long-bodied) and we are emending the description of M. aegypti based on our revision of the type material. Also, we discuss on the distribution of the species of the sanguinea-group and on the relevancy of taxonomically robust studies when dealing with species of commercial interest having the potential of being globally spread through human activities, as well as on the misunderstandings caused by the incorrect use of the "cosmopolitan species" concept.}, } @article {pmid31954181, year = {2020}, author = {Lannes-Costa, PS and Baraúna, RA and Ramos, JN and Veras, JFC and Conceição, MVR and Vieira, VV and de Mattos-Guaraldi, AL and Ramos, RTJ and Doran, KS and Silva, A and Nagao, PE}, title = {Comparative genomic analysis and identification of pathogenicity islands of hypervirulent ST-17 Streptococcus agalactiae Brazilian strain.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {80}, number = {}, pages = {104195}, doi = {10.1016/j.meegid.2020.104195}, pmid = {31954181}, issn = {1567-7257}, mesh = {Brazil/epidemiology ; Computational Biology/methods ; *Genome, Bacterial ; *Genomics/methods ; Humans ; Molecular Sequence Annotation ; Phylogeny ; Public Health Surveillance ; Streptococcal Infections/*epidemiology/*microbiology ; Streptococcus agalactiae/*classification/*genetics/isolation & purification/pathogenicity ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Streptococcus agalactiae are important pathogenic bacteria that cause severe infections in humans, especially neonates. The mechanism by which ST-17 causes invasive infections than other STs is not well understood. In this study, we sequenced the first genome of a S. agalactiae ST-17 strain isolated in Brazil using the Illumina HiSeq 2500 technology. S. agalactiae GBS90356 ST-17 belongs to the capsular type III and was isolated from a neonatal with a fatal case of meningitis. The genome presented a size of 2.03 Mbp and a G + C content of 35.2%. S. agalactiae has 706 genes in its core genome and an open pan-genome with a size of 5.020 genes, suggesting a high genomic plasticity. GIPSy software was used to identify 10 Pathogenicity islands (PAIs) which corresponded to 15% of the genome size. IslandViewer4 corroborated the prediction of six PAIs. The pathogenicity islands showed important virulence factors genes for S. agalactiae e.g. neu, cps, dlt, fbs, cfb, lmb. SignalP detected 20 proteins with signal peptides among the 352 proteins found in PAIs, which 60% were located in the SagPAI_5. SagPAI_2 and 5 were mainly detected in ST-17 strains studied. Moreover, we identified 51 unique genes, 9 recombination regions and a large number of SNPs with an average of 760.3 polymorphisms, which can be related with high genomic plasticity and virulence during host-pathogen interactions. Our results showed implications for pathogenesis, evolution, concept of species and in silico analysis value to understand the epidemiology and genome plasticity of S. agalactiae.}, } @article {pmid35275133, year = {2020}, author = {Warwick, C}, title = {Zoonoplasticity as an intuitive risk protocol for companion-animal-linked zoonoses.}, journal = {Revue scientifique et technique (International Office of Epizootics)}, volume = {39}, number = {3}, pages = {817-830}, doi = {10.20506/rst.39.3.3180}, pmid = {35275133}, issn = {0253-1933}, abstract = {Zoonoses are diseases transmissible between non-human and human animals. Over 200 zoonoses are known, of which at least 60 are associated with (especially exotic) companion animals. Current risk-impact assessment approaches for zoonoses are largely cumbersome and, to be meaningful, may require extensive detailed information. A literature search and review were conducted for current risk assessment protocols for common zoonoses, with subsequent development of two novel rapid scoring methods for evaluating potential risk associated with companion-animal-linked zoonoses. Accordingly, a novel, two-tier methodological concept - ‘zoonoplasticity' - was prepared using an intuitive risk approach. The first tier considers risk principles for companion animals and husbandry practices, and pre-weights animals by class or species. The second tier considers established pathogen- or disease-based questions and assigns a degree of risk. Thus, the zoonoplasticity concept enables pathogens or their resultant zoonoses to be scored and provides a clear points-based protocol offering guidance concerning potential threat, in particular where more quantifiable risk assessment is unavailable because of information deficits. The zoonoplasticity concept was tested with 15 animal species and 22 known zoonoses against European Centre for Disease Prevention and Control (ECDC) operational guidance as a comparative system. Risk categorisation was 100% consistent for 21 of the 22 specific zoonoses, while requiring minimal information input, and the overall comparison rate was 98.85%. Zoonoplasticity is not intended to provide an absolute measure of risk or to replace existing methodologies, rather it is an attempt to standardise a practical judgement protocol that accounts for various relevant issues, and to offer a potentially helpful indicator of concern. The zoonoplasticity concept will be relevant to remits for medical professionals, veterinary medical professionals, public health professionals, government administrators, biomedical researchers and others.}, } @article {pmid33929010, year = {2020}, author = {Pavey, CR}, title = {The recognition concept and conservation management of species.}, journal = {Theoretical biology forum}, volume = {113}, number = {1-2}, pages = {91-94}, doi = {10.19272/202011402012}, pmid = {33929010}, issn = {2282-2593}, mesh = {Animals ; *Conservation of Natural Resources ; *Endangered Species ; Recognition, Psychology ; }, } @article {pmid33929006, year = {2020}, author = {Hereward, JP and Brookes, DR and Walter, GH}, title = {The recognition concept and genetic approaches to interpreting species.}, journal = {Theoretical biology forum}, volume = {113}, number = {1-2}, pages = {67-70}, doi = {10.19272/202011402008}, pmid = {33929006}, issn = {2282-2593}, mesh = {Animals ; Genetic Speciation ; *Mating Preference, Animal ; }, abstract = {1. Introduction. 2. The Specific-mate Recognition System (SMRS). 3. The Genetic Change As sociated with Speciation.}, } @article {pmid31885493, year = {2019}, author = {Pfingstl, T and Baumann, J and Lienhard, A}, title = {The Caribbean enigma: the presence of unusual cryptic diversity in intertidal mites (Arachnida, Acari, Oribatida).}, journal = {Organisms, diversity & evolution}, volume = {19}, number = {4}, pages = {609-623}, pmid = {31885493}, issn = {1439-6092}, support = {P 28597/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The definition, as well as the existence of cryptic species, is still a subject of controversial debates. Some scientists claim that cryptic diversity is a real phenomenon that should be extensively studied while others argue that cryptic species do not exist as they are nothing more than an incompatibility of species concepts. We investigated the enigmatic case of two widely distributed Caribbean intertidal oribatid mites, Carinozetes bermudensis and Carinozetes mangrovi, consisting of five distinct genetic lineages. Morphological features allowing to clearly distinguish between these lineages are absent, and despite certain congruence with genetic data, comprehensive morphometric analyses also do not show clear separation. Species delimitation analyses based on COI sequence data, on the other hand, suggest five distinct genetic species. Despite the lack of diagnostic characters for these suggested species, the lineages can be classified at least into two morphological groups, the bermudensis and the mangrovi group which can only be distinguished by the arrangement of cuticular ventral carinae. Specimens within a group show nearly identical phenotypes, impeding morphological identification and hence rendering the found diversity cryptic. Stabilizing selection caused by the extreme conditions of the intertidal environment is suggested to be responsible for the found morphological stasis. The genetic lineages show more or less clear geographic patterns; in C. mangrovi, there is a northern, an Antillean, and a Pacific lineage, whereas in C. bermudensis, there is a Bermudian and a Caribbean lineage. In a few places, e.g., the Bahamas and Panama, distributions may overlap. Neither the found biogeographic pattern nor the observed ecological needs could explain the reason for the genetic diversification of Caribbean Carinozetes.}, } @article {pmid31879098, year = {2020}, author = {Liao, JY and Fan, C and Huang, YZ and Pei, KJ}, title = {Distribution of residual agricultural pesticides and their impact assessment on the survival of an endangered species.}, journal = {Journal of hazardous materials}, volume = {389}, number = {}, pages = {121871}, doi = {10.1016/j.jhazmat.2019.121871}, pmid = {31879098}, issn = {1873-3336}, mesh = {Agriculture ; Animals ; Dietary Exposure/*adverse effects ; *Endangered Species ; Environmental Monitoring ; Lethal Dose 50 ; No-Observed-Adverse-Effect Level ; *Panthera ; Pesticides/analysis/*toxicity ; Risk Assessment ; Soil Pollutants/analysis/*toxicity ; Taiwan ; }, abstract = {This study aimed to assess the distribution of spent pesticides in an agro-farming area and to evaluate their impact on the ecological risk for an endangered species combing the health risk assessment concept with the modelling algorithm proposed by European Food Safety Authority (EFSA). An agricultural area in western Taiwan was chosen to investigate the ecological risk on Prionailurus bengalensis. Their ecological stability was evaluated in the context of the residuals' distribution of the spent pesticides in the investigated area. The pesticide residues accumulated and correlated highly to the adverse health impact on the leopard cat. In the present study, 67 pesticides were detected from 79 collected soil samples. The hazard index (HI) was found related to land use patterns and the HI values in Yuanli and Zhuolan were significantly higher than those in the other areas, increasing poisoning probability of the leopard cat. The locations of agro-chemical utilization were highly overlapped with leopard cats' activity zone, supporting the hypothesis that pesticide residues posed a potential threat to the leopard cats' health. The proposed risk assessment framework was capable of estimating the risk caused by pesticide residues and no similar study has been reported before.}, } @article {pmid31837544, year = {2020}, author = {Xu, H and Zhang, S and Ma, G and Zhang, Y and Li, Y and Pei, H}, title = {18S rRNA gene sequencing reveals significant influence of anthropogenic effects on microeukaryote diversity and composition along a river-to-estuary gradient ecosystem.}, journal = {The Science of the total environment}, volume = {705}, number = {}, pages = {135910}, doi = {10.1016/j.scitotenv.2019.135910}, pmid = {31837544}, issn = {1879-1026}, mesh = {Animals ; China ; *Ecosystem ; Environmental Monitoring ; Estuaries ; Genes, rRNA ; Humans ; RNA, Ribosomal, 18S ; Rivers ; }, abstract = {Microeukaryotes play key roles in the structure and functioning of lotic ecosystems; however, little is known about the relative importance of the processes that drive planktonic microeukaryotic biogeography in rivers, especially the effects of anthropogenic inputs (e.g., wastewater discharge and pesticide and fertilizer use) on the taxonomic and functional diversity of microeukaryotes. Herein 18S ribosomal RNA sequencing was used to examine the assembly of microeukaryotes in samples from Xiaoqing River, a mid-sized river in north China that runs through urban and agricultural areas and then discharges into the Bohai Sea. We found that diversity of microeukaryote declined obviously due to the excessive disturbance of the urban and agricultural activities in the midstream of the river. Our results support the concept that species sorting caused by local pollution can largely determine microeukaryotic community structure when significant environmental gradients exist in polluted running-water ecosystems and that compositional dissimilarity increased with increases in the Euclidean distance of environmental variables. Variation of microeukaryotic diversity was mainly determined by changes in levels of nutrients, dissolved oxygen, turbidity, and salinity and they can affect the rare subcommunities significantly. Furthermore, zooplankton were dominated in rare taxa, meanwhile phytoplankton was composed by the abundant taxa mainly. These findings confirmed the dynamic character of riverine ecosystems and the significance of human activities in shaping microeukaryote diversity in rivers.}, } @article {pmid31833026, year = {2019}, author = {Ashton, NJ and Ide, M and Zetterberg, H and Blennow, K}, title = {Salivary Biomarkers for Alzheimer's Disease and Related Disorders.}, journal = {Neurology and therapy}, volume = {8}, number = {Suppl 2}, pages = {83-94}, pmid = {31833026}, issn = {2193-8253}, abstract = {The search for accessible and cost-effective biomarkers to complement current cerebrospinal fluid (CSF) and imaging biomarkers in the accurate detection of Alzheimer disease (AD) and other common neurodegenerative disorders remains a challenging task. The advances in ultra-sensitive detection methods has highlighted blood biomarkers (e.g. amyloid-β and neurofilament light) as a valuable and realistic tool in a diagnostic or screening process. Saliva, however, is also a rich source of potential biomarkers for disease detection and offers several practical advantages over biofluids that are currently examined for neurodegenerative disorders. However, while this may be true for the general population, challenges in collecting saliva from an elderly population should be seriously considered. In this review, we begin by discussing how saliva is produced and how age-related conditions can modify saliva production and composition. We then focus on the data available which support the concept of salivary amyloid-β, tau species and novel biomarkers in detecting AD and alpha-synuclein (α-syn) in Parkinson's disease (PD).}, } @article {pmid31782770, year = {2021}, author = {Nakashima, Y and Sakai, Y and Mizuno, Y and Furuno, K and Hirono, K and Takatsuki, S and Suzuki, H and Onouchi, Y and Kobayashi, T and Tanabe, K and Hamase, K and Miyamoto, T and Aoyagi, R and Arita, M and Yamamura, K and Tanaka, T and Nishio, H and Takada, H and Ohga, S and Hara, T}, title = {Lipidomics links oxidized phosphatidylcholines and coronary arteritis in Kawasaki disease.}, journal = {Cardiovascular research}, volume = {117}, number = {1}, pages = {96-108}, doi = {10.1093/cvr/cvz305}, pmid = {31782770}, issn = {1755-3245}, mesh = {Adaptor Proteins, Signal Transducing/blood ; Arteritis/*blood/diagnosis/etiology ; Biomarkers/blood ; Case-Control Studies ; Child ; Child, Preschool ; Chromatography, Liquid ; Coronary Artery Disease/*blood/diagnosis/etiology ; Female ; Humans ; Japan ; *Lipidomics ; Lipoproteins, LDL/blood ; Male ; Mucocutaneous Lymph Node Syndrome/*blood/complications/diagnosis ; Oxidation-Reduction ; Phenylalanine/blood ; Phosphatidylcholines/*blood ; Prospective Studies ; Scavenger Receptors, Class E/blood ; Tandem Mass Spectrometry ; }, abstract = {AIMS: Coronary arteritis is a life-threatening complication that may arise in the acute stage of Kawasaki disease (KD), the leading cause of systemic vasculitis in childhood. Various microorganisms and molecular pathogens have been reported to cause KD. However, little is known about the key molecules that contribute to the development of coronary arteritis in KD.

METHODS AND RESULTS: To identify causative molecules for coronary arteritis in KD, we prospectively recruited 105 patients with KD and 65 disease controls in four different parts of Japan from 2015 to 2018. During this period, we conducted lipidomics analyses of their sera using liquid chromatography-mass spectrometry (LC-MS). The comprehensive LC-MS system detected a total of 27 776 molecules harbouring the unique retention time and m/z values. In the first cohort of 57 KD patients, we found that a fraction of these molecules showed enrichment patterns that varied with the sampling region and season. Among them, 28 molecules were recurrently identified in KD patients but not in controls. The second and third cohorts of 48 more patients with KD revealed that these molecules were correlated with inflammatory markers (leucocyte counts and C-reactive proteins) in the acute stage. Notably, two of these molecules (m/z values: 822.55 and 834.59) were significantly associated with the development of coronary arteritis in the acute stage of KD. Their fragmentation patterns in the tandem MS/MS analysis were consistent with those of oxidized phosphatidylcholines (PCs). Further LC-MS/MS analysis supported the concept that reactive oxygen species caused the non-selective oxidization of PCs in KD patients. In addition, the concentrations of LOX-1 ligand containing apolipoprotein B in the plasma of KD patients were significantly higher than in controls.

CONCLUSION: These data suggest that inflammatory signals activated by oxidized phospholipids are involved in the pathogenesis of coronary arteritis in KD. Because the present study recruited only Japanese patients, further examinations are required to determine whether oxidized PCs might be useful biomarkers for the development of coronary arteritis in broad populations of KD.}, } @article {pmid31768539, year = {2020}, author = {Goddard, J and Allerdice, M and Portugal, JS and Moraru, GM and Paddock, CD and King, J}, title = {What Is Going on With the Genus Dermacentor? Hybridizations, Introgressions, Oh My!.}, journal = {Journal of medical entomology}, volume = {57}, number = {3}, pages = {653-656}, doi = {10.1093/jme/tjz219}, pmid = {31768539}, issn = {1938-2928}, mesh = {Animals ; Dermacentor/*genetics ; *Genetic Introgression ; *Hybridization, Genetic ; }, abstract = {In the 1930s, R. A. Cooley noted that Dermacentor occidentalis (Acarina: Ixodidae) and Dermacentor andersoni were closely related and could hybridize. Decades later, James Oliver discovered that crosses of Dermacentor variabilis, D. andersoni, and D. occidentalis could, on occasion, produce hybrids. A recent molecular analysis (both mtDNA and nDNA) in our laboratory revealed that certain specimens of Dermacentor andersoni nested with Dermacentor parumapertus. Does this close relationship, along with the mito-nuclear discordance we have observed, mean D. andersoni and D. parumapertus are a single species? By contemporary taxonomic criteria, this seems improbable based on their distinctly different morphologies, host associations, and ecologies. This paper explores ideas related to mito-nuclear discordance, hybridization, and introgression (primarily) not only in these two species but also other members of the genus Dermacentor. Both D. andersoni and D. parumapertus can be found on the same hosts and have sympatric distributions, so introgression of genetic material by occasional cross-mating between these two species is possible. Further, the difficulty in applying specific species concepts in ticks has been recently pointed out and a unified agreement on an integrative species concepts could clearly be useful in this situation. With the discovery of D. parumapertus as a potential vector of Rickettsia parkeri and the historically recognized role of D. andersoni in transmission of Rickettsia rickettsii, understanding the specific status of each lineage of these species (and others in the genus) is extremely important from a public health perspective.}, } @article {pmid31739583, year = {2019}, author = {Walther, G and Wagner, L and Kurzai, O}, title = {Updates on the Taxonomy of Mucorales with an Emphasis on Clinically Important Taxa.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {5}, number = {4}, pages = {}, pmid = {31739583}, issn = {2309-608X}, abstract = {Fungi of the order Mucorales colonize all kinds of wet, organic materials and represent a permanent part of the human environment. They are economically important as fermenting agents of soybean products and producers of enzymes, but also as plant parasites and spoilage organisms. Several taxa cause life-threatening infections, predominantly in patients with impaired immunity. The order Mucorales has now been assigned to the phylum Mucoromycota and is comprised of 261 species in 55 genera. Of these accepted species, 38 have been reported to cause infections in humans, as a clinical entity known as mucormycosis. Due to molecular phylogenetic studies, the taxonomy of the order has changed widely during the last years. Characteristics such as homothallism, the shape of the suspensors, or the formation of sporangiola are shown to be not taxonomically relevant. Several genera including Absidia, Backusella, Circinella, Mucor, and Rhizomucor have been amended and their revisions are summarized in this review. Medically important species that have been affected by recent changes include Lichtheimia corymbifera, Mucor circinelloides, and Rhizopus microsporus. The species concept of Rhizopus arrhizus (syn. R. oryzae) is still a matter of debate. Currently, species identification of the Mucorales is best performed by sequencing of the internal transcribed spacer (ITS) region. Ecologically, the Mucorales represent a diverse group but for the majority of taxa, the ecological role and the geographic distribution remain unknown. Understanding the biology of these opportunistic fungal pathogens is a prerequisite for the prevention of infections, and, consequently, studies on the ecology of the Mucorales are urgently needed.}, } @article {pmid31735146, year = {2020}, author = {Fitch, WT}, title = {Animal cognition and the evolution of human language: why we cannot focus solely on communication.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1789}, pages = {20190046}, pmid = {31735146}, issn = {1471-2970}, mesh = {*Animal Communication ; Animals ; *Biological Evolution ; Cognition/*physiology ; *Communication ; Humans ; *Language ; Primates ; Vocalization, Animal ; }, abstract = {Studies of animal communication are often assumed to provide the 'royal road' to understanding the evolution of human language. After all, language is the pre-eminent system of human communication: doesn't it make sense to search for its precursors in animal communication systems? From this viewpoint, if some characteristic feature of human language is lacking in systems of animal communication, it represents a crucial gap in evolution, and evidence for an evolutionary discontinuity. Here I argue that we should reverse this logic: because a defining feature of human language is its ability to flexibly represent and recombine concepts, precursors for many important components of language should be sought in animal cognition rather than animal communication. Animal communication systems typically only permit expression of a small subset of the concepts that can be represented and manipulated by that species. Thus, if a particular concept is not expressed in a species' communication system this is not evidence that it lacks that concept. I conclude that if we focus exclusively on communicative signals, we sell the comparative analysis of language evolution short. Therefore, animal cognition provides a crucial (and often neglected) source of evidence regarding the biology and evolution of human language. This article is part of the theme issue 'What can animal communication teach us about human language?'}, } @article {pmid31732260, year = {2020}, author = {Yong, TC and Chiu, PH and Chen, CH and Hung, CH and Chen, CN}, title = {Disruption of thin- and thick-wall microalgae using high pressure gases: Effects of gas species, pressure and treatment duration on the extraction of proteins and carotenoids.}, journal = {Journal of bioscience and bioengineering}, volume = {129}, number = {4}, pages = {502-507}, doi = {10.1016/j.jbiosc.2019.10.008}, pmid = {31732260}, issn = {1347-4421}, mesh = {Biomass ; Carotenoids/*isolation & purification/metabolism ; Cell Fractionation/*methods ; Cell Wall/*chemistry ; Fungal Proteins/*isolation & purification/metabolism ; Gases/*pharmacology ; Humans ; Microalgae/*chemistry/drug effects/growth & development/metabolism ; *Pressure ; Protein Stability ; Stress, Mechanical ; Subcellular Fractions/chemistry/metabolism ; Time Factors ; }, abstract = {Industrial scale microalgal cell disruption requires low cost, high efficiency and structural conservation of biomolecules for biorefinery. Many cultivated microalgae have thick walls and these walls are barriers for efficient cell disruption. Until recently, despite the high biodiversity of microalgae, little attention has been paid to thin-wall microalgal species in the natural environment for the production and recovery of valuable biomolecules. Instead of developing high power cell disruption devices, utilization of thin-wall species would be a better approach. The present paper describes a simple device that was assembled to evaluate the viability and effectiveness of biomolecule extraction from both thin- and thick-wall species as a proof of concept. This device was tested with high-pressure gases including N2, CO2 plus N2, and air as the disruption force. The highest nitrogen pressure, 110 bar, was not able to disrupt the thick-wall microalgal cells. On the other hand, the thin-wall species was disrupted to different degrees using different pressures and treatment durations. In the same treatment duration, higher nitrogen pressure gave better cell disruption efficiency than the lower pressure. However, in the same pressure, longer treatment duration did not give better efficiency than the shorter duration. High pressure CO2 treatments resulted in low soluble protein levels in the media. The best conditions to disrupt the thin-wall microalgal cells were 110 bar N2 or air for 1 min among these tests. In these conditions, not only were the disruption efficiencies high, but also the biomolecules were well preserved.}, } @article {pmid31719781, year = {2019}, author = {Cabarroi-Hernández, M and Villalobos-Arámbula, AR and Mabel Gisela Torres-Torres, and Decock, C and Guzmán-Dávalos, L}, title = {The Ganoderma weberianum-resinaceum lineage: multilocus phylogenetic analysis and morphology confirm G. mexicanum and G. parvulum in the Neotropics.}, journal = {MycoKeys}, volume = {59}, number = {}, pages = {95-131}, pmid = {31719781}, issn = {1314-4049}, abstract = {Many species of Ganoderma exhibit a high phenotypic plasticity. Hence, particularly among them, the morphological species concept remains difficult to apply, resulting in a currently confused taxonomy; as a consequence, the geographical distribution range of many species also remains very uncertain. One of the areas with a strong uncertainty, as far as morphological species concept is concerned, is the Neotropics. It is common that names of species described from other regions, mainly from northern temperate areas, have been applied to Neotropical species. The aim of the present study was to determine which species might lay behind the G. weberianum complex in the Neotropics, using morphological studies and phylogenetic inferences based on both single (ITS) and multilocus (ITS, rpb2, and tef1-α) sequences. The results indicated that G. weberianum sensu Steyaert, which is the usually accepted concept for this taxon, was absent from the Neotropics. In this area, G. weberianum sensu Steyaert encompassed at least two phylogenetic species, which are tentatively, for the time being, identified as belonging to G. mexicanum and G. parvulum. These two species could be distinguished morphologically, notably by the ornamentation or its absence on their chlamydospores. The results also showed that additional species from the Neotropics might still exist, including, e.g., G. perzonatum, but their circumscription remains uncertain until now because of the paucity of material available. Furthermore, it was found that the current concept of G. resinaceum embraced a complex of species.}, } @article {pmid31717080, year = {2019}, author = {Yang, X and Shi, K and Heller, K and Menzel, F and Huang, J and Wu, H}, title = {Morphology and DNA barcodes of two species of Bradysia Winnertz from China (Diptera, Sciaridae), with the description of Bradysia minorlobus Yang, Shi amp; Huang sp. n.}, journal = {Zootaxa}, volume = {4612}, number = {1}, pages = {zootaxa.4612.1.5}, doi = {10.11646/zootaxa.4612.1.5}, pmid = {31717080}, issn = {1175-5334}, mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; *Diptera/genetics ; Nematocera ; }, abstract = {Two morphologically similar species of the fungicola species group of Bradysia Winnertz, 1867 were studied in China: Bradysia chenjinae Yang, Zhang Yang, 1993 and Bradysia minorlobus Yang, Shi Huang sp. n. The morphological species concepts were supported by the DNA barcodes of COI sequences. The genetic distances of 16 Bradysia fungicola group species were analyzed and a neighbor-joining tree was constructed. The morphological characters of both Chinese species were described and illustrated.}, } @article {pmid31716982, year = {2019}, author = {Khaustov, AA and Frolov, AV}, title = {Revision of the genus Athyreacarus (Acari: Athyreacaridae).}, journal = {Zootaxa}, volume = {4647}, number = {1}, pages = {zootaxa.4647.1.14}, doi = {10.11646/zootaxa.4647.1.14}, pmid = {31716982}, issn = {1175-5334}, mesh = {Animals ; Bolivia ; Brazil ; *Coleoptera ; Mexico ; *Mites ; }, abstract = {Mites of the genus Athyreacarus (Acari: Athyreacaridae) associated with bolboceratine beetles (Coleoptera: Geotrupidae: Bolboceratine) of New World are revised, a new generic concept provided, and the family concept modified. Nine new species are described: A. grandis sp. nov. on Neoathyreus lanuginosus in Brazil; A. magnificus sp. nov. on Athyreus tuberifer in Brazil; A. variabilis sp. nov. on Neoathyreus cf. anthracinus in Brazil; A. similis sp. nov. on Neoathyreus centromaculatus in Bolivia; A. vazdemelloi sp. nov. on Parathyreus rectus in Brazil; A. pusillus sp. nov. on Athyreus brasilicus in Brazil; A. latus sp. nov. on Athyreus cf. bifurcatus from unknown locality; A. angustus sp. nov. on Bolbelasmus horni in USA; and A. ovalis sp. nov. on Bolbelasmus variabilis in Mexico. Bolbapium striatopunctatum, B. minutum, and B. sculpturatum are recorded as new phoretic host beetles for Athyreacarus primitivus. A key to genera and species of the family Athyreacaridae is provided.}, } @article {pmid31716742, year = {2019}, author = {Grubbs, SA and Baumann, RW}, title = {Soyedina Ricker, 1952 (Plecoptera: Nemouridae) in the eastern Nearctic: review of species concepts, proposed morphology-based species groups, and description of a new species from North Carolina.}, journal = {Zootaxa}, volume = {4658}, number = {2}, pages = {zootaxa.4658.2.2}, doi = {10.11646/zootaxa.4658.2.2}, pmid = {31716742}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; Appalachian Region ; *Insecta ; *Lepidoptera ; North Carolina ; }, abstract = {The eastern Nearctic species of the genus Soyedina Ricker, 1952 (Plecoptera: Nemouridae) are reviewed. Two morphology-based species groups are proposed based on epiproct characteristics. Soyedina sheldoni sp. nov. is described from the southern Appalachian Highland region of western North Carolina. A distribution map and a dichotomous key to all nine Nearctic species are provided.}, } @article {pmid31716519, year = {2019}, author = {Smith, BP and Cairns, KM and Adams, JW and Newsome, TM and Fillios, M and Déaux, EC and Parr, WCH and Letnic, M and VAN Eeden, LM and Appleby, RG and Bradshaw, CJA and Savolainen, P and Ritchie, EG and Nimmo, DG and Archer-Lean, C and Greenville, AC and Dickman, CR and Watson, L and Moseby, KE and Doherty, TS and Wallach, AD and Morrant, DS and Crowther, MS}, title = {Taxonomic status of the Australian dingo: the case for Canis dingo Meyer, 1793.}, journal = {Zootaxa}, volume = {4564}, number = {1}, pages = {zootaxa.4564.1.6}, doi = {10.11646/zootaxa.4564.1.6}, pmid = {31716519}, issn = {1175-5334}, mesh = {Animals ; Australia ; *Canidae ; Dogs ; Phylogeny ; *Wolves ; }, abstract = {The taxonomic status and systematic nomenclature of the Australian dingo remain contentious, resulting in decades of inconsistent applications in the scientific literature and in policy. Prompted by a recent publication calling for dingoes to be considered taxonomically as domestic dogs (Jackson et al. 2017, Zootaxa 4317, 201-224), we review the issues of the taxonomy applied to canids, and summarise the main differences between dingoes and other canids. We conclude that (1) the Australian dingo is a geographically isolated (allopatric) species from all other Canis, and is genetically, phenotypically, ecologically, and behaviourally distinct; and (2) the dingo appears largely devoid of many of the signs of domestication, including surviving largely as a wild animal in Australia for millennia. The case of defining dingo taxonomy provides a quintessential example of the disagreements between species concepts (e.g., biological, phylogenetic, ecological, morphological). Applying the biological species concept sensu stricto to the dingo as suggested by Jackson et al. (2017) and consistently across the Canidae would lead to an aggregation of all Canis populations, implying for example that dogs and wolves are the same species. Such an aggregation would have substantial implications for taxonomic clarity, biological research, and wildlife conservation. Any changes to the current nomen of the dingo (currently Canis dingo Meyer, 1793), must therefore offer a strong, evidence-based argument in favour of it being recognised as a subspecies of Canis lupus Linnaeus, 1758, or as Canis familiaris Linnaeus, 1758, and a successful application to the International Commission for Zoological Nomenclature - neither of which can be adequately supported. Although there are many species concepts, the sum of the evidence presented in this paper affirms the classification of the dingo as a distinct taxon, namely Canis dingo.}, } @article {pmid31715944, year = {2019}, author = {Kundrata, R and Mertlik, J and Németh, T}, title = {Unexpected diversity of Lacon Laporte, 1838 (Coleoptera: Elateridae: Agrypninae) in the Levant: revised species concepts, new species, and an identification key.}, journal = {Zootaxa}, volume = {4679}, number = {3}, pages = {zootaxa.4679.3.1}, doi = {10.11646/zootaxa.4679.3.1}, pmid = {31715944}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; *Coleoptera ; Cyprus ; Israel ; Jordan ; Lebanon ; Syria ; Turkey ; }, abstract = {The species of genus Lacon Laporte, 1838 from the Levant are taxonomically revised. Currently, 18 species are known from the area covering the island of Cyprus and mainland from Hatay province of Turkey to Israel. Six species are described as new for science: Lacon mucheibensis sp. nov. (Israel), L. qatanensis sp. nov. (Syria), L. platiai sp. nov. (Jordan), L. safitensis sp. nov. (Syria), L. tafilensis sp. nov. (Jordan), and L. zenobiae sp. nov. (Lebanon, Syria). Lacon freidbergi Platia, 2010 is synonymized with L. lithophilus (Candèze, 1857), and L. kapleri Platia Schimmel, 1994 with L. graecus (Candèze, 1857). Lacon drusus (Marseul, 1870) is recorded for the first time from Israel. Lacon lithophilus is recorded for the first time from Israel and Jordan. Lacon graecus is removed from the fauna of Levant, because all earlier reports of this species from Lebanon and Syria were based on misidentifications. Figures of habitus and main diagnostic features are provided for all species and an identification key to the Lacon species of the Levant is given.}, } @article {pmid31692070, year = {2019}, author = {Tasneem, F and Shakoori, FR and Ilyas, M and Shahzad, N and Potekhin, A and Shakoori, AR}, title = {Genetic diversity of Paramecium species on the basis of multiple loci analysis and ITS secondary structure models.}, journal = {Journal of cellular biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/jcb.29546}, pmid = {31692070}, issn = {1097-4644}, abstract = {Among ciliates, Paramecium has become a privileged model for the study of "species problem" particularly in the case of the "Paramecium aurelia complex" that has been intensely investigated. Despite extensive studies, the taxonomy of Paramecium is still challenging. The major problem is an uneven sampling of Paramecium with relatively few representatives of each species. To investigate species from the less discovered region (Pakistan), 10 isolates of Paramecium species including a standing-alone FT8 strain previously isolated by some of us were subjected to molecular characterization. Fragments of 18S recombinant DNA (rDNA), ITS1-5.8S-ITS2-5'LSU rDNA, cytochrome c oxidase subunit II, and hsp70 genes were used as molecular markers for phylogenetic analysis of particular isolates. The nucleotide sequences of polymerase chain reaction products of all markers were compared with the available sequences of relevant markers of other Paramecium species from GenBank. Phylogenetic trees based on all molecular markers showed that all the nine strains had a very close relationship with Paramecium primaurelia except for the FT8 strain. FT8 consistently showed its unique position in comparison to all other species in the phylogenetic trees. Available sequences of internal transcribed spacer 1 (ITS1) and ITS2 and some other ciliate sequences from GenBank were used for the construction of secondary models. Two highly conserved helices supported by compensatory base changes among all ciliates of ITS2 secondary structures were found similar to other eukaryotes. Therefore, the most conserved 120 to 180 base pairs regions were identified for their comparative studies. We found that out of the three helices in ITS1 structure, helix B was more conserved in Paramecium species. Despite various substitutions in the primary sequence, it was observed that secondary structures of ITS1 and ITS2 could be helpful in interpreting the phylogenetic relationships both at species as well as at generic level.}, } @article {pmid31679484, year = {2019}, author = {Monsarrat, S and Jarvie, S and Svenning, JC}, title = {Anthropocene refugia: integrating history and predictive modelling to assess the space available for biodiversity in a human-dominated world.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1788}, pages = {20190219}, pmid = {31679484}, issn = {1471-2970}, mesh = {*Biodiversity ; *Conservation of Natural Resources/methods ; Ecosystem ; Human Activities ; *Refugium ; }, abstract = {During periods of strong environmental change, some areas may serve as refugia, where components of biodiversity can find protection, persist and potentially expand from should conditions again become favourable. The refugia concept has previously been used in the context of climatic change, to describe climatically stable areas in which taxa survived past Quaternary glacial-interglacial oscillations, or where they might persist in the future under anthropogenic climate change. However, with the recognition that Earth has entered the Anthropocene, an era in which human activities are the dominant driving force on ecosystems, it is critical to also consider human pressures on the environment as factors limiting species distributions. Here, we present a novel concept, Anthropocene refugia, to refer to areas that provide spatial and temporal protection from human activities and that will remain suitable for a given taxonomic unit in the long-term. It integrates a deep-time perspective on species biogeography that provides information on the natural rather than current-day relictual distribution of species, with spatial information on modern and future anthropogenic threats. We define the concept and propose a methodology to effectively identify and map realized and potential current and future refugia, using examples for two megafaunal species as a proof of concept. We argue that identifying Anthropocene refugia will improve biodiversity conservation and restoration by allowing better prediction of key areas for conservation and potential for re-expansions today and in the future. More generally, it forms a new conceptual framework to assess and manage the impact of anthropogenic activities on past, current and future patterns of species distributions. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'}, } @article {pmid31662456, year = {2019}, author = {Chase, AB and Arevalo, P and Brodie, EL and Polz, MF and Karaoz, U and Martiny, JBH}, title = {Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31662456}, issn = {2150-7511}, mesh = {Actinobacteria/genetics ; Bacteria/classification/*genetics ; Ecology ; Ecosystem ; Gene Flow ; Genetic Variation ; Genome, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; }, abstract = {For free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several obstacles to the study of the processes contributing to microbial diversification. These obstacles are particularly high in soil, where high bacterial diversity inhibits the study of closely related genotypes and therefore the factors structuring microbial populations. Here, we isolated strains within a single Curtobacterium ecotype from surface soil (leaf litter) across a regional climate gradient and investigated the phylogenetic structure, recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. Our results indicate that microbial populations are delineated by gene flow discontinuities, with distinct populations cooccurring at multiple sites. Bacterial population structure was further delineated by genomic features allowing for the identification of candidate genes possibly contributing to local adaptation. These results suggest that the genetic structure within this bacterium is maintained both by ecological specialization in localized microenvironments (isolation by environment) and by dispersal limitation between geographic locations (isolation by distance).IMPORTANCE Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit equivalent to a eukaryotic species, defined as highly clustered genotypic and phenotypic strains with the same ecological niche. Using a combination of genomic and computational analyses, we assessed the phylogenetic structure, extent of recombination, and flexible gene content of this genomic diversity to infer patterns of gene flow. To our knowledge, this study is the first to do so for a dominant soil bacterium. Our results indicate that bacterial soil populations, similarly to those in other environments, are structured by gene flow discontinuities and exhibit distributional patterns consistent with both isolation by distance and isolation by environment. Thus, both dispersal limitation and local environments contribute to the divergence among closely related soil bacteria as observed in macroorganisms.}, } @article {pmid31640818, year = {2020}, author = {Wongnikong, W and van Brunschot, SL and Hereward, JP and De Barro, PJ and Walter, GH}, title = {Testing mate recognition through reciprocal crosses of two native populations of the whitefly Bemisia tabaci (Gennadius) in Australia.}, journal = {Bulletin of entomological research}, volume = {110}, number = {3}, pages = {328-339}, doi = {10.1017/S0007485319000683}, pmid = {31640818}, issn = {1475-2670}, mesh = {Animals ; Australia ; Female ; Hemiptera/*classification/genetics/*physiology ; Male ; Microsatellite Repeats ; *Sexual Behavior, Animal ; Species Specificity ; }, abstract = {Bemisia tabaci (Gennadius) represents a relatively large cryptic species complex. Australia has at least two native populations of B. tabaci sensu lato and these were first found on different host plants in different parts of Australia. The species status of these populations has not been resolved, although their mitochondrial sequences differ by 3.82-4.20%. We addressed the question of whether these AUSI and AUSII B. tabaci populations are distinct species. We used reciprocal cross-mating tests to establish whether the insects from these different populations recognize one another as potential mating partners. The results show that the two native Australian populations of B. tabaci have a mating sequence with four phases, each of which is described. Not all pairs in the control crosses mated and the frequency of mating differed across them. Some pairs in the AUSI-M × AUSII-F did mate (15%) and did produce female progeny, but the frequency was extremely low relative to controls. Microsatellite genotyping of the female progeny produced in the crosses showed these matings were successful. None of the AUSII-M × AUSI-F crosses mated although some of the males did search for females. These results demonstrate the critical role of the mate recognition process and the need to assess this directly in cross-mating tests if the species status of different populations is to be tested realistically. In short, AUSI and AUSII B. tabaci populations are distinct species because the individual males and females do not recognize individuals of the alternative population as potential mating partners.}, } @article {pmid31632650, year = {2019}, author = {König, K and Zundel, P and Krimmer, E and König, C and Pollmann, M and Gottlieb, Y and Steidle, JLM}, title = {Reproductive isolation due to prezygotic isolation and postzygotic cytoplasmic incompatibility in parasitoid wasps.}, journal = {Ecology and evolution}, volume = {9}, number = {18}, pages = {10694-10706}, pmid = {31632650}, issn = {2045-7758}, abstract = {The reproductive barriers that prevent gene flow between closely related species are a major topic in evolutionary research. Insect clades with parasitoid lifestyle are among the most species-rich insects and new species are constantly described, indicating that speciation occurs frequently in this group. However, there are only very few studies on speciation in parasitoids. We studied reproductive barriers in two lineages of Lariophagus distinguendus (Chalcidoidea: Hymenoptera), a parasitoid wasp of pest beetle larvae that occur in human environments. One of the two lineages occurs in households preferably attacking larvae of the drugstore beetle Stegobium paniceum ("DB-lineage"), the other in grain stores with larvae of the granary weevil Sitophilus granarius as main host ("GW-lineage"). Between two populations of the DB-lineage, we identified slight sexual isolation as intraspecific barrier. Between populations from both lineages, we found almost complete sexual isolation caused by female mate choice, and postzygotic isolation, which is partially caused by cytoplasmic incompatibility induced by so far undescribed endosymbionts which are not Wolbachia or Cardinium. Because separation between the two lineages is almost complete, they should be considered as separate species according to the biological species concept. This demonstrates that cryptic species within parasitoid Hymenoptera also occur in Central Europe in close contact to humans.}, } @article {pmid31628939, year = {2019}, author = {Huston, DC and Cutmore, SC and Cribb, TH}, title = {An identity crisis in the Indo-Pacific: molecular exploration of the genus Koseiria (Digenea: Enenteridae).}, journal = {International journal for parasitology}, volume = {49}, number = {12}, pages = {945-961}, doi = {10.1016/j.ijpara.2019.07.001}, pmid = {31628939}, issn = {1879-0135}, mesh = {Animals ; Biometry ; Cluster Analysis ; DNA, Helminth/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fishes/*parasitology ; Microscopy ; Pacific Ocean ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; Trematoda/*anatomy & histology/*classification/genetics/isolation & purification ; }, abstract = {We explore the growing issue of cryptic speciation in the Digenea through study of museum material and newly collected specimens consistent with the enenterid genus Koseiria from five species of the Kyphosidae and Chaetodontoplus meredithi Kuiter (Pomacanthidae) collected in the Indo-Pacific. We use an integrated approach, employing traditional morphometrics, principal components analysis (PCA), and molecular data (ITS2 and 28S rDNA). Our results support recombination of Koseiria allanwilliamsi Bray & Cribb, 2002 as Proenenterum allanwilliamsi (Bray & Cribb, 2002) n. comb. and transfer of Koseiria huxleyi Bray & Cribb, 2001 to a new genus as Enenterageitus huxleyi (Bray & Cribb, 2002) n. comb. Molecular data indicate the presence of four further species consistent with Koseiria, one from Western Australia (sequence data only) and three from eastern Australia. All three eastern Australian species are morphologically consistent with Koseiria xishaensis Gu & Shen, 1983, but distinct from all other previously described species. Although K. xishaensis has been reported from Australia, we conclude that the similarity of the present forms to the original description of K. xishaensis means records of this species from Japan, Palau and Australia are unreliable. Because the eastern Australian forms cannot be reliably ascribed to K. xishaensis, we describe Koseiria argalea n. sp., Koseiria laiphopharophora n. sp., and Koseiria pyknophora n. sp., following application of PCAs and iterative refinement of species concepts and type series. These analyses did not allow convincing identification hypotheses for all specimens examined. In this genus, both morphological and molecular data, together with reliable host identifications, are essential for species recognition, and thus we refrain from attempting to name samples lacking molecular data. The issues presented by these taxa encapsulate those of trematodes in the region as a whole. Many records require dramatically improved supporting data, leading to substantial uncertainly in the identification of this fauna.}, } @article {pmid31621946, year = {2020}, author = {Akçakaya, HR and Rodrigues, ASL and Keith, DA and Milner-Gulland, EJ and Sanderson, EW and Hedges, S and Mallon, DP and Grace, MK and Long, B and Meijaard, E and Stephenson, PJ}, title = {Assessing ecological function in the context of species recovery.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {34}, number = {3}, pages = {561-571}, doi = {10.1111/cobi.13425}, pmid = {31621946}, issn = {1523-1739}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; *Ecosystem ; *Endangered Species ; }, abstract = {Species interactions matter to conservation. Setting an ambitious recovery target for a species requires considering the size, density, and demographic structure of its populations such that they fulfill the interactions, roles, and functions of the species in the ecosystems in which they are embedded. A recently proposed framework for an International Union for Conservation of Nature Green List of Species formalizes this requirement by defining a fully recovered species in terms of representation, viability, and functionality. Defining and quantifying ecological function from the viewpoint of species recovery is challenging in concept and application, but also an opportunity to insert ecological theory into conservation practice. We propose 2 complementary approaches to assessing a species' ecological functions: confirmation (listing interactions of the species, identifying ecological processes and other species involved in these interactions, and quantifying the extent to which the species contributes to the identified ecological process) and elimination (inferring functionality by ruling out symptoms of reduced functionality, analogous to the red-list approach that focuses on symptoms of reduced viability). Despite the challenges, incorporation of functionality into species recovery planning is possible in most cases and it is essential to a conservation vision that goes beyond preventing extinctions and aims to restore a species to levels beyond what is required for its viability. This vision focuses on conservation and recovery at the species level and sees species as embedded in ecosystems, influencing and being influenced by the processes in those ecosystems. Thus, it connects and integrates conservation at the species and ecosystem levels.}, } @article {pmid31611298, year = {2020}, author = {Ng, SC and Kamm, MA and Yeoh, YK and Chan, PKS and Zuo, T and Tang, W and Sood, A and Andoh, A and Ohmiya, N and Zhou, Y and Ooi, CJ and Mahachai, V and Wu, CY and Zhang, F and Sugano, K and Chan, FKL}, title = {Scientific frontiers in faecal microbiota transplantation: joint document of Asia-Pacific Association of Gastroenterology (APAGE) and Asia-Pacific Society for Digestive Endoscopy (APSDE).}, journal = {Gut}, volume = {69}, number = {1}, pages = {83-91}, pmid = {31611298}, issn = {1468-3288}, mesh = {Anti-Bacterial Agents/pharmacology ; Clostridioides difficile ; Endoscopy, Gastrointestinal ; Enterocolitis, Pseudomembranous/therapy ; Fecal Microbiota Transplantation/*methods ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/physiology ; Humans ; Inflammatory Bowel Diseases/therapy ; Prognosis ; Recurrence ; Tissue Donors ; Treatment Outcome ; }, abstract = {OBJECTIVE: The underlying microbial basis, predictors of therapeutic outcome and active constituent(s) of faecal microbiota transplantation (FMT) mediating benefit remain unknown. An international panel of experts presented key elements that will shape forthcoming FMT research and practice.

DESIGN: Systematic search was performed, FMT literature was critically appraised and a 1-day round-table discussion was conducted to derive expert consensus on key issues in FMT research.

RESULTS: 16 experts convened and discussed five questions regarding (1) the role of donor and recipient microbial (bacteria, viruses, fungi) parameters in FMT; (2) methods to assess microbiota alterations; (3) concept of keystone species and microbial predictors of FMT, (4) influence of recipient profile and antibiotics pretreatment on FMT engraftment and maintenance and (5) new developments in FMT formulations and delivery. The panel considered that variable outcomes of FMT relate to compositional and functional differences in recipient's microbiota, and likely donor-associated and recipient-associated physiological and genetic factors. Taxonomic composition of donor intestinal microbiota may influence the efficacy of FMT in recurrent Clostridioides difficile infections and UC. FMT not only alters bacteria composition but also establishes trans-kingdom equilibrium between gut fungi, viruses and bacteria to promote the recovery of microbial homeostasis. FMT is not a one size fits all and studies are required to identify microbial components that have specific effects in patients with different diseases.

CONCLUSION: FMT requires optimisation before their therapeutic promise can be evaluated for different diseases. This summary will guide future directions and priorities in advancement of the science and practice of FMT.}, } @article {pmid31566155, year = {2020}, author = {Pienaar, R and Josemans, A and Latif, AA and Mans, BJ}, title = {The host-specificity of Theileria sp. (sable) and Theileria sp. (sable-like) in African Bovidae and detection of novel Theileria in antelope and giraffe.}, journal = {Parasitology}, volume = {147}, number = {2}, pages = {213-224}, doi = {10.1017/S003118201900132X}, pmid = {31566155}, issn = {1469-8161}, mesh = {Animals ; Antelopes/parasitology ; Giraffes/parasitology ; Host Specificity ; RNA, Ribosomal, 18S/genetics ; Real-Time Polymerase Chain Reaction ; Ruminants/*parasitology ; Sensitivity and Specificity ; Theileria/*genetics ; Theileriasis/*diagnosis/*parasitology ; }, abstract = {Tick-borne diseases caused by Theileria are of economic importance in domestic and wildlife ruminants. The majority of Theileria infects a limited number of host species, supporting the concept of host specificity. However, some Theileria seem to be generalists challenging the host specificity paradigm, such as Theileria sp. (sable) reported from various vertebrate hosts, including African buffalo, cattle, dogs and different antelope species. We tested the hypothesis that T. sp. (sable) uses Bovidae as hosts in general using a real-time polymerase chain reaction assay specific for T. sp. (sable) and a closely related genotype: T. sp. (sable-like). Various antelope species from the Tragelaphini (black wildebeest, blesbuck, blue wildebeest, gemsbuck, sable and waterbuck) tested positive for either T. sp. (sable) or T. sp. (sable-like). However, no African buffalo (n = 238) or cattle (n = 428) sampled in the current study tested positive, suggesting that these latter species are not carrier hosts. The results were confirmed using next-generation sequencing which also indicated at least 13 new genotypes or species found in various antelope and giraffes. Genotypes were found in single host species or in evolutionarily related hosts, suggesting that host specificity in Theileria may be a lineage specific phenomenon likely associated with tick-host-parasite co-evolution.}, } @article {pmid31551615, year = {2019}, author = {Boluda, CG and Rico, VJ and Divakar, PK and Nadyeina, O and Myllys, L and McMullin, RT and Zamora, JC and Scheidegger, C and Hawksworth, DL}, title = {Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae).}, journal = {Persoonia}, volume = {42}, number = {}, pages = {75-100}, pmid = {31551615}, issn = {0031-5850}, abstract = {In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach - including morphological, chemical, molecular, and distributional characters - to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.}, } @article {pmid31529041, year = {2020}, author = {Qing, X and Wang, M and Karssen, G and Bucki, P and Bert, W and Braun-Miyara, S}, title = {PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {4}, pages = {1052-1056}, doi = {10.1093/bioinformatics/btz707}, pmid = {31529041}, issn = {1367-4811}, mesh = {Animals ; *Nematoda ; Phylogeny ; *Plants ; Software ; }, abstract = {MOTIVATION: The phylum Nematoda comprises the most cosmopolitan and abundant metazoans on Earth and plant-parasitic nematodes represent one of the most significant nematode groups, causing severe losses in agriculture. Practically, the demands for accurate nematode identification are high for ecological, agricultural, taxonomic and phylogenetic researches. Despite their importance, the morphological diagnosis is often a difficult task due to phenotypic plasticity and the absence of clear diagnostic characters while molecular identification is very difficult due to the problematic database and complex genetic background.

RESULTS: The present study attempts to make up for currently available databases by creating a manually-curated database including all up-to-date authentic barcoding sequences. To facilitate the laborious process associated with the interpretation and identification of a given query sequence, we developed an automatic software pipeline for rapid species identification. The incorporated alignment function facilitates the examination of mutation distribution and therefore also reveals nucleotide autapomorphies, which are important in species delimitation. The implementation of genetic distance, plot and maximum likelihood phylogeny analysis provides more powerful optimality criteria than similarity searching and facilitates species delimitation using evolutionary or phylogeny species concepts. The pipeline streamlines several functions to facilitate more precise data analyses, and the subsequent interpretation is easy and straightforward.

The pipeline was written in vb.net, developed on Microsoft Visual Studio 2017 and designed to work in any Windows environment. The PPNID is distributed under the GNU General Public License (GPL). The executable file along with tutorials is available at https://github.com/xueqing4083/PPNID.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid31499461, year = {2019}, author = {Remm, L and Lõhmus, A and Leibak, E and Kohv, M and Salm, JO and Lõhmus, P and Rosenvald, R and Runnel, K and Vellak, K and Rannap, R}, title = {Restoration dilemmas between future ecosystem and current species values: The concept and a practical approach in Estonian mires.}, journal = {Journal of environmental management}, volume = {250}, number = {}, pages = {109439}, doi = {10.1016/j.jenvman.2019.109439}, pmid = {31499461}, issn = {1095-8630}, mesh = {Animals ; *Conservation of Natural Resources ; *Ecosystem ; Endangered Species ; Estonia ; Wetlands ; }, abstract = {Ecosystem restoration is gaining political and economic support worldwide, but its exact targets and costs often remain unclear. A key issue, both for predicting restoration success and assessing the costs, is the uncertainty of post-restoration development of the ecosystem. A specific combination of uncertainties emerges when ecosystem restoration would negatively affect pre-restoration species conservation values. Such dilemma appears to be common, but largely ignored in restoration planning; for example, in historically degraded forests, wetlands and grasslands that provide novel habitats for some threatened species. We present a framework of linked options for resolving the dilemma, and exemplify its application in extensive mire restoration in Estonia. The broad options include: redistributing the risks by timing; relocating restoration sites; modifying restoration techniques; and managing for future habitats of the species involved. In Estonia, we assessed these options based on spatially explicit mapping of expected future states of the ecosystem, their uncertainty, and the distribution of species at risk. Such planning documentation, combined with follow-up monitoring and experimentation, can be used for adaptive management, by funding organizations and for academic research.}, } @article {pmid31483800, year = {2019}, author = {Tapanila, L and Pruitt, J}, title = {Redefining species concepts for the Pennsylvanian scissor tooth shark, Edestus.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0220958}, pmid = {31483800}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; *Fossils ; Models, Anatomic ; Sharks/*anatomy & histology/classification ; Tooth/*anatomy & histology ; }, abstract = {This study reevaluates the tooth morphology used to define species within the genus Edestus (Chondrichthyes, Euchondrocephali). Known as the scissor tooth shark, Edestus produced a unique dentition of spiraled tooth families positioned in the symphysis (midline) of the upper and lower jaws. Morphometric analysis of more than 200 ejected teeth and intact spiral tooth whorls demonstrates that teeth from the upper and lower whorls differ in shape and ontogeny. Comparison of these data to the type specimens of 13 existing species reduces the number of morphologically distinct Edestus to just four species and refines the stratigraphic occurrence and expansion of the group. E. triserratus has a narrow bullet-shaped crown that points anteriorly and has roots of intermediate length. E. minor crowns have a wider triangular base, whereas the crowns of E. heinrichi form nearly equilateral triangles and are supported by an elongated root. E. vorax, which also has roughly equilateral triangular crowns, has short and deep roots, and is only known from very large specimens that are distinct from the growth series of E. heinrichi. Tooth and whorl morphologies among the species are consistent with cranial anatomy observed in a juvenile E. heinrichi and with transverse tooth-wear patterns to suggest Edestus used a forward to backward slicing motion to bite its prey. Extrapolating body size from tooth whorl length provides a conservative estimate that E. heinrichi could exceed 6.7 m in length. Edestus fossils are recovered from coastal marine to estuarine deposits spanning roughly six million years (313-307 Ma). Edestus first appears in England during the latest Bashkirian (313 Ma, Carboniferous), a few million years after its most closely resembling genus Lestrodus. Diversification and range expansion of Edestus coincides with the Moscovian transgression that flooded Laurentia and the Russian platform.}, } @article {pmid31475654, year = {2020}, author = {Govers, LC and Harper, AP and Finger, BJ and Mattiske, DM and Pask, AJ and Green, MP}, title = {Atrazine induces penis abnormalities including hypospadias in mice.}, journal = {Journal of developmental origins of health and disease}, volume = {11}, number = {3}, pages = {246-249}, pmid = {31475654}, issn = {2040-1752}, support = {R01 DK096263/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Atrazine/administration & dosage/*toxicity ; Disease Models, Animal ; Female ; Herbicides/administration & dosage/*toxicity ; Humans ; Hypospadias/*chemically induced ; Male ; Mice ; Penis/*abnormalities/drug effects/embryology ; Pregnancy ; Prenatal Exposure Delayed Effects/*chemically induced ; Proof of Concept Study ; }, abstract = {Use of the herbicide atrazine (ATR) is banned in the European Union; yet, it is still widely used in the USA and Australia. ATR is known to alter testosterone and oestrogen production and thus reproductive characteristics in numerous species. In this proof of concept study, we examined the effect of ATR exposure, at a supra-environmental dose (5 mg/kg bw/day), beginning on E9.5 in utero, prior to sexual differentiation of the reproductive tissues, until 26 weeks of age, on the development of the mouse penis. Notably, this is the first study to specifically investigate whether ATR can affect penis characteristics. We show that ATR exposure, beginning in utero, causes a shortening (demasculinisation) of penis structures and increases the incidence of hypospadias in mice. These data indicate the need for further studies of ATR on human reproductive development and fertility, especially considering its continued and widespread use.}, } @article {pmid31465043, year = {2019}, author = {Muntel, J and Gandhi, T and Verbeke, L and Bernhardt, OM and Treiber, T and Bruderer, R and Reiter, L}, title = {Surpassing 10 000 identified and quantified proteins in a single run by optimizing current LC-MS instrumentation and data analysis strategy.}, journal = {Molecular omics}, volume = {15}, number = {5}, pages = {348-360}, doi = {10.1039/c9mo00082h}, pmid = {31465043}, issn = {2515-4184}, mesh = {Chromatography, Liquid/*instrumentation/methods ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Mass Spectrometry/*instrumentation/methods ; Neoplastic Stem Cells/*chemistry/metabolism ; Proteome ; Proteomics/*methods ; Testicular Neoplasms/metabolism ; }, abstract = {Comprehensive proteome quantification is crucial for a better understanding of underlying mechanisms of diseases. Liquid chromatography mass spectrometry (LC-MS) has become the method of choice for comprehensive proteome quantification due to its power and versatility. Even though great advances have been made in recent years, full proteome coverage for complex samples remains challenging due to the high dynamic range of protein expression. Additionally, when studying disease regulatory proteins, biomarkers or potential drug targets are often low abundant, such as for instance kinases and transcription factors. Here, we show that with improvements in chromatography and data analysis the single shot proteome coverage can go beyond 10 000 proteins in human tissue. In a testis cancer study, we quantified 11 200 proteins using data independent acquisition (DIA). This depth was achieved with a false discovery rate of 1% which was experimentally validated using a two species test. We introduce the concept of hybrid libraries which combines the strength of direct searching of DIA data as well as the use of large project-specific or published DDA data sets. Remarkably deep proteome coverage is possible using hybrid libraries without the additional burden of creating a project-specific library. Within the testis cancer set, we found a large proportion of proteins in an altered expression (in total: 3351; 1453 increased in cancer). Many of these proteins could be linked to the hallmarks of cancer. For example, the complement system was downregulated which helps to evade the immune response and chromosomal replication was upregulated indicating a dysregulated cell cycle.}, } @article {pmid31446446, year = {2020}, author = {Mitsui, R and Lee, K and Uchiyama, A and Hayakawa, S and Kinoshita, F and Kajioka, S and Eto, M and Hashitani, H}, title = {Contractile elements and their sympathetic regulations in the pig urinary bladder: a species and regional comparative study.}, journal = {Cell and tissue research}, volume = {379}, number = {2}, pages = {373-387}, doi = {10.1007/s00441-019-03088-6}, pmid = {31446446}, issn = {1432-0878}, mesh = {Actins/metabolism ; Aged ; Aged, 80 and over ; Animals ; Female ; Guinea Pigs ; Humans ; Male ; Middle Aged ; Mucous Membrane/physiology ; Muscle Contraction/*physiology ; Muscle, Smooth/physiology ; *Organ Specificity ; Species Specificity ; Swine ; Sympathetic Nervous System/*physiology ; Urinary Bladder/*innervation/*physiology ; }, abstract = {Contractile behaviour of the urinary bladder and its sympathetic inhibition during storage phases are not well understood. Here, we explore muscularis mucosae (MM) as a predominant mucosal contractile element and the capability of sympathetic nerves to relax detrusor smooth muscle (DSM) or MM. Distribution of α-smooth muscle actin (α-SMA)-immunoreactive cells was compared in pig, human, guinea pig, rat and mouse bladders by immunohistochemistry, while contractility of the bladder mucosa was compared in these species by isometric tension recordings. In pig, human and guinea pig bladders, DSM and MM located in the lamina propria expressed α-SMA immunoreactivity, while both rat and mouse bladders lacked a MM. Consistent with this presence or absence of MM, bladder mucosa of pig, human and guinea pig but not rat and mouse developed spontaneous phasic contractions (SPCs). Distribution of tyrosine hydroxylase (TH)-immunoreactive sympathetic nerve fibres was compared in pig DSM, MM, trigone and urethra, as were their sympathetic nerve-evoked contractile/relaxing responses examined. In pig DSM or MM, where TH-immunoreactive sympathetic fibres exclusively projected to the vasculature, sympathetic relaxations were difficult to demonstrate. In contrast, sympathetic contractions were invariably evoked in pig trigone and urethra where the smooth muscle cells receive TH-immunoreactive sympathetic innervations. Thus, SPCs of bladder mucosa appear to predominantly arise from the MM displaying species differences. Despite the currently accepted concept of sympathetic nerve-mediated DSM relaxation during the storage phase, it is unlikely that neurally released noradrenaline acts on β-adrenoceptors to relax either DSM or MM due to the anatomical lack of sympathetic innervation.}, } @article {pmid31427708, year = {2019}, author = {Lyons, K and Kacev, D and Preti, A and Gillett, D and Dewar, H}, title = {Organic contaminants as an ecological tool to explore niche partitioning: a case study using three pelagic shark species.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {12080}, pmid = {31427708}, issn = {2045-2322}, mesh = {Animals ; *Ecology ; Ecosystem ; Humans ; Organic Chemicals/*chemistry/isolation & purification ; Seafood/analysis ; Seawater/*chemistry ; Sharks/*metabolism ; }, abstract = {Chemical contaminant profiles are linked to an animal's niche, providing a potential tool by which to assess resource partitioning in pelagic species. As proof of concept, we examined contaminant signatures in three species of sharks (Isurus oxyrinchus, Prionace glauca, and Alopias vulpinus) known to overlap in both space and time. Since these sharks comprise a predatory guild within the Southern California Bight (SCB), we predicted that species may partition spatial and dietary resources to limit the extent of competitive exclusion. Indeed, species were distinguishable by both total contaminant loads and their contaminant fingerprint, as random forest analysis found that species could be correctly classified 96% of the time. Our results demonstrate the utility of chemical analyses for ecological studies, and how contaminant tracers can be used in combination with traditional methods to elucidate how species may undergo niche partitioning to reduce competition for overlapping resources within predatory guilds.}, } @article {pmid31418654, year = {2019}, author = {Walck-Shannon, E and Batzli, J and Pultorak, J and Boehmer, H}, title = {Biological Variation as a Threshold Concept: Can We Measure Threshold Crossing?.}, journal = {CBE life sciences education}, volume = {18}, number = {3}, pages = {ar36}, pmid = {31418654}, issn = {1931-7913}, mesh = {Cross-Sectional Studies ; Curriculum ; Female ; Humans ; *Learning ; Male ; Students ; }, abstract = {Threshold concepts are fundamental to a discipline and, once understood, transform students' understanding and perception of the subject. Despite the value of threshold concepts as a learning "portal" for heuristic purposes, there is limited empirical evidence of threshold crossing or achieving mastery. As a threshold concept, biological variation within species is fundamental to understanding evolution and provides a target for analyzing threshold crossing. We aimed to 1) examine student understanding of variation using four dimensions of a threshold concept (discursive, troublesome, liminal, and integrative), 2) measure "threshold crossing," and 3) investigate the utility of the threshold concept framework to curriculum design. We conducted semistructured interviews of 29 students affiliated with a "variation-enriched" curriculum in a cross-sectional design with precurriculum, current, and postcurriculum groups (Pre, Current, and Post) and an outgroup of three postbaccalaureate advanced learners (Outgroup). Interview transcripts revealed that Current students expand their "variation discourse," while the Post group and Outgroup displayed conformity in word choice about variation. The Post and Current groups displayed less troublesome and more integrative responses. Pre, Post, and Outgroup explanations' revealed liminality, with discomfort and uncertainty regardless of accuracy. When we combined all four threshold concept dimensions for each respondent, patterns indicative of threshold crossing emerged along with new insight regarding curricular design.}, } @article {pmid31415905, year = {2019}, author = {Zhao, L and de Hoog, S and Hagen, F and Kang, Y and Al-Hatmi, AMS}, title = {Species borderlines in Fusarium exemplified by F. circinatum/F. subglutinans.}, journal = {Fungal genetics and biology : FG & B}, volume = {132}, number = {}, pages = {103262}, doi = {10.1016/j.fgb.2019.103262}, pmid = {31415905}, issn = {1096-0937}, mesh = {Fusarium/*classification ; Gene Expression Regulation, Fungal ; Genes, Mating Type, Fungal/genetics ; Microbial Interactions/*genetics ; Peptide Elongation Factor 1/*genetics ; Phylogeny ; Plant Diseases/microbiology ; RNA Polymerase II/genetics ; *Recombination, Genetic ; }, abstract = {Fusarium species are known as cross-kingdom pathogens, causing infections in both plants and animals. This ecological variation challenges the species concept of closely similar lineages in the genus. The present paper describes various types of genetic interaction between strains of two neighboring model species with different predilection, F. circinatum and F. subglutinans. Parameters include sequencing of the translation elongation factor 1α (TEF1) and the second largest subunit of RNA polymerase (RPB2), sexual crossing, and vegetative compatibility groups (VCGs). Successful interspecific crosses resulted in either recombination or in homothallic fruiting, the latter being limited to F. subglutinans MAT1 parents. Crossings were skewed, as Fusarium circinatum recombined more often than F. subglutinans. We hypothesize that genetic exchange in Fusarium species is finely regulated with an arsenal of options, which are applied when partners are phylogenetically closely related, leading to fluent species borderlines.}, } @article {pmid31404391, year = {2019}, author = {Costa, WJEM}, title = {Description of a new species of cynopoeciline killifish (Cyprinodontiformes, Aplocheilidae), possibly extinct, from the Atlantic Forest of south-eastern Brazil.}, journal = {ZooKeys}, volume = {867}, number = {}, pages = {73-85}, pmid = {31404391}, issn = {1313-2989}, abstract = {Specimens found between 1985 and 1988 in the Magé River Basin, south-eastern Brazil were misidentified as L. splendens. The recent rediscovery of other specimens in the Estrela River Basin near the type locality of L. splendens has clarified the species' concept, making it possible to recognise the Magé River Basin specimens as a new species. The new species is herein described as Leptopanchax sanguineus sp. nov. and is distinguished from all other cynopoecilines by a unique colour pattern in males, including red bars with sinuous margins. It was collected in a well-preserved, temporary shallow swampy area within dense moist forest, but since 1990 the species has not been found again. Leptopanchax sanguineus sp. nov. is one of three species of cynopoeciline killifishes living in lowland moist forests of the coastal plains of Rio de Janeiro State, where the greatest diversity of endemic cynopoecilines is concentrated. Each of these species has been recorded a single time in the last 30 years, a surprisingly low record attributable to intense deforestation during the last several decades resulting in small fragmented lowland moist forests of today. This study indicates that seasonal killifishes adapted to uniquely live in this kind of habitat should be regarded with special concern in studies evaluating conservation priorities.}, } @article {pmid31398339, year = {2019}, author = {Arevalo, P and VanInsberghe, D and Elsherbini, J and Gore, J and Polz, MF}, title = {A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations.}, journal = {Cell}, volume = {178}, number = {4}, pages = {820-834.e14}, doi = {10.1016/j.cell.2019.06.033}, pmid = {31398339}, issn = {1097-4172}, mesh = {Adaptation, Physiological/genetics ; Alleles ; Clostridiales/*genetics ; Colitis, Ulcerative/microbiology ; Crohn Disease/microbiology ; *Gene Flow ; Gene Transfer, Horizontal ; Genome, Bacterial ; Humans ; Microbiota/*genetics ; Models, Genetic ; Mutation Rate ; Phylogeny ; Polymorphism, Single Nucleotide ; Prochlorococcus/genetics ; Sulfolobus/genetics ; Vibrio/genetics ; }, abstract = {Delineating ecologically meaningful populations among microbes is important for identifying their roles in environmental and host-associated microbiomes. Here, we introduce a metric of recent gene flow, which when applied to co-existing microbes, identifies congruent genetic and ecological units separated by strong gene flow discontinuities from their next of kin. We then develop a pipeline to identify genome regions within these units that show differential adaptation and allow mapping of populations onto environmental variables or host associations. Using this reverse ecology approach, we show that the human commensal bacterium Ruminococcus gnavus breaks up into sharply delineated populations that show different associations with health and disease. Defining populations by recent gene flow in this way will facilitate the analysis of bacterial and archaeal genomes using ecological and evolutionary theory developed for plants and animals, thus allowing for testing unifying principles across all biology.}, } @article {pmid31380462, year = {2019}, author = {Verma, A and Xu, K and Du, T and Zhu, P and Liang, Z and Liao, S and Zhang, J and Raizada, MK and Grant, MB and Li, Q}, title = {Expression of Human ACE2 in Lactobacillus and Beneficial Effects in Diabetic Retinopathy in Mice.}, journal = {Molecular therapy. Methods & clinical development}, volume = {14}, number = {}, pages = {161-170}, pmid = {31380462}, issn = {2329-0501}, support = {R01 HL102033/HL/NHLBI NIH HHS/United States ; R01 EY028858/EY/NEI NIH HHS/United States ; R01 EY012601/EY/NEI NIH HHS/United States ; R01 EY024564/EY/NEI NIH HHS/United States ; P30 DK079626/DK/NIDDK NIH HHS/United States ; R01 EY021752/EY/NEI NIH HHS/United States ; P30 EY003039/EY/NEI NIH HHS/United States ; P30 EY008571/EY/NEI NIH HHS/United States ; P30 EY021721/EY/NEI NIH HHS/United States ; }, abstract = {The angiotensin converting enzyme 2 (ACE2) catalyzes the degradation of Angiotensin II (Ang II) to generate Angiotensin-(1-7), which reduces inflammation and oxidative stress stimulated by Ang II. ACE2 has been shown to be protective in cardiovascular and metabolic diseases including diabetes and its complications. However, the challenge for its clinical application is large-scale production of high-quality ACE2 with sufficient target tissue bioavailability. We developed an expression and delivery system based on the use of probiotic species Lactobacillus paracasei (LP) to serve as a live vector for oral delivery of human ACE2. We show that codon-optimized ACE2 can be efficiently expressed in LP. Mice treated with the recombinant LP expressing the secreted ACE2 in fusion with the non-toxic subunit B of cholera toxin, which acts as a carrier to facilitate transmucosal transport, showed increased ACE2 activities in serum and tissues. ACE2-LP administration reduced the number of acellular capillaries, blocked retinal ganglion cell loss, and decreased retinal inflammatory cytokine expression in two mouse models of diabetic retinopathy. These results provide proof of concept for feasibility of using engineered probiotic species as live vector for delivery of human ACE2 with enhanced tissue bioavailability for treating diabetic retinopathy, as well as other diabetic complications.}, } @article {pmid31370425, year = {2019}, author = {Park, J}, title = {Emergence of oscillatory coexistence with exponentially decayed waiting times in a coupled cyclic competition system.}, journal = {Chaos (Woodbury, N.Y.)}, volume = {29}, number = {7}, pages = {071107}, doi = {10.1063/1.5118833}, pmid = {31370425}, issn = {1089-7682}, abstract = {Interpatch migration between two environments is generally considered as a spatial concept and can affect species biodiversity in each patch by inducing flux of population such as inflow and outflow quantities of species. In this paper, we explore the effect of interpatch migration, which can be generally considered as a spatial concept and may affect species biodiversity between two different patches in the perspective of the macroscopic level by exploiting the coupling of two systems, where each patch is occupied by cyclically competing three species who can stably coexist by exhibiting periodic orbits. For two simple scenarios of interpatch migration either single or all species migration, we found that two systems with independently stable coexisting species in each patch are eventually synchronized, and oscillatory behaviors of species densities in two patches become identical, i.e., the synchronized coexistence emerges. In addition, we find that, whether single or all species interpatch migration occurs, the waiting time for the synchronization is exponentially decreasing as the coupling strength is intensified. Our findings suggest that the synchronized behavior of species as a result of migration between different patches can be easily predicted by the coupling of systems and additional information such as waiting times and sensitivity of initial densities.}, } @article {pmid31363173, year = {2019}, author = {Pérez-Carrascal, OM and Terrat, Y and Giani, A and Fortin, N and Greer, CW and Tromas, N and Shapiro, BJ}, title = {Coherence of Microcystis species revealed through population genomics.}, journal = {The ISME journal}, volume = {13}, number = {12}, pages = {2887-2900}, pmid = {31363173}, issn = {1751-7370}, mesh = {Brazil ; Canada ; Ecosystem ; Evolution, Molecular ; Fresh Water/microbiology ; Genome, Bacterial ; Metagenomics ; Microcystins/metabolism ; Microcystis/classification/*genetics/*isolation & purification/metabolism ; Phylogeny ; }, abstract = {Microcystis is a genus of freshwater cyanobacteria, which causes harmful blooms in ecosystems worldwide. Some Microcystis strains produce harmful toxins such as microcystin, impacting drinking water quality. Microcystis colony morphology, rather than genetic similarity, is often used to classify Microcystis into morphospecies. Yet colony morphology is a plastic trait, which can change depending on environmental and laboratory culture conditions, and is thus an inadequate criterion for species delineation. Furthermore, Microcystis populations are thought to disperse globally and constitute a homogeneous gene pool. However, this assertion is based on relatively incomplete characterization of Microcystis genomic diversity. To better understand these issues, we performed a population genomic analysis of 33 newly sequenced genomes mainly from Canada and Brazil. We identified 17 Microcystis clusters of genomic similarity, five of which correspond to monophyletic clades containing at least three newly sequenced genomes. Four out of these five clades match to named morphospecies. Notably, M. aeruginosa is paraphyletic, distributed across 12 genomic clusters, suggesting it is not a coherent species. A few clades of closely related isolates are specific to a unique geographic location, suggesting biogeographic structure over relatively short evolutionary time scales. Higher homologous recombination rates within than between clades further suggest that monophyletic groups might adhere to a Biological Species-like concept, in which barriers to gene flow maintain species distinctness. However, certain genes-including some involved in microcystin and micropeptin biosynthesis-are recombined between monophyletic groups in the same geographic location, suggesting local adaptation.}, } @article {pmid31352635, year = {2019}, author = {Ranius, T and Hämäläinen, A and Sjögren, J and Hiron, M and Jonason, D and Kubart, A and Schroeder, M and Dahlberg, A and Thor, G and Jonsell, M}, title = {The evolutionary species pool concept does not explain occurrence patterns of dead-wood-dependent organisms: implications for logging residue extraction.}, journal = {Oecologia}, volume = {191}, number = {1}, pages = {241-252}, pmid = {31352635}, issn = {1432-1939}, mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; Ecosystem ; Forestry ; Sweden ; *Trees ; *Wood ; }, abstract = {Emulation of natural disturbances is often regarded as a key measure to make forestry biodiversity-oriented. Consequently, extraction of logging residues is assumed to have little negative effect in comparison to extraction of dead wood mainly formed at natural disturbances. This is consistent with the evolutionary species pool hypothesis, which suggests that most species are evolutionary adapted to the naturally most abundant habitats. We tested this hypothesis for dead-wood-dependent macrofungi, lichens, and beetles in a boreal forest landscape in central Sweden, assuming that species are adapted to conditions similar to today's unmanaged forest. No occurrence patterns, for the species groups which we investigated, were consistent with the hypothesis. Overall, stumps and snags had the highest habitat quality (measured as average population density with equal weight given to each species) and fine woody debris the lowest, which was unexpected, since stumps were the rarest dead-wood type in unmanaged forest. We conclude that the evolutionary species pool concept did not explain patterns of species' occurrences, and for two reasons, the concept is not reliable as a general rule of thumb: (1) what constitute habitats harbouring different species communities can only be understood from habitat-specific studies and (2) the suitability of habitats is affected by their biophysical characteristics. Thus, emulation of natural disturbances may promote biodiversity, but empirical studies are needed for each habitat to understand how natural disturbances should be emulated. We also conclude that stump extraction for bioenergy is associated with larger risks for biodiversity than fine woody debris extraction.}, } @article {pmid31314770, year = {2019}, author = {Pradhan, N and Sharma, AN and Sherchan, AM and Chhetri, S and Shrestha, P and Kilpatrick, CW}, title = {Further assessment of the Genus Neodon and the description of a new species from Nepal.}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0219157}, pmid = {31314770}, issn = {1932-6203}, mesh = {Animals ; Arvicolinae/anatomy & histology/*classification/genetics ; Cytochromes b/genetics ; DNA/genetics ; Discriminant Analysis ; Ecosystem ; Evolution, Molecular ; Female ; Genetic Variation ; Male ; Molar/anatomy & histology ; Nepal ; Phylogeny ; Species Specificity ; }, abstract = {Recent molecular systematic studies of arvicoline voles of the genera Neodon, Lasiopodomys, Phaiomys, and Microtus from Central Asia suggest the inclusion of Phaiomys leucurus, Microtus clarkei, and Lasiopodomys fuscus into Neodon and moving Neodon juldaschi into Microtus (Blanfordimys). In addition, three new species of Neodon (N. linzhiensis, N. medogensis, and N. nyalamensis) have recently been described from Tibet. Analyses of concatenated mitochondrial (Cytb, COI) and nuclear (Ghr, Rbp3) genes recovered Neodon as a well-supported monophyletic clade including all the recently described and relocated species. Kimura-2-parameter distance between Neodon from western Nepal compared to N. sikimensis (K2P = 13.1) and N. irene (K2P = 13.4) was equivalent to genetic distances observed between recognized species of this genus. The specimens sampled from western Nepal were recovered sister to N. sikimensis in the concatenated analysis. However, analyses conducted exclusively with mitochondrial loci did not support this relationship. The occlusal patterns of the first lower (m1) and third upper (M3) molars were simpler in specimens from western Nepal in comparison to N. sikimensis from eastern Nepal and India. Twelve craniodental characters and four external field measurements were examined from specimens of N. sikimensis from eastern Nepal and India, N. irene, and Neodon from western Nepal. Neodon from western Nepal were significantly different from N. sikimensis from eastern Nepal and India in ten out of 16 characters measured and from N. irene for all characters except ear height. Specimens from western Nepal were smaller in size than N. sikimensis from Eastern Nepal and India and larger than N. irene. Together the results of the molecular and morphological analyses indicate that Neodon from western Nepal are distinct under the phylogenetic, genetic and morpho species concepts.}, } @article {pmid31282925, year = {2019}, author = {McKenzie, JL and Chung, DJ and Healy, TM and Brennan, RS and Bryant, HJ and Whitehead, A and Schulte, PM}, title = {Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {925-937}, doi = {10.1093/icb/icz124}, pmid = {31282925}, issn = {1557-7023}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/*physiology ; Fundulidae/genetics/*physiology ; Genetic Speciation ; *Genome ; Genome, Mitochondrial ; Mitochondria/genetics/*physiology ; }, abstract = {The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.}, } @article {pmid31259097, year = {2019}, author = {Jacobs, SJ and Herzog, S and Tank, DC}, title = {Quantifying morphological variation in the Castilleja pilosa species complex (Orobanchaceae).}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7090}, pmid = {31259097}, issn = {2167-8359}, abstract = {Robustly delimited species are of paramount importance, the identification of which relies on our ability to discern boundaries between one species and the next. This is not difficult to do when species are very distinct from one another. However, in recently evolved lineages where putative species may have relatively few diagnostic features (e.g., species complexes composed of very similar species, the boundaries between which are often unclear), defining species boundaries can be more challenging. Hence, the field of species delimitation has widely advocated the use of multiple lines of evidence to delimit species, particularly in species complexes. Excessive taxonomic confusion, often the result of species descriptions that shift through time (e.g., during revisionary work and regional treatments), can further complicate the search for diagnostic features in species complexes. Here, as a first step in robustly delimiting species boundaries, we quantify and describe morphological variation in the Castilleja pilosa species complex. We first infer the morphospace of the species complex and use fuzzy-clustering techniques to explore the morphological variation in the system. Next, we hypothesize the position of type specimens within that morphospace. In so doing, we aim to visualize the impact that regional treatments have had on the conceptualization of taxa through time. We find that there is limited morphological variation among members of this complex, and we determine that the morphological concept of these species have shifted through time and are no longer accurately represented by species descriptions.}, } @article {pmid31255695, year = {2020}, author = {Curry-Hyde, A and Ueberham, U and Arendt, T and Janitz, M}, title = {Neural circular transcriptomes across mammalian species.}, journal = {Genomics}, volume = {112}, number = {2}, pages = {1162-1166}, doi = {10.1016/j.ygeno.2019.06.030}, pmid = {31255695}, issn = {1089-8646}, mesh = {Animals ; Brain/*metabolism ; Conserved Sequence ; *Evolution, Molecular ; Humans ; RNA, Circular/chemistry/*genetics/metabolism ; *Transcriptome ; }, abstract = {Circular RNAs (circRNAs) have recently attracted significant interest in the realm of science and the evolution of species. Given the lack of information available on circRNAs due to various barriers related to sequencing techniques and bioinformatics tools, little regarding their function is known. It has been predicted that circRNAs contribute to gene expression regulation, but aside from a few specific cases, this contention has yet to be proven. Although the role of circRNAs in evolution remains elusive, from the few studies that have shown circRNA conservation in mammalian species, tissue specificity in brain regions, and the abundance of circRNAs in the brains of various species, the concept is becoming more likely with much gravitas. The proposed functional role of circRNAs being gene regulators is of great interest and would provide a basis to further understand not only the functional capabilities of organisms, but also the evolution of mammalian species.}, } @article {pmid31231665, year = {2019}, author = {Guzmán-Verri, C and Suárez-Esquivel, M and Ruíz-Villalobos, N and Zygmunt, MS and Gonnet, M and Campos, E and Víquez-Ruiz, E and Chacón-Díaz, C and Aragón-Aranda, B and Conde-Álvarez, R and Moriyón, I and Blasco, JM and Muñoz, PM and Baker, KS and Thomson, NR and Cloeckaert, A and Moreno, E}, title = {Genetic and Phenotypic Characterization of the Etiological Agent of Canine Orchiepididymitis Smooth Brucella sp. BCCN84.3.}, journal = {Frontiers in veterinary science}, volume = {6}, number = {}, pages = {175}, pmid = {31231665}, issn = {2297-1769}, support = {//Wellcome Trust/United Kingdom ; }, abstract = {Members of the genus Brucella cluster in two phylogenetic groups: classical and non-classical species. The former group is composed of Brucella species that cause disease in mammals, including humans. A Brucella species, labeled as Brucella sp. BCCN84.3, was isolated from the testes of a Saint Bernard dog suffering orchiepididymitis, in Costa Rica. Following standard microbiological methods, the bacterium was first defined as "Brucella melitensis biovar 2." Further molecular typing, identified the strain as an atypical "Brucella suis." Distinctive Brucella sp. BCCN84.3 markers, absent in other Brucella species and strains, were revealed by fatty acid methyl ester analysis, high resolution melting PCR and omp25 and omp2a/omp2b gene diversity. Analysis of multiple loci variable number of tandem repeats and whole genome sequencing demonstrated that this isolate was different from the currently described Brucella species. The smooth Brucella sp. BCCN84.3 clusters together with the classical Brucella clade and displays all the genes required for virulence. Brucella sp. BCCN84.3 is a species nova taxonomical entity displaying pathogenicity; therefore, relevant for differential diagnoses in the context of brucellosis. Considering the debate on the Brucella species concept, there is a need to describe the extant taxonomical entities of these pathogens in order to understand the dispersion and evolution.}, } @article {pmid31227902, year = {2019}, author = {Darienko, T and Kang, W and Orzechowski, AK and Pröschold, T}, title = {Pleurastrosarcina terriformae, a new species of a rare desert trebouxiophycean alga discovered by an integrative approach.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {5}, pages = {573-586}, pmid = {31227902}, issn = {1433-4909}, mesh = {Chlorophyta/classification/*genetics ; DNA Barcoding, Taxonomic ; *Desert Climate ; Microsatellite Repeats ; Phylogeny ; Soil ; }, abstract = {Biological soil crusts of extreme habitats (semi-deserts and deserts) are dominated by cyanobacteria and microalgae. The most abundant taxa are green algae belonging to the classes Chlorophyceae and Trebouxiophyceae. Specimens with sarcinoid-like morphology (cells arranged in packages) represent one group of these microalgae. The genus Pleurastrosarcina consists of two species, which were originally described as Chlorosarcina (P. brevispinosa and P. longispinosa). Both species are exclusively found from arid soils. However, these species were only reported few times and probably overlooked especially if no akinetes were present. During studying soil samples collected from different regions of the Atacama desert (Chile), we isolated two strains, which were morphologically similar to both Pleurastrosarcina species. The phylogenetic analyses confirmed that they belong to this genus. The ITS-2/CBC approach revealed that both new isolates represent a new species, P. terriformae. The comparison with other available strains demonstrated that this new species is not restricted to South America and was also found in coastal area in Europe. The six investigated strains showed a high phenotypic plasticity, which is reflected in the descriptions of several varieties.}, } @article {pmid31209597, year = {2019}, author = {Van Regenmortel, MHV}, title = {Solving the species problem in viral taxonomy: recommendations on non-Latinized binomial species names and on abandoning attempts to assign metagenomic viral sequences to species taxa.}, journal = {Archives of virology}, volume = {164}, number = {9}, pages = {2223-2229}, doi = {10.1007/s00705-019-04320-y}, pmid = {31209597}, issn = {1432-8798}, mesh = {Animals ; *Genome, Viral ; Humans ; Metagenomics ; Phylogeny ; Virus Diseases/*virology ; Viruses/*classification/genetics/isolation & purification ; }, abstract = {Properties useful for defining virus species are phenotypic properties of viruses that can be altered by a few mutations. Such properties include the natural host range, cell and tissue tropism, symptomatology, pathogenicity and mode of transmission. All these properties are not necessarily present in identical form in all the members of a species; therefore, a virus species is a polythetic class of viruses defined by a variable combination of several properties rather than by a single conserved property present in all the members of the species. This review will discuss current controversies about what virus species actually are as well as which names should be given to them. It will be emphasized that most species-defining properties are so-called relational properties that arise because viruses necessarily interact with biological partners such as vectors, hosts and immune systems. Although these relational properties are of utmost importance to laboratory and clinical virologists, they remain unknown if only the viral genome is available and the relational partners of the virus have not yet been identified. Since the International Committee on Taxonomy of Viruses (ICTV) in 2013 ratified a new definition of virus species, which no longer accepts that species are polythetic classes but instead are monophyletic groups, the implications of this new definition for viral taxonomy and nomenclature will be analyzed. In my private capacity, I also make the following recommendations regarding current debates on proposed new names for virus species as well as on the feasibility of assigning viral sequences found in metagenomic databases to individual species taxa in the current ICTV classification. 1) The ICTV should abandon the current rule that the names of virus species (for instance Measles virus) should differ from the virus name (measles virus) only by typography. 2) Non-Latinized binomial species names based on familiar virus and genus names should become the norm. This would obviate the need to create about 5000 hard-to-memorize Latinized species names. 3) Virus species are defined not by the intrinsic properties of virions and viral genomes but by the relational properties of viruses that arise from their interactions with host and vector partners. Since the hosts and vectors associated with nearly all viral sequences found in metagenomic databases are unknown, the phenotypic properties of the putative viruses also remain unknown, and these viral sequences cannot be allocated to established species in the ICTV classification.}, } @article {pmid31196521, year = {2019}, author = {Sundaresan, N and Sahu, AK and Jagan, EG and Pandi, M}, title = {Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota - A pilot study.}, journal = {Fungal biology}, volume = {123}, number = {7}, pages = {517-527}, doi = {10.1016/j.funbio.2019.05.002}, pmid = {31196521}, issn = {1878-6146}, mesh = {Ascomycota/*classification/*genetics ; Base Sequence ; DNA, Fungal/*chemistry/genetics ; DNA, Ribosomal Spacer/*chemistry/genetics ; Evolution, Molecular ; Genetic Variation ; Nucleic Acid Conformation ; *Phylogeny ; Pilot Projects ; Species Specificity ; }, abstract = {Exploring the secondary structure information of nuclear ribosomal internal transcribed spacer 2 (ITS2) has been a promising approach in species delimitation. However, Compensatory base changes (CBC) concept employed in this approach turns futile when CBC is absent. This prompted us to investigate the utility of insertion/deletion (INDELs) and substitutions in fungal delineation at species level. Upon this rationale, 116 strains representing 97 species, belonging to 6 genera (Colletotrichum, Boeremia, Leptosphaeria, Peyronellaea, Plenodomus and Stagonosporopsis) of Ascomycota were retrieved from Q-bank for molecular morphometric analysis. CBC, INDELs and substitutions between the species of their respective genus were recorded. Most species combinations lacked CBC. Among the substitution events, transitions were predominant. INDELs were less frequent than the substitutions. These evolutionary events were mapped upon the helices to discern species specific variation sites. In 68 species unique variation sites were recognised. The remaining 29 species shared absolute similarity with distinctly named species. The variation sites catalogued in them overlapped with other distinct species and resulted in the blurring of species boundaries. Species specific variation sites recognized in this study are the preliminary results and they could be discerned with absolute confidence when larger datasets encompassing all described species of genera were investigated. They could be of potential use in barcoding fungi at species level. This study also concludes that the ITS2 molecular morphometric analysis is an efficient third dimensional study of the fungal species delimitation. This may help to avoid the false positives in species delimitations and to alleviate the challenges in molecular characterization.}, } @article {pmid31189587, year = {2019}, author = {Su, H and Packeu, A and Ahmed, SA and Al-Hatmi, AMS and Blechert, O and İlkit, M and Hagen, F and Gräser, Y and Liu, W and Deng, S and Hendrickx, M and Xu, J and Zhu, M and de Hoog, S}, title = {Species Distinction in the Trichophyton rubrum Complex.}, journal = {Journal of clinical microbiology}, volume = {57}, number = {9}, pages = {}, pmid = {31189587}, issn = {1098-660X}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Humans ; Microbiological Techniques ; Microscopy ; Phylogeny ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tinea/microbiology ; Trichophyton/*classification/genetics/isolation & purification/physiology ; }, abstract = {The Trichophyton rubrum species complex comprises commonly encountered dermatophytic fungi with a worldwide distribution. The members of the complex usually have distinct phenotypes in culture and cause different clinical symptoms, despite high genome similarity. In order to better delimit the species within the complex, molecular, phenotypic, and physiological characteristics were combined to reestablish a natural species concept. Three groups, T. rubrum, T. soudanense, and T. violaceum, could be distinguished based on the sequence of the internal transcribed spacer (ITS) ribosomal DNA barcode gene. On average, strains within each group were similar by colony appearance, microscopy, and physiology, but strains between groups showed significant differences. Trichophyton rubrum strains had higher keratinase activity, whereas T. violaceum strains tended to be more lipophilic; however, none of the phenotypic features were diagnostic. The results of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and amplified fragment length polymorphism (AFLP) were partially consistent with the ITS data but failed to distinguish the species unambiguously. Despite their close similarity, T. violaceum, T. soudanense, and T. rubrum can be regarded as independent species with distinct geographical distributions and clinical predilections. Trichophyton soudanense is pheno- and genotypically intermediate between T. rubrum and T. violaceum For routine diagnostics, ITS sequencing is recommended.}, } @article {pmid31182532, year = {2019}, author = {Wagner, L and de Hoog, S and Alastruey-Izquierdo, A and Voigt, K and Kurzai, O and Walther, G}, title = {A Revised Species Concept for Opportunistic Mucor Species Reveals Species-Specific Antifungal Susceptibility Profiles.}, journal = {Antimicrobial agents and chemotherapy}, volume = {63}, number = {8}, pages = {}, pmid = {31182532}, issn = {1098-6596}, mesh = {Amphotericin B/pharmacology ; Antifungal Agents/*pharmacology ; Humans ; Itraconazole/pharmacology ; Microbial Sensitivity Tests/methods ; Mucor/*drug effects ; Mucormycosis/drug therapy/microbiology ; Natamycin/pharmacology ; Nitriles/pharmacology ; Pyridines/pharmacology ; Rhizopus/drug effects ; Species Specificity ; Terbinafine/pharmacology ; Triazoles/pharmacology ; }, abstract = {Recently, the species concept of opportunistic Mucor circinelloides and its relatives has been revised, resulting in the recognition of its classical formae as independent species and the description of new species. In this study, we used isolates of all clinically relevant Mucor species and performed susceptibility testing using the EUCAST reference method to identify potential species-specific susceptibility patterns. In vitro susceptibility profiles of 101 mucoralean strains belonging to the genus Mucor (72), the closely related species Cokeromyces recurvatus (3), Rhizopus (12), Lichtheimia (10), and Rhizomucor (4) to six antifungals (amphotericin B, natamycin, terbinafine, isavuconazole, itraconazole, and posaconazole) were determined. The most active drug for all Mucorales was amphotericin B. Antifungal susceptibility profiles of pathogenic Mucor species were specific for isavuconazole, itraconazole, and posaconazole. The species formerly united in M. circinelloides showed clear differences in their antifungal susceptibilities. Cokeromyces recurvatus, Mucor ardhlaengiktus, Mucor lusitanicus (M. circinelloides f. lusitanicus), and Mucor ramosissimus exhibited high MICs to all azoles tested. Mucor indicus presented high MICs for isavuconazole and posaconazole, and Mucor amphibiorum and Mucor irregularis showed high MICs for isavuconazole. MIC values of Mucor spp. for posaconazole, isavuconazole, and itraconazole were high compared to those for Rhizopus and the Lichtheimiaceae (Lichtheimia and Rhizomucor). Molecular identification combined with in vitro susceptibility testing is recommended for Mucor species, especially if azoles are applied in treatment.}, } @article {pmid31181921, year = {2019}, author = {Nothias-Esposito, M and Nothias, LF and Da Silva, RR and Retailleau, P and Zhang, Z and Leyssen, P and Roussi, F and Touboul, D and Paolini, J and Dorrestein, PC and Litaudon, M}, title = {Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation.}, journal = {Journal of natural products}, volume = {82}, number = {6}, pages = {1459-1470}, doi = {10.1021/acs.jnatprod.8b00916}, pmid = {31181921}, issn = {1520-6025}, mesh = {Chikungunya Fever ; Chikungunya virus/*drug effects ; Crystallography, X-Ray ; Diterpenes/*chemistry/isolation & purification/*pharmacology ; Esters/chemistry/pharmacology ; Euphorbia/*chemistry ; Molecular Structure ; Virus Replication/*drug effects ; }, abstract = {The species Euphorbia pithyusa and Euphorbia cupanii are two closely related Mediterranean spurges for which their taxonomic relationships are still being debated. Herein, the diterpene ester content of E. cupanii was investigated using liquid chromatography coupled to tandem mass spectrometry. The use of molecular networking coupled to unsupervised substructure annotation (MS2LDA) indicated the presence of new premyrsinane/myrsinane diterpene esters in the E. cupanii fractions. A structure-guided isolation procedure yielded 16 myrsinane (11a-h, 12, and 13) and premyrsinane esters (14a-c and 15a-c), along with four 4β-phorbol esters (16a-c and 17) that showed inhibitory activity against chikungunya virus replication. The structures of the 16 new compounds (11a-c, 11h, 12, 13, 14a-c, 15a-c, 16a-c, and 17) were characterized by NMR spectroscopy and X-ray crystallography. To further uncover the diterpene ester content of these two species, the concept of combinatorial network annotation propagation (C-NAP) was developed. By leveraging the fact that the diterpene esters of Euphorbia species are made up of limited building blocks, a combinatorial database of theoretical structures was created and used for C-NAP that made possible the annotation of 123 premyrsinane or myrsinane esters, from which 74% are not found in any compound database.}, } @article {pmid31180508, year = {2020}, author = {Chambers, EA and Hillis, DM}, title = {The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa.}, journal = {Systematic biology}, volume = {69}, number = {1}, pages = {184-193}, doi = {10.1093/sysbio/syz042}, pmid = {31180508}, issn = {1076-836X}, mesh = {Animals ; Classification/*methods ; Phylogeny ; *Phylogeography ; Snakes/classification/genetics ; }, abstract = {Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.}, } @article {pmid31179175, year = {2019}, author = {Jablonski, D and Kukushkin, OV and Avcı, A and Bunyatova, S and Kumlutaş, Y and Ilgaz, Ç and Polyakova, E and Shiryaev, K and Tuniyev, B and Jandzik, D}, title = {The biogeography of Elaphe sauromates (Pallas, 1814), with a description of a new rat snake species.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6944}, pmid = {31179175}, issn = {2167-8359}, abstract = {BACKGROUND: The rat snake genus Elaphe once comprised several dozens of species distributed in temperate through tropical zones of the New and Old World. Based on molecular-genetic analyses in early 2000s, the genus was split into several separate genera, leaving only 15 Palearctic and Oriental species as its members. One of the three species also occurring in Europe is Elaphe sauromates, a robust snake from the Balkans, Anatolia, Caucasus, Ponto-Caspian steppes, and Levant that has been suspected to be composed of two or more genetically diverse populations. Here, we studied the genetic structure and morphological variation of E. sauromates, aiming to better understand its inter-population relationships and biogeography, and subsequently revise its taxonomy.

METHODS: We reconstructed the phylogeography and analyzed the genetic structure of E. sauromates populations originating from most of its geographic range using both mitochondrial (COI, ND4) and nuclear (C-MOS, MC1R, PRLR, RAG1) DNA gene fragments. We employed Maximum likelihood and Bayesian inference methods for the phylogenetic tree reconstructions, supplemented with species delimitation methods, analysis of haplotype networks, and calculation of uncorrected p-distances. Morphological variation in 15 metric and 18 meristic characters was studied using parametric univariate tests as well as multivariate general linearized models. In total, we analyzed sequences originating from 63 specimens and morphological data from 95 specimens of E. sauromates sensu lato.

RESULTS: The molecular phylogeny identified two clearly divergent sister lineages within E. sauromates, with both forming a lineage sister to E. quatuorlineata. The genetic distance between them (5.80-8.24% in mtDNA) is similar to the distances among several other species of the genus Elaphe. Both lineages are also moderately morphologically differentiated and, while none of the characters are exclusively diagnostic, their combination can be used for confident lineage identification. Here, following the criteria of genetic and evolutionary species concepts, we describe the lineage from eastern Anatolia and parts of the Lesser and Great Caucasus as a new species E. urartica sp. nov.

DISCUSSION: Elaphe urartica sp. nov. represents a cryptic species whose ancestors presumably diverged from their common ancestor with E. sauromates around the Miocene-Pliocene boundary. The intraspecific genetic structure indicates that the recent diversity of both species has been predominantly shaped by Pleistocene climatic oscillations, with glacial refugia mainly located in the Balkans, Crimea, and/or Anatolia in E. sauromates and Anatolia and/or the Caucasus in E. urartica sp. nov.}, } @article {pmid31177615, year = {2019}, author = {Williams, MA and O'Grady, J and Ball, B and Carlsson, J and de Eyto, E and McGinnity, P and Jennings, E and Regan, F and Parle-McDermott, A}, title = {The application of CRISPR-Cas for single species identification from environmental DNA.}, journal = {Molecular ecology resources}, volume = {19}, number = {5}, pages = {1106-1114}, doi = {10.1111/1755-0998.13045}, pmid = {31177615}, issn = {1755-0998}, mesh = {Animals ; *Biota ; *Clustered Regularly Interspaced Short Palindromic Repeats ; DNA, Environmental/analysis/*genetics ; Gene Editing/*methods ; Nucleic Acid Amplification Techniques/*methods ; Salmo salar/*classification/*genetics ; Sensitivity and Specificity ; Temperature ; }, abstract = {We report the first application of CRISPR-Cas technology to single species detection from environmental DNA (eDNA). Organisms shed and excrete DNA into their environment such as in skin cells and faeces, referred to as environmental DNA (eDNA). Utilising eDNA allows noninvasive monitoring with increased specificity and sensitivity. Current methods primarily employ PCR-based techniques to detect a given species from eDNA samples, posing a logistical challenge for on-site monitoring and potential adaptation to biosensor devices. We have developed an alternative method; coupling isothermal amplification to a CRISPR-Cas12a detection system. This utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA. We used the target species Salmo salar as a proof-of-concept test of the specificity of the assay among closely related species and to show the assay is successful at a single temperature of 37°C with signal detection at 535 nM. The specific assay, detects at attomolar sensitivity with rapid detection rates (<2.5 hr). This approach simplifies the challenge of building a biosensor device for rapid target species detection in the field and can be easily adapted to detect any species from eDNA samples from a variety of sources enhancing the capabilities of eDNA as a tool for monitoring biodiversity.}, } @article {pmid31157378, year = {2019}, author = {Leszczyńska, J and Grzybkowska, M and Głowacki, Ł and Dukowska, M}, title = {Environmental Variables Influencing Chironomid Assemblages (Diptera: Chironomidae) in Lowland Rivers of Central Poland.}, journal = {Environmental entomology}, volume = {48}, number = {4}, pages = {988-997}, doi = {10.1093/ee/nvz057}, pmid = {31157378}, issn = {1938-2936}, mesh = {Animals ; Bayes Theorem ; *Chironomidae ; Ecosystem ; Environmental Monitoring ; Poland ; *Rivers ; }, abstract = {Chironomids (Diptera: Chironomidae) are a family of dipterans with a global distribution. Owing to their great functional diversity and ability to adapt to a wide range of environmental conditions, they often dominate in freshwater macroinvertebrate communities, playing a key role in the cycling of organic matter and the flow of energy in aquatic ecosystems. Our aim was to analyze the structure of chironomid assemblages and identify the environmental factors, including current velocity, river width, water depth, water temperature, dissolved oxygen, percentage of substrate covered by vascular plants, inorganic bottom substrate, and quantity of benthic (BPOM) and transported (TPOM) particulate organic matter, that underpin variation in species richness across a set of lowland rivers in central Poland, differing by stream order and abiotic parameters. Using an Information Theoretic Approach, we formulated a set of alternative models based on previously published work, with models fitted in a Bayesian framework using Integrated Nested Laplace Approximation. The species richness of chironomids increased with river order, achieving a maximum in third and fourth order rivers, but decreased at higher orders. The best-fitting models included a positive effect of inorganic substrate index and dissolved oxygen on chironomid species richness. The quality structure of chironomid assemblages reflected the assumptions of the River Continuum Concept showing that species richness was under the influence of factors operating at both a micro- (inorganic bottom substrate) and macro-scale (dissolved oxygen).}, } @article {pmid31152554, year = {2019}, author = {Li, M and Zhao, H and Zhao, F and Jiang, L and Peng, H and Zhang, W and Simmons, MP}, title = {Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae).}, journal = {Annals of botany}, volume = {124}, number = {2}, pages = {233-243}, pmid = {31152554}, issn = {1095-8290}, mesh = {*Corydalis ; DNA, Ribosomal Spacer ; Nucleic Acid Conformation ; *Papaveraceae ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND AND AIMS: Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models.

METHODS: We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing.

KEY RESULTS: Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models.

CONCLUSIONS: Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.}, } @article {pmid31147849, year = {2019}, author = {Lazarowski, L and Goodman, A and Galizio, M and Bruce, K}, title = {Effects of set size on identity and oddity abstract-concept learning in rats.}, journal = {Animal cognition}, volume = {22}, number = {5}, pages = {733-742}, doi = {10.1007/s10071-019-01270-5}, pmid = {31147849}, issn = {1435-9456}, mesh = {Animals ; *Concept Formation ; *Discrimination Learning ; Learning ; Rats ; Transfer, Psychology ; }, abstract = {Match (MTS) and non-match-to-sample (NMTS) procedures are used to assess concepts of identity and oddity across species and are measured by transfer performance to novel stimuli. The number of exemplars used in training (set size) has been shown to affect learning with evidence of larger set sizes promoting concept learning in several species. The present study explored the effects of set size and procedure on concept learning in rats using olfactory stimuli. Concept learning was assessed for 20 rats via transfer tests consisting of novel stimuli after rats were initially trained to either MTS or NMTS with two or ten stimuli as exemplars. No difference was found in acquisition or transfer between MTS and NMTS, but rats trained with ten stimuli performed better on novel transfer tests than rats trained with two. When set size was expanded for rats originally trained with two stimuli and rats were re-tested with ten novel stimuli, performance showed full transfer demonstrating that training with multiple exemplars facilitates concept learning.}, } @article {pmid31143925, year = {2019}, author = {Hundsdoerfer, AK and Lee, KM and Kitching, IJ and Mutanen, M}, title = {Genome-wide SNP Data Reveal an Overestimation of Species Diversity in a Group of Hawkmoths.}, journal = {Genome biology and evolution}, volume = {11}, number = {8}, pages = {2136-2150}, pmid = {31143925}, issn = {1759-6653}, mesh = {Animals ; *Evolution, Molecular ; *Genome ; Metagenomics/*methods ; Moths/*classification/*genetics ; Phylogeny ; *Polymorphism, Single Nucleotide ; Species Specificity ; }, abstract = {The interface between populations and evolving young species continues to generate much contemporary debate in systematics depending on the species concept(s) applied but which ultimately reduces to the fundamental question of "when do nondiscrete entities become distinct, mutually exclusive evolutionary units"? Species are perceived as critical biological entities, and the discovery and naming of new species is perceived by many authors as a major research aim for assessing current biodiversity before much of it becomes extinct. However, less attention is given to determining whether these names represent valid biological entities because this is perceived as both a laborious chore and an undesirable research outcome. The charismatic spurge hawkmoths (Hyles euphorbiae complex, HEC) offer an opportunity to study this less fashionable aspect of systematics. To elucidate this intriguing systematic challenge, we analyzed over 10,000 ddRAD single nucleotide polymorphisms from 62 individuals using coalescent-based and population genomic methodology. These genome-wide data reveal a clear overestimation of (sub)species-level diversity and demonstrate that the HEC taxonomy has been seriously oversplit. We conclude that only one valid species name should be retained for the entire HEC, namely Hyles euphorbiae, and we do not recognize any formal subspecies or other taxonomic subdivisions within it. Although the adoption of genetic tools has frequently revealed morphologically cryptic diversity, the converse, taxonomic oversplitting of species, is generally (and wrongly in our opinion) accepted as rare. Furthermore, taxonomic oversplitting is most likely to have taken place in intensively studied popular and charismatic organisms such as the HEC.}, } @article {pmid31139008, year = {2019}, author = {Petrželová, I and Sochor, M}, title = {How useful is the current species recognition concept for the determination of true morels? Insights from the Czech Republic.}, journal = {MycoKeys}, volume = {52}, number = {}, pages = {17-43}, pmid = {31139008}, issn = {1314-4049}, abstract = {The phylogentic diversity of the genus Morchella has only been sporadically studied in Central Europe. In this study, a molecular taxonomic revision of the Morchella species of the Czech Republic was performed using available fungarium specimens, fresh collections, and axenic cultures. Molecular phylogenetic analyses based on either ITS or five-locus (ITS, LSU, RPB1, RPB2, and EF-1α) sequencing and the application of principles of the genealogical concordance phylogenetic species recognition (GCPSR) have revealed the occurrence of 11 phylogenetic species in the region, but only six of them could be assigned unequivocally to the previously published phylospecies: Mel-3 (M.semilibera), Mel-10 (M.importuna), Mel-19 (M.eohespera), Mes-4 (M.americana), Mes-5 and Mes-8 (M.esculenta). One lineage was identified as a new phylospecies and is designated as Mel-39. Four lineages grouped together with two or more previously published phylospecies: Mel-13/26 (M.deliciosa), Mel-15/16 (M.angusticeps / M.eximioides), Mel-20/34 (M.purpurascens), and Mel-23/24/31/32 (M.pulchella). Our phylogenetic analyses and literature review shed light on the pitfalls of current molecular taxonomy of morels and highlight the ambiguities of present species recognition concepts. The main source of the problems seems to be rooted in the application of different methods (multigene vs single-gene sequencing, phenotypic determination) and approaches (monophyly vs paraphyly, the application or not of GCPSR, degree of differentiation between accepted species, etc.) by various authors for the delimitation of new phylospecies. Therefore, we propose five criteria for distinguishing new phylospecies in the genus Morchella based on molecular data, and recommend a more conservative approach in species delimitation.}, } @article {pmid31114737, year = {2019}, author = {Palazzolo, MA and Postemsky, PD and Kurina-Sanz, M}, title = {From agro-waste to tool: biotechnological characterization and application of Ganoderma lucidum E47 laccase in dye decolorization.}, journal = {3 Biotech}, volume = {9}, number = {6}, pages = {213}, pmid = {31114737}, issn = {2190-572X}, abstract = {The culture of fungal species from agro-waste allows for the sustainable preparation of valuable biotechnological products and contributes to establish the Circular Economy concept. The Ganoderma lucidum species is well known as producer of laccases (EC 1.10.3.2), which serves as a tool to oxidize chemicals. When producing G. lucidum E47 basidiomes with edible purposes out of rice crop residues, its laccase remains as by-product. In this work, we report the biotechnological characterization and application of the laccase recovered from spent cultures of the G. lucidum E47 strain. We detected at least one polypeptide (ca. 59 kDa) which displays attractive activity and stability values when used in the range of 18-45 °C in mildly acidic environment (pH 4.8-5.8). These parameters can be enhanced in the presence of organic cosolvents such as butyl acetate and methyl iso-butyl ketone, but the opposite effect is observed with solvents of lower log P. The best activity-stability performance is reached when the biocatalyst is used in pH 4.8 buffer with 5% (v/v) butyl acetate at 37 °C. The laccase was capable of decolorizing xanthene, azo and triarylmethane dyes, exhibiting excellent selectivity on bromocresol green and bromocresol purple. Furthermore, the biocatalyst displayed an attractive activity when assessed for the decolorization of bromocresol green in a proof-of-concept effluent biotreatment.}, } @article {pmid31106730, year = {2019}, author = {Haelewaters, D and Boer, P and Báthori, F and Rádai, Z and Reboleira, ASPS and Tartally, A and Pfliegler, WP and De Kesel, A and Nedvěd, O}, title = {Studies of Laboulbeniales on Myrmica ants (IV): host-related diversity and thallus distribution patterns of Rickia wasmannii.}, journal = {Parasite (Paris, France)}, volume = {26}, number = {}, pages = {29}, pmid = {31106730}, issn = {1776-1042}, mesh = {Animals ; Ants/*microbiology ; Ascomycota/*physiology ; *Host-Parasite Interactions ; Hungary ; Mycoses ; Phylogeny ; }, abstract = {Fungal species identities are often based on morphological features, but current molecular phylogenetic and other approaches almost always lead to the discovery of multiple species in single morpho-species. According to the morphological species concept, the ant-parasitic fungus Rickia wasmannii (Ascomycota, Laboulbeniales) is a single species with pan-European distribution and a wide host range. Since its description, it has been reported from ten species of Myrmica (Hymenoptera, Formicidae), of which two belong to the rubra-group and the other eight to the phylogenetically distinct scabrinodis-group. We found evidence for R. wasmannii being a single phylogenetic species using sequence data from two loci. Apparently, the original morphological description (dating back to 1899) represents a single phylogenetic species. Furthermore, the biology and host-parasite interactions of R. wasmannii are not likely to be affected by genetic divergence among different populations of the fungus, implying comparability among studies conducted on members of different ant populations. We found no differences in total thallus number on workers between Myrmica species, but we did observe differences in the pattern of thallus distribution over the body. The locus of infection is the frontal side of the head in Myrmica rubra and M. sabuleti whereas in M. scabrinodis the locus of infection differs between worker ants from Hungary (gaster tergites) and the Netherlands (frontal head). Possible explanations for these observations are differences among host species and among populations of the same species in (i) how ant workers come into contact with the fungus, (ii) grooming efficacy, and (iii) cuticle surface characteristics.}, } @article {pmid31106407, year = {2019}, author = {Kahlert, M and Kelly, MG and Mann, DG and Rimet, F and Sato, S and Bouchez, A and Keck, F}, title = {Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta).}, journal = {Journal of phycology}, volume = {55}, number = {4}, pages = {948-970}, doi = {10.1111/jpy.12886}, pmid = {31106407}, issn = {1529-8817}, mesh = {*Diatoms ; Genes, Chloroplast ; Genetic Markers ; Phylogeny ; }, abstract = {This paper explores the diversity and taxonomy of species within Fragilaria sensu stricto, an abundant and ecologically important diatom genus, taking advantage of cultured and DNA-barcoded material. The goal is to facilitate the identification of European taxa within this complex, providing a unified view on morphological and molecular diversity. There is a general agreement that the separation of species within the group of Fragilaria is difficult because morphological descriptions of species are not consistent between authorities, ongoing taxonomic revisions have resulted in species described with standards of the late 20th and 21st centuries alongside descriptions based on 19th century (light microscopical) criteria, and because not all diagnostic characters can be seen in all specimens encountered in routine analyses. Consequent confusion could blur potentially important ecological distinctions between species. Our study demonstrated that some species defined on morphological criteria could be confirmed using the rbcL chloroplast gene as a genetic marker, for example, Fragilaria gracilis, Fragilaria tenera, Fragilaria perminuta, and Fragilaria subconstricta. However, even for those species, preliminary identifications based on morphology often differed from identifications based on phylogenetic clustering combined with detailed morphological study. Clades were well-defined by rbcL, but based on morphology, the terminal taxa of these clades did not match the currently described Fragilaria species. To clarify recognition of these taxa, we describe three new species: Fragilaria agnesiae, Fragilaria heatherae, and Fragilaria joachimii.}, } @article {pmid31098690, year = {2019}, author = {Brasch, J and Gläser, R}, title = {[Dynamic diversity of dermatophytes].}, journal = {Der Hautarzt; Zeitschrift fur Dermatologie, Venerologie, und verwandte Gebiete}, volume = {70}, number = {8}, pages = {575-580}, pmid = {31098690}, issn = {1432-1173}, mesh = {Arthrodermataceae/*classification/genetics/isolation & purification ; Classification/*methods ; Dermatomycoses/*diagnosis ; Humans ; Mycological Typing Techniques ; Mycology/*methods ; *Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Many dermatologists do not understand the perpetual adjustments in the dermatophyte nomenclature.

OBJECTIVES: The aim is to explain the background and the development of methods that have led to previous and current changes of dermatophyte taxonomy and to the detection of new dermatophytes.

METHODS: In this article we evaluate the recent literature on this topic and our own results in the fields of dermatophyte identification, their detection, and of the associated taxonomic developments.

RESULTS: Today, the phylogenetic species concept is the basis of taxonomic classification, including that of dermatophytes. Genetic techniques have decisively advanced this and are state of the art nowadays. The detection of new dermatophyte species was often triggered by clinical observations and by morphologically conspicuous cultures that prompted their subsequent exact mycological characterization. Even today not all species of dermatophytes are unequivocally defined.

CONCLUSIONS: By exclusively using selected genetic characteristics for the construction of phylogenetic trees additional taxonomically relevant features are neglected. Therefore it is necessary to better integrate data derived from morphologic, physiologic, ecologic and pathophysiologic observations into phylogenetic analyses. Dermatologists are still asked to contribute such information.}, } @article {pmid31096128, year = {2019}, author = {Van den Brink, PJ and Buijert-de Gelder, DM and Brock, TCM and Roessink, I and Focks, A}, title = {Exposure pattern-specific species sensitivity distributions for the ecological risk assessments of insecticides.}, journal = {Ecotoxicology and environmental safety}, volume = {180}, number = {}, pages = {252-258}, doi = {10.1016/j.ecoenv.2019.05.022}, pmid = {31096128}, issn = {1090-2414}, mesh = {Animals ; Chlorpyrifos/toxicity ; Environmental Exposure ; Insecticides/*toxicity ; Neonicotinoids/toxicity ; Nitriles/toxicity ; Nitro Compounds/toxicity ; Pyrethrins/toxicity ; Risk Assessment ; Species Specificity ; }, abstract = {In the higher tiers of pesticide risk assessment, the Species Sensitivity Distribution (SSD) concept is often used to establish the effect threshold defined as the concentration protecting 95% of the species (Hazardous Concentration 5%, HC5). The toxicity data included in SSDs are normally established using a constant exposure regime. However, the exposure of pesticides in the field is often characterised by a variable exposure regime. Toxicokinetic-toxicodynamic (TKTD) models can be used to extrapolate the toxic effects of a chemical to a specific, time-variable exposure regime. The aim of this paper was to develop Exposure Pattern Specific SSDs (EPS-SSDs) for three insecticides using TKTD models and to compare the HC5 of different exposure patterns with the same time-weighted average concentration to evaluate whether the use of EPS-SSDs would change the outcome of the ecological risk assessment. The EPS-SSDs were developed by estimating TKTD parameters for the compounds chlorpyrifos, imidacloprid and lambda-cyhalothrin using results from standard, 96 h, single species tests. These parameter estimates were used for TKTD modelling to determine toxicity thresholds (e.g. LC10 and LC50) for contrasting exposure patterns after certain evaluation times (4, 10 or 100 days). HC5 values were constructed with TKTD-predicted LC10- and LC50- values for different exposure patterns characterised by similar time-weighted average concentrations. Differences between those HC5 values ranged from a factor 1 to a factor 2.3 for the short evaluation period (4 d). This difference was smaller when using an evaluation period of 10 days instead of 4 days and selecting the TKTD-predicted LC10 instead of TKTD-predicted LC50 based HC5s. For the long term evaluation period (100 d), a maximum difference of a factor of 30 was found.}, } @article {pmid31059905, year = {2019}, author = {Ratier, A and Lopes, C and Labadie, P and Budzinski, H and Delorme, N and Quéau, H and Peluhet, L and Geffard, O and Babut, M}, title = {A Bayesian framework for estimating parameters of a generic toxicokinetic model for the bioaccumulation of organic chemicals by benthic invertebrates: Proof of concept with PCB153 and two freshwater species.}, journal = {Ecotoxicology and environmental safety}, volume = {180}, number = {}, pages = {33-42}, doi = {10.1016/j.ecoenv.2019.04.080}, pmid = {31059905}, issn = {1090-2414}, mesh = {Amphipoda/*drug effects/metabolism ; Animals ; Bayes Theorem ; Chironomidae/*drug effects/metabolism ; Fresh Water/*chemistry ; Geologic Sediments/*chemistry ; Larva/drug effects/metabolism ; Models, Theoretical ; Polychlorinated Biphenyls/metabolism/*toxicity ; Toxicokinetics ; Water Pollutants, Chemical/metabolism/*toxicity ; }, abstract = {Toxicokinetic (TK) models are relevant and widely used to predict chemical concentrations in biological organisms. The importance of dietary uptake for aquatic invertebrates has been increasingly assessed in recent years. However, the model parameters are estimated on limited specific laboratory data sets that are bounded by several uncertainties. The aim of this study was to implement a Bayesian framework for simultaneously estimating the parameters of a generic TK model for benthic invertebrate species from all data collected. We illustrate our approach on the bioaccumulation of PCB153 by two species with different life traits and therefore exposure routes: Chironomus riparius larvae exposed to spiked sediment for 7 days and Gammarus fossarum exposed to spiked sediment and/or leaves for 7 days and then transferred to a clean media for 7 more days. The TK models assuming first-order kinetics were fitted to the data using Bayesian inference. The median model predictions and their 95% credibility intervals showed that the model fit the data well. From a methodological point of view, this paper illustrates that simultaneously estimating all model parameters from all available data by Bayesian inference, while considering the correlation between parameters and different types of data, is a real added value for TK modeling. Moreover, we demonstrated the ability of a generic TK model considering uptake and elimination routes as modules to add according to the availability of the data measured. From an ecotoxicological point of view, we show differences in PCB153 bioaccumulation between chironomids and gammarids, explained by the different life traits of these two organisms.}, } @article {pmid31057520, year = {2019}, author = {Eriksson, P and Lindskog, C and Lorente-Leal, V and Waldenström, J and González-Acuna, D and Järhult, JD and Lundkvist, Å and Olsen, B and Jourdain, E and Ellström, P}, title = {Attachment Patterns of Human and Avian Influenza Viruses to Trachea and Colon of 26 Bird Species - Support for the Community Concept.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {815}, pmid = {31057520}, issn = {1664-302X}, abstract = {Avian influenza A viruses (AIVs) have a broad host range, but are most intimately associated with waterfowl (Anseriformes) and, in the case of the H13 and H16 subtypes, gulls (Charadriiformes). Host associations are multifactorial, but a key factor is the ability of the virus to bind host cell receptors and thereby initiate infection. The current study aims at investigating the tissue attachment pattern of a panel of AIVs, comprising H3N2, H6N1, H12N5, and H16N3, to avian trachea and colon tissue samples obtained from host species of different orders. Virus attachment was not restricted to the bird species or order from which the virus was isolated. Instead, extensive virus attachment was observed to several distantly related avian species. In general, more virus attachment and receptor expression were observed in trachea than in colon samples. Additionally, a human seasonal H3N2 virus was studied. Unlike the studied AIVs, this virus mainly attached to tracheae from Charadriiformes and a very limited set of avian cola. In conclusion, the reported results highlight the importance of AIV attachment to trachea in many avian species. Finally, the importance of chickens and mallards in AIVs dynamics was illustrated by the abundant AIV attachment observed.}, } @article {pmid31043629, year = {2019}, author = {Korshunova, T and Picton, B and Furfaro, G and Mariottini, P and Pontes, M and Prkić, J and Fletcher, K and Malmberg, K and Lundin, K and Martynov, A}, title = {Multilevel fine-scale diversity challenges the 'cryptic species' concept.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6732}, pmid = {31043629}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Gastropoda/anatomy & histology/*classification/*genetics/ultrastructure ; *Genetic Speciation ; Genetic Variation ; Phylogeny ; Species Specificity ; }, abstract = {'Cryptic' species are an emerging biological problem that is broadly discussed in the present study. Recently, a cryptic species definition was suggested for those species which manifest low morphological, but considerable genetic, disparity. As a case study we present unique material from a charismatic group of nudibranch molluscs of the genus Trinchesia from European waters to reveal three new species and demonstrate that they show a dual nature: on one hand, they can be considered a 'cryptic' species complex due to their overall similarity, but on the other hand, stable morphological differences as well as molecular differences are demonstrated for every species in that complex. Thus, this species complex can equally be named 'cryptic', 'pseudocryptic' or 'non-cryptic'. We also present evidence for an extremely rapid speciation rate in this species complex and link the species problem with epigenetics. Available metazoan-wide data, which are broadly discussed in the present study, show the unsuitability of a 'cryptic' species concept because the degree of crypticity represents a continuum when a finer multilevel morphological and molecular scale is applied to uncover more narrowly defined species making the 'cryptic' addition to 'species' redundant. Morphological and molecular methods should be applied in concordance to form a fine-scale multilevel taxonomic framework, and not necessarily implying only an a posteriori transformation of exclusively molecular-based 'cryptic' species into morphologically-defined 'pseudocryptic' ones. Implications of the present study have importance for many fields, including conservation biology and fine-scale biodiversity assessments.}, } @article {pmid31012104, year = {2019}, author = {González-Resendiz, L and Johansen, JR and León-Tejera, H and Sánchez, L and Segal-Kischinevzky, C and Escobar-Sánchez, V and Morales, M}, title = {A bridge too far in naming species: a total evidence approach does not support recognition of four species in Desertifilum (Cyanobacteria).}, journal = {Journal of phycology}, volume = {55}, number = {4}, pages = {898-911}, doi = {10.1111/jpy.12867}, pmid = {31012104}, issn = {1529-8817}, mesh = {*Cyanobacteria ; DNA, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {A population of Desertifilum (Cyanobacteria, Oscillatoriales) from an oligotrophic desertic biotope was isolated and characterized using a polyphasic approach including molecular, morphological, and ecological information. The population was initially assumed to be a new species based on ecological and biogeographic separation from other existing species, however, phylogenetic analyses based on sequences of the 16S rRNA gene and 16S-23S ITS region, placed this strain clearly within the type species, Desertifilum tharense. Comparative analysis of morphology, 16S rRNA gene similarity, 16S-23S ITS secondary structure, and percent dissimilarity of the ITS regions for all characterized strains supports placing the six Desertifilum strains (designated as PD2001/TDC17, UAM-C/S02, CHAB7200, NapGTcm17, IPPAS B-1220, and PMC 872.14) into D. tharense. The recognition of Desertifilum salkalinema and Desertifilum dzianense is not supported, although our analysis does support continued recognition of Desertifilum fontinale. Pragmatic criteria for recognition of closely related species are proposed based on this study and others, and more rigorous review of future taxonomic papers is recommended.}, } @article {pmid30986507, year = {2019}, author = {Fan, X and Xu, W and Han, J and Jiang, X and Wink, M and Wu, G}, title = {Antimicrobial peptide hybrid fluorescent protein based sensor array discriminate ten most frequent clinic isolates.}, journal = {Biochimica et biophysica acta. General subjects}, volume = {1863}, number = {6}, pages = {1158-1166}, doi = {10.1016/j.bbagen.2019.04.010}, pmid = {30986507}, issn = {1872-8006}, mesh = {Anti-Bacterial Agents/*chemistry ; Antimicrobial Cationic Peptides/*chemistry/genetics ; Bacteria/*growth & development/isolation & purification ; Green Fluorescent Proteins/*chemistry/genetics ; Humans ; *Quartz Crystal Microbalance Techniques ; Recombinant Fusion Proteins/*chemistry/genetics ; }, abstract = {Antimicrobial peptides killed bacteria through intercalating into the bacterial membrane. Their antimicrobial efficiencies varied in bacterial species and were affected by ion strength in the culture medium. A recombinant IGP protein consisted of an antimicrobial peptide, Ib-AMP4 fused with the Green Fluorescent Protein was expressed from E. coli cells and was found to maintain the antimicrobial activity. We demonstrated the interaction between the lipid membranes with IGP by quartz crystal microbalance with dissipation and tried to elucidate the effect of calcium ions by lipopolysaccharide monolayer surface isotherm assays. Ten most frequent clinic isolates were subjected to IGP incubation in buffers containing different calcium ion concentrations. The yielded fluorescent intensities ranging from several thousand to several million, differed greatly between species allowing big coefficient of variances that rendered this method a superior reproducibility and resolution. The classification and data treatment were performed by pattern identification with linear discriminant analysis. Seventy-nine isolates of the 10 most frequent clinic species were classified in the blind test with accuracy >70% by a single measurement and with a 100% accuracy by combined measurements for each species. In conclusion, the concept is based on a solid fact that antimicrobial proteins inhibit bacterial growth at a constant minimal inhibitory concentration through intercalating into the biomembrane. The developed method has a good resolution and high-faulty tolerance rate in discriminating bacteria.}, } @article {pmid30976300, year = {2019}, author = {Galtier, N}, title = {Delineating species in the speciation continuum: A proposal.}, journal = {Evolutionary applications}, volume = {12}, number = {4}, pages = {657-663}, pmid = {30976300}, issn = {1752-4571}, abstract = {Delineating species is a difficult and seemingly uninteresting issue that is still essential to address. Taxonomic methodology is heterogeneous according to the taxa and scientists involved due to the disparate data quality and quantity and disagreements over the species concept. This has negative impacts on basic and applied research. Genomic data substantially enhance our understanding of the speciation process but do not provide a ubiquitous solution to the species problem. The relevance of comparative approaches in speciation research has nevertheless recently been demonstrated. I suggest moving towards a more unified taxonomic classification through a reference-based decision procedure.}, } @article {pmid30970025, year = {2019}, author = {Aguado, MT and Capa, M and Lago-Barcia, D and Gil, J and Pleijel, F and Nygren, A}, title = {Species delimitation in Amblyosyllis (Annelida, Syllidae).}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0214211}, pmid = {30970025}, issn = {1932-6203}, mesh = {Animals ; Annelida/*anatomy & histology/classification/genetics ; DNA, Mitochondrial/genetics ; *Phylogeny ; *Phylogeography ; Polychaeta/classification/*genetics ; Species Specificity ; }, abstract = {Amblyosyllis is a worldwide distributed group of annelids mainly found in coastal environments. It is well known among the polychaete specialists mostly because of its notable beauty, showing bright colourful patterns and outstanding long and coiled appendices. Amblyosyllis is a monophyletic genus easy to identify due to its distinct diagnostic features; however, the species and their boundaries are, in most cases, not well defined. Herein, we provide an extensive sample of Amblyosyllis material (115 specimens) from several world geographic areas. We have studied the morphological features of each specimen and photographed them alive. Two mitochondrial DNA markers (COI and 16S) and one nuclear gene fragment (28S, D1 region) were sequenced. We performed phylogenetic analyses based on each DNA partition, as well as the combined data sets, obtaining congruent results. Species delimitation methods such as distance analyses, statistical parsimony networks and multi-rate Poisson tree processes were also applied. The combined results obtained from different methodologies and data sets are used to differentiate between, at least, 19 lineages compatible with the separately evolving meta-populations species concept. Four of these lineages are identified as nominal species, including the type species of Amblyosyllis, A. rhombeata. For three other lineages previously synonymized names are recovered, and seven lineages are described as new species. All of these species are described and supported by appropriate iconography. We recognize several morphological characters useful to identify species of Amblyosyllis, which in some cases should also be combined with molecular methods for species delineation. The genetic divergence in the genus is high, contrary to the morphological homogeneity observed. Two species show a wide geographical distribution, while the rest have a more restricted distribution. There are several examples of species with overlapping distribution patterns.}, } @article {pmid30957604, year = {2019}, author = {Velamala, GR and Naranji, MK and Kondamudi, RB and Netto-Ferreira, AL}, title = {DNA barcoding of commercially important snapper species (Lutjaniformes; Lutjanidae; Lutjanus) from Visakhapatnam, Central Eastern coast of India.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {30}, number = {4}, pages = {585-591}, doi = {10.1080/24701394.2018.1551387}, pmid = {30957604}, issn = {2470-1408}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics/metabolism ; Fishes/*genetics ; Genome, Mitochondrial/genetics ; India ; Phylogeny ; Species Specificity ; }, abstract = {Snappers are commercially important fishes in Indian waters, currently belonging to the order Lutjaniformes, family Lutjanidae. Generally, recognizing species of Lutjanus is a challenging task not only because of overlapping morphological characters, such as shapes, size groups, or colour patterns, but also based on the definition of the species concept or the definition of the threshold for speciation. In India there has not been any updated and accurate study of the genus so far. Besides, identification of the group based on ecological aspects and DNA barcoding tools were confined to limited laboratories. In the present study, ten species of snappers were identified from samples obtained from the major fish landing centres in the Visakhapatnam, Central Eastern coast of India. Snapper species were identified using COI (Cytochrome oxidase I) sequences for DNA barcoding. The validity of the conjecture species-level taxonomy based on COI is assisted with high equivalence search (98-100%) both in BOLD and BLAST, well-distributed genetic distance values.}, } @article {pmid30937430, year = {2019}, author = {Hill, GE}, title = {Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {912-924}, doi = {10.1093/icb/icz019}, pmid = {30937430}, issn = {1557-7023}, mesh = {*Biological Evolution ; Cell Nucleus/*genetics ; Eukaryota/*genetics ; Genetic Introgression ; Genome, Mitochondrial/*genetics ; Genotype ; }, abstract = {The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.}, } @article {pmid30936888, year = {2019}, author = {Gao, YD and Gao, XF and Harris, A}, title = {Species Boundaries and Parapatric Speciation in the Complex of Alpine Shrubs, Rosa sericea (Rosaceae), Based on Population Genetics and Ecological Tolerances.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {321}, pmid = {30936888}, issn = {1664-462X}, abstract = {Discerning species boundaries among closely related taxa is fundamental to studying evolution and biodiversity. However, species boundaries can be difficult to access in plants because ongoing divergence and speciation may leave an evolutionary footprint similar to introgression, which occurs frequently among species and genera. In this study, we sought to determine species boundaries between two closely related alpine shrubs, Rosa sericea and Rosa omeiensis, using population genetics, environmental data and ecological niche modeling, and morphological traits. We analyzed populations of R. sericea and R. omeiensis using genetic markers comprising a fragment of the single-copy nuclear gene, LEAFY, micro-satellites (EST-SSR), and plastid DNA sequences. The DNA sequence data suggested clusters of populations consistent with geography but not with previously proposed species boundaries based on morphology. Nevertheless, we found that the ecological niches of the previously proposed species only partially overlap. Thus, we suspect that these species are in the process of parapatric speciation; that is, differentiating along an ecological gradient, so that they exhibit differing morphology. Morphology has previously been the basis of recognizing the species R. sericea and R. omeiensis, which are the most widely distributed species within a broader R. sericea complex that includes several other narrow endemics. Here, we recognize R. sericea and R. omeiensis as independent species based on morphological and ecological data under the unified species concept, which emphasizes that these data types are of equal value to DNA for determining species boundaries and refining taxonomic treatments. While the DNA data did not delimit species within the R. sericea complex, we expect to develop and utilize new, robust DNA tools for understanding speciation within this group in future studies.}, } @article {pmid30918087, year = {2019}, author = {Joyce, W and White, DW and Raven, PB and Wang, T}, title = {Weighing the evidence for using vascular conductance, not resistance, in comparative cardiovascular physiology.}, journal = {The Journal of experimental biology}, volume = {222}, number = {Pt 6}, pages = {}, doi = {10.1242/jeb.197426}, pmid = {30918087}, issn = {1477-9145}, mesh = {Animals ; *Cardiovascular Physiological Phenomena ; Cardiovascular System ; Hemodynamics ; *Movement ; Physiology, Comparative ; Vascular Resistance/*physiology ; }, abstract = {Vascular resistance and conductance are reciprocal indices of vascular tone that are often assumed to be interchangeable. However, in most animals in vivo, blood flow (i.e. cardiac output) typically varies much more than arterial blood pressure. When blood flow changes at a constant pressure, the relationship between conductance and blood flow is linear, whereas the relationship between resistance and blood flow is non-linear. Thus, for a given change in blood flow, the change in resistance depends on the starting point, whereas the attendant change in conductance is proportional to the change in blood flow regardless of the starting conditions. By comparing the effects of physical activity at different temperatures or between species - concepts at the heart of comparative cardiovascular physiology - we demonstrate that the difference between choosing resistance or conductance can be marked. We also explain here how the ratio of conductance in the pulmonary and systemic circulations provides a more intuitive description of cardiac shunt patterns in the reptilian cardiovascular system than the more commonly used ratio of resistance. Finally, we posit that, although the decision to use conductance or resistance should be made on a case-by-case basis, in most circumstances, conductance is a more faithful portrayal of cardiovascular regulation in vertebrates.}, } @article {pmid33267027, year = {2019}, author = {Feng, J and Liu, Z and Feng, H and Sutcliffe, RFE and Liu, J and Han, J}, title = {A New Phylogenetic Inference Based on Genetic Attribute Reduction for Morphological Data.}, journal = {Entropy (Basel, Switzerland)}, volume = {21}, number = {3}, pages = {}, pmid = {33267027}, issn = {1099-4300}, abstract = {To address the instability of phylogenetic trees in morphological datasets caused by missing values, we present a phylogenetic inference method based on a concept decision tree (CDT) in conjunction with attribute reduction. First, a reliable initial phylogenetic seed tree is created using a few species with relatively complete morphological information by using biologists' prior knowledge or by applying existing tools such as MrBayes. Second, using a top-down data processing approach, we construct concept-sample templates by performing attribute reduction at each node in the initial phylogenetic seed tree. In this way, each node is turned into a decision point with multiple concept-sample templates, providing decision-making functions for grafting. Third, we apply a novel matching algorithm to evaluate the degree of similarity between the species' attributes and their concept-sample templates and to determine the location of the species in the initial phylogenetic seed tree. In this manner, the phylogenetic tree is established step by step. We apply our algorithm to several datasets and compare it with the maximum parsimony, maximum likelihood, and Bayesian inference methods using the two evaluation criteria of accuracy and stability. The experimental results indicate that as the proportion of missing data increases, the accuracy of the CDT method remains at 86.5%, outperforming all other methods and producing a reliable phylogenetic tree.}, } @article {pmid30886774, year = {2019}, author = {Buck, T and Bruchmann, I and Zumstein, P and Drees, C}, title = {Just a small bunch of flowers: the botanical knowledge of students and the positive effects of courses in plant identification at German universities.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6581}, pmid = {30886774}, issn = {2167-8359}, abstract = {BACKGROUND: In the light of the ongoing loss of species the knowledge about and the ability to identify species becomes increasingly important for effective monitoring and conservation measures. Learning about identifying biodiversity is a central task for future biologists and biology teachers and universities play an important role in educating future experts and multipliers. It builds one basis for conservation literacy.

METHODS: We analyzed undergraduate students' prior knowledge on plant species, identification and their knowledge gain from introductory plant identification courses at eight German universities. Using the Visual Classification Method-a combination of a presentation and standardized questionnaires-we evaluated the learning success of more than 500 students regarding (a) 'declarative species knowledge' of plant species names and (b) 'taxonomic concept knowledge', which is seen as knowledge on a higher level of complexity. From comparison of paired pre- and post-tests we calculated the individual knowledge gain. Using Linear Mixed Effects Models (LMMs) we analyzed effects of knowledge levels, learner-specific resources and learning environment on the knowledge gain.

RESULTS: We found that university course instructors have to start teaching at an almost zero level with respect to undergraduates' prior knowledge: on average 2.6 of 32 common plant species were known. Overall, the introductory courses resulted in a significant but weak knowledge gain. We detected a higher knowledge gain in 'taxonomic concept knowledge' than in 'declarative species knowledge'. We showed that the learning success was influenced by learner-specific resources, such as prior knowledge or aspects of motivation towards the subject matter, and by learning environment such as teaching methodology.

DISCUSSION: We discuss didactical demands and aspects of teaching methodologies that could facilitate learning the complex task of plant identification in university courses. Plant identification should be taught and supervised by experienced, highly motivated course instructors with profound expertise and outstanding didactical skills. In order to qualify future generations of biologists, biology teachers, or conservationists universities should aim at and encourage high-quality teaching.}, } @article {pmid30879639, year = {2019}, author = {Zhu, X and Yin, L and Theisen, M and Zhuo, J and Siddiqui, S and Levy, B and Presnyak, V and Frassetto, A and Milton, J and Salerno, T and Benenato, KE and Milano, J and Lynn, A and Sabnis, S and Burke, K and Besin, G and Lukacs, CM and Guey, LT and Finn, PF and Martini, PGV}, title = {Systemic mRNA Therapy for the Treatment of Fabry Disease: Preclinical Studies in Wild-Type Mice, Fabry Mouse Model, and Wild-Type Non-human Primates.}, journal = {American journal of human genetics}, volume = {104}, number = {4}, pages = {625-637}, pmid = {30879639}, issn = {1537-6605}, mesh = {Animals ; Disease Models, Animal ; Endocytosis ; Enzyme Replacement Therapy ; Fabry Disease/*genetics/*therapy ; Genetic Therapy ; Humans ; Lipids/chemistry ; Lysosomes/metabolism ; Macaca fascicularis ; Male ; Mice ; Mice, Knockout ; RNA, Messenger/pharmacokinetics/*therapeutic use ; Tissue Distribution ; Trihexosylceramides/metabolism ; alpha-Galactosidase/*genetics ; }, abstract = {Fabry disease is an X-linked lysosomal storage disease caused by loss of alpha galactosidase A (α-Gal A) activity and is characterized by progressive accumulation of globotriaosylceramide and its analogs in all cells and tissues. Although enzyme replacement therapy (ERT) is considered standard of care, the long-term effects of ERT on renal and cardiac manifestations remain uncertain and thus novel therapies are desirable. We herein report preclinical studies evaluating systemic messenger RNA (mRNA) encoding human α-Gal A in wild-type (WT) mice, α-Gal A-deficient mice, and WT non-human primates (NHPs). The pharmacokinetics and distribution of h-α-Gal A mRNA encoded protein in WT mice demonstrated prolonged half-lives of α-Gal A in tissues and plasma. Single intravenous administration of h-α-Gal A mRNA to Gla-deficient mice showed dose-dependent protein activity and substrate reduction. Moreover, long duration (up to 6 weeks) of substrate reductions in tissues and plasma were observed after a single injection. Furthermore, repeat i.v. administration of h-α-Gal A mRNA showed a sustained pharmacodynamic response and efficacy in Fabry mice model. Lastly, multiple administrations to non-human primates confirmed safety and translatability. Taken together, these studies across species demonstrate preclinical proof-of-concept of systemic mRNA therapy for the treatment of Fabry disease and this approach may be useful for other lysosomal storage disorders.}, } @article {pmid30871454, year = {2019}, author = {Naz, K and Naz, A and Ashraf, ST and Rizwan, M and Ahmad, J and Baumbach, J and Ali, A}, title = {PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {123}, pmid = {30871454}, issn = {1471-2105}, mesh = {Bacterial Vaccines/pharmacology/*therapeutic use ; Genomics/*methods ; Humans ; Proteomics/*methods ; Vaccinology/*methods ; }, abstract = {BACKGROUND: A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine designing and development process. Reverse vaccinology is considered as a cost-effective and proficient approach to screen the entire pathogen genome. To look for broad-spectrum immunogenic targets and analysis of closely-related bacterial species, the assimilation of pangenome concept into reverse vaccinology approach is essential. The categories of species pangenome such as core, accessory, and unique genes sets can be analyzed for the identification of vaccine candidates through reverse vaccinology.

RESULTS: We have designed an integrative computational pipeline term as "PanRV" that employs both the pangenome and reverse vaccinology approaches. PanRV comprises of four functional modules including i) Pangenome Estimation Module (PGM) ii) Reverse Vaccinology Module (RVM) iii) Functional Annotation Module (FAM) and iv) Antibiotic Resistance Association Module (ARM). The pipeline is tested by using genomic data from 301 genomes of Staphylococcus aureus and the results are verified by experimentally known antigenic data.

CONCLUSION: The proposed pipeline has proved to be the first comprehensive automated pipeline that can precisely identify putative vaccine candidates exploiting the microbial pangenome. PanRV is a Linux based package developed in JAVA language. An executable installer is provided for ease of installation along with a user manual at https://sourceforge.net/projects/panrv2/ .}, } @article {pmid30870979, year = {2019}, author = {Chandra, N and Frängsmyr, L and Arnberg, N}, title = {Decoy Receptor Interactions as Novel Drug Targets against EKC-Causing Human Adenovirus.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, pmid = {30870979}, issn = {1999-4915}, mesh = {A549 Cells ; Adenovirus Infections, Human/drug therapy/virology ; Adenoviruses, Human/*drug effects ; Binding Sites ; DNA, Viral ; Drug Repositioning ; Genome, Viral ; Humans ; Keratoconjunctivitis/drug therapy/*virology ; Phylogeny ; Proof of Concept Study ; Receptors, Virus/*metabolism ; Sequence Analysis, DNA ; Suramin/*pharmacology ; Virus Attachment/*drug effects ; }, abstract = {Epidemic keratoconjunctivitis (EKC) is a severe ocular disease and can lead to visual impairment. Human adenovirus type-37 (HAdV-D37) is one of the major causative agents of EKC and uses sialic acid (SA)-containing glycans as cellular receptors. Currently, there are no approved antivirals available for the treatment of EKC. Recently, we have reported that sulfated glycosaminoglycans (GAGs) bind to HAdV-D37 via the fiber knob (FK) domain of the viral fiber protein and function as decoy receptors. Based on this finding, we speculated that GAG-mimetics may act as artificial decoy receptors and inhibit HAdV-D37 infection. Repurposing of approved drugs to identify new antivirals has drawn great attention in recent years. Here, we report the antiviral effect of suramin, a WHO-approved drug and a widely known GAG-mimetic, against HAdV-D37. Commercially available suramin analogs also show antiviral effects against HAdV-D37. We demonstrate that suramin exerts its antiviral activity by inhibiting the attachment of HAdV-D37 to cells. We also reveal that the antiviral effect of suramin is HAdV species-specific. Collectively, in this proof of concept study, we demonstrate for the first time that virus binding to a decoy receptor constitutes a novel and an unexplored target for antiviral drug development.}, } @article {pmid30870675, year = {2019}, author = {Strbova, K and Ruzickova, J and Raclavska, H}, title = {Application of multivariate statistical analysis using organic compounds: Source identification at a local scale (Napajedla, Czechia).}, journal = {Journal of environmental management}, volume = {238}, number = {}, pages = {434-441}, doi = {10.1016/j.jenvman.2019.03.035}, pmid = {30870675}, issn = {1095-8630}, mesh = {*Air Pollutants ; *Air Pollution ; Czech Republic ; Environmental Monitoring ; Multivariate Analysis ; Particulate Matter ; }, abstract = {The study aimed to apply novel source classification tool for local scale air pollution assessment reducing the total number of organic compounds in the model. Samples of particulate matter (PM) were collected in the town of Napajedla (South-eastern Czech Republic) in 2016. The industrial sector of the town is represented by plastics processing and manufacturing, as well as by mechanical engineering. Analytical technique of pyrolysis chromatography with mass spectroscopy detection was employed to identify organic species in the PM10 fraction. Two datasets (465 determined organic compounds and 50 selected organic markers) were used and compared by multivariate analysis - principal component analysis followed with hierarchical clustering on principal components incorporating compositional data approach. Three resulting clusters were observed in both cases. The cluster representing measurements near plastic processing and manufacturing plants was identical in both the analysed datasets with the same organic compounds that characterized resulting cluster Consequently, leading markers for plastic processing and manufacturing sources were suggested (bumetrizole, bis(tridecyl)phthalate, mono(2-ethylhexyl)phthalate). Other two clusters varied among the analysed datasets, however, dataset with selected markers showed more reliable outcomes. The results imply that concept of using only selected organic marker species with the compositional approach in multivariate statistical methods is sufficient and allows properly distinguishing the main air pollution sources between sampling locations even at a small urban scale.}, } @article {pmid30858753, year = {2019}, author = {Riebesehl, J and Yurchenko, E and Nakasone, KK and Langer, E}, title = {Phylogenetic and morphological studies in Xylodon (Hymenochaetales, Basidiomycota) with the addition of four new species.}, journal = {MycoKeys}, volume = {47}, number = {}, pages = {97-137}, pmid = {30858753}, issn = {1314-4049}, abstract = {Xylodon (Hymenochaetales, Basidiomycota) is the largest segregate genus of Hyphodontia s.l. Based on molecular and morphological data, 77 species are accepted in Xylodon to date. Phylogenetic analyses of ITS and 28S sequences, including 38 new ITS and 20 28S sequences of Xylodon species, revealed four species new to science. The new taxa X.exilis, X.filicinus, X.follis and X.pseudolanatus from Taiwan, Nepal, Réunion, Belize, and USA are described and illustrated. In addition, species concepts for Odontiavesiculosa from New Zealand and Xylodonlanatus from U.S.A. are revised and the new name X.vesiculosus is proposed. Phylogenetic analyses of the ITS region placed X.spathulatus, X.bubalinus and X.chinensis in a strongly supported clade and demonstrated that they are conspecific. Palifer and Odontiopsis are synonymised under Xylodon based on morphological and sequence data. The following new combinations are proposed: X.erikssonii, X.gamundiae, X.hjortstamii, X.hyphodontinus, X.septocystidiatus and X.verecundus. Line drawings of X.cystidiatus, X.hyphodontinus, X.lanatus and X.vesiculosus, as well as photographs of X.raduloides basidiomata, are provided. A key to X.lanatus and similar species is presented.}, } @article {pmid30853974, year = {2019}, author = {Telschow, A and Gadau, J and Werren, JH and Kobayashi, Y}, title = {Genetic Incompatibilities Between Mitochondria and Nuclear Genes: Effect on Gene Flow and Speciation.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {62}, pmid = {30853974}, issn = {1664-8021}, abstract = {The process of speciation is, according to the biological species concept, the reduction in gene flow between genetically diverging populations. Most of the previous theoretical studies analyzed the effect of nuclear genetic incompatibilities on gene flow. There is, however, an increasing number of empirical examples suggesting that cytoplasmically inherited genetic elements play an important role in speciation. Here, we present a theoretical analysis of mitochondrial driven speciation, in which genetic incompatibilities occur between mitochondrial haplotypes and nuclear alleles. Four population genetic models with mainland-island structure were analyzed that differ with respect to the type of incompatibility and the underlying genetics. Gene flow reduction was measured on selectively neutral alleles of an unlinked locus and quantified by the effective migration rate. Analytical formulae for the different scenarios were derived using the fitness graph method. For the models with haploid genetics, we found that mito-nuclear incompatibilities (MtNI) are as strong as nuclear-nuclear incompatibilities (NNI) in reducing gene flow at the unlinked locus, but only if males and females migrate in equal number. For models with diploid genetics, we found that MtNI reduce gene flow stronger than NNI when incompatibilities are recessive, but weaker when they are dominant. For both haploid and diploid MtNI, we found that gene flow reduction is stronger if females are the migrating sex, but weaker than NNI when males are the migrating sex. These results encourage further examination on the role of mitochondria on genetic divergence and speciation and point toward specific factors (e.g., migrating sex) that could be the focus of an empirical test.}, } @article {pmid30846812, year = {2019}, author = {Jaiswal, S and Iquebal, MA and Arora, V and Sheoran, S and Sharma, P and Angadi, UB and Dahiya, V and Singh, R and Tiwari, R and Singh, GP and Rai, A and Kumar, D}, title = {Development of species specific putative miRNA and its target prediction tool in wheat (Triticum aestivum L.).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3790}, pmid = {30846812}, issn = {2045-2322}, mesh = {Chromosomes, Plant ; Computational Biology/*methods ; Databases, Genetic ; Genome, Plant ; Machine Learning ; MicroRNAs/chemistry/*genetics ; Models, Genetic ; RNA, Plant/*genetics ; Reproducibility of Results ; *Software ; Support Vector Machine ; Triticum/*genetics ; User-Computer Interface ; }, abstract = {MicroRNA are 20-24 nt, non-coding, single stranded molecule regulating traits and stress response. Tissue and time specific expression limits its detection, thus is major challenge in their discovery. Wheat has limited 119 miRNAs in MiRBase due to limitation of conservation based methodology where old and new miRNA genes gets excluded. This is due to origin of hexaploid wheat by three successive hybridization, older AA, BB and younger DD subgenome. Species specific miRNA prediction (SMIRP concept) based on 152 thermodynamic features of training dataset using support vector machine learning approach has improved prediction accuracy to 97.7%. This has been implemented in TamiRPred (http://webtom.cabgrid.res.in/tamirpred). We also report highest number of putative miRNA genes (4464) of wheat from whole genome sequence populated in database developed in PHP and MySQL. TamiRPred has predicted 2092 (>45.10%) additional miRNA which was not predicted by miRLocator. Predicted miRNAs have been validated by miRBase, small RNA libraries, secondary structure, degradome dataset, star miRNA and binding sites in wheat coding region. This tool can accelerate miRNA polymorphism discovery to be used in wheat trait improvement. Since it predicts chromosome-wise miRNA genes with their respective physical location thus can be transferred using linked SSR markers. This prediction approach can be used as model even in other polyploid crops.}, } @article {pmid30832573, year = {2019}, author = {Aghová, T and Palupčíková, K and Šumbera, R and Frynta, D and Lavrenchenko, LA and Meheretu, Y and Sádlová, J and Votýpka, J and Mbau, JS and Modrý, D and Bryja, J}, title = {Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {69}, pmid = {30832573}, issn = {1471-2148}, mesh = {Africa ; Africa, Eastern ; Africa, Northern ; Africa, Western ; Animals ; Arabia ; Biological Evolution ; DNA, Mitochondrial/chemistry/genetics ; *Ecosystem ; Middle East ; Murinae/classification/*genetics ; Phylogeny ; *Phylogeography ; }, abstract = {BACKGROUND: Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept.

RESULTS: The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated "out-of-East-Africa" dispersal events into western Africa, the Mediterranean region and Arabia.

CONCLUSIONS: The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa.}, } @article {pmid30821344, year = {2019}, author = {Denk, TRA and Kraus, D and Kiese, R and Butterbach-Bahl, K and Wolf, B}, title = {Constraining N cycling in the ecosystem model LandscapeDNDC with the stable isotope model SIMONE.}, journal = {Ecology}, volume = {100}, number = {5}, pages = {e02675}, doi = {10.1002/ecy.2675}, pmid = {30821344}, issn = {1939-9170}, support = {BU1173/15-1//German Research Foundation (DFG)/International ; }, mesh = {*Ecosystem ; Isotopes ; Nitrogen ; Nitrogen Isotopes ; Nitrous Oxide ; *Soil ; Switzerland ; }, abstract = {The isotopic composition (ic) of soil nitrogen (N) and, more recently, the intramolecular distribution of [15] N in the N2 O molecule (site preference, SP) are powerful instruments to identify dominant N turnover processes, and to attribute N2 O emissions to their source processes. Despite the process information contained in the ic of N species and the associated potential for model validation, the implementation of isotopes in ecosystem models has lagged behind. To foster the validation of ecosystem models based on the ic of N species, we developed the stable isotope model for nutrient cycles (SIMONE). SIMONE uses fluxes between ecosystem N pools (soil organic N, mineral N, plants, microbes) calculated by biogeochemical models, and literature isotope effects for these processes to calculate the ic of N species. Here, we present the concept of SIMONE, apply it to simulations of the biogeochemical model LandscapeDNDC, and assess the capability of [15] N-N2 O and, to our knowledge for the first time, SP, to constrain simulated N fluxes by LandscapeDNDC. LandscapeDNDC successfully simulated N2 O emission, soil nitrate, and ammonium, as well as soil environmental conditions of an intensively managed grassland site in Switzerland. Accordingly, the dynamics of [15] N-N2 O and SP of soil N2 O fluxes as simulated by SIMONE agreed well with measurements, though [15] N-N2 O was on average underestimated and SP overestimated (root-mean-square error [RMSE] of 8.4‰ and 7.3‰, respectively). Although [15] N-N2 O could not constrain the N cycling process descriptions of LandscapeDNDC, the overestimation of SP indicated an overestimation of simulated nitrification rates by 10-59% at low water content, suggesting the revision of the corresponding model parameterization. Our findings show that N isotope modeling in combination with only recently available high- frequency measurements of the N2 O ic are promising tools to identify and address weaknesses in N cycling of ecosystem models. This will finally contribute to augmenting the development of model-based strategies for mitigating N pollution.}, } @article {pmid30793996, year = {2019}, author = {Demin, KA and Sysoev, M and Chernysh, MV and Savva, AK and Koshiba, M and Wappler-Guzzetta, EA and Song, C and De Abreu, MS and Leonard, B and Parker, MO and Harvey, BH and Tian, L and Vasar, E and Strekalova, T and Amstislavskaya, TG and Volgin, AD and Alpyshov, ET and Wang, D and Kalueff, AV}, title = {Animal models of major depressive disorder and the implications for drug discovery and development.}, journal = {Expert opinion on drug discovery}, volume = {14}, number = {4}, pages = {365-378}, doi = {10.1080/17460441.2019.1575360}, pmid = {30793996}, issn = {1746-045X}, mesh = {Animals ; Antidepressive Agents/*pharmacology ; Depressive Disorder, Major/*drug therapy/physiopathology ; Disease Models, Animal ; Drug Development/methods ; Drug Discovery/*methods ; Humans ; Translational Research, Biomedical/methods ; }, abstract = {Depression is a highly debilitating psychiatric disorder that affects the global population and causes severe disabilities and suicide. Depression pathogenesis remains poorly understood, and the disorder is often treatment-resistant and recurrent, necessitating the development of novel therapies, models and concepts in this field. Areas covered: Animal models are indispensable for translational biological psychiatry, and markedly advance the study of depression. Novel approaches continuously emerge that may help untangle the disorder heterogeneity and unclear categories of disease classification systems. Some of these approaches include widening the spectrum of model species used for translational research, using a broader range of test paradigms, exploring new pathogenic pathways and biomarkers, and focusing more closely on processes beyond neural cells (e.g. glial, inflammatory and metabolic deficits). Expert opinion: Dividing the core symptoms into easily translatable, evolutionarily conserved phenotypes is an effective way to reevaluate current depression modeling. Conceptually novel approaches based on the endophenotype paradigm, cross-species trait genetics and 'domain interplay concept', as well as using a wider spectrum of model organisms and target systems will enhance experimental modeling of depression and antidepressant drug discovery.}, } @article {pmid30721036, year = {2019}, author = {Siegenthaler, KD and Sevier, CS}, title = {Working Together: Redox Signaling between the Endoplasmic Reticulum and Mitochondria.}, journal = {Chemical research in toxicology}, volume = {32}, number = {3}, pages = {342-344}, doi = {10.1021/acs.chemrestox.8b00379}, pmid = {30721036}, issn = {1520-5010}, mesh = {Endoplasmic Reticulum/*metabolism ; Mitochondria/*metabolism ; Oxidation-Reduction ; Reactive Oxygen Species/*metabolism ; *Signal Transduction ; }, abstract = {The concept that reactive oxygen species (ROS) are primarily toxic, mitochondria-generated molecules has persisted for decades. Here we highlight the emerging complexity for ROS-based events, emphasizing the evolving importance of the endoplasmic reticulum as a source and platform for redox signaling.}, } @article {pmid30719428, year = {2019}, author = {Wilson, BC and Vatanen, T and Cutfield, WS and O'Sullivan, JM}, title = {The Super-Donor Phenomenon in Fecal Microbiota Transplantation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {2}, pmid = {30719428}, issn = {2235-2988}, mesh = {Clostridium Infections/*therapy ; Fecal Microbiota Transplantation/*methods ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; *Tissue Donors ; }, abstract = {Fecal microbiota transplantation (FMT) has become a highly effective bacteriotherapy for recurrent Clostridium difficile infection. Meanwhile the efficacy of FMT for treating chronic diseases associated with microbial dysbiosis has so far been modest with a much higher variability in patient response. Notably, a number of studies suggest that FMT success is dependent on the microbial diversity and composition of the stool donor, leading to the proposition of the existence of FMT super-donors. The identification and subsequent characterization of super-donor gut microbiomes will inevitably advance our understanding of the microbial component of chronic diseases and allow for more targeted bacteriotherapy approaches in the future. Here, we review the evidence for super-donors in FMT and explore the concept of keystone species as predictors of FMT success. Possible effects of host-genetics and diet on FMT engraftment and maintenance are also considered. Finally, we discuss the potential long-term applicability of FMT for chronic disease and highlight how super-donors could provide the basis for dysbiosis-matched FMTs.}, } @article {pmid30714895, year = {2019}, author = {McCarthy, CGP and Fitzpatrick, DA}, title = {Pan-genome analyses of model fungal species.}, journal = {Microbial genomics}, volume = {5}, number = {2}, pages = {}, pmid = {30714895}, issn = {2057-5858}, mesh = {Evolution, Molecular ; Fungi/*classification/genetics ; *Genome, Fungal ; Genome-Wide Association Study ; Genomics ; Phylogeny ; }, abstract = {The concept of the species 'pan-genome', the union of 'core' conserved genes and all 'accessory' non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. Between 80 and 90 % of gene models per strain in each of these species are core genes that are highly conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species, the remaining 'accessory' gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance. Analysis of the ancestry of species core and accessory genomes suggests that fungal pan-genomes evolve by strain-level innovations such as gene duplication as opposed to wide-scale horizontal gene transfer. Our findings lend further supporting evidence to the existence of species pan-genomes in eukaryote taxa.}, } @article {pmid30686927, year = {2019}, author = {Murphy, JC and Braswell, AL and Charles, SP and Auguste, RJ and Rivas, GA and Orzée, A and Lehtinen, RM and Jowers, MJ}, title = {A new species of Erythrolamprus from the oceanic island of Tobago (Squamata, Dipsadidae).}, journal = {ZooKeys}, volume = {}, number = {817}, pages = {131-157}, pmid = {30686927}, issn = {1313-2989}, abstract = {Tobago is a small island on the southeast edge of the Caribbean Plate with a continental flora and fauna. Using DNA sequences from Genbank, new sequences, and morphological data from the snakes Erythrolamprusepinephalus, E.melanotus, E.reginae, and E.zweifeli, the species status of specimens of a Tobago snake previously considered to be Erythrolamprusreginae was assessed. Erythrolampruszweifeli, long considered a subspecies of E.reginae, was found to be a northern Venezuela-Trinidad endemic and the sister to E.reginae. The trans-Andean species E.epinephalus is shown to be non-monophyletic while the Costa Rican lineage of E.epinephalus is weakly supported as the sister to the Tobago population. The Tobago Erythrolamprus is described as a distinct taxon based upon five specimens from four localities in lower montane rainforest. Much of the new species range includes the Main Ridge Forest Reserve of Tobago, the oldest protected forest in the Western Hemisphere. All known locations fall within a 400-ha area, and its total geographic distribution is likely to be less than 4,566 ha. The restricted distribution of this new snake makes it a likely candidate for threatened status. The new species also becomes another biogeographic link between northern Venezuela and Tobago.}, } @article {pmid30672345, year = {2020}, author = {Djebrouni, M and Wolbring, G}, title = {Impact of robotics and human enhancement on occupation: what does it mean for rehabilitation?.}, journal = {Disability and rehabilitation}, volume = {42}, number = {11}, pages = {1518-1528}, doi = {10.1080/09638288.2018.1527401}, pmid = {30672345}, issn = {1464-5165}, mesh = {*Disabled Persons ; Humans ; *Occupational Therapy ; Occupations ; *Robotics ; }, abstract = {Purpose: People with disabilities face participation challenges in all occupations. Scientific and technological advancements impact the occupational landscape of humans. This scoping review aimed to ascertain the academic engagement with occupation in relation to robotics and human enhancement focusing in particular on how people with disabilities and rehabilitation were mentioned.Method: SCOPUS and the 70 databases of EBSCO host were searched. Manifest and latent content coding and thematic grouping of codes relevant to answering the review questions was performed.Results: Only four articles engaged with occupation in relation to human enhancement. As to occupation and robotics, some occupational fields were visible and not others; occupational health and safety was the most visible one; people with disabilities were covered from a medical, therapeutic angle and not in relation to social issues caused by the occupational impact of robotics. Change in the scope, meaning, and clients of rehabilitation efforts related to occupation enabled by human enhancement and robotics was not covered.Conclusions: The gaps found should be filled. The impact of robotics and human enhancement on the occupational landscape indicates the need for rehabilitation to think beyond recovery to the species typical as a goal. The ultrabilitation concept could help to meet this need.Implications for rehabilitationAdvances in robotics and human enhancement beyond species-typical levels modify the occupational landscape, human ability expectations in this setting, and the meaning and scope of disability and rehabilitation (clinical and community based).There is a need to elucidate the impact of these changes on the meaning, scope and goals of recovery-oriented rehabilitation.The recently coined term "ultrabilitation" creates space to discuss an ability expectation creep triggered by developments in robotics and human enhancement, particularly within occupation focused rehabilitation.}, } @article {pmid30647342, year = {2018}, author = {Garibian, PG and Neretina, AN and Klimovsky, AI and Kotov, AA}, title = {A new case of West-East differentiation of the freshwater fauna in Northern Eurasia: the Pleuroxus trigonellus species group (Crustacea: Cladocera: Chydoridae).}, journal = {Zootaxa}, volume = {4532}, number = {4}, pages = {451-482}, doi = {10.11646/zootaxa.4532.4.1}, pmid = {30647342}, issn = {1175-5334}, mesh = {Animals ; *Cladocera ; Europe ; Female ; Fresh Water ; Male ; Parthenogenesis ; }, abstract = {Cladocerans (Crustacea: Branchiopoda) of Northern Eurasia traditionally belong to the most intensively studied groups of freshwater microcrustaceans. However, despite a significant progress in our knowledge of different aspects on their biology, some intriguing questions remain unresolved. The hypothesis of cladoceran faunas differentiation between the western and eastern parts of Northern Eurasia agrees with the continental endemism concept. But to date few cladoceran species groups have been investigated through the whole North Eurasian range. Our current work contributes to the confirmation of this hypothesis through a revision of the poorly studied Pleuroxus trigonellus species group. Based on material from Europe, we redescibed morphology of Pleuroxus trigonellus (O.F. Müller, 1776) s.str. and found that its distribution range is potentially restricted to the western portion of Northern Eurasia. At the same time, morphologically similar populations from the eastern portion of Eurasia belong to a new species, Pleuroxus yakutensis sp. nov. These two species are basically similar in general morphology of parthenogenetic and gamogenetic females, but have clear differences in the male morphology. Additionally we offer an identification key for discrimination of the P. trigonellus group from P. uncinatus (Baird, 1850) according to morphological features of the males.}, } @article {pmid30647339, year = {2018}, author = {Freyhof, J and BayÇelebİ, E and Geiger, M}, title = {Review of the genus Cobitis in the Middle East, with the description of eight new species (Teleostei: Cobitidae).}, journal = {Zootaxa}, volume = {4535}, number = {1}, pages = {1-75}, doi = {10.11646/zootaxa.4535.1.1}, pmid = {30647339}, issn = {1175-5334}, mesh = {Animals ; Black Sea ; *Cypriniformes ; Male ; Middle East ; *Perciformes ; }, abstract = {The diversity of Cobitis in the Middle East is reviewed, resulting in the recognition of 30 species, of which eight are described herein as new. Two species, C. amphilekta and C. kellei, seem to be extinct. Hypotheses on species-level diversity derived from distance and Poisson tree process analyses of DNA barcode data are tested against morphometric and morphological characters including colour patterns. For species pairs separated by small K2P distances in COI sequence data we follow a practitioner-oriented diagnostic species concept, in which we recognise species only if differentiated morphologically (including by colour pattern). For all 30 species we provide diagnoses and identification keys. Cobitis afifeae, new species, from the Büyük Menderes River drainage in the Aegean Sea basin, is distinguished by having two laminae circularis in the male, a row of blotches below Z4, a small, roundish or comma-shaped black spot at the upper caudal-fin base, and elevated mental lobes. Cobitis aliyeae, new species, from the lower Seyhan and Ceyhan River drainages, is distinguished by having two laminae circularis in the male, the blotches in Z2 and Z4 anterior to the dorsal-fin origin usually well separated from each other, and the pigmentation in Z1 well distinguished from the pigmentation in Z2. Cobitis anabelae, new species, from the lower Orontes River drainage, is distinguished by having two laminae circularis in the male, the pigmentation in Z2 formed by small, brown spots, always much smaller than blotches in Z3, much smaller than the pupil diameter, Z2 and Z3 well separated, and no pigmentation below Z4. Cobitis erkakanae, new species, from the Gölbasi Lakes, adjacent to the Ceyhan River drainage, is distinguished by having two laminae circularis in the male, no blotches below Z4, the blotches in Z2 and Z4 being horizontally elongated and often fused with adjacent ones, and the caudal fin with 4-6 wide, regularly-shaped, brown bands. Cobitis emrei, new species, from the Lake Sapanca basin is distinguished by having one lamina circularis in the male, a large black spot at the upper caudal-fin base, and Z3 fully covered by very small spots forming a sand-like pattern. Cobitis joergbohleni, new species, from the Sultan marshes in Central Anatolia is distinguished by having two laminae circularis in the male, and the flank colour pattern being completely disorganised, not following the Gambetta zones. Cobitis pirii, new species, from the endorheic Lake Eğirdir basin and the Mediterranean Aksu and Köprü Rivers, is distinguished by having two laminae circularis in the male, a simple external part of the suborbital spine and two distinct rows of small blotches in Z4, one along the lateral midline and one distinctly below. Cobitis troasensis, new species, from the Tuzla River drainage, is distinguished by having one lamina circularis in the male and 25-36 small, comma-shaped brown blotches in Z4. A lectotype is designated for Cobitis battalgilae. As First Revisers, priority is given to Cobitis fahireae over C. kurui. Cobitis damlae and C. kurui are treated as synonyms of C. fahireae. Cobitis strumicae and C. taenia are recorded for the first time from Anatolia and C. saniae is newly documented from the Black Sea basin in Georgia. The Poisson tree process analysis of COI data proposed 31 groups, most of which could be distinguished by morphological characters. Cobitis troasensis is described based on morphological data alone.}, } @article {pmid30633772, year = {2019}, author = {Fotedar, S and Lukehurst, S and Jackson, G and Snow, M}, title = {Molecular tools for identification of shark species involved in depredation incidents in Western Australian fisheries.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210500}, pmid = {30633772}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Bites and Stings/epidemiology/physiopathology ; Conservation of Natural Resources/*methods ; Cytochromes b/genetics ; DNA/*analysis/genetics ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fish Proteins/genetics ; *Fisheries ; Incidence ; Sequence Homology, Nucleic Acid ; Sharks/classification/*genetics/physiology ; Species Specificity ; Western Australia/epidemiology ; }, abstract = {Shark depredation is an issue of concern in some Western Australian recreational and commercial fisheries where it can have economic, social and ecological consequences. Knowledge of the shark species involved is fundamental to developing effective management strategies to mitigate the impacts of depredation. Identification of the species responsible is difficult as direct observation of depredation events is uncommon and evaluating bite marks on fish has a high degree of uncertainty. The use of trace DNA techniques has provided an alternative method for species identification. We demonstrate proof of concept for a targeted DNA barcoding approach to identify shark species using trace DNA found at bite marks on recovered remains of hooked fish. Following laboratory validation, forensic analysis of swabs collected from samples of bitten demersal fish, led to the definitive identification of shark species involved in 100% of the incidences of depredation (n = 16).}, } @article {pmid30631643, year = {2019}, author = {Craig, CA and Maikoetter, JD and Bonner, TH}, title = {Temperature-mediated feeding between spring-associated and riverine-associated congeners, with implications for community segregation.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6144}, pmid = {30631643}, issn = {2167-8359}, abstract = {Freshwater fish communities segregate along water temperature gradients attributed in part to temperature-mediated physiological processes that affect species fitness. In spring complexes of southwest USA, spring complexes with narrow range of water temperatures are dominated by a community of fishes (i.e., spring-associated fishes), whereas riverine habitats with wide-range of water temperatures are dominated by a different community of fishes (i.e., riverine-associated fishes). The purpose of this study was to test a prediction of the concept that temperature-mediated species performance is a mechanism in maintaining community segregation. We predicted that a spring-associated fish (Largespring Gambusia Gambusia geiseri) would feed first and more often in a pairing with a riverine-associated fish (Western Mosquitofish G. affinis) at an average spring temperature (23 °C) and that the riverine-associated fish would feed first and more often in a pairing with the spring-associated fish at a warm riverine temperature (30 °C). Among four trails consisting of 30 pairings, at the spring complex temperature (23 °C), Largespring Gambusia had a greater number of first feeds (mean ± 1 SD, 5.0 ± 0.82) than Western Mosquitofish (2.5 ± 1.73) and had greater mean number of total feeds (1.9 ± 0.31) than Western Mosquitofish (0.81 ± 0.70). At the riverine environment temperature (30 °C), Western Mosquitofish had a greater number of first feeds (5.25 ± 1.71) than Largespring Gambusia (2.5 ± 1.73) and had greater mean number of total feeds (2.78 ± 1.05) than Largespring Gambusia (0.94 ± 0.68). Our findings suggest that temperature-mediated species performance could be maintaining segregation between the two fish communities. This study benefits our understanding of distributional patterns and improves threat assessments of stenothermal aquatic organisms.}, } @article {pmid30622886, year = {2018}, author = {Lawrence, DP and Holland, LA and Nouri, MT and Travadon, R and Abramians, A and Michailides, TJ and Trouillas, FP}, title = {Molecular phylogeny of Cytospora species associated with canker diseases of fruit and nut crops in California, with the descriptions of ten new species and one new combination.}, journal = {IMA fungus}, volume = {9}, number = {}, pages = {333-370}, pmid = {30622886}, issn = {2210-6340}, abstract = {Cytospora species are destructive canker and dieback pathogens of woody hosts in natural and agroecosystems around the world. In this genus, molecular identification has been limited due to the paucity of multi-locus sequence typing studies and the lack of sequence data from type specimens in public repositories, stalling robust phylogenetic reconstructions. In most cases a morphological species concept could not be applied due to the plasticity of characters and significant overlap of morphological features such as spore dimensions and fruiting body characters. In this study, we employed a molecular phylogenetic framework with the inclusion of four nuclear loci (ITS, translation elongation factor 1-alpha, actin, and beta-tubulin) to unveil the biodiversity and taxonomy of this understudied important genus of plant pathogens. Phylogenetic inferences based on 150 Californian isolates revealed 15 Cytospora species associated with branch and twig cankers and dieback of almond, apricot, cherry, cottonwood, olive, peach, pistachio, plum, pomegranate, and walnut trees in California. Of the 15 species recovered in this study, 10 are newly described and typified, in addition to one new combination. The pathogenic status of the newly described Cytospora species requires further investigation as most species were associated with severe dieback and decline of diverse and economically important fruit and nut crops in California.}, } @article {pmid30612225, year = {2019}, author = {Machado-de-Souza, T and Campos, RP and Devoto, M and Varassin, IG}, title = {Local drivers of the structure of a tropical bird-seed dispersal network.}, journal = {Oecologia}, volume = {189}, number = {2}, pages = {421-433}, pmid = {30612225}, issn = {1432-1939}, mesh = {Animals ; Birds ; Brazil ; Ecology ; Forests ; *Seed Dispersal ; }, abstract = {One of the major challenges in ecology is to understand the relative importance of neutral- and niche-based processes structuring species interactions within communities. The concept of neutral-based processes posits that network structure is a result of interactions between species based on their abundance. On the other hand, niche-based processes presume that network structure is shaped by constraints to interactions. Here, we evaluated the relative importance of neutral-based process, represented by species' abundance (A) and fruit production (F) models, and niche-based process, represented by spatial overlap (S), temporal overlap (T) and morphological barrier (M) models, in shaping the structure of a bird-seed dispersal network from the Brazilian Atlantic Forest. We evaluated the ability of each model, singly or in combination, to predict the general structure [represented by connectance, nestedness (NODF), weight nestedness (WNODF), interaction evenness and complementary specialization] and microstructure of the network (i.e., the frequency of pairwise interactions). Only nestedness (both NODF and WNODF) was predicted by at least one model. NODF and WNODF were predicted by a neutral-based process (A), by a combination of niche-based processes (ST and STM) and by both neutral- and niche-based processes (AM). NODF was also predicted by F and FM model. Regarding microstructure, temporal overlap (T) was the most parsimonious model able to predict it. Our findings reveal that a combination of neutral- and niche-based processes is a good predictor of the general structure (NODF and WNODF) of the bird-seed dispersal network and a niche-based process is the best predictor of the network's microstructure.}, } @article {pmid30607025, year = {2019}, author = {Lu, HP and Yeh, YC and Shiah, FK and Gong, GC and Hsieh, CH}, title = {Evolutionary constraints on species diversity in marine bacterioplankton communities.}, journal = {The ISME journal}, volume = {13}, number = {4}, pages = {1032-1041}, pmid = {30607025}, issn = {1751-7370}, mesh = {Bacteria/*isolation & purification ; *Biodiversity ; *Biological Evolution ; Environment ; Phylogeny ; Plankton/*isolation & purification ; Seawater/microbiology ; }, abstract = {Variation in microbial species diversity has typically been explained as the outcome of local ecological factors driving species coexistence, overlooking the roles of evolutionary constraints. Here, we argue that macro-evolutionary niche conservatism and unequal diversification rates among phylum-level lineages are strong determinants of diversity-environment relationships in bacterial systems. That is, apart from stochasticity, environmental effects operate most strongly on phylum composition, which in turn dictates the species diversity of bacterial communities. This concept is demonstrated using bacterioplankton in the surface seawaters of the East China Sea. Furthermore, we show that the species richness of a local bacterioplankton community can generally be estimated based on the relative abundances of phyla and their contributions of species numbers in the global seawater pool-highlighting the important influence of evolutionary constraints on local community diversity.}, } @article {pmid32214496, year = {2019}, author = {Lombard, L and Sandoval-Denis, M and Lamprecht, SC and Crous, PW}, title = {Epitypification of Fusarium oxysporum - clearing the taxonomic chaos.}, journal = {Persoonia}, volume = {43}, number = {}, pages = {1-47}, pmid = {32214496}, issn = {0031-5850}, abstract = {Fusarium oxysporum is the most economically important and commonly encountered species of Fusarium. This soil-borne fungus is known to harbour both pathogenic (plant, animal and human) and non-pathogenic strains. However, in its current concept F. oxysporum is a species complex consisting of numerous cryptic species. Identification and naming these cryptic species is complicated by multiple subspecific classification systems and the lack of living ex-type material to serve as basic reference point for phylogenetic inference. Therefore, to advance and stabilise the taxonomic position of F. oxysporum as a species and allow naming of the multiple cryptic species recognised in this species complex, an epitype is designated for F. oxysporum. Using multi-locus phylogenetic inference and subtle morphological differences with the newly established epitype of F. oxysporum as reference point, 15 cryptic taxa are resolved in this study and described as species.}, } @article {pmid30548156, year = {2019}, author = {Filker, S and Kühner, S and Heckwolf, M and Dierking, J and Stoeck, T}, title = {A fundamental difference between macrobiota and microbial eukaryotes: protistan plankton has a species maximum in the freshwater-marine transition zone of the Baltic Sea.}, journal = {Environmental microbiology}, volume = {21}, number = {2}, pages = {603-617}, doi = {10.1111/1462-2920.14502}, pmid = {30548156}, issn = {1462-2920}, support = {03F0682//EU & German BMBF/International ; //TU Nachwuchsring/International ; }, mesh = {Bacteria/classification/genetics/*isolation & purification ; Baltic States ; Eukaryota/classification/genetics/*isolation & purification ; Fresh Water/*chemistry/microbiology/parasitology ; Plankton/classification/genetics/*isolation & purification ; Saline Waters/chemistry ; Salinity ; Seawater/*chemistry/microbiology/parasitology ; }, abstract = {Remane's Artenminimum at the horohalinicum is a fundamental concept in ecology to describe and explain the distribution of organisms along salinity gradients. However, a recent metadata analysis challenged this concept for protists, proposing a species maximum in brackish waters. Due to data bias, this literature-based investigation was highly discussed. Reliable data verifying or rejecting the species minimum for protists in brackish waters were critically lacking. Here, we sampled a pronounced salinity gradient along a west-east transect in the Baltic Sea and analysed protistan plankton communities using high-throughput eDNA metabarcoding. A strong salinity barrier at the upper limit of the horohalinicum and 10 psu appeared to select for significant shifts in protistan community structures, with dinoflagellates being dominant at lower salinities, and dictyochophytes and diatoms being keyplayers at higher salinities. Also in vertical water column gradients in deeper basins (Kiel Bight, Arkona and Bornholm Basin) appeared salinity as significant environmental determinant influencing alpha- and beta-diversity patterns. Importantly, alpha-diversity indices revealed species maxima in brackish waters, that is, indeed contrasting Remane's Artenminimum concept. Statistical analyses confirmed salinity as the major driving force for protistan community structuring with high significance. This suggests that macrobiota and microbial eukaryotes follow fundamentally different rules regarding diversity patterns in the transition zone from freshwater to marine waters.}, } @article {pmid30547247, year = {2019}, author = {El-Sherry, S and Ogedengbe, ME and Hafeez, MA and Sayf-Al-Din, M and Gad, N and Barta, JR}, title = {Cecal coccidiosis in turkeys: Comparative biology of Eimeria species in the lower intestinal tract of turkeys using genetically typed, single oocyst-derived lines.}, journal = {Parasitology research}, volume = {118}, number = {2}, pages = {583-598}, pmid = {30547247}, issn = {1432-1955}, mesh = {Animals ; Coccidiosis/parasitology/*veterinary ; Eimeria/*classification/genetics/*physiology ; Intestinal Mucosa/parasitology ; Intestines/*parasitology ; Oocysts/genetics/isolation & purification ; Poultry Diseases/*parasitology ; Species Specificity ; Turkeys/parasitology ; }, abstract = {Differentiating the Eimeria species causing cecal coccidiosis in turkeys is challenging. To obtain benchmark biological data for Eimeria gallopavonis Hawkins 1952 and Eimeria meleagridis Tyzzer 1929 and to support the stability of the species concept for each, genetically typed, single oocyst-derived lines of E. gallopavonis Weybridge strain and E. meleagridis USAR97-01 were used to redescribe the biological, pathological, and morphological features of these parasites. Oocysts of E. meleagridis and E. gallopavonis overlap in dimensions, but oocysts of the former have a single polar granule compared with multiple in the latter. Mature first-generation meronts of E. gallopavonis were observed histologically as early as 48 h post-inoculation alongside the villi in jejunum (before and after Meckel's diverticulum), ileum, cecal neck and rectum, but not cecal pouches. Three asexual cycles were observed suggesting that early workers apparently overlooked one asexual cycle. Examination of endogenous development of a culture labeled "Eimeria adenoeides Weybridge strain" suggested that this strain (found in a number of publications as a large oocyst strain of "Eimeria adenoeides") matched the species description of E. gallopavonis and so has been renamed herein. Macroscopic lesions induced by E. gallopavonis consisted of caseous material distally from posterior of the yolk stalk through the remaining intestinal tract, excluding the cecal pouches. For E. meleagridis, only the first asexual generation was observed outside of the cecal pouches within the jejunum around the yolk stalk. Second- and 3rd-generation asexual stages developed almost exclusively in the cecal pouches (but not cecal necks). Macroscopic lesions described for E. meleagridis were similar to those of E. adenoeides. Marked corrugation of the cecal serosal surface was observed. Cecal pouches contained creamy colored, caseous material varying from loose material to granular. Distinguishing features of the Eimeria species infecting the lower part of the small intestine are summarized in the present study, and new type specimens were designated for E. gallopavonis and E. meleagridis to provide a stable reference for future work with these parasites.}, } @article {pmid30523201, year = {2019}, author = {Wood, HN and Sidders, AE and Brumsey, LE and Morozkin, ES and Gerasimova, YV and Rohde, KH}, title = {Species Typing of Nontuberculous Mycobacteria by Use of Deoxyribozyme Sensors.}, journal = {Clinical chemistry}, volume = {65}, number = {2}, pages = {333-341}, pmid = {30523201}, issn = {1530-8561}, support = {R21 AI123876/AI/NIAID NIH HHS/United States ; }, mesh = {Colorimetry ; DNA, Catalytic/*metabolism ; Fluorescent Dyes/chemistry ; Humans ; Limit of Detection ; Mycobacterium Infections, Nontuberculous/diagnosis ; Mycobacterium tuberculosis/genetics/isolation & purification ; Nontuberculous Mycobacteria/*genetics/isolation & purification ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; }, abstract = {BACKGROUND: Nontuberculous mycobacteria (NTM) species are a rising threat, especially to patients living with pulmonary comorbidities. Current point-of-care diagnostics fail to adequately identify and differentiate NTM species from Mycobacterium tuberculosis (Mtb). Definitive culture- and molecular-based testing can take weeks to months and requires sending samples out to specialized diagnostic laboratories.

METHODS: In this proof-of-concept study, we developed an assay based on PCR amplification of 16S ribosomal RNA (rRNA) rrs genes by using universal mycobacterial primers and interrogation of the amplified fragments with a panel of binary deoxyribozyme (BiDz) sensors to enable species-level identification of NTM (BiDz-NTMST). Each BiDz sensor consists of 2 subunits of an RNA-cleaving deoxyribozyme, which form an active deoxyribozyme catalytic core only in the presence of the complimentary target sequence. The target-activated BiDz catalyzes cleavage of a reporter substrate, thus triggering either fluorescent or colorimetric (visually observed) signal depending on the substrate used. The panel included BiDz sensors for differentiation of 6 clinically relevant NTM species (Mycobacterium abscessus, Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium fortuitum, Mycobacterium kansasii, and Mycobacterium gordonae) and Mtb.

RESULTS: Using the fluorescent BiDz-NTMST assay, we successfully identified the species of 38 clinical isolates. In addition, a subset of strains was tested with visual BiDz sensors, providing proof-of-concept for species typing of NTM by the naked eye.

CONCLUSIONS: The BiDz-NTMST assay is a novel platform for rapid identification of NTM species. This method is highly specific and significantly faster than current tools and is easily adaptable for onsite diagnostic laboratories in hospitals or clinical laboratories.}, } @article {pmid30535961, year = {2019}, author = {Spirin, V and Malysheva, V and Haelewaters, D and Larsson, KH}, title = {Studies in the Stypella vermiformis group (Auriculariales, Basidiomycota).}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {5}, pages = {753-764}, pmid = {30535961}, issn = {1572-9699}, mesh = {Basidiomycota/*classification/genetics/growth & development/isolation & purification ; Brazil ; Europe ; Norway ; Phylogeny ; Spores, Fungal/classification/genetics/growth & development/isolation & purification ; }, abstract = {Stypella vermiformis is a heterobasidiomycete producing minute gelatinous basidiocarps on rotten wood of conifers in the Northern Hemisphere. In the current literature, Stypella papillata, the genus type of Stypella (described from Brazil), is treated as a taxonomic synonym of S. vermiformis. In the present paper, we revise the type material of S. papillata and a number of specimens addressed to S. vermiformis. As a result, the presumed synonymy of S. papillata and S. vermiformis is rejected and the genus Stypella is restricted to the single species S. papillata. Morphological and molecular phylogenetic studies of specimens from the Northern Hemisphere corresponding to the current concept of S. vermiformis uncovered three species from two newly described genera. S. vermiformis s.str. is distributed in temperate Europe and has small-sized basidia and basidiospores, and it is placed in a new genus, Mycostilla. Another genus, Stypellopsis, is created for two other species, the North American Stypellopsis farlowii, comb. nov., and the North European Stypellopsis hyperborea, sp. nov. Basidia and basidiospores of Stypellopsis spp. are larger than in Mycostilla vermiformis but other morphological characters are very similar. In addition, Spiculogloea minuta (Spiculogloeomycetes, Pucciniomycotina) is reported as new to Norway, parasitising basidiocarps of M. vermiformis and Tulasnella spp.}, } @article {pmid30535845, year = {2019}, author = {Manceau, M and Lambert, A}, title = {The Species Problem from the Modeler's Point of View.}, journal = {Bulletin of mathematical biology}, volume = {81}, number = {3}, pages = {878-898}, doi = {10.1007/s11538-018-00536-2}, pmid = {30535845}, issn = {1522-9602}, mesh = {Animals ; *Biological Evolution ; Genetic Speciation ; Mathematical Concepts ; *Models, Genetic ; Mutation ; *Phylogeny ; Species Specificity ; Systems Biology ; }, abstract = {How to define a partition of individuals into species is a long-standing question called the species problem in systematics. Here, we focus on this problem in the thought experiment where individuals reproduce clonally and both the differentiation process and the population genealogies are explicitly known. We specify three desirable properties of species partitions: (A) Heterotypy between species, (B) Homotypy within species and (M) Genealogical monophyly of each species. We then ask: How and when is it possible to delineate species in a way satisfying these properties? We point out that the three desirable properties cannot in general be satisfied simultaneously, but that any two of them can. We mathematically prove the existence of the finest partition satisfying (A) and (M) and the coarsest partition satisfying (B) and (M). For each of them, we propose a simple algorithm to build the associated phylogeny out of the genealogy. The ways we propose to phrase the species problem shed new light on the interaction between the genealogical and phylogenetic scales in modeling work. The two definitions centered on the monophyly property can readily be used at a higher taxonomic level as well, e.g., to cluster species into monophyletic genera.}, } @article {pmid30534598, year = {2018}, author = {Chung, M and Munro, JB and Tettelin, H and Dunning Hotopp, JC}, title = {Using Core Genome Alignments To Assign Bacterial Species.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, pmid = {30534598}, issn = {2379-5077}, support = {U19 AI110820/AI/NIAID NIH HHS/United States ; }, abstract = {With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in the Rickettsiales. In this study, we generated nucleotide-based core genome alignments for a wide range of genera with classically defined species, as well as those within the Rickettsiales. We created a workflow that uses the length, sequence identity, and phylogenetic relationships inferred from core genome alignments to assign genus and species designations that recapitulate classically obtained results. Using this method, most classically defined bacterial genera have a core genome alignment that is ≥10% of the average input genome length. Both Anaplasma and Neorickettsia fail to meet this criterion, indicating that the taxonomy of these genera should be reexamined. Consistently, genomes from organisms with the same species epithet have ≥96.8% identity of their core genome alignments. Additionally, these core genome alignments can be used to generate phylogenomic trees to identify monophyletic clades that define species and neighbor-network trees to assess recombination across different taxa. By these criteria, Wolbachia organisms are delineated into species different from the currently used supergroup designations, while Rickettsia organisms are delineated into 9 distinct species, compared to the current 27 species. By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method to guide bacterial nomenclature that is aligned with classically obtained results. IMPORTANCE With the increasing availability of genome sequences, we sought to develop and apply a robust, portable, and high-resolution method for the assignment of genera and species designations that can recapitulate classically defined taxonomic designations. Using cutoffs derived from the lengths and sequence identities of core genome alignments along with phylogenetic analyses, we sought to evaluate or reevaluate genus- and species-level designations for diverse taxa, with an emphasis on the order Rickettsiales, where species designations have been applied inconsistently. Our results indicate that the Rickettsia genus has an overabundance of species designations, that the current Anaplasma and Neorickettsia genus designations are both too broad and need to be divided, and that there are clear demarcations of Wolbachia species that do not align precisely with the existing supergroup designations.}, } @article {pmid30520563, year = {2019}, author = {Marais, BJ and Buddle, BM and de Klerk-Lorist, LM and Nguipdop-Djomo, P and Quinn, F and Greenblatt, C}, title = {BCG vaccination for bovine tuberculosis; conclusions from the Jerusalem One Health workshop.}, journal = {Transboundary and emerging diseases}, volume = {66}, number = {2}, pages = {1037-1043}, doi = {10.1111/tbed.13089}, pmid = {30520563}, issn = {1865-1682}, mesh = {Animals ; BCG Vaccine/*administration & dosage ; Cattle ; Congresses as Topic ; Israel ; *Mycobacterium bovis ; One Health ; Tuberculosis, Bovine/*prevention & control ; Vaccination/*veterinary ; }, abstract = {The global burden of bovine tuberculosis (bTB) remains poorly characterized, with spill-over impacts on multiple species. The "One Health" concept is especially relevant given the bidirectional risk of cattle infecting humans with Mycobacterium bovis and humans infecting cattle with Mycobacterium tuberculosis. "Test and cull" is the traditional bTB control method, but the strategy may not be economically feasible or culturally acceptable where cattle are highly prized or their killing is a religious taboo; it is also less effective when there are wildlife reservoirs of infection. Vaccination with M. bovis bacille Calmette-Guerin (BCG) provides protection against bTB, but its use in animals has been limited. The Jerusalem One Health workshop considered key bTB knowledge gaps and innovative solutions. Knowledge gaps identified included (a) the poorly quantified prevalence of M. bovis infection and disease in cattle, domestic camelids and human populations in developing countries, (b) the absence of alternatives to a "test and cull" strategy in settings where the killing of infected animals is culturally or economically unacceptable, or where affected species are protected and (c) an understanding of the induction of mucosal immunity against bTB. We summarize discussions on the use of BCG vaccination in domestic animals and wildlife and list potential projects to address the knowledge gaps identified.}, } @article {pmid30508066, year = {2019}, author = {Train, CM and Pignatelli, M and Altenhoff, A and Dessimoz, C}, title = {iHam and pyHam: visualizing and processing hierarchical orthologous groups.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {14}, pages = {2504-2506}, pmid = {30508066}, issn = {1367-4811}, support = {BB/M015009/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Biological Evolution ; Genome ; *Software ; }, abstract = {SUMMARY: The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species.

iHam's code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam's code is available at https://github.com/DessimozLab/pyHam and or via the pip package 'pyham'.}, } @article {pmid30505002, year = {2018}, author = {Doungsa-Ard, C and McTaggart, AR and Geering, ADW and Shivas, RG}, title = {Diversity of gall-forming rusts (Uromycladium, Pucciniales) on Acacia in Australia.}, journal = {Persoonia}, volume = {40}, number = {}, pages = {221-238}, pmid = {30505002}, issn = {0031-5850}, abstract = {Uromycladium tepperianum has been reported on over 100 species of Acacia, as well as on the closely related plant genera, Falcataria, Racosperma and Paraserianthes. Previous studies have indicated that U. tepperianum may represent a complex of host-specific, cryptic species. The phylogenetic relationships between 79 specimens of Uromycladium were determined based on a concatenated dataset of the Small Subunit, the Internal Transcribed Spacer and the Large Subunit regions of nuclear ribosomal DNA, and the mitochondrial cytochrome c oxidase subunit 3. This study showed that the host range of U. tepperianum s.str. was restricted to species of Acacia in the 'A. bivenosa group' sensu Chapman & Maslin (1992). An epitype of U. tepperianum on A. ligulata is designated to create a stable taxonomy for the application of this name. Sixteen novel species of Uromycladium are described, based on host preference, morphology and a phylogenetic species concept.}, } @article {pmid32467889, year = {2018}, author = {Heuchert, B and Braun, U and Diederich, P and Ertz, D}, title = {Taxonomic monograph of the genus Taeniolella s. lat. (Ascomycota).}, journal = {Fungal systematics and evolution}, volume = {2}, number = {}, pages = {69-261}, pmid = {32467889}, issn = {2589-3831}, abstract = {A taxonomic monograph of the ascomycete genus Taeniolella (asexual dematiaceous hyphomycetes, sexual morphs unknown) is provided. Recent phylogenetic analyses demonstrated the polyphyly of this genus. The type species of Taeniolella pertains to the Kirschsteiniotheliaceae within Dothideomycetes, while other saprobic species clustered far away within Sordariomycetes, Savoryellaceae s. lat., and Lindgomycetaceae, whereas lichenicolous species belong to a monophyletic clade that represents the order Asterotexiales, but for most species assigned to Taeniolella sequence data and phylogenetic analyses are not yet available. The main focus of the present taxonomic study was on a revision of the lichenicolous Taeniolella species. Since the currently available phylogenetic analyses do not allow final taxonomic conclusions at generic rank, the exclusion of lichenicolous species from Taeniolella s. lat. has been postponed pending a broader sampling and more phylogenetic data of allied ascomycete genera within the order Asterotexiales. For the interim, Taeniolella s. lat., including lichenicolous and saprobic species, is maintained. The taxonomic background, history, generic description and discrimination from morphologically confusable genera, phylogeny, biology, host range and distribution, and species concept of Taeniolella species are briefly outlined and discussed. Keys to the species of Taeniolella divided by ecological groups (lichenicolous taxa, saprobic taxa) are provided, supplemented by a tabular key to lichenicolous species based on host (lichen) families and genera. Twenty-nine lichenicolous species and a Taeniolella sp. (putative asexual morph of Sphaerellothecium thamnoliae) as well as 16 saprobic species are described in detail and illustrated by drawings, macroscopic photographs, light microscopic and SEM micrographs, including six new lichenicolous species (T. arctoparmeliae on Arctoparmelia separata, T. lecanoricola on Lecanora rupicola, T. thelotrematis on Thelotrema, T. umbilicariae and T. umbilicariicola on Umbilicaria, T. weberi on Thelotrema weberi), three new saprobic species (T. filamentosa on Salix, T. ravenelii on Quercus, T. stilbosporoides on Salix caprea), and one new combination, T. arthoniae. Most saprobic Taeniolella species are wood-inhabiting (on bark, decorticated trunks and twigs, rotten wood), whereas lichenicolous species grow on thalli and fruiting bodies (mostly apothecia) of lichens, mostly without causing any evident damage, but they are nevertheless confined to their host lichens, or they are obviously pathogenic and cause either disease of the thalli (e.g., Taeniolella chrysothricis and T. delicata) or at least thallus discolorations or necroses (e.g., T. christiansenii, T. chrysothricis, T. cladinicola, T. pseudocyphellariae, and T. strictae). Taeniolella atricerebrina and T. rolfii induce the formation of distinct galls. The range of micro-morphological traits for taxonomic purposes is limited in Taeniolella species, but size, shape and septation of conidiophores and conidia, including surface ornamentation, provided basic characters. Mycelium, stromata and arrangement of conidiophores are less important for the differentiation of species. Lichenicolous species are widespread on a wide range of lichens, with a focus in the northern hemisphere, mainly in northern temperate regions, including arctic-subartic habitats (18 species, i.e., 62 % of the lichenicolous species). Eleven lichenicolous species, e.g., T. pseudocyphellariae, T. santessonii, T. thelotrematis, T. umbilicariae, are also known from collections in non-temperate Asia, Australia and South America (38 % of the species). Most collections deposited in herbaria are from northern temperate to arctic-subarctic regions, which may reflect activities of lichenologists and mycologist dealing with lichenicolous fungi in general and Taeniolella in particular. Most lichenicolous Taeniolella species are confined to hosts of a single lichen genus or few closely allied genera (26 species, i.e., 97 % of the lichenicolous species), but only three species, T. delicata, T. punctata, and T. verrucosa, have wider hosts ranges. Excluded, doubtful and insufficiently known species assigned to Taeniolella are listed at the end, discussed, described and in some cases illustrated, including Talpapellis beschiana comb. nov. (≡ Taeniolella beschiana), Corynespora laevistipitata (≡ Taeniolella laevistipitata), Stanjehughesia lignicola comb. nov. (≡ Taeniolella lignicola), Sterigmatobotrys rudis (≡ Taeniolella rudis), and Taeniolina scripta (≡ Taeniolella scripta).}, } @article {pmid32467888, year = {2018}, author = {Martín, MP and Zhang, LF and Fernández-López, J and Dueñas, M and Rodríguez-Armas, JL and Beltrán-Tejera, E and Telleria, MT}, title = {Hyphoderma paramacaronesicum sp. nov. (Meruliaceae, Polyporales, Basidiomycota), a cryptic lineage to H. macaronesicum.}, journal = {Fungal systematics and evolution}, volume = {2}, number = {}, pages = {57-68}, pmid = {32467888}, issn = {2589-3831}, abstract = {This article re-evaluates the taxonomy of Hyphoderma macaronesicum based on various strategies, including the cohesion species recognition method through haplotype networks, multilocus genetic analyses using the genealogical concordance phylogenetic concept, as well as species tree reconstruction. The following loci were examined: the internal transcribed spacers of nuclear ribosomal DNA (ITS nrDNA), the intergenic spacers of nuclear ribosomal DNA (IGS nrDNA), two fragments of the protein-coding RNA polymerase II subunit 2 (RPB2), and two fragments of the translation elongation factor 1-α (EF1-α). Our results indicate that the name H. macaronesicum includes at least two separate species, one of which is newly described as Hyphoderma paramacaronesicum. The two species are readily distinguished based on the various loci analysed, namely ITS, IGS, RPB2 and EF1-α.}, } @article {pmid30487454, year = {2018}, author = {Sharma, L and Marques, G}, title = {Fusarium, an Entomopathogen-A Myth or Reality?.}, journal = {Pathogens (Basel, Switzerland)}, volume = {7}, number = {4}, pages = {}, pmid = {30487454}, issn = {2076-0817}, abstract = {The Fusarium species has diverse ecological functions ranging from saprophytes, endophytes, and animal and plant pathogens. Occasionally, they are isolated from dead and alive insects. However, research on fusaria-insect associations is very limited as fusaria are generalized as opportunistic insect-pathogens. Additionally, their phytopathogenicity raises concerns in their use as commercial biopesticides. Insect biocontrol potential of Fusarium is favored by their excellent soil survivability as saprophytes, and sometimes, insect-pathogenic strains do not exhibit phytopathogenicity. In addition, a small group of fusaria, those belonging to the Fusarium solani species complex, act as insect mutualists assisting in host growth and fecundity. In this review, we summarize mutualism and pathogenicity among fusaria and insects. Furthermore, we assert on Fusarium entomopathogenicity by analyzing previous studies clearly demonstrating their natural insect-pathogenicity in fields, and their presence in soils. We also review the presence and/or production of a well-known insecticidal metabolite beauvericin by different Fusarium species. Lastly, some proof-of-concept studies are also summarized, which demonstrate the histological as well as immunological changes that a larva undergoes during Fusarium oxysporum pathogenesis. These reports highlight the insecticidal properties of some Fusarium spp., and emphasize the need of robust techniques, which can distinguish phytopathogenic, mutualistic and entomopathogenic fusaria.}, } @article {pmid30486085, year = {2018}, author = {Brower, AVZ}, title = {Alternative facts: a reconsideration of putatively natural interspecific hybrid specimens in the genus Heliconius (Lepidoptera: Nymphalidae).}, journal = {Zootaxa}, volume = {4499}, number = {1}, pages = {1-87}, doi = {10.11646/zootaxa.4499.1.1}, pmid = {30486085}, issn = {1175-5334}, mesh = {Animals ; Biological Evolution ; *Butterflies ; Genome ; *Hybridization, Genetic ; }, abstract = {Mallet et al. (2007 BMC Evolutionary Biology, 7, 28) employed a database of putative interspecific hybrid specimens of the genus Heliconius to advance a hypothesis of "the species boundary as a continuum." Here, each of those specimens, as well as subsequently documented specimens, is individually reassessed regarding its phenotype, potential parentage and chain of custody in collections. Using a quantified scale of reliability, most of the specimens are interpreted differently than Mallet et al.'s identifications, and the actual number of interspecific hybrids is estimated to be much smaller than they proposed. To be specific, of 163 putative hybrid specimens examined, 11% suffered from ambiguous identity, 5% from confounding issues with their data labels, 50% were arguably intraspecific (depending upon alternative species concepts), and 22% were almost certainly reared, commercial specimens. Only eleven of the specimens meet the criteria established here to be legitimate and reliable interspecific hybrids, and all of those are between closely-related species. This result has potentially important implications for current hypotheses of frequent genomic introgression of wing pattern alleles among Heliconius clades.}, } @article {pmid30486046, year = {2018}, author = {Beaulieu, F and Beard, JJ}, title = {Acarine biocontrol agents Neoseiulus californicus sensu Athias-Henriot (1977) and N. barkeri Hughes (Mesostigmata: Phytoseiidae) redescribed, their synonymies assessed, and the identity of N. californicus (McGregor) clarified based on examination of types.}, journal = {Zootaxa}, volume = {4500}, number = {4}, pages = {451-507}, doi = {10.11646/zootaxa.4500.4.1}, pmid = {30486046}, issn = {1175-5334}, mesh = {Animals ; California ; Citrus ; Female ; Male ; *Mites ; Pest Control, Biological ; *Predatory Behavior ; }, abstract = {In 1954, McGregor described two species of phytoseiids from lemon, in California, USA: Typhlodromus californicus McGregor and T. mungeri McGregor, the former represented by one male, and the latter by two females. Since its description, T. mungeri was synonymised under T. californicus, and the name T. (now Neoseiulus) californicus has been used extensively to represent a species that is now commonly used as a biocontrol agent of crop pests worldwide. However, the true identity of the biocontrol agent is uncertain because the original descriptions of T. californicus and T. mungeri were not adequate enough to allow an irrefutable identification, with each description being based on specimens of a single sex. An examination of the types of N. californicus and N. mungeri revealed that they are morphologically identical to the male and female of N. barkeri Hughes, 1948, respectively, and that they are in fact junior synonyms of N. barkeri-and are therefore distinct from the biocontrol agent globally called N. californicus (sensu Athias-Henriot, 1977; see Griffiths, 2015). This is further supported by a comparison with male and female syntypes of N. barkeri, as well as other specimens of N. barkeri including some collected from the type host in the vicinity of the type location (i.e. lemon in southern California, 1952-1958). We redescribe the male and female of both N. barkeri and N. californicus sensu Athias-Henriot (1977), based on representative specimens from at least 14 and 19 populations, respectively. Based on examination of types, we confirm the synonymy of N. mckenziei (Schuster Pritchard, 1963), N. picketti (Specht, 1968), and N. oahuensis (Prasad, 1968) with N. barkeri, and that the names N. chilenensis (Dosse, 1958b) and N. wearnei (Schicha, 1987) represent the same species as N. californicus sensu Athias-Henriot (1977). We also provide a hypothesis as to why Chant (1959) had erroneously synonymised T. californicus and T. mungeri under T. marinus (Willmann). Finally, we suggest maintaining the prevailing usage of the name N. californicus (McGregor) for the species concept of Athias-Henriot (1977) as followed by subsequent authors, through submission of a separate application to the International Commission of Zoological Nomenclature (ICZN). In the meantime, the current meaning of N. californicus should be maintained until a ruling by the ICZN is made on the application.}, } @article {pmid30485588, year = {2018}, author = {Jacobs, RL and Baker, BW}, title = {The species dilemma and its potential impact on enforcing wildlife trade laws.}, journal = {Evolutionary anthropology}, volume = {27}, number = {6}, pages = {261-266}, doi = {10.1002/evan.21751}, pmid = {30485588}, issn = {1520-6505}, mesh = {Animals ; *Animals, Wild ; Conservation of Natural Resources ; Endangered Species/*legislation & jurisprudence ; Forensic Sciences ; Law Enforcement ; *Primates ; United States ; }, abstract = {The varied answers to the question "What is a species?" provoke more than lively debates in academic circles. They pose practical problems for law enforcement. Commercial wildlife trade threatens many primate species and is regulated through such laws and international agreements as the U.S. Endangered Species Act and the Convention on International Trade in Endangered Species of Wild Fauna and Flora. Enforcing legislation relies on the ability to identify when violations occur. Species-defining characters may not be preserved in wildlife trade items. For example, pelage patterns and behavioral characters (e.g., vocalizations) are absent from skulls. Accordingly, identifying victims of illegal trade can be difficult, which hinders enforcement. Moreover, identifying new species and "splitting" of currently recognized species can result in enforcement lags and regulatory loopholes. Although such negative consequences should not hinder scientific advancement, we suggest that they be considered by primate taxonomists and provide recommendations to prevent unintended conservation consequences.}, } @article {pmid30481372, year = {2019}, author = {Klimešová, M and Rindi, F and Škaloud, P}, title = {DNA cloning demonstrates high genetic heterogeneity in populations of the subaerial green alga Trentepohlia (Trentepohliales, Chlorophyta).}, journal = {Journal of phycology}, volume = {55}, number = {1}, pages = {224-235}, doi = {10.1111/jpy.12817}, pmid = {30481372}, issn = {1529-8817}, mesh = {*Chlorophyta ; Cloning, Molecular ; DNA ; Europe ; *Genetic Heterogeneity ; Phylogeny ; }, abstract = {Mats of the green alga Trentepohlia, a genus widely distributed in the tropics as well as temperate regions, have always been perceived as homogeneous (i.e., formed by only one species). As such, their general nature and specific feature play a supportive role in the species delimitation. However, the presence of morphologically dissimilar thalli was observed under the light microscope and when cultivating a piece of a single mat. To address this, we performed DNA cloning of the rbcL gene on mat fragments of T. abietina, T. annulata, T. jolithus and T. umbrina sampled in Europe to reveal if they are composed of one or more species. We revealed that more Trentepohlia haplotypes may coexist in a single mat. In consideration of this, we conclude that the use of material isolated in unialgal culture will be almost mandatory for a taxonomic reassessment of this complicated genus. Another direct implication of this problem is that herbarium specimens consisting of field-collected material should not be used for direct sequencing. We further hypothesize the reasons why multiple haplotypes of Trentepohlia occur more frequently in the tuft-like mats. Possibly, fragments and/or cells of other microalgae, including other species of Trentepohlia, might be retained in such mats more easily than in the crustose trentepohlialean mats.}, } @article {pmid30462683, year = {2018}, author = {Koch, JB and Rodriguez, J and Pitts, JP and Strange, JP}, title = {Phylogeny and population genetic analyses reveals cryptic speciation in the Bombus fervidus species complex (Hymenoptera: Apidae).}, journal = {PloS one}, volume = {13}, number = {11}, pages = {e0207080}, pmid = {30462683}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; Bees/classification/*genetics ; Female ; Gene Frequency ; North America ; Phenotype ; Phylogeny ; Pigmentation/genetics ; Species Specificity ; }, abstract = {Bumble bees (Bombus Latrielle) are significant pollinators of flowering plants due to their large body size, abundant setae, and generalist foraging strategies. However, shared setal coloration patterns among closely and distantly related bumble bee species makes identification notoriously difficult. The advent of molecular genetic techniques has increased our understanding of bumble bee evolution and taxonomy, and enables effective conservation policy and management. Individuals belonging to the North American Bombus fervidus species-complex (SC) are homogenous in body structure but exhibit significant body color phenotype variation across their geographic distribution. Given the uncertainty of the genealogical boundaries within the SC, some authors have synonymized all members of the B. fervidus SC within a single taxon, while others propose an alternative two taxa hypothesis. Operating under the phylogenetic species concept, our analysis supports the hypothesis that there are two independent lineages of bumble bees within the B. fervidus SC. With the current evidence, however, it is not possible to assign valid names to either of them, because both lineages include the color phenotypes found in the original species descriptions of B. fervidus and B. californicus. Cryptic speciation does not seem to be the product of Müllerian mimicry between the clades, because diverging coloration patterns are observed when the distribution of the clades overlaps. Furthermore, within each lineage there is evidence for strong population differentiation that is correlated with geographic distribution rather than color phenotype. In our study, we demonstrate the importance of obtaining a broad sample of multiple populations when conducting lower-level phylogenetic analyses. In addition to improving our knowledge of bumble bee diversification patterns, characterizing the evolutionary history of these pollinators provides the foundation needed to guide contemporary conservation assessments and management strategies.}, } @article {pmid30449355, year = {2018}, author = {Letcher, PM and Powell, MJ}, title = {Morphology, zoospore ultrastructure, and phylogenetic position of Polyphlyctis willoughbyi, a new species in Chytridiales (Chytridiomycota).}, journal = {Fungal biology}, volume = {122}, number = {12}, pages = {1171-1183}, doi = {10.1016/j.funbio.2018.08.003}, pmid = {30449355}, issn = {1878-6146}, mesh = {Chytridiomycota/*classification/*cytology/genetics/ultrastructure ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Microscopy ; Microscopy, Electron, Transmission ; New South Wales ; *Phylogeny ; RNA, Fungal/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; Spores, Fungal/*classification/*cytology/genetics/ultrastructure ; }, abstract = {The purpose of our research is to investigate the morphology, zoospore ultrastructure, and molecular phylogenetic placement of a chytrid from Australia. From a survey of chytrid fungi in New South Wales, Australia, we isolated strain PL AUS 026 and putatively identified it as Polyphlyctis unispina. Light microscopic evaluation determined strain PL AUS 026 to be similar to two other strains of P. unispina characterized in the literature but to have a more complex thallus than that of the type. Molecular phylogenetic analyses placed our strain as sister of or basal to Chytridiaceae, Chytridiales. Ultrastructural analysis of the zoospore of strain PL AUS 026 revealed unique features. On the basis of our analyses we designate strain PL AUS 026 as a new species, Polyphlyctis willoughbyi. This research extends our concept of Chytridiaceae systematics and ultrastructural variation in the Chytridiales zoospore.}, } @article {pmid30443676, year = {2019}, author = {Hettiarachchige, IK and Elkins, AC and Reddy, P and Mann, RC and Guthridge, KM and Sawbridge, TI and Forster, JW and Spangenberg, GC}, title = {Genetic modification of asexual Epichloë endophytes with the perA gene for peramine biosynthesis.}, journal = {Molecular genetics and genomics : MGG}, volume = {294}, number = {2}, pages = {315-328}, pmid = {30443676}, issn = {1617-4623}, mesh = {Alkaloids/genetics ; Animals ; Disease Resistance/genetics ; Endophytes/*genetics ; Epichloe/*genetics/growth & development ; Gene Editing ; Heterocyclic Compounds, 2-Ring/*metabolism ; Pest Control, Biological ; Phylogeny ; Plant Diseases/genetics/microbiology ; Poaceae/*genetics/microbiology ; Polyamines/*metabolism ; Reproduction, Asexual/genetics ; Symbiosis/genetics ; Weevils/genetics/pathogenicity ; }, abstract = {Development of grass-endophyte associations with minimal or no detrimental effects in combination with beneficial characteristics is important for pastoral agriculture. The feasibility of enhancing production of an endophyte-derived beneficial alkaloid through introduction of an additional gene copy was assessed in a proof-of-concept study. Sexual and asexual Epichloë species that form symbiotic associations with cool-season grasses of the Poaceae sub-family Pooideae produce bioactive alkaloids that confer resistance to herbivory by a number of organisms. Of these, peramine is thought to be crucial for protection of perennial ryegrass (Lolium perenne L.) from the Argentinian stem weevil, an economically important exotic pest in New Zealand, contributing significantly to pasture persistence. A single gene (perA) has been identified as solely responsible for peramine biosynthesis and is distributed widely across Epichloë taxa. In the present study, a functional copy of the perA gene was introduced into three recipient endophyte genomes by Agrobacterium tumefaciens-mediated transformation. The target strains included some that do not produce peramine, and others containing different perA gene copies. Mitotically stable transformants generated from all three endophyte strains were able to produce peramine in culture and in planta at variable levels. In summary, this study provides an insight into the potential for artificial combinations of alkaloid biosynthesis in a single endophyte strain through transgenesis, as well as the possibility of using novel genome editing techniques to edit the perA gene of non-peramine producing strains.}, } @article {pmid30415103, year = {2018}, author = {Schuler, GA and Tice, AK and Pearce, RA and Foreman, E and Stone, J and Gammill, S and Willson, JD and Reading, C and Silberman, JD and Brown, MW}, title = {Phylogeny and Classification of Novel Diversity in Sainouroidea (Cercozoa, Rhizaria) Sheds Light on a Highly Diverse and Divergent Clade.}, journal = {Protist}, volume = {169}, number = {6}, pages = {853-874}, doi = {10.1016/j.protis.2018.08.002}, pmid = {30415103}, issn = {1618-0941}, mesh = {Cercozoa/*classification/cytology/genetics/*isolation & purification ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Environmental Microbiology ; Microscopy ; Microscopy, Electron, Transmission ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Sainouroidea is a molecularly diverse clade of cercozoan flagellates and amoebae in the eukaryotic supergroup Rhizaria. Previous 18S rDNA environmental sequencing of globally collected fecal and soil samples revealed great diversity and high sequence divergence in the Sainouroidea. However, a very limited amount of this diversity has been observed or described. The two described genera of amoebae in this clade are Guttulinopsis, which displays aggregative multicellularity, and Rosculus, which does not. Although the identity of Guttulinopsis is straightforward due to the multicellular fruiting bodies they form, the same is not true for Rosculus, and the actual identity of the original isolate is unclear. Here we isolated amoebae with morphologies like that of Guttulinopsis and Rosculus from many environments and analyzed them using 18S rDNA sequencing, light microscopy, and transmission electron microscopy. We define a molecular species concept for Sainouroidea that resulted in the description of 4 novel genera and 12 novel species of naked amoebae. Aggregative fruiting is restricted to the genus Guttulinopsis, but other than this there is little morphological variation amongst these taxa. Taken together, simple identification of these amoebae is problematic and potentially unresolvable without the 18S rDNA sequence.}, } @article {pmid30409685, year = {2019}, author = {Sun, WB and Ma, YP and Blackmore, S}, title = {How a New Conservation Action Concept Has Accelerated Plant Conservation in China.}, journal = {Trends in plant science}, volume = {24}, number = {1}, pages = {4-6}, doi = {10.1016/j.tplants.2018.10.009}, pmid = {30409685}, issn = {1878-4372}, mesh = {China ; *Conservation of Natural Resources ; *Endangered Species ; *Plants ; }, abstract = {Since 2005, a new conservation action concept has been implemented to address the most threatened plant species requiring priority conservation in China. The concept is now widely recognized at different levels of governmental departments and by the general public, and is leading to great achievements for plant conservation in China.}, } @article {pmid30405566, year = {2018}, author = {Holzapfel, M and Girault, G and Keriel, A and Ponsart, C and O'Callaghan, D and Mick, V}, title = {Comparative Genomics and in vitro Infection of Field Clonal Isolates of Brucella melitensis Biovar 3 Did Not Identify Signature of Host Adaptation.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2505}, pmid = {30405566}, issn = {1664-302X}, abstract = {Brucella spp. are responsible for brucellosis, a widespread zoonosis causing reproductive disorders in animals. Species-classification within this monophyletic genus is based on bacteriological and biochemical phenotyping. Traditionally, Brucella species are reported to have a preferential, but not exclusive mammalian host. However, this concept can be challenged since many Brucella species infect a wide range of animal species. Adaptation to a specific host can be a driver of pathogen variation. It is generally thought that Brucella species have highly stable and conserved genomes, however the degree of genomic variation during natural infection has not been documented. Here, we investigated potential genetic diversity and virulence of Brucella melitensis biovar 3 field isolates obtained from a single outbreak but from different host species (human, bovine, small ruminants). A unique MLVA-16 pattern suggested all isolates were clonal. Comparative genomic analyses showed an almost non-existent genetic diversity among isolates (only one SNP; no architectural rearrangements) and did not highlight any signature specific to host adaptation. Similarly, the strains showed identical capacities to enter and replicate in an in vitro model of macrophage infection. In our study, the absence of genomic variability and similar virulence underline that B. melitensis biovar 3 is a broad-host-range pathogen without the need to adapt to different hosts.}, } @article {pmid30397261, year = {2019}, author = {Meziti, A and Tsementzi, D and Rodriguez-R, LM and Hatt, JK and Karayanni, H and Kormas, KA and Konstantinidis, KT}, title = {Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient.}, journal = {The ISME journal}, volume = {13}, number = {3}, pages = {767-779}, pmid = {30397261}, issn = {1751-7370}, mesh = {Bacteria/*genetics/isolation & purification ; Bacterial Proteins/genetics ; Ecosystem ; Fresh Water/microbiology ; *Genetic Variation ; Genome, Bacterial/*genetics ; Greece ; Microbiota/*genetics ; Rivers/*microbiology ; Seasons ; Time Factors ; }, abstract = {Recent diversity studies have revealed that microbial communities of natural environments are dominated by species-like, sequence-discrete populations. However, how stable the sequence and gene-content diversity are within these populations and especially in highly dynamic lotic habitats remain unclear. Here we quantified the dynamics of intra-population diversity in samples spanning two years and five sites in the Kalamas River (Northwest Greece). A significant positive correlation was observed between higher intra-population sequence diversity and longer persistence over time, revealing that more diverse populations tended to represent more autochthonous (vs. allochthonous) community members. Assessment of intra-population gene-content changes caused by strain replacement or gene loss over time revealed different profiles with the majority of populations exhibiting gene-content changes close to 10% of the total genes, while one population exhibited ~21% change. The variable genes were enriched in hypothetical proteins and mobile elements, and thus, were probably functionally neutral or attributable to phage predation. A few notable exceptions to this pattern were also noted such as phototrophy-related proteins in summer vs. winter populations. Taken together, these results revealed that some freshwater genomes are remarkably dynamic, even across short time and spatial scales, and have implications for the bacterial species concept and microbial source tracking.}, } @article {pmid30376154, year = {2018}, author = {Castorani, MCN and Reed, DC and Miller, RJ}, title = {Loss of foundation species: disturbance frequency outweighs severity in structuring kelp forest communities.}, journal = {Ecology}, volume = {99}, number = {11}, pages = {2442-2454}, doi = {10.1002/ecy.2485}, pmid = {30376154}, issn = {0012-9658}, support = {1232779//National Science Foundation/International ; }, mesh = {Animals ; Ecosystem ; Forests ; Invertebrates ; *Kelp ; *Macrocystis ; }, abstract = {Disturbances often cause the disproportionate loss of foundation species but understanding how the frequency and severity of disturbance to such organisms influence biological communities remains unresolved. This gap in knowledge exists in part because of the rarity of ecologically meaningful studies capable of disentangling different elements of disturbance. Hence, we carried out a long-term (9 yr), large-scale (2,000 m[2] plots), spatially replicated (4 sites) field experiment in which we manipulated disturbance to a globally distributed marine foundation species, the giant kelp Macrocystis pyrifera, and tracked community responses over time. To distinguish the effects of disturbance frequency and severity on the biodiversity and composition of temperate rocky reef communities, we simulated the repeated loss of giant kelp from destructive winter waves across a background of natural variation in disturbance. By following the response of over 200 taxa from the surrounding community, we discovered that the frequency of disturbance to giant kelp changed the biomass, diversity, and composition of community guilds in a manner commensurate with their dependence on the physical (i.e., benthic light and space), trophic (i.e., living and detrital biomass), and habitat (i.e., biogenic structure) resources mediated by this foundation species. Annual winter disturbance to giant kelp reduced living and detrital giant kelp biomass by 57% and 40%, respectively, enhanced bottom light by 22%, and halved the seafloor area covered by giant kelp holdfasts. Concomitantly, the biomass of understory algae and epilithic sessile invertebrates more than doubled, while the biomass of rock-boring clams, mobile invertebrates, and fishes decreased 30-61%. Frequent loss of giant kelp boosted understory algal richness by 82% and lowered sessile invertebrate richness by 13% but did not affect the biodiversity of mobile fauna. In contrast to changes driven by disturbance frequency, interannual variation in the severity of disturbance to giant kelp had weaker, less consistent effects, causing only modest changes in assemblages of sessile invertebrates, mobile invertebrate herbivores, and fishes. Our results broaden the foundation species concept by demonstrating that repeated disturbance to a dominant habitat-forming species can outweigh the influence of less frequent but severe disturbances for the surrounding community.}, } @article {pmid30374135, year = {2018}, author = {Haelewaters, D and De Kesel, A and Pfister, DH}, title = {Integrative taxonomy reveals hidden species within a common fungal parasite of ladybirds.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15966}, pmid = {30374135}, issn = {2045-2322}, mesh = {Animals ; Ascomycota/classification/genetics/isolation & purification/*physiology ; Coleoptera/*parasitology ; DNA, Fungal/chemistry/genetics/metabolism ; DNA, Ribosomal Spacer/chemistry/genetics/metabolism ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA ; }, abstract = {Our understanding of fungal diversity is far from complete. Species descriptions generally focus on morphological features, but this approach may underestimate true diversity. Using the morphological species concept, Hesperomyces virescens (Ascomycota, Laboulbeniales) is a single species with global distribution and wide host range. Since its description 120 years ago, this fungal parasite has been reported from 30 species of ladybird hosts on all continents except Antarctica. These host usage patterns suggest that H. virescens could be made up of many different species, each adapted to individual host species. Using sequence data from three gene regions, we found evidence for distinct clades within Hesperomyces virescens, each clade corresponding to isolates from a single host species. We propose that these lineages represent separate species, driven by adaptation to different ladybird hosts. Our combined morphometric, molecular phylogenetic and ecological data provide support for a unified species concept and an integrative taxonomy approach.}, } @article {pmid30371872, year = {2019}, author = {Zink, RM and Vázquez-Miranda, H}, title = {Species Limits and Phylogenomic Relationships of Darwin's Finches Remain Unresolved: Potential Consequences of a Volatile Ecological Setting.}, journal = {Systematic biology}, volume = {68}, number = {2}, pages = {347-357}, doi = {10.1093/sysbio/syy073}, pmid = {30371872}, issn = {1076-836X}, mesh = {Animals ; *Ecosystem ; Ecuador ; Finches/*classification/genetics ; Genetic Variation ; Genome/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin's finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin's finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies of prior data and analytic methods explained different proposed classifications, we were surprised to observe that three new phylogenetic hypotheses derived mostly from the same genomics data were topologically inconsistent. We found that the differences between some of these genomics trees were as great as one would expect between two random trees with the same number of taxa. Thus, the phylogeny of Darwin's finches remains unresolved, as it has for more than a century. A component of phylogenetic uncertainty comes from unclear species limits, under any species concept, in the ground finches (Geospiza) and tree finches (Camarhynchus). We suggest that past authors should have tested the species limits of Lack, rather than uncritically accepting them. In fact, the impressive amount of genomics data do not provide unambiguous hypotheses of the number of species of Geospiza or Camarhynchus, although they imply greater species diversity than Lack's taxonomy. We suggest that insufficient sampling of species populations across islands (35.6% for morphometrics and 20.4% for genomics) prevents accurate diagnoses of species limits. However, it is unknown whether samples from a greater number of islands might result in bridging differences between species, or reveal many new ones. We conclude that attempts to interpret patterns of variation among the finches under standard evolutionary paradigms have obscured some major messages, most specifically the ongoing reciprocal interactions between geographic isolation and lineage divergence, and dispersal and gene flow caused by the volatile ecological conditions in the islands. Although the finches provide textbook examples of natural selection, better understanding of species limits and a robust phylogenetic hypothesis are required to corroborate past hypotheses of speciation and adaptive radiation in the finches of the Galapagos.}, } @article {pmid30367487, year = {2018}, author = {Vernygora, OV and Davis, CS and Murray, AM and Sperling, FAH}, title = {Delimitation of Alosa species (Teleostei: Clupeiformes) from the Sea of Azov: integrating morphological and molecular approaches.}, journal = {Journal of fish biology}, volume = {93}, number = {6}, pages = {1216-1228}, doi = {10.1111/jfb.13847}, pmid = {30367487}, issn = {1095-8649}, mesh = {Animals ; Biological Evolution ; Body Size ; Cytochromes b/chemistry/genetics ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/chemistry/genetics ; Fishes/anatomy & histology/classification/*genetics ; Gills ; Phylogeography ; Polymorphism, Single Nucleotide ; Species Specificity ; }, abstract = {Shads of the genus Alosa are essential to commercial fisheries across North America and Europe, but in some areas their species boundaries remain controversial. Traditional morphology-based taxonomy of Alosa spp. has relied heavily on the number of gill rakers and body proportions, but these can be highly variable. We use mitochondrial (mt)DNA (coI and cytb) and genome-wide single nucleotide polymorphisms (SNP) along with morphological characters to assess differentiation among endemic Ponto-Caspian shads in the Sea of Azov. Morphological species assignments based on gill-raker number were not congruent with genetic lineages shown by mtDNA and SNPs. Iterative analysis revealed that genetic lineages were associated with sampling location and several other morphometric traits (caudal peduncle depth, pre-anal length and head length). Phylogenetic analysis of the genus placed Ponto-Caspian Alosa spp. in the same evolutionary lineage as endangered Alosa spp. endemic to Greece, highlighting the importance of these findings to conservation management. We conclude that gill-raker number is not reliable for delimiting species of Alosa. This taxonomic uncertainty should be addressed by examining type material to provide a robust integrative classification for these commercially important fishes.}, } @article {pmid30343986, year = {2018}, author = {Dantas-Torres, F}, title = {Species Concepts: What about Ticks?.}, journal = {Trends in parasitology}, volume = {34}, number = {12}, pages = {1017-1026}, doi = {10.1016/j.pt.2018.09.009}, pmid = {30343986}, issn = {1471-5007}, mesh = {Animals ; *Classification ; Species Specificity ; *Ticks ; }, abstract = {Since ancient times, philosophers and taxonomists have tried to classify forms of life. This is what taxonomy is about: the science of identifying, naming, classifying, and describing organisms. In this article I address the issue of the species concept in tick taxonomy. While the typological species concept is still the most widely used, the biological and phylogenetic species concepts are growing in popularity among tick taxonomists. The integrative approach is increasingly being used, but the question is how to define a tick species when using this approach, particularly if data are incongruent. The adoption of an integrative species concept is discussed, in light of recent advances in our understanding of the genetics, morphology, and biology of ticks.}, } @article {pmid30341078, year = {2019}, author = {Suga, H and Arai, M and Fukasawa, E and Motohashi, K and Nakagawa, H and Tateishi, H and Fuji, SI and Shimizu, M and Kageyama, K and Hyakumachi, M}, title = {Genetic Differentiation Associated with Fumonisin and Gibberellin Production in Japanese Fusarium fujikuroi.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {1}, pages = {}, pmid = {30341078}, issn = {1098-5336}, mesh = {Drug Resistance, Fungal/*genetics ; Fumonisins/*metabolism ; Fungicides, Industrial/*pharmacology ; Fusarium/drug effects/*genetics/pathogenicity ; Gibberellins/*metabolism ; Japan ; Oryza/microbiology ; Plant Diseases/microbiology ; *Polymorphism, Genetic ; Thiophanate/*pharmacology ; Virulence ; }, abstract = {Fusarium fujikuroi is a pathogenic fungus that infects rice. It produces several important mycotoxins, such as fumonisins. Fumonisin production has been detected in strains of maize, strawberry, and wheat, whereas it has not been detected in strains from rice seedlings infested with bakanae disease in Japan. We investigated the genetic relationships, pathogenicity, and resistance to a fungicide, thiophanate-methyl (TM), in 51 fumonisin-producing strains and 44 nonproducing strains. Phylogenetic analyses based on amplified fragment length polymorphism (AFLP) markers and two specific genes (a combined sequence of translation elongation factor 1α [TEF1α] and RNA polymerase II second-largest subunit [RPB2]) indicated differential clustering between the fumonisin-producing and -nonproducing strains. One of the AFLP markers, EATMCAY107, was specifically present in the fumonisin-producing strains. A specific single nucleotide polymorphism (SNP) between the fumonisin-producing and nonproducing strains was also detected in RPB2, in addition to an SNP previously found in TEF1α. Gibberellin production was higher in the nonproducing than in the producing strains according to an in vitro assay, and the nonproducing strains had the strongest pathogenicity with regard to rice seedlings. TM resistance was closely correlated with the cluster of fumonisin-nonproducing strains. The results indicate that intraspecific evolution in Japanese F. fujikuroi is associated with fumonisin production and pathogenicity. Two subgroups of Japanese F. fujikuroi, designated G group and F group, were distinguished based on phylogenetic differences and the high production of gibberellin and fumonisin, respectively.IMPORTANCEFusarium fujikuroi is a pathogenic fungus that causes rice bakanae disease. Historically, this pathogen has been known as Fusarium moniliforme, along with many other species based on a broad species concept. Gibberellin, which is currently known as a plant hormone, is a virulence factor of F. fujikuroi Fumonisin is a carcinogenic mycotoxin posing a serious threat to food and feed safety. Although it has been confirmed that F. fujikuroi produces gibberellin and fumonisin, production varies among strains, and individual production has been obscured by the traditional appellation of F. moniliforme, difficulties in species identification, and variation in the assays used to determine the production of these secondary metabolites. In this study, we discovered two phylogenetic subgroups associated with fumonisin and gibberellin production in Japanese F. fujikuroi.}, } @article {pmid30336287, year = {2019}, author = {Pei, P and Sun, C and Tao, W and Li, J and Yang, X and Wang, J}, title = {ROS-sensitive thioketal-linked polyphosphoester-doxorubicin conjugate for precise phototriggered locoregional chemotherapy.}, journal = {Biomaterials}, volume = {188}, number = {}, pages = {74-82}, doi = {10.1016/j.biomaterials.2018.10.010}, pmid = {30336287}, issn = {1878-5905}, mesh = {Animals ; Antibiotics, Antineoplastic/*administration & dosage/pharmacokinetics/therapeutic use ; Cell Line, Tumor ; Chlorophyllides ; Delayed-Action Preparations/*chemistry ; Doxorubicin/*administration & dosage/pharmacokinetics/therapeutic use ; Drug Delivery Systems ; Drug Liberation ; Female ; Light ; Mice ; Mice, Inbred BALB C ; Nanoparticles/chemistry ; Neoplasms/drug therapy/metabolism/pathology ; Photosensitizing Agents/*administration & dosage/pharmacokinetics/therapeutic use ; Porphyrins/*administration & dosage/pharmacokinetics/therapeutic use ; Reactive Oxygen Species/*metabolism ; }, abstract = {Minimizing drug leakage at off-target sites and triggering sufficient drug release in tumor tissue are major objectives for effective nanoparticle (NP)-based cancer therapy. The current covalent and cleavable drug-NP conjugation strategy is promising but lacks high controllability to realize tumor-specific release. As a proof-of-concept, the reactive oxygen species (ROS)-activatable thioketal (TK) bond was explored as the linkage between doxorubicin (DOX) and polyphosphoester (PPE-TK-DOX). The Ce6@PPE-TK-DOX NPs constructed by co-self-coassembly of PPE-TK-DOX and the photosensitizer Ce6 efficiently prevented premature drug leakage in the off-target tissue and cells because of the high stability of the TK bond under physiological conditions. Once circulating into the tumor site, the 660-nm red light was precisely employed to irradiate the tumor area under the guidance of fluorescence/magnetic resonance (MR) dual-model imaging, which can induce localized ROS generation, resulting in rapid cleavage of the TK bond. Consequently, the DOX prodrug was locoregionally released and activated, achieving tumor-specific drug delivery with high controllability by light. Such phototriggered prodrug release and activation at the desired site significantly enhanced the therapeutic efficacy and minimized the side effect, providing new avenues to develop drug delivery systems for remote on-demand drug delivery in vivo.}, } @article {pmid30319671, year = {2018}, author = {Lazcano-Ramírez, HG and Gómez-Felipe, A and Díaz-Ramírez, D and Durán-Medina, Y and Sánchez-Segura, L and de Folter, S and Marsch-Martínez, N}, title = {Non-destructive Plant Morphometric and Color Analyses Using an Optoelectronic 3D Color Microscope.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1409}, pmid = {30319671}, issn = {1664-462X}, abstract = {Gene function discovery in plants, as other plant science quests, is aided by tools that image, document, and measure plant phenotypes. Tools that acquire images of plant organs and tissues at the microscopic level have evolved from qualitative documentation tools, to advanced tools where software-assisted analysis of images extracts quantitative information that allows statistical analyses. They are useful to perform morphometric studies that describe plant physical characteristics and quantify phenotypes, aiding gene function discovery. In parallel, non-destructive, versatile, robust, and user friendly technologies have also been developed for surface topography analysis and quality control in the industrial manufacture sector, such as optoelectronic three-dimensional (3D) color microscopes. These microscopes combine optical lenses, electronic image sensors, motorized stages, graphics engines, and user friendly software to allow the visualization and inspection of objects of diverse sizes and shapes from different angles. This allow the integration of different automatically obtained images along the Z axis of an object, into a single image with a large depth-of-field, or a 3D model in color. In this work, we explored the performance of an optoelectronic microscope to study plant morphological phenotypes and plant surfaces in different model species. Furthermore, as a "proof-of-concept," we included the phenotypic characterization (morphometric analyses at the organ level, color, and cell size measurements) of Arabidopsis mutant leaves. We found that the microscope tested is a suitable, practical, and fast tool to routinely and precisely analyze different plant organs and tissues, producing both high-quality, sharp color images and morphometric and color data in real time. It is fully compatible with live plant tissues (no sample preparation is required) and does not require special conditions, high maintenance, nor complex training. Therefore, though barely reported in plant scientific studies, optoelectronic microscopes should emerge as convenient and useful tools for phenotypic characterization in plant sciences.}, } @article {pmid30314212, year = {2018}, author = {GÓmez, P and GonzÁlez-Acosta, B and SÁnchez-ortÍz, C and Hoffman, Z and HernÁndez-Guerrero, CJ}, title = {Amended definitions for Aplysinidae and Aplysina (Porifera, Demospongiae, Verongiida): on three new species from a remarkable population in the Gulf of California.}, journal = {Zootaxa}, volume = {4455}, number = {2}, pages = {322-342}, doi = {10.11646/zootaxa.4455.2.4}, pmid = {30314212}, issn = {1175-5334}, mesh = {Animals ; California ; *Porifera ; Sympatry ; }, abstract = {Verongiid sponges inhabiting the La Paz region, Gulf of California are described herein as new species. Although morphological evidence was sufficient to determine the identity between species, we have confirmed their uniqueness and relationships with molecular (CO1 and ITS1 and 2), and ecological studies. An amended definition of family Aplysinidae and genus Aplysina is presented to highlight a novel skeletal trait for the latter, clearly described herein as a complex of dendritic fibers sustained by anastomosed fibers deep in the choanosome. This novel fiber arrangement combination is a constant trait of Aplysina encarnacionae sp. nov. and A. airapii sp. nov., which otherwise conform to our current concept of Aplysina. The former species has a long tubular morphology, reddish purple color, with the longest dendritic fibers; while A. airapii sp. nov. is a short tubular sponge, yellow with reddish tints, and smaller choanosomal dendritic fibers that depart from a uniplanar anastomosed skeleton. A third species, A. sinuscaliforniensis sp. nov., is characterized by a completely anastomosed skeleton, massive habit with short tubes superimposed one over the other, sympatric with the other new species. Comparisons with Suberea azteca verified that the same novel skeletal architecture described here occurs in the latter, while Aiolochroia thiona examined as well, proved to bear an anastomosed skeleton only, besides sharing more features with Aplysina than with any other genera in Verongiida. Moreover, molecular sequencing recovered "S." azteca nested in the Aplysina clade, prompting us to reallocate it in Aplysina, as originally proposed. The new species described herein are probably endemics within the Gulf of California since they have not been recorded elsewhere along the Mexican Pacific coast.}, } @article {pmid30281867, year = {2019}, author = {Lewis, AM and Chan, AN and LaJeunesse, TC}, title = {New Species of Closely Related Endosymbiotic Dinoflagellates in the Greater Caribbean have Niches Corresponding to Host Coral Phylogeny.}, journal = {The Journal of eukaryotic microbiology}, volume = {66}, number = {3}, pages = {469-482}, doi = {10.1111/jeu.12692}, pmid = {30281867}, issn = {1550-7408}, mesh = {Animals ; Anthozoa/*parasitology ; Caribbean Region ; *Coral Reefs ; DNA, Protozoan/analysis ; Dinoflagellida/*classification/physiology ; Florida ; Gulf of Mexico ; Phylogeny ; *Symbiosis ; }, abstract = {Symbiotic dinoflagellates in the genus Breviolum (formerly Symbiodinium Clade B) dominate coral communities in shallow waters across the Greater Caribbean. While some formally described species exist, mounting genetic, and ecological evidence indicate that numerous more comprise this genus, many of which are closely related. To test this, colonies of common reef-building corals were sampled across a large geographical range. Phylogenetic and population genetic markers then used to examine evolutionary divergence and delineate boundaries of genetic recombination. Three new candidate species were distinguished by fixed differences in nucleotide sequences from nuclear and chloroplast DNA. Population connectivity was evident within each lineage over thousands of kilometers, however, substantial genetic structure persisted between lineages co-occurring within sampling locations, signifying reproductive isolation. While geographically widespread with overlapping distributions, each species is ecologically distinct, exhibiting specific mutualisms with phylogenetically distinct coral hosts. Moreover, significant differences in mean cell sizes provide some morphological evidence substantiating formal species distinctions. In providing evidence that satisfies the biological, phylogenetic, ecological, and morphological species concepts, we classify and formally name Breviolum faviinorum n. sp., primarily associated with Caribbean corals belonging to the Caribbean subfamily Faviinae; B. meandrinium n. sp., associated with corals belonging to the family Meandrinidae; and B. dendrogyrum n. sp., a symbiont harbored exclusively by the threatened coral Dendrogyra cylindrus. These findings support the primary importance of niche diversification (i.e. host habitat) in the speciation of symbiotic dinoflagellates.}, } @article {pmid30271536, year = {2018}, author = {Bernardi, G and Nelson, P and Paddack, M and Rulmal, J and Crane, N}, title = {Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes.}, journal = {Ecology and evolution}, volume = {8}, number = {17}, pages = {8676-8685}, pmid = {30271536}, issn = {2045-7758}, abstract = {The current ease of obtaining thousands of molecular markers challenges the notion that full phylogenetic concordance, as proposed by phylogenetic species concepts, is a requirement for defining species delimitations. Indeed, the presence of genomic islands of divergence, which may be the cause, or in some cases the consequence, of speciation, precludes concordance. Here, we explore this issue using thousands of RAD markers on two sister species of surgeonfishes (Teleostei: Acanthuridae), Zebrasoma flavescens and Z. scopas, and several populations within each species. Species are readily distinguished based on their colors (solid yellow and solid brown, respectively), yet populations and species are neither distinguishable using mitochondrial markers (cytochrome c oxidase 1), nor using 5193 SNPs (pairwise Φst = 0.034). In contrast, when using outlier loci, some of them presumably under selection, species delimitations, and strong population structure follow recognized taxonomic positions (pairwise Φst = 0.326). Species and population delimitation differences based on neutral and selected markers are likely due to local adaptation, thus being consistent with the idea that these genomic islands of divergence arose as a consequence of isolation. These findings, which are not unique, raise the question of a potentially important pathway of divergence based on local adaptation that is only evident when looking at thousands of loci.}, } @article {pmid30262692, year = {2018}, author = {Zachos, FE}, title = {(New) Species concepts, species delimitation and the inherent limitations of taxonomy.}, journal = {Journal of genetics}, volume = {97}, number = {4}, pages = {811-815}, pmid = {30262692}, issn = {0973-7731}, mesh = {Animals ; *Biodiversity ; *Classification ; Phylogeny ; *Species Specificity ; }, abstract = {The species problem, despite decades of heated debates, has not been resolved yet. Recently, two new species concepts have been published, the mitonuclear compatibility species concept and the inclusive species concept. I briefly discuss them, together with a recent attempt at standardizing taxonomic decisions, in the broader framework of what I believe is an inherent limitation of taxonomy-imposing a discrete system on a continuous process (evolution) that leads to fuzzy boundaries in nature. In the light of this, taxonomists, biologists in general and conservationists alike will have to accept the fact that completely nonarbitrary species delimitation is impossible. This has serious ramifications in all disciplines that rely on species, and particularly species counts, as a basic currency for quantitative analyses (ecology, evolutionary biology) and practical decision-making (conservation and environmental policy).}, } @article {pmid30258001, year = {2018}, author = {Schenk, C and Meyrath, M and Warnken, U and Schnölzer, M and Mier, W and Harak, C and Lohmann, V}, title = {Characterization of a Threonine-Rich Cluster in Hepatitis C Virus Nonstructural Protein 5A and Its Contribution to Hyperphosphorylation.}, journal = {Journal of virology}, volume = {92}, number = {24}, pages = {}, pmid = {30258001}, issn = {1098-5514}, mesh = {Cell Line ; Hepacivirus/*physiology ; Humans ; Mass Spectrometry ; Mutation ; Phosphorylation ; Proteomics ; Threonine/*metabolism ; Viral Nonstructural Proteins/chemistry/*genetics/*metabolism ; Virus Assembly ; Virus Replication ; }, abstract = {Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a phosphoprotein with key functions in regulating viral RNA replication and assembly. Two phosphoisoforms are discriminated by their different apparent molecular weights: a basally phosphorylated (p56) and a hyperphosphorylated (p58) variant. The precise mechanisms governing p58 synthesis and specific functions of the isoforms are poorly understood. Our study aimed at a deeper understanding of determinants involved in p58 synthesis. We analyzed two variants of p56 and p58 of isolate JFH-1 separately by mass spectrometry using an expression model and thereby identified a threonine-rich phosphopeptide exclusively found in the hyperphosphorylated variant. Individual exchange of possible phosphoacceptor sites to phosphoablatant or -mimetic residues had little impact on HCV replication or assembly in cell culture. A phosphospecific antibody recognizing pT242 revealed that this position was indeed phosphorylated only in p58 and depended on casein kinase Iα. Importantly, phosphoablative mutations at positions T244 and S247 abrogated pT242 detection without substantial effects on global p58 levels, whereas mutations in the preceding serine-rich cluster dramatically reduced total p58 levels but had minor impact on pT242 levels, suggesting the existence of distinct subspecies of hyperphosphorylated NS5A. Mass spectrometry analyses of different genotypes showed variable phosphorylation patterns across NS5A and suggested that the threonine-rich region is also phosphorylated at T242 in gt4a and at S249 in gt1a, gt1b, and gt4a. Our data therefore indicate that p58 is not a single homogenously phosphorylated protein species but rather a population of various phosphoisoforms, with high variability between genotypes.IMPORTANCE Hepatitis C virus infections affect 71 million people worldwide and cause severe chronic liver disease. Recently, efficient antiviral therapies have been established, with inhibitors of nonstructural protein NS5A as a cornerstone. NS5A is a central regulator of HCV replication and assembly but is still enigmatic in its molecular functions. It exists in two phosphoisoforms, p56 and p58. We identified a phosphopeptide exclusively found in p58 and analyzed the determinants involved in phosphorylation of this region. We found evidence for very different phosphorylation patterns resulting in p58. These results challenge the concept of p58 being a homogenous species of NS5A molecules phosphorylated at the same positions and argues for at least two independently phosphorylated variants showing the same electrophoretic mobility, likely serving different functions.}, } @article {pmid30253250, year = {2018}, author = {Yesinowski, JP and Miller, JB and Klug, CA and Ricks-Laskoski, HL}, title = {Optorelaxers: Achieving real-time control of NMR relaxation.}, journal = {Solid state nuclear magnetic resonance}, volume = {96}, number = {}, pages = {1-9}, doi = {10.1016/j.ssnmr.2018.09.002}, pmid = {30253250}, issn = {1527-3326}, abstract = {We present an approach to increase the detection sensitivity of NMR by shortening the spin-lattice relaxation time using transient paramagnetic species created by light irradiation of "optorelaxer" molecules. In the ultimate implementation of this concept, not yet realized here, these transient species are absent during the detection period, thereby avoiding the loss of spectral resolution caused by inhomogeneous broadening from paramagnetic species. Real-time control of NMR relaxation by visible light is demonstrated with Fe(II)(ptz)6(BF4)2, (ptz = 1-propyltetrazole), abbreviated FePTZ. Illumination of FePTZ at 30 K results in a decrease of the [1]H NMR spin-lattice relaxation time T1 due to formation of a high spin photoexcited state. The [1]H NMR of polystyrene containing a low concentration of FePTZ molecules shows a similar reduction in T1, establishing that FePTZ can act as an optorelaxer for the protons of a matrix. Numerical modeling of the spin-diffusion processes from the protons in a FePTZ core to those in a shell of polystyrene accounts for the observed T1 effects under both dark and light conditions. Additionally, [1]H MAS (magic-angle spinning) NMR results for pure FePTZ provide information on the isotropic and anisotropic portions of the electron-nuclear hyperfine interactions.}, } @article {pmid30247671, year = {2018}, author = {Lachance, MA}, title = {C. P. Kurtzman's evolving concepts of species, genus and higher categories.}, journal = {FEMS yeast research}, volume = {18}, number = {8}, pages = {}, doi = {10.1093/femsyr/foy103}, pmid = {30247671}, issn = {1567-1364}, mesh = {Classification/*methods ; *Evolution, Molecular ; History, 20th Century ; History, 21st Century ; Mycology/history/*methods ; *Phylogeny ; Yeasts/*classification/*genetics ; }, abstract = {Cletus P. Kurtzman transformed the way yeast systematists practice their trade and how they perceive the yeast species. He redefined many genera of ascomycetous yeasts and provided a sound basis upon which to base higher taxonomic categories. Within his extraordinary corpus lies a trail of elements that can be used to reconstruct his evolving vision of the concepts that underlie the species and the genus, rarely set in a theoretical framework. While occasionally tipping his hat to the biological and phylogenetic species, Kurtzman espoused a concept founded primarily on genetic distance, even when claiming otherwise. In contrast, his notion of genus incorporated components of both genetic distance and phylogenetic structure, and possibly a size consideration. A phylogenetic approach predominated with higher taxa.}, } @article {pmid30236150, year = {2018}, author = {Xie, Y and Zhao, B and Hoberg, EP and Li, M and Zhou, X and Gu, X and Lai, W and Peng, X and Yang, G}, title = {Genetic characterisation and phylogenetic status of whipworms (Trichuris spp.) from captive non-human primates in China, determined by nuclear and mitochondrial sequencing.}, journal = {Parasites & vectors}, volume = {11}, number = {1}, pages = {516}, pmid = {30236150}, issn = {1756-3305}, mesh = {Animals ; Biological Evolution ; Cercopithecidae ; China/epidemiology ; DNA, Helminth/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Electron Transport Complex IV/genetics ; Female ; *Genetic Variation ; Host Specificity ; Hylobates ; Male ; Phylogeny ; Primates ; Sequence Analysis, DNA/veterinary ; Trichuriasis/epidemiology/parasitology/*veterinary ; Trichuris/classification/*genetics/isolation & purification ; }, abstract = {BACKGROUND: Whipworms (Nematoda: Trichuridae), among the most common soil-transmitted helminths (STHs), can cause the socioeconomically important disease trichuriasis in various mammalian hosts including humans and non-human primates. For many years, Trichuris from non-human primates has been assigned to the same species as the one infecting humans Trichuris trichiura. More recently, several molecular reports challenged this assumption following recognition of a Trichuris species complex observed in humans and non-human primates. A refined concept for species limits within Trichuris contributes to an understanding of diversity and the potential (zoonotic) transmission among humans and non-human primates. In this study, we expanded previous investigations by exploring the diversity of Trichuris among eight primates including three Asian autochthonous species (i.e. Rhinopithecus roxellana, Rhinopithecus bieti and Nomascus leucogenys). Species-level identification, whether novel or assignable to known lineages of Trichuris, was based on analyses of nuclear internal transcribed spacers (ITS) and mitochondrial cytochrome c oxidase subunit 1 (cox1) genes.

RESULTS: In total, seven genetically distinct subgroups of whipworms were determined to be present among the primates sampled. Most Trichuris lineages, including Subgroups 1, 1', 3, 5 and 6, showed a broad host range and were not restricted to particular primate species; in addition to T. trichiura, a complex of Trichuris species was shown infecting primates. Furthermore, it was assumed that Trichuris spp. from either N. leucogenys and P. hamadryas or R. roxellana and R. bieti, respectively, were conspecific. Each pair was indicated to be a discrete lineage of Trichuris, designated, respectively, as Subgroups 1 or 1' and 2, based on integrated genetic and phylogenetic evidence.

CONCLUSION: These results emphasise that the taxonomy and genetic variations of Trichuris are more complicated than previously acknowledged. These cumulative molecular and phylogenetic data provide a better understanding of the taxonomy, genetics and evolutionary biology of the whipworms.}, } @article {pmid30230155, year = {2019}, author = {Saro, I and García-Verdugo, C and González-Pérez, MA and Naranjo, A and Santana, A and Sosa, PA}, title = {Genetic structure of the Canarian palm tree (Phoenix canariensis) at the island scale: does the 'island within islands' concept apply to species with high colonisation ability?.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {21}, number = {1}, pages = {101-109}, doi = {10.1111/plb.12913}, pmid = {30230155}, issn = {1438-8677}, mesh = {Genetic Variation ; Genetics, Population ; Phoeniceae/*genetics ; Seed Dispersal/*physiology ; Spain ; Species Specificity ; Trees/*genetics ; }, abstract = {Oceanic islands are dynamic settings that often promote within-island patterns of strong population differentiation. Species with high colonisation abilities, however, are less likely to be affected by genetic barriers, but island size may impact on species genetic structure regardless of dispersal ability. The aim of the present study was to identify the patterns and factors responsible for the structure of genetic diversity at the island scale in Phoenix canariensis, a palm species with high dispersal potential. To this end, we conducted extensive population sampling on the three Canary Islands where the species is more abundant and assessed patterns of genetic variation at eight microsatellite loci, considering different within-island scales. Our analyses revealed significant genetic structure on each of the three islands analysed, but the patterns and level of structure differed greatly among islands. Thus, genetic differentiation fitted an isolation-by-distance pattern on islands with high population densities (La Gomera and Gran Canaria), but such a pattern was not found on Tenerife due to strong isolation between colonised areas. In addition, we found a positive correlation between population geographic isolation and fine-scale genetic structure. This study highlights that island size is not necessarily a factor causing strong population differentiation on large islands, whereas high colonisation ability does not always promote genetic connectivity among neighbouring populations. The spatial distribution of populations (i.e. landscape occupancy) can thus be a more important driver of plant genetic structure than other island, or species' life-history attributes.}, } @article {pmid30210181, year = {2019}, author = {Wang, XW and Yang, FY and Meijer, M and Kraak, B and Sun, BD and Jiang, YL and Wu, YM and Bai, FY and Seifert, KA and Crous, PW and Samson, RA and Houbraken, J}, title = {Redefining Humicola sensu stricto and related genera in the Chaetomiaceae.}, journal = {Studies in mycology}, volume = {93}, number = {}, pages = {65-153}, pmid = {30210181}, issn = {0166-0616}, abstract = {The traditional concept of the genus Humicola includes species that produce pigmented, thick-walled and single-celled spores laterally or terminally on hyphae or minimally differentiated conidiophores. More than 50 species have been described in the genus. Species commonly occur in soil, indoor environments, and compost habitats. The taxonomy of Humicola and morphologically similar genera is poorly understood in modern terms. Based on a four-locus phylogeny, the morphological concept of Humicola proved to be polyphyletic. The type of Humicola, H. fuscoatra, belongs to the Chaetomiaceae. In the Chaetomiaceae, species producing humicola-like thick-walled spores are distributed among four lineages: Humicola sensu stricto, Mycothermus, Staphylotrichum, and Trichocladium. In our revised concept of Humicola, asexual and sexually reproducing species both occur. The re-defined Humicola contains 24 species (seven new and thirteen new combinations), which are described and illustrated in this study. The species in this genus produce conidia that are lateral, intercalary or terminal on/in hyphae, and conidiophores are not formed or are minimally developed (micronematous). The ascospores of sexual Humicola species are limoniform to quadrangular in face view and bilaterally flattened with one apical germ pore. Seven species are accepted in Staphylotrichum (four new species, one new combination). Thick-walled conidia of Staphylotrichum species usually arise either from hyphae (micronematous) or from apically branched, seta-like conidiophores (macronematous). The sexual morph represented by Staphylotrichum longicolleum (= Chaetomium longicolleum) produces ascomata with long necks composed of a fused basal part of the terminal hairs, and ascospores that are broad limoniform to nearly globose, bilaterally flattened, with an apical germ pore. The Trichocladium lineage has a high morphological diversity in both asexual and sexual structures. Phylogenetic analysis revealed four subclades in this lineage. However, these subclades are genetically closely related, and no distinctive phenotypic characters are linked to any of them. Fourteen species are accepted in Trichocladium, including one new species, twelve new combinations. The type species of Gilmaniella, G. humicola, belongs to the polyphyletic family Lasiosphaeriaceae (Sordariales), but G. macrospora phylogenetically belongs to Trichocladium. The thermophilic genus Mycothermus and the type species My. thermophilum are validated, and one new Mycothermus species is described. Phylogenetic analyses show that Remersonia, another thermophilic genus, is sister to Mycothermus and two species are known, including one new species. Thermomyces verrucosus produces humicola-like conidia and is transferred to Botryotrichum based on phylogenetic affinities. This study is a first attempt to establish an inclusive modern classification of Humicola and humicola-like genera of the Chaetomiaceae. More research is needed to determine the phylogenetic relationships of "humicola"-like species outside the Chaetomiaceae.}, } @article {pmid30197212, year = {2019}, author = {Overmann, J and Huang, S and Nübel, U and Hahnke, RL and Tindall, BJ}, title = {Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms.}, journal = {Systematic and applied microbiology}, volume = {42}, number = {1}, pages = {22-29}, doi = {10.1016/j.syapm.2018.08.009}, pmid = {30197212}, issn = {1618-0984}, mesh = {Archaea/*classification ; Bacteria/*classification ; Classification/*methods ; Phenotype ; *Terminology as Topic ; }, abstract = {To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.}, } @article {pmid30177778, year = {2018}, author = {Waters, AJ and Capriotti, P and Gaboriau, DCA and Papathanos, PA and Windbichler, N}, title = {Rationally-engineered reproductive barriers using CRISPR & CRISPRa: an evaluation of the synthetic species concept in Drosophila melanogaster.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13125}, pmid = {30177778}, issn = {2045-2322}, support = {335724/ERC_/European Research Council/International ; }, mesh = {Animals ; Base Sequence ; CRISPR-Associated Protein 9/genetics/metabolism ; *CRISPR-Cas Systems ; Drosophila Proteins/*genetics ; Drosophila melanogaster/*genetics ; Female ; Gene Editing/*methods ; *Genes, Insect ; Genes, Lethal ; Genetic Fitness ; Genetic Loci ; *Genome, Insect ; Homeodomain Proteins/*genetics ; INDEL Mutation ; Male ; Population Control/methods ; Promoter Regions, Genetic ; RNA, Guide/genetics/metabolism ; Reproductive Isolation ; Sequence Alignment ; Transcription Factors/*genetics ; Transcriptional Activation ; }, abstract = {The ability to erect rationally-engineered reproductive barriers in animal or plant species promises to enable a number of biotechnological applications such as the creation of genetic firewalls, the containment of gene drives or novel population replacement and suppression strategies for genetic control. However, to date no experimental data exist that explores this concept in a multicellular organism. Here we examine the requirements for building artificial reproductive barriers in the metazoan model Drosophila melanogaster by combining CRISPR-based genome editing and transcriptional transactivation (CRISPRa) of the same loci. We directed 13 single guide RNAs (sgRNAs) to the promoters of 7 evolutionary conserved genes and used 11 drivers to conduct a misactivation screen. We identify dominant-lethal activators of the eve locus and find that they disrupt development by strongly activating eve outside its native spatio-temporal context. We employ the same set of sgRNAs to isolate, by genome editing, protective INDELs that render these loci resistant to transactivation without interfering with target gene function. When these sets of genetic components are combined we find that complete synthetic lethality, a prerequisite for most applications, is achievable using this approach. However, our results suggest a steep trade-off between the level and scope of dCas9 expression, the degree of genetic isolation achievable and the resulting impact on fly fitness. The genetic engineering strategy we present here allows the creation of single or multiple reproductive barriers and could be applied to other multicellular organisms such as disease vectors or transgenic organisms of economic importance.}, } @article {pmid30172296, year = {2018}, author = {Khan, F and Jain, S and Oloketuyi, SF}, title = {Bacteria and bacterial products: Foe and friends to Caenorhabditis elegans.}, journal = {Microbiological research}, volume = {215}, number = {}, pages = {102-113}, doi = {10.1016/j.micres.2018.06.012}, pmid = {30172296}, issn = {1618-0623}, mesh = {Animals ; Bacteria/*metabolism/pathogenicity ; Bacterial Infections/microbiology ; *Bacterial Physiological Phenomena ; Caenorhabditis elegans/immunology/*microbiology/*physiology ; Disease Resistance ; Environment ; Escherichia coli ; Host-Pathogen Interactions ; Humans ; Immunity, Innate ; Life Cycle Stages ; Longevity ; Metabolome ; Microbiota/*physiology ; Models, Animal ; Secondary Metabolism ; Virulence ; }, abstract = {Caenorhabditis elegans is a model organism for the study of different molecular, biochemical, microbial and immunity-related mechanisms. In its natural habitat, C. elegans survives by feeding microorganisms (mainly bacteria), though majorly on Escherichia coli OP50 when grown in the laboratory. Numerous bacteria are shown to influence the lifespan, behavioural responses and innate immunity of C. elegans. The secondary metabolites produced by bacteria have shown to play key role in C. elegans longevity. This behaviour provides insights for potential development of new strategies for the treatment of diseases in other species, including humans. This review explains the concept of C. elegans microbiome, different mechanisms employed in its longevity and resistance against bacterial pathogens and the effects of various bacteria (both beneficial and harmful) as well as their products on the life cycle of C. elegans.}, } @article {pmid30145700, year = {2018}, author = {Gallego-Tévar, B and Curado, G and Grewell, BJ and Figueroa, ME and Castillo, JM}, title = {Realized niche and spatial pattern of native and exotic halophyte hybrids.}, journal = {Oecologia}, volume = {188}, number = {3}, pages = {849-862}, pmid = {30145700}, issn = {1432-1939}, mesh = {*Ecosystem ; Hybridization, Genetic ; Poaceae ; *Salt-Tolerant Plants ; Wetlands ; }, abstract = {Interspecific hybridization is an important and common evolutionary mechanism, but field-based evaluations of changes in realized niches and zonation patterns of native and exotic hybrids relative to those of their parental plant species are rare. Would native hybrids forming hybrid zones between their parental species show realized niches similar to that of their parents, whereas would exotic hybrids show larger realized niches than their parents, and alter zonation patterns of native species? To address these questions, we examined key sediment characteristics in plots representing realized niches of native Sarcocornia hybrids, invasive Spartina hybrids and parental species in 14 salt marshes from four estuaries in the Gulf of Cadiz, Southwest Iberian Peninsula. In one representative marsh, the presence of plant taxa relative to intertidal plant zonation was recorded. Results documented that native and fertile hybrids of Sarcocornia had similar realized niche dimensions as their parental species and co-occurred with other plant species, supporting community diversity. However, exotic sterile hybrids of Spartina had realized niche dimensions lower than those of their parental species and occurred in monocultures. The native hybrids played a community structuring role, whereas the exotic Spartina hybrids were a disruptive influence that changed native halophyte zonation pattern and decreased diversity. This negative functional role could intensify if the sterile hybrids evolve and become fertile. Our study suggests the ecological niche dimension concept is an important tool for understanding species roles in ecosystems, incorporating many ideas from the individual to ecosystem levels.}, } @article {pmid30115317, year = {2018}, author = {Lay, CY and Hamel, C and St-Arnaud, M}, title = {Taxonomy and pathogenicity of Olpidium brassicae and its allied species.}, journal = {Fungal biology}, volume = {122}, number = {9}, pages = {837-846}, doi = {10.1016/j.funbio.2018.04.012}, pmid = {30115317}, issn = {1878-6146}, mesh = {Chytridiomycota/*classification/*pathogenicity ; Host Specificity ; Plant Diseases/microbiology ; Virulence ; }, abstract = {The classification and physiology of the zoosporic plant-pathogen Olpidium brassicae and its relationships with the closely-related species are often confusing. This review focuses on these species and intends to differentiate them based on the literatures published since the discovery and establishment of the species by Woronin in 1878 under the name of Chytridium brassicae to current molecular era. The goal of this review is to help researchers better understand the taxonomy, the host range, and the potential role in plant health of O. brassicae-related species. To reach the goal, we reviewed the rationales behind the creation or reduction in synonymy of the different names for O. brassicae and its allied species in order to elucidate the evolution of the species concept on them based on the traditional morphological studies. Furthermore, the studies by molecular biology methods improve our knowledge and perspectives on O. brassicae and its host specificity. In particular, we clarify the differences between O. brassicae and Olpidium virulentus, and propose potential new research avenues. We therefore hope that this review will give a better perspective on Olpidium spp. and their potential role in the root microbiome of plants in natural environments and in agricultural settings.}, } @article {pmid30110337, year = {2018}, author = {Valledor, M and Myers, RS and Schiller, PC}, title = {Herpes ICP8 protein stimulates homologous recombination in human cells.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0200955}, pmid = {30110337}, issn = {1932-6203}, support = {F31 GM089125/GM/NIGMS NIH HHS/United States ; I01 BX000952/BX/BLRD VA/United States ; }, mesh = {Bacteriophage lambda ; DNA, Single-Stranded ; DNA-Binding Proteins/*metabolism ; Genetic Engineering/methods ; Green Fluorescent Proteins/genetics/metabolism ; HEK293 Cells ; Homologous Recombination/*physiology ; Humans ; Proof of Concept Study ; Viral Proteins/*metabolism ; }, abstract = {Recombineering has transformed functional genomic analysis. Genome modification by recombineering using the phage lambda Red homologous recombination protein Beta in Escherichia coli has approached 100% efficiency. While highly efficient in E. coli, recombineering using the Red Synaptase/Exonuclease pair (SynExo) in other organisms declines in efficiency roughly correlating with phylogenetic distance from E. coli. SynExo recombinases are common to double-stranded DNA viruses infecting a variety of organisms, including humans. Human Herpes virus 1 (HHV1) encodes a SynExo comprised of ICP8 synaptase and UL12 exonuclease. In a previous study, the Herpes SynExo was reconstituted in vitro and shown to catalyze a model recombination reaction. Here we describe stimulation of gene targeting to edit a novel fluorescent protein gene in the human genome using ICP8 and compared its efficiency to that of a "humanized" version of Beta protein from phage λ. ICP8 significantly enhanced gene targeting rates in HEK 293T cells while Beta was not only unable to catalyze recombineering but inhibited gene targeting using endogenous recombination functions, despite both synaptases being well-expressed and localized to the nucleus. This proof of concept encourages developing species-specific SynExo recombinases for genome engineering.}, } @article {pmid30098801, year = {2018}, author = {Skovmand, LH and Xu, CCY and Servedio, MR and Nosil, P and Barrett, RDH and Hendry, AP}, title = {Keystone Genes.}, journal = {Trends in ecology & evolution}, volume = {33}, number = {9}, pages = {689-700}, doi = {10.1016/j.tree.2018.07.002}, pmid = {30098801}, issn = {1872-8383}, mesh = {*Biological Evolution ; Ecology/*methods ; Ecosystem ; *Genes ; *Genetic Techniques ; Phenotype ; }, abstract = {The keystone species concept is used in ecology to describe individual species with disproportionately large effects on their communities. We extend this idea to the level of genes with disproportionately large effects on ecological processes. Such 'keystone genes' (KGs) would underlie traits involved in species interactions or causing critical biotic and/or abiotic changes that influence emergent community and ecosystem properties. We propose a general framework for how KGs could be identified, while keeping KGs under the umbrella of 'ecologically important genes' (EIGs) that also include categories such as 'foundation genes', 'ecosystem engineering genes', and more. Although likely rare, KGs and other EIGs could dominate certain ecological processes; thus, their discovery and study are relevant for understanding eco-evolutionary dynamics.}, } @article {pmid30073009, year = {2018}, author = {Rosbakh, S and Pacini, E and Nepi, M and Poschlod, P}, title = {An Unexplored Side of Regeneration Niche: Seed Quantity and Quality Are Determined by the Effect of Temperature on Pollen Performance.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1036}, pmid = {30073009}, issn = {1664-462X}, abstract = {In 1977, Peter Grubb introduced the regeneration niche concept, which assumes that a plant species cannot persist if the environmental conditions are only suitable for adult plant growth and survival, but not for seed production, dispersal, germination, and seedling establishment. During the last decade, this concept has received considerable research attention as it helps to better understand community assembly, population dynamics, and plant responses to environmental changes. Yet, in its present form, it focuses too much on the post-fertilization stages of plant sexual reproduction, neglecting the fact that the environment can operate as a constraint at many points in the chain of processes necessary for successful regeneration. In this review, we draw the attention of the plant ecology research community to the pre-fertilization stages of plant sexual reproduction, an almost ignored but important aspect of the regeneration niche, and their potential consequences for successful seed production. Particularly, we focus on how temperature affects pollen performance and determines plant reproduction success by playing an important role in the temporal and spatial variations in seed quality and quantity. We also review the pollen adaptations to temperature stresses at different levels of plant organization and discuss the plasticity of the performance of pollen under changing temperature conditions. The reviewed literature demonstrates that pre-fertilization stages of seed production, particularly the extreme sensitivity of male gametophyte performance to temperature, are the key determinants of a species' regeneration niche. Thus, we suggest that previous views stating that the regeneration niche begins with the production of seeds should be modified to include the preceding stages. Lastly, we identify several gaps in pollen-related studies revealing a framework of opportunities for future research, particularly how these findings could be used in the field of plant biology and ecology.}, } @article {pmid30070419, year = {2018}, author = {Svigelj, R and Dossi, N and Toniolo, R and Miranda-Castro, R and de-Los-Santos-Álvarez, N and Lobo-Castañón, MJ}, title = {Selection of Anti-gluten DNA Aptamers in a Deep Eutectic Solvent.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {57}, number = {39}, pages = {12850-12854}, doi = {10.1002/anie.201804860}, pmid = {30070419}, issn = {1521-3773}, mesh = {Aptamers, Nucleotide/*chemistry/metabolism ; Base Sequence ; Biotinylation ; Glutens/*analysis/metabolism ; SELEX Aptamer Technique/*methods ; Solvents/*chemistry ; Water/chemistry ; }, abstract = {Herein, we show the feasibility of using deep eutectic solvents as a faster way of selecting aptamers targeting poorly water-soluble species. This unexplored concept is illustrated for gluten proteins. In this way, aptamer-based gluten detection can be performed directly in the extraction media with improved detectability. We envision deep implications for applications not only in food safety control but also in biomedicine.}, } @article {pmid30066110, year = {2018}, author = {Grodwohl, JB and Porto, F and El-Hani, CN}, title = {The instability of field experiments: building an experimental research tradition on the rocky seashores (1950-1985).}, journal = {History and philosophy of the life sciences}, volume = {40}, number = {3}, pages = {45}, doi = {10.1007/s40656-018-0209-y}, pmid = {30066110}, issn = {0391-9714}, mesh = {Animals ; Aquatic Organisms/*physiology ; Ecology/*history ; *Ecosystem ; History, 20th Century ; Hydrobiology/*history ; *Life History Traits ; Models, Biological ; Predatory Behavior ; }, abstract = {In many experimental sciences, like particle physics or molecular biology, the proper place for establishing facts is the laboratory. In the sciences of population biology, however, the laboratory is often seen as a poor approximation of what occurs in nature. Results obtained in the field are usually more convincing. This raises special problems: it is much more difficult to obtain stable, repeatable results in the field, where environmental conditions vary out of the experimenter's control, than in the laboratory. We examine here how this problem affected an influential experimental research tradition in community ecology, the study of the ecology of the rocky seashores. In the 1960s, a handful of North-American ecologists, most notably Joseph Connell, Robert Paine and Paul Dayton, made the rocky seashores a model study system for experimenting in the field. Their experiments were deceptively simple: they removed species living on the seashore and described the resulting effects on the local ecology. These experiments exerted a deep influence on community ecology. They provided evidence for speculative developments concerning the theory of interspecific competition, the factors responsible for species richness and the ecology of food webs. They also stimulated novel conceptual developments. In particular, Paine developed the predation hypothesis, which states that the presence of predators can favour species richness, before introducing the keystone species concept, according to which some species exert disproportionate effects on ecological systems. More broadly, these experiments gave support to a methodological trend in favour of field experimentation. Only controlled perturbations in the field, it seemed, provided a reliable method to get insights into the structure of ecological communities. However, as experiments were continued in time and repeated in different sites, divergent results appeared. We analyse here how intertidal researchers coped with the variability of environmental conditions and tried to stabilize their results. In the process, they reconsidered not only their early conclusions, but also the exclusive status given to field experiments. Expanding on this case study, we discuss some significant differences between laboratory and field experiments.}, } @article {pmid30057481, year = {2018}, author = {Korhonen, A and Seelan, JSS and Miettinen, O}, title = {Cryptic species diversity in polypores: the Skeletocutis nivea species complex.}, journal = {MycoKeys}, volume = {}, number = {36}, pages = {45-82}, pmid = {30057481}, issn = {1314-4049}, abstract = {We propose a taxonomic revision of the two closely related white-rot polypore species, Skeletocutis nivea (Jungh.) Jean Keller and S. ochroalba Niemelä (Incrustoporiaceae, Basidiomycota), based on phylogenetic analyses of nuclear ribosomal internal transcribed spacer (ITS) and translation elongation factor EF-1α sequences. We show that prevailing morphological species concepts of S. nivea and S. ochroalba are non-monophyletic and we delineate new species boundaries based on phylogenetic inference. We recognise eleven species within the prevailing species concept of S. nivea (S. calidasp. nov., S. coprosmae comb. nov., S. futilissp. nov., S. imperviasp. nov., S. ipuletiisp. nov., S. lepidasp. nov., S. nemoralissp. nov., S. nivea sensu typi, S. semipileata comb. nov., S. unguinasp. nov. and S. yuchengiisp. nov.) and assign new sequenced epitypes for S. nivea and S. semipileata. The traditional concept of S. ochroalba comprises two independent lineages embedded within the S. nivea species complex. The Eurasian conifer-dwelling species S. cummatasp. nov. is recognised as separate from the North American S. ochroalba sensu stricto. Despite comprehensive microscopic examination, the majority of the recognised species are left without stable diagnostic character combinations that would enable species identification based solely on morphology and ecology.}, } @article {pmid30036698, year = {2018}, author = {Cornejo, C and Chabanenko, S and Scheidegger, C}, title = {Are species-pairs diverging lineages? A nine-locus analysis uncovers speciation among species-pairs of the Lobaria meridionalis-group (Ascomycota).}, journal = {Molecular phylogenetics and evolution}, volume = {129}, number = {}, pages = {48-59}, doi = {10.1016/j.ympev.2018.07.011}, pmid = {30036698}, issn = {1095-9513}, mesh = {Ascomycota/*genetics ; Far East ; *Genetic Loci ; *Genetic Speciation ; Genetics, Population ; Geography ; Microsatellite Repeats/genetics ; *Phylogeny ; Reproduction/genetics ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {In spite of considerable effort to verify the theory of species-pairs, uncertainty still exists about the relationship between sexually or vegetatively reproducing populations of morphologically indistinguishable, sympatric lichen species. The current paper studies putative species-pairs within the Asian Lobaria meridionalis-group, using a nine-locus and time calibrated species-tree approach. Analyses demonstrate that pairs of sexually or vegetatively reproducing lineages split into highly supported monophyletic clades-confirming molecularly the species-pair concept for the L. meridionalis-group. In the broader context of evolution and speciation dynamics in lichenized fungi, this paper attempts to synthesize molecular findings from the last two decades to promote a more modern perception of the species-pair concept. Taxonomically, eight species were found to currently conform to the L. meridionalis-group, which differentiated during the Pliocene and Pleistocene. The coincidence of paleoclimatic events with estimated dates of divergence support a bioclimatic hypothesis for the evolution of species in the L. meridionalis-group, which also explains their current eco-geographic distribution patterns. Greater recognition for species with a long and independent evolutionary history, which merit high conservation priority, will be especially critical for preserving geographically restricted endemics from Southeast Asia, where habitat loss is driving rapid declines.}, } @article {pmid30033565, year = {2018}, author = {Posso-Terranova, A and Andrés, J}, title = {Multivariate species boundaries and conservation of harlequin poison frogs.}, journal = {Molecular ecology}, volume = {27}, number = {17}, pages = {3432-3451}, doi = {10.1111/mec.14803}, pmid = {30033565}, issn = {1365-294X}, mesh = {Animals ; Anura/*classification/genetics ; Bayes Theorem ; Colombia ; *Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Endangered Species ; *Genetic Speciation ; Haplotypes ; Likelihood Functions ; Microsatellite Repeats ; Phylogeny ; }, abstract = {In this study, we present an iterative method for delimiting species under the general lineage concept (GLC) based on the multivariate clustering of morphological, ecological and genetic data. Our rationale is that distinct multivariate groups correspond to evolutionarily independent metapopulation lineages because they reflect the common signal of different secondary defining properties (environmental and genetic distinctiveness, phenotypic diagnosability, etc.) that imply the existence of barriers preventing or limiting gene exchange. We applied this method to study a group of endangered poison frogs, the Oophaga histrionica complex. In our study case, we used next-generation targeted amplicon sequencing to obtain a robust genetic data set that we combined with patterns of morphological and ecological features. Our analyses revealed the existence of at least five different species in the histrionica complex (three, new to science), some of them, occurring in small isolated populations outside any protected areas. The lineage delimitation proposed here has important conservation implications as it revealed that some of the Oophaga species should be considered among the most vulnerable of the Neotropical frogs. More broadly, our study exemplifies how multiple-amplicon and multivariate statistical techniques can be integrated to successfully identify species and their boundaries.}, } @article {pmid30026123, year = {2018}, author = {Niu, YT and Jabbour, F and Barrett, RL and Ye, JF and Zhang, ZZ and Lu, KQ and Lu, LM and Chen, ZD}, title = {Combining complete chloroplast genome sequences with target loci data and morphology to resolve species limits in Triplostegia (Caprifoliaceae).}, journal = {Molecular phylogenetics and evolution}, volume = {129}, number = {}, pages = {15-26}, doi = {10.1016/j.ympev.2018.07.013}, pmid = {30026123}, issn = {1095-9513}, mesh = {Base Sequence ; Caprifoliaceae/*genetics ; Chloroplasts/genetics ; Genes, Plant ; *Genetic Loci ; *Genome, Chloroplast ; Geography ; Phylogeny ; Plant Leaves/anatomy & histology ; Pollen/ultrastructure ; Species Specificity ; }, abstract = {Species represent the most basic unit of taxonomy. As such, species delimitation represents a crucial issue for biodiversity conservation. Taxonomic practices were revolutionized in the last three decades due to the increasing availability of molecular phylogenetic data. The genus Triplostegia (Caprifoliaceae) traditionally consists of two species, T. glandulifera and T. grandiflora, distinguishable mainly based on quantitative morphological features. In this study, we sequenced nine chloroplast loci (i.e., accD, psbK-psbI, rbcL-accD, rpoB-trnC, rps16-trnQ, trnE-trnT, trnF-ndhJ, trnH-psbA, trnS-trnG) and one nuclear locus (ITS) of 16 individuals of Triplostegia representing the entire distribution range of both species recognized. Furthermore, we also obtained whole chloroplast sequences for 11 of the 16 individuals for which silica gel-dried leaves were available. Our phylogenetic analyses integrating chloroplast genome sequences and multiple loci data revealed that Triplostegia includes four main clades that largely match geography. Neither T. grandiflora nor T. glandulifera was recovered as monophyletic and no diagnosable differences in leaf, flower, and pollen traits were detected between the two species, indicating the need for a revised species circumscription within Triplostegia. Our study highlights the importance of combining data from different sources while defining species limits.}, } @article {pmid30018871, year = {2018}, author = {Fourie, G and Van der Merwe, NA and Wingfield, BD and Bogale, M and Wingfield, MJ and Steenkamp, ET}, title = {Mitochondrial introgression and interspecies recombination in the Fusarium fujikuroi species complex.}, journal = {IMA fungus}, volume = {9}, number = {1}, pages = {37-48}, pmid = {30018871}, issn = {2210-6340}, abstract = {The Fusarium fujikuroi species complex (FFSC) is an economically important monophyletic lineage in the genus Fusarium. Incongruence observed among mitochondrial gene trees, as well as the multiple non-orthologous copies of the internal transcribed spacer region of the ribosomal RNA genes, suggests that the origin and history of this complex likely involved interspecies gene flow. Based on this hypothesis, the mitochondrial genomes of non-conspecific species should harbour signatures of introgression or introgressive hybridization. The aim of this study was therefore to search for recombination between the mitochondrial genomes of different species in the FFSC. Using methods based on mt genome sequence similarity, five significant recombinant regions in both gene and intergenic regions were detected. Using coalescent-based methods and the sequences for individual mt genes, various ancestral recombination events between different lineages of the FFSC were also detected. These findings suggest that interspecies gene flow and introgression are likely to have played key roles in the evolution of the FFSC at both ancient and more recent time scales.}, } @article {pmid30002790, year = {2018}, author = {Tsang, CC and Tang, JYM and Lau, SKP and Woo, PCY}, title = {Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era - Past, present and future.}, journal = {Computational and structural biotechnology journal}, volume = {16}, number = {}, pages = {197-210}, pmid = {30002790}, issn = {2001-0370}, abstract = {Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evolutionary relationships and define criteria for species recognition. With the advancement of various biological, biochemical and computational technologies, different approaches have been adopted for the taxonomy of Aspergillus, Penicillium and Talaromyces; for example, from traditional morphotyping, phenotyping to chemotyping (e.g. lipotyping, proteotypingand metabolotyping) and then mitogenotyping and/or phylotyping. Since different taxonomic approaches focus on different sets of characters of the organisms, various classification and identification schemes would result. In view of this, the consolidated species concept, which takes into account different types of characters, is recently accepted for taxonomic purposes and, together with the lately implemented 'One Fungus - One Name' policy, is expected to bring a more stable taxonomy for Aspergillus, Penicillium and Talaromyces, which could facilitate their evolutionary studies. The most significant taxonomic change for the three genera was the transfer of Penicillium subgenus Biverticillium to Talaromyces (e.g. the medically important thermally dimorphic 'P. marneffei' endemic in Southeast Asia is now named T. marneffei), leaving both Penicillium and Talaromyces as monophyletic genera. Several distantly related Aspergillus-like fungi were also segregated from Aspergillus, making this genus, containing members of both sexual and asexual morphs, monophyletic as well. In the current omics era, application of various state-of-the-art omics technologies is likely to provide comprehensive information on the evolution of Aspergillus, Penicillium and Talaromyces and a stable taxonomy will hopefully be achieved.}, } @article {pmid29983205, year = {2018}, author = {Cabrini, TMB and Barboza, CAM and Skinner, VB and Hauser-Davis, RA and Rocha, RC and Saint'Pierre, TD and Valentin, JL and Cardoso, RS}, title = {Investigating heavy metal bioaccumulation by macrofauna species from different feeding guilds from sandy beaches in Rio de Janeiro, Brazil.}, journal = {Ecotoxicology and environmental safety}, volume = {162}, number = {}, pages = {655-662}, doi = {10.1016/j.ecoenv.2018.06.077}, pmid = {29983205}, issn = {1090-2414}, mesh = {Animals ; Biological Availability ; Brazil ; Environmental Monitoring ; Geologic Sediments/chemistry ; Invertebrates/classification/*metabolism ; Metals, Heavy/*pharmacokinetics ; Water Pollutants, Chemical/*pharmacokinetics ; }, abstract = {The relationship between metal accumulation and feeding behavior of macrofauna species is a key concept to understand the bioavailability of different metals in the marine environment. We examined and compared the concentrations of eight heavy metals (Cr, Zn, Pb, Ni, Cu, Cd, Co and V) in different feeding guilds of macrofauna species, from a data set including 68 sandy beaches along the Rio de Janeiro coast. For this purpose, macrofauna species were classified in five feeding guild categories: carnivorous, herbivorous, detritivorous, suspensivorous and filter feeders. The coast of Rio de Janeiro was divided into seven regions according to environmental characteristics and historical human activities. For each region, generalized linear models were adjusted to test for differences between feeding guild abundances. Redundancy Analysis was performed to explore the relationship among the feeding guilds composition and the environmental variables. We found high variability in abundance and composition among feeding guilds, linked with environmental heterogeneity. In general, carnivorous species showed a higher heavy metal concentrations compared to other trophic guilds evaluated. However, bioaccumulation across the feeding guild was not the rule and patterns varied across regions. Our hypothesis is that variations are probably related to the different magnitudes of metal contamination along the coast as also in to the trophic structure found in each beach. This data highlighted the crucial role of the relationship between variability of environmental drivers and bioaccumulation in macrofauna species in sandy beaches ecosystem.}, } @article {pmid29966912, year = {2018}, author = {De Decker, S and Vanormelingen, P and Pinseel, E and Sefbom, J and Audoor, S and Sabbe, K and Vyverman, W}, title = {Incomplete Reproductive Isolation Between Genetically Distinct Sympatric Clades of the Pennate Model Diatom Seminavis robusta.}, journal = {Protist}, volume = {169}, number = {4}, pages = {569-583}, doi = {10.1016/j.protis.2018.05.003}, pmid = {29966912}, issn = {1618-0941}, mesh = {Animals ; Belgium ; Diatoms/classification/*genetics ; Gene Flow ; Phylogeny ; *Reproductive Isolation ; Sympatry/*genetics ; }, abstract = {Incomplete reproductive isolation between genetically distinct taxa provides an interesting opportunity for speciation and adaptation studies. This phenomenon is well-described in macro-organisms, but less experimental evidence is available for unicellular eukaryotes. Here, we document the sympatric occurrence of genetically differentiated populations of the pennate model diatom Seminavis robusta in coastal subtidal biofilm communities and show widespread potential for gene flow between them. Based on sequence variation in the plastid-encoded rbcL gene, three distinct clades were identified. Morphological variation between the clades reflected their phylogenetic relationships, with subtle differences in valve morphology in the most distant clade compared to the other two clades, which were indistinguishable. Using a large number of experimental crosses we showed that, although reproductive output was significantly lower compared to the majority of within-clade crosses, approximately 34.5% of the inter-clade crosses resulted in viable and fertile progeny. While the nature of the incomplete reproductive isolation remains unknown, its occurrence in natural diatom populations represents an additional mechanism contributing to population genetic structuring and adaptation and can spur further research into the mechanisms of species divergence and the maintenance of species identity in the presence of gene flow.}, } @article {pmid29940429, year = {2018}, author = {Carruthers, P}, title = {Comparative psychology without consciousness.}, journal = {Consciousness and cognition}, volume = {63}, number = {}, pages = {47-60}, doi = {10.1016/j.concog.2018.06.012}, pmid = {29940429}, issn = {1090-2376}, mesh = {Animals ; *Consciousness ; Humans ; Psychological Theory ; *Psychology, Comparative ; }, abstract = {The goal of this paper is to establish the truth of the following conditional: if a global workspace theory of phenomenal consciousness is correct, and is fully reductive in nature, then we should stop asking questions about consciousness in nonhuman animals-not because those questions are too hard to answer, but because there are no substantive facts to discover. The argument in support of this conditional turns on the idea that while global broadcasting is all-or-nothing in the human mind, it is framed in terms that imply gradations across species. Yet our concept of phenomenal consciousness doesn't permit mental states to be to some degree conscious. Before getting to that argument, however, and in order to motivate the subsequent discussion, some of the virtues of global workspace theory are displayed.}, } @article {pmid29927707, year = {2018}, author = {Feurtey, A and Stukenbrock, EH}, title = {Interspecific Gene Exchange as a Driver of Adaptive Evolution in Fungi.}, journal = {Annual review of microbiology}, volume = {72}, number = {}, pages = {377-398}, doi = {10.1146/annurev-micro-090817-062753}, pmid = {29927707}, issn = {1545-3251}, mesh = {*Adaptation, Biological ; *Evolution, Molecular ; Fungi/*genetics ; *Gene Transfer, Horizontal ; *Recombination, Genetic ; }, abstract = {Throughout evolutionary history in the kingdom Fungi, taxa have exchanged genetic information among species, as revealed in particular by analyses of genome sequences. In fungi, hybridization can occur by sexual mating or by fusion of vegetative structures giving rise to new species or leaving traces of introgression in the genome. Furthermore, gene exchange can occur by horizontal gene transfer between species and can even include organisms outside the kingdom Fungi. In several cases, interspecific gene exchange has been instrumental in rapid adaptive evolution of fungal species and has notably played a role in the emergence of new pathogens. Here we summarize mechanisms and examples of gene exchange in fungi with a particular focus on the genomic context. We emphasize the need for and potential of applying population genetic approaches to better understand the processes and the impact of interspecific gene exchange in rapid adaptive evolution and species diversification. The broad occurrence of gene exchange among fungal species challenges our species concepts in the kingdom Fungi.}, } @article {pmid29910521, year = {2018}, author = {Zhan, P and Dukik, K and Li, D and Sun, J and Stielow, JB and Gerrits van den Ende, B and Brankovics, B and Menken, SBJ and Mei, H and Bao, W and Lv, G and Liu, W and de Hoog, GS}, title = {Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. violaceum.}, journal = {Studies in mycology}, volume = {89}, number = {}, pages = {153-175}, pmid = {29910521}, issn = {0166-0616}, abstract = {Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrum complex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3 and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrum and T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrum and T. violaceum was observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceum contains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrum and T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrum and T. violaceum underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.}, } @article {pmid29899129, year = {2018}, author = {Tatarenkov, A and Earley, RL and Taylor, DS and Davis, WP and Avise, JC}, title = {Natural hybridization between divergent lineages in a selfing hermaphroditic fish.}, journal = {Biology letters}, volume = {14}, number = {6}, pages = {}, pmid = {29899129}, issn = {1744-957X}, mesh = {Animals ; Bahamas ; Cyprinodontiformes/classification/*genetics ; Female ; Hermaphroditic Organisms/*genetics ; *Hybridization, Genetic ; Male ; Microsatellite Repeats ; Phylogeny ; Self-Fertilization ; Sympatry ; }, abstract = {By definition, mating between individuals is infrequent in highly selfing organisms, and so too, therefore, hybridization should be rare between genetically divergent lineages in predominantly self-fertilizing species. Notwithstanding these expectations, here we report a remarkable case of natural hybridization between highly diverged phylogeographic lineages of the mangrove rivulus, a small killifish that reproduces predominantly by self-fertilization and typically is found as highly homozygous lines in most parts of its extensive geographical range. Two distinctive genetic lineages (Kryptolebias marmoratus and a 'Central clade' closely related to K. hermaphroditus) previously were not known in sympatry, but were found by us to co-occur on San Salvador, Bahamas. Genetic analyses of a mitochondrial and multiple nuclear markers determined the direction of a cross producing a hybrid fish. Furthermore, we show that this hybrid individual was viable, as it successfully reproduced by self-fertilization for two generations. Additional sampling of this population will be necessary to determine if backcrossing of hybrids to the parental lineages occurs in nature and to analyse whether such backcross progeny are viable. Application of the biological species concept (BSC) is traditionally difficult in clonally reproducing organisms. Our results show that although mangrove rivulus fish are mostly highly selfing in nature (resulting in isogenic, effectively clonal and homozygous progeny), classification within this taxonomic complex need not be incompatible with the BSC.}, } @article {pmid29895946, year = {2018}, author = {Sutherland, C and Fuller, AK and Royle, JA and Hare, MP and Madden, S}, title = {Large-scale variation in density of an aquatic ecosystem indicator species.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8958}, pmid = {29895946}, issn = {2045-2322}, mesh = {Animals ; *Ecosystem ; *Environmental Monitoring ; Mink/*physiology ; Population Density ; *Rivers ; }, abstract = {Monitoring indicator species is a pragmatic approach to natural resource assessments, especially when the link between the indicator species and ecosystem state is well justified. However, conducting ecosystem assessments over representative spatial scales that are insensitive to local heterogeneity is challenging. We examine the link between polychlorinated biphenyl (PCB) contamination and population density of an aquatic habitat specialist over a large spatial scale using non-invasive genetic spatial capture-recapture. Using American mink (Neovison vison), a predatory mammal and an indicator of aquatic ecosystems, we compared estimates of density in two major river systems, one with extremely high levels of PCB contamination (Hudson River), and a hydrologically independent river with lower PCB levels (Mohawk River). Our work supports the hypothesis that mink densities are substantially (1.64-1.67 times) lower in the contaminated river system. We demonstrate the value of coupling the indicator species concept with well-conceived and spatially representative monitoring protocols. PCBs have demonstrable detrimental effects on aquatic ecosystems, including mink, and these effects are likely to be profound and long-lasting, manifesting as population-level impacts. Through integrating non-invasive data collection, genetic analysis, and spatial capture-recapture methods, we present a monitoring framework for generating robust density estimates across large spatial scales.}, } @article {pmid29842921, year = {2019}, author = {Kruepunga, N and Hakvoort, TBM and Hikspoors, JPJM and Köhler, SE and Lamers, WH}, title = {Anatomy of rodent and human livers: What are the differences?.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1865}, number = {5}, pages = {869-878}, doi = {10.1016/j.bbadis.2018.05.019}, pmid = {29842921}, issn = {1879-260X}, mesh = {Animals ; Biological Evolution ; Gallbladder/anatomy & histology/blood supply ; Humans ; Liver/*anatomy & histology/blood supply ; Rodentia ; }, abstract = {The size of the liver of terrestrial mammals obeys the allometric scaling law over a weight range of >3 ∗ 10[6]. Since scaling reflects adaptive changes in size or scale among otherwise similar animals, we can expect to observe more similarities than differences between rodent and human livers. Obvious differences, such as the presence (rodents) or absence (humans) of lobation and the presence (mice, humans) or absence (rats) of a gallbladder, suggest qualitative differences between the livers of these species. After review, however, we conclude that these dissimilarities represent relatively small quantitative differences. The microarchitecture of the liver is very similar among mammalian species and best represented by the lobular concept, with the biggest difference present in the degree of connective tissue development in the portal tracts. Although larger mammals have larger lobules, increasing size of the liver is mainly accomplished by increasing the number of lobules. The increasing role of the hepatic artery in lobular perfusion of larger species is, perhaps, the most important and least known difference between small and large livers, because it profoundly affects not only interventions like liver transplantations, but also calculations of liver function.}, } @article {pmid29803933, year = {2018}, author = {Ren, XD and Hao, XY and Li, HC and Ke, MR and Zheng, BY and Huang, JD}, title = {Progress in the development of nanosensitizers for X-ray-induced photodynamic therapy.}, journal = {Drug discovery today}, volume = {23}, number = {10}, pages = {1791-1800}, doi = {10.1016/j.drudis.2018.05.029}, pmid = {29803933}, issn = {1878-5832}, mesh = {Animals ; Drug Development/methods ; Humans ; Molecular Targeted Therapy ; Neoplasms/*drug therapy/pathology ; Photochemotherapy/*methods ; Photosensitizing Agents/*administration & dosage ; Reactive Oxygen Species/metabolism ; X-Rays ; }, abstract = {In recent years, photodynamic therapy has been applied in cancer treatment because of its high selectivity and marginal invasion properties. However, the excitation light used has limited ability to penetrate tissue, which creates a stumbling block for its future development. To overcome this, X-rays have been introduced to transmit energy to deeper tissues. Given that a large number of X-ray-induced sensitizers have been designed to facilitate X-ray excitation and generate reactive oxygen species (ROS), this has led to the concept of X-ray-induced photodynamic therapy (X-PDT). After 10 years of development, this treatment now shows good therapeutic effects as well as shortcomings. Going forward, it will be important to improve tumor targeting and a standard deep-seated tumor model should be established.}, } @article {pmid29789066, year = {2018}, author = {von Reuss, SH}, title = {Exploring Modular Glycolipids Involved in Nematode Chemical Communication.}, journal = {Chimia}, volume = {72}, number = {5}, pages = {297-303}, doi = {10.2533/chimia.2018.297}, pmid = {29789066}, issn = {0009-4293}, mesh = {*Animal Communication ; Animals ; Caenorhabditis elegans/*physiology ; Communication ; Glycolipids/*physiology ; Hexoses ; }, abstract = {Chemical communication in nematodes has been known for over half a century, but the underlying molecular basis remained largely elusive. Recent advances in analytical techniques facilitated the characterization of a modular glycolipid library based on the dideoxysugar L-ascarylose, which modulates behavior and development in the model organism C. elegans. Ascaroside signaling is highly conserved in nematodes and represents a key factor in nematode chemical ecology. Ascaroside biosynthesis depends on the co-option of the peroxisomal β-oxidation cycle and in addition integrates a large diversity of additional building blocks derived from various primary metabolic pathways to give rise to species-specific modular assemblies, thus, transcending the concept of strictly segregated primary versus secondary metabolism.}, } @article {pmid29784828, year = {2018}, author = {Bobay, LM and Ochman, H}, title = {Biological species in the viral world.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {23}, pages = {6040-6045}, pmid = {29784828}, issn = {1091-6490}, support = {R35 GM118038/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics ; Biological Evolution ; Genetic Speciation ; Genome, Viral/genetics ; Host Specificity/genetics ; Phylogeny ; *Species Specificity ; Virus Diseases/genetics ; Viruses/*genetics ; }, abstract = {Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.}, } @article {pmid29781421, year = {2018}, author = {Laurimäe, T and Kinkar, L and Moks, E and Romig, T and Omer, RA and Casulli, A and Umhang, G and Bagrade, G and Irshadullah, M and Sharbatkhori, M and Mirhendi, H and Ponce-Gordo, F and Soriano, SV and Varcasia, A and Rostami-Nejad, M and Andresiuk, V and Saarma, U}, title = {Molecular phylogeny based on six nuclear genes suggests that Echinococcus granulosus sensu lato genotypes G6/G7 and G8/G10 can be regarded as two distinct species.}, journal = {Parasitology}, volume = {145}, number = {14}, pages = {1929-1937}, doi = {10.1017/S0031182018000719}, pmid = {29781421}, issn = {1469-8161}, mesh = {Animals ; Bayes Theorem ; Echinococcosis ; Echinococcus granulosus/*classification/*genetics ; Evolution, Molecular ; Gene Flow ; *Genes, Helminth ; Genetic Variation ; *Genotype ; Humans ; *Phylogeny ; Zoonoses/parasitology ; }, abstract = {Tapeworms of the species complex of Echinococcus granulosus sensu lato (s. l.) are the cause of a severe zoonotic disease - cystic echinococcosis, which is listed among the most severe parasitic diseases in humans and is prioritized by the World Health Organization. A stable taxonomy of E. granulosus s. l. is essential to the medical and veterinary communities for accurate and effective communication of the role of different species in this complex on human and animal health. E. granulosus s. l. displays high genetic diversity and has been divided into different species and genotypes. Despite several decades of research, the taxonomy of E. granulosus s. l. has remained controversial, especially the species status of genotypes G6-G10. Here the Bayesian phylogeny based on six nuclear loci (7387 bp in total) demonstrated, with very high support, the clustering of G6/G7 and G8/G10 into two separate clades. According to the evolutionary species concept, G6/G7 and G8/G10 can be regarded as two distinct species. Species differentiation can be attributed to the association with distinct host species, largely separate geographical distribution and low level of cross-fertilization. These factors have limited the gene flow between genotypic groups G6/G7 and G8/G10, resulting in the formation of distinct species. We discuss ecological and epidemiological differences that support the validity of these species.}, } @article {pmid29771275, year = {2018}, author = {Bobay, LM and Ellis, BS and Ochman, H}, title = {ConSpeciFix: classifying prokaryotic species based on gene flow.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {21}, pages = {3738-3740}, pmid = {29771275}, issn = {1367-4811}, support = {R35 GM118038/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gene Flow ; *Software ; }, abstract = {SUMMARY: Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life.

ConSpeciFix's webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML.}, } @article {pmid29766525, year = {2018}, author = {Imholt, C and Abdulla, T and Stevens, A and Edwards, P and Jacob, J and Woods, D and Rogers, E and Aarons, L and Segelcke, D}, title = {Establishment and validation of microsampling techniques in wild rodents for ecotoxicological research.}, journal = {Journal of applied toxicology : JAT}, volume = {38}, number = {9}, pages = {1244-1250}, doi = {10.1002/jat.3635}, pmid = {29766525}, issn = {1099-1263}, mesh = {Administration, Intravenous ; Animals ; Arvicolinae/*blood ; Blood Specimen Collection/*methods ; Dioxoles/administration & dosage/blood/pharmacokinetics/*toxicity ; Ecotoxicology/*methods ; Environmental Exposure/*adverse effects ; Environmental Monitoring/*methods ; Female ; Fungicides, Industrial/administration & dosage/blood/pharmacokinetics/*toxicity ; Male ; Pyrimidines/administration & dosage/blood/pharmacokinetics/*toxicity ; Pyrroles/administration & dosage/blood/pharmacokinetics/*toxicity ; Reproducibility of Results ; Risk Assessment ; Toxicokinetics ; }, abstract = {Compounds and products in the biocide and plant protection sector can only be registered after formal risk assessment to ensure safety for users and the environment. In bird and mammal risk assessment, this is routinely done using generic focal species as models, which are of particular exposure risk. Such a species is the common vole (Microtus arvalis) due to its high food intake relative to the low body weight. For wild species, biological samples, data and hence realistic exposure estimations are particularly difficult to obtain. In recent years, advances have been made in the techniques related to serial microsampling of laboratory mice and rats that allow for a reduction in sampling volumes. Similar progress in wild species sampling is missing. This study presents a proof of concept to dose wild rodents with relevant compounds and to draw serial, low volume blood samples suitable for state-of-the art toxicokinetic analyses. For the first time, the jugular vein of common voles was used to administer compounds (two frequently used fungicidal components). This procedure and the following microsampling of blood (2 × 10 μl six times within 24 hours) from the lateral tail vein did not affect body weight and mortality of voles. Samples were sufficient to detect dissipation patterns of the compounds from blood in toxicokinetic analysis. These results suggest that microsampling can be well translated from laboratory mice to wild rodent species and help to obtain realistic exposure estimates in wild rodents for ecotoxicological studies as well as to promote the 3R concept in studies with wild rodent species.}, } @article {pmid29743130, year = {2019}, author = {Stock, SP and Campos-Herrera, R and El-Borai, FE and Duncan, LW}, title = {Steinernema khuongi n. sp. (Panagrolaimomorpha, Steinernematidae), a new entomopathogenic nematode species from Florida, USA.}, journal = {Journal of helminthology}, volume = {93}, number = {2}, pages = {226-241}, doi = {10.1017/S0022149X18000081}, pmid = {29743130}, issn = {1475-2697}, mesh = {Animals ; DNA, Helminth/genetics ; DNA, Ribosomal/genetics ; Florida ; Larva/parasitology ; Moths/parasitology ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Rhabditida/anatomy & histology/*classification/*pathogenicity ; Sequence Analysis, DNA ; Soil/parasitology ; }, abstract = {In this study, molecular (ribosomal sequence data), morphological and cross-hybridization properties were used to identify a new Steinernema sp. from Florida, USA. Molecular and morphological data provided evidence for placing the novel species into Clade V, or the 'glaseri-group' of Steinernema spp. Within this clade, analysis of sequence data of the rDNA genes, 28S and internal transcribed spacer (ITS), depicted the novel species as a distinctive entity and closely related to S. glaseri and S. cubanum. Additionally, cross-hybridization assays showed that the new species is unable to interbreed with either of the latter two species, reinforcing its uniqueness from a biological species concept standpoint. Key morphological diagnostic characters for S. khuongi n. sp. include the mean morphometric features of the third-stage infective juveniles: total body length (average: 1066 μm), tail length (average: 65 μm), location of the excretory pore (average: 80.5 μm) and the values of c (average: 16.4), D% (average: 60.5), E% (average: 126) and H% (average: 46.6). Additionally, males can be differentiated from S. glaseri and S. cubanum by the values of several ratios: D% (average: 68), E% (average: 323) and SW% (average: 120). The natural distribution of this species in Florida encompasses both natural areas and citrus groves, primarily in shallow groundwater ecoregions designated as 'flatwoods'. The morphological, molecular, phylogenetic and ecological data associated with this nematode support its identity as a new species in the S. glaseri-group.}, } @article {pmid29729946, year = {2019}, author = {Mehta, RS and Rosenberg, NA}, title = {The probability of reciprocal monophyly of gene lineages in three and four species.}, journal = {Theoretical population biology}, volume = {129}, number = {}, pages = {133-147}, pmid = {29729946}, issn = {1096-0325}, support = {R01 GM117590/GM/NIGMS NIH HHS/United States ; }, mesh = {*Models, Genetic ; *Phylogeny ; Probability ; Trees/*genetics ; }, abstract = {Reciprocal monophyly, a feature of a genealogy in which multiple groups of descendant lineages each consist of all of the descendants of their respective most recent common ancestors, has been an important concept in studies of species delimitation, phylogeography, population history reconstruction, systematics, and conservation. Computations involving the probability that reciprocal monophyly is observed in a genealogy have played a key role in criteria for defining taxonomic groups and inferring divergence times. The probability of reciprocal monophyly under a coalescent model of population divergence has been studied in detail for groups of gene lineages for pairs of species. Here, we extend this computation to generate corresponding probabilities for sets of gene lineages from three and four species. We study the effects of model parameters on the probability of reciprocal monophyly, finding that it is driven primarily by species tree height, with lesser but still substantial influences of internal branch lengths and sample sizes. We also provide an example application of our results to data from maize and teosinte.}, } @article {pmid29729925, year = {2018}, author = {Pazzola, M and Stocco, G and Paschino, P and Dettori, ML and Cipolat-Gotet, C and Bittante, G and Vacca, GM}, title = {Modeling of coagulation, curd firming, and syneresis of goat milk from 6 breeds.}, journal = {Journal of dairy science}, volume = {101}, number = {8}, pages = {7027-7039}, doi = {10.3168/jds.2018-14397}, pmid = {29729925}, issn = {1525-3198}, mesh = {Animals ; *Breeding ; Cheese/*analysis ; Dairy Products ; *Goats ; Milk/*chemistry ; }, abstract = {Traditional milk coagulation properties are used to predict the suitability of milk for cheese-making. In bovine and ovine species, the introduction of the concept of curd firming over time, continuously recorded by a lactodynamograph during prolonged tests, provides additional information about milk coagulation, curd-firming, and syneresis processes. The aims of present study were (1) to test the adaptability of a 4-parameter curd-firming model in the assessment of goat milk (also comparing published data of other species); (2) to describe variability of coagulation, curd firming, and syneresis processes among individual goat milk samples; (3) to quantify the effects of farm and animal factors (breed, parity, and stage of lactation); and (4) to compare 6 goat breeds for their model parameters. Milk samples from 1,272 goats reared in 35 farms were collected. Goats were of 6 breeds: Saanen and Camosciata delle Alpi for the Alpine type; and Murciano-Granadina, Maltese, Sarda, and Sarda Primitiva for the Mediterranean type. During a lactodynamographic analysis (60 min), 240 measures of curd firmness (mm) were recorded for each milk sample. The modeling of curd firming allowed us to achieve the rennet coagulation time estimated on the basis of all the data points (min); the curd firming and the curd syneresis instant rate constants; the asymptotical potential value of curd firming; the actual maximum curd firmness; and the time at which the curd firming maximum level is attained. Modeling parameter data were analyzed using a linear mixed model. Comparison with other dairy species showed several differences: goat milk coagulated later than sheep but earlier than bovine, and curd firming and curd syneresis instant rate constants were greater in small ruminants. Modeling parameters of goat milk were mostly affected by the farm effect (37% of the total variance, on average) compared with the results found for bovine and ovine samples, and this was probably attributable to the marked differences among goat farming systems. Small differences were demonstrated between Alpine and Mediterranean breeds, but the time of maximum curd firmness was lower in Murciano-Granadina compared with Maltese, Sarda, and Sarda Primitiva. Sarda and Sarda Primitiva were very similar and exhibited the most favorable coagulation properties of milk. For almost all the model parameters, the direct effect of breed was increased after correction for milk yield and composition. In conclusion, this approach allowed us to fully depict the effects of the different factors on coagulation of goat milk, and clarified the different renneting pattern among goat breeds, and with other species. Results could be used for the valorization of goat dairy products, also when these are linked to particular local breeds, and to stimulate further studies about relationships between coagulation and cheese-making traits.}, } @article {pmid29726914, year = {2018}, author = {Mora-Márquez, F and Vázquez-Poletti, JL and López de Heredia, U}, title = {NGScloud: RNA-seq analysis of non-model species using cloud computing.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {19}, pages = {3405-3407}, doi = {10.1093/bioinformatics/bty363}, pmid = {29726914}, issn = {1367-4811}, mesh = {*Cloud Computing ; Computational Biology ; RNA ; *Sequence Analysis, RNA ; *Software ; }, abstract = {SUMMARY: RNA-seq analysis usually requires large computing infrastructures. NGScloud is a bioinformatic system developed to analyze RNA-seq data using the cloud computing services of Amazon that permit the access to ad hoc computing infrastructure scaled according to the complexity of the experiment, so its costs and times can be optimized. The application provides a user-friendly front-end to operate Amazon's hardware resources, and to control a workflow of RNA-seq analysis oriented to non-model species, incorporating the cluster concept, which allows parallel runs of common RNA-seq analysis programs in several virtual machines for faster analysis.

NGScloud is freely available at https://github.com/GGFHF/NGScloud/. A manual detailing installation and how-to-use instructions is available with the distribution.}, } @article {pmid29720606, year = {2018}, author = {Beermann, J and Westbury, MV and Hofreiter, M and Hilgers, L and Deister, F and Neumann, H and Raupach, MJ}, title = {Cryptic species in a well-known habitat: applying taxonomics to the amphipod genus Epimeria (Crustacea, Peracarida).}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6893}, pmid = {29720606}, issn = {2045-2322}, mesh = {Amphipoda/anatomy & histology/*classification/*genetics ; Animals ; Biodiversity ; DNA Barcoding, Taxonomic ; *Ecosystem ; Genome, Mitochondrial ; Genomics/methods ; RNA, Ribosomal, 18S ; RNA, Transfer ; }, abstract = {Taxonomy plays a central role in biological sciences. It provides a communication system for scientists as it aims to enable correct identification of the studied organisms. As a consequence, species descriptions should seek to include as much available information as possible at species level to follow an integrative concept of 'taxonomics'. Here, we describe the cryptic species Epimeria frankei sp. nov. from the North Sea, and also redescribe its sister species, Epimeria cornigera. The morphological information obtained is substantiated by DNA barcodes and complete nuclear 18S rRNA gene sequences. In addition, we provide, for the first time, full mitochondrial genome data as part of a metazoan species description for a holotype, as well as the neotype. This study represents the first successful implementation of the recently proposed concept of taxonomics, using data from high-throughput technologies for integrative taxonomic studies, allowing the highest level of confidence for both biodiversity and ecological research.}, } @article {pmid29720294, year = {2018}, author = {Hérault, F and Duby, C and Baéza, E and Diot, C}, title = {Adipogenic genes expression in relation to hepatic steatosis in the liver of two duck species.}, journal = {Animal : an international journal of animal bioscience}, volume = {12}, number = {12}, pages = {2571-2577}, doi = {10.1017/S1751731118000897}, pmid = {29720294}, issn = {1751-732X}, mesh = {Adipocytes/metabolism ; *Adipogenesis ; Adipose Tissue/metabolism ; Animals ; Down-Regulation ; Ducks ; Fatty Liver/genetics/metabolism/*veterinary ; *Gene Expression Regulation ; Liver/metabolism ; Male ; Mice ; Organ Specificity ; Peroxisome Proliferator-Activated Receptors/*genetics ; Poultry Diseases/genetics/*metabolism ; Species Specificity ; Up-Regulation ; }, abstract = {Some studies have shown that expression of peroxisome proliferator-activated receptor gamma (PPARG), a key regulator of adipogenesis, and of some adipocyte-specific genes or adipokines are expressed in hepatic steatosis, leading to the concept of 'adipogenic hepatic steatosis' or 'hepatic adiposis.' Most of these studies were conducted in genetic obese mouse models or after manipulation of gene expression. The relevance of this concept to other species and more physiological models was here addressed in ducks which are able to develop hepatic steatosis after overfeeding. The expression of PPARG and other adipocyte-specific genes was thus analyzed in the liver of ducks fed ad libitum or overfed and compared with those observed in adipose tissues. Pekin (Anas platyrhynchos) and Muscovy ducks (Cairina moschata) were analyzed, as metabolic responses to overfeeding differ according to these two species, Muscovy ducks having a greater ability to synthesize and store lipids in the liver than Pekin ducks. Our results indicate that adipocyte-specific genes are expressed in the liver of ducks, PPARG and fatty acid-binding protein 4 being upregulated and adiponectin and leptin receptor downregulated by overfeeding. However, these expression levels are much lower than those observed in adipose tissue suggesting that fatty liver cells are not transformed to adipocytes, although some hepato-specific functions are decreased in fatty liver when compared with normal liver.}, } @article {pmid29690436, year = {2018}, author = {Rognes, K}, title = {Revision of the Bengalia torosa Wiedemann, 1819 species-group (Diptera: Calliphoridae), with notes on the systematic position of B. robertsi Kurahashi, 1987 and B. subnitida James, 1964.}, journal = {Zootaxa}, volume = {4391}, number = {1}, pages = {1-71}, doi = {10.11646/zootaxa.4391.1.1}, pmid = {29690436}, issn = {1175-5334}, mesh = {Animals ; China ; Classification ; *Diptera ; Female ; Male ; Muscidae ; }, abstract = {The mainly Oriental Bengalia torosa Wiedemann species-group is revised on the basis of males. Species concepts are based on male terminalia. Monophyly of the species-group is established on the basis of two unique synapomorphies of the distiphallus. Eleven species are recognized as valid, viz. Bengalia chekiangensis Fan, 1965, Bengalia chiangmaiensis Kurahashi Tumrasvin, 1979, Bengalia concava Malloch, 1927, Bengalia escheri Bezzi, 1913, Bengalia fuscipennis Bezzi, 1913, Bengalia jejuna (Fabricius, 1787), Bengalia kanoi Kurahashi Magpayo, 2000, Bengalia martinleakei Senior-White, 1930, Bengalia recurva Malloch, 1927, Bengalia torosa (Wiedemann, 1819), Bengalia xanthopyga Senior-White, 1924, and their geographical distributions are updated. The following new synonymies are proposed: Bezzigalia rivanella Lehrer, 2005 is a junior synonym of B. escheri, syn. nov.; Bengalia siamensis Senior-White, 1924, Gangelomyia kosungana Lehrer, 2007 and G. laoziella Lehrer, 2007 are junior synonyms of B. fuscipennis, syn. nov.; Gangelomyia evafoneae Lehrer, 2005 and G. senausmarta Lehrer, 2005 are junior synonyms of B. jejuna, syn. nov.; Gangelomyia indipyga Lehrer, 2005, G. philipyga Lehrer, 2005, G. schiavoae Lehrer, 2005, G. shivanella Lehrer, 2005, G. tagaloga Lehrer, 2005 and G. phantastika Lehrer, 2007 are junior synonyms of B. kanoi, syn. nov.; Gangelomyia gandhiana Lehrer, 2005 and G. krishna Lehrer, 2005 are junior synonyms of B. martinleakei, syn. nov.; Laoziana camerina Lehrer, 2005, L. mandarina Lehrer, 2005 and L. singhasaria Lehrer, 2005 are junior synonyms of B. recurva, syn. nov. Lectotypes are designated for Musca favillacea Walker, 1859 and Bengalia escheri Bezzi, 1913. A male syntype of Musca torosa Wiedemann, 1819 has been located in NHMD and a female syntype of the same nominal species has been located in NMW. A male specimen in NHMD is proposed as neotype for Musca jejuna Fabricius, 1787, to replace the three existing female syntypes. A male specimen in NHMD is proposed as neotype for Musca torosa Wiedemann, 1819, to replace the newly located syntypes. The ICZN Commission will be requested, in a forthcoming paper, to formally set aside the existing name-bearing types of both nominal species and designate the proposed specimens as neotypes, in order to preserve the current usage of both names. Musca favillacea Walker, 1859 is removed from synonymy with Bengalia jejuna and treated as an unplaced name in the Bengalia torosa species-group. Bengalia robertsi Kurahashi, 1987 is removed from the Bengalia torosa species-group and re-assigned to the Bengalia labialis Robineau-Desvoidy species-group. Bengalia subnitida James, 1964 is assigned to the Bengalia peuhi Villeneuve species-group even though it lacks discal setae on the fifth abdominal tergite. Two new terms are introduced for description of the distiphallus of the B. torosa species-group. Bengalia recurva Malloch is reported for the first time from China.}, } @article {pmid29690385, year = {2018}, author = {Webb, JM and Jacobus, LM and Sullivan, SP}, title = {The state of systematics of North American Baetis Leach, 1815 (Ephemeroptera: Baetidae), with recommendations for identification of larvae.}, journal = {Zootaxa}, volume = {4394}, number = {1}, pages = {105-127}, doi = {10.11646/zootaxa.4394.1.6}, pmid = {29690385}, issn = {1175-5334}, mesh = {Animals ; *Ephemeroptera ; Fabaceae ; Larva ; United States ; }, abstract = {The North American species of Baetis Leach (Ephemeroptera: Baetidae) are reviewed. Nearly one-third of species are either unknown or inadequately described in the larval stage, a fact not reflected in most keys or standard taxonomic efforts for bioassessment, which typically recommend species-level identifications of larvae. Furthermore, our new observations indicate that some previously published stage associations should be viewed as only tentative, and molecular evidence suggests that current species taxonomy does not reflect biological species. In order to acknowledge these deficiencies, but at the same time provide a degree of higher taxonomic resolution beyond the genus level, we recommend a scheme for identifications incorporating previously established species groups and the species complexes and species included within them. Species complexes are proposed for instances when there are either multiple species that cannot be differentiated in the larval stage or when multiple lines of evidence indicate more than one actual species is included in a single species concept. Complexes include B. flavistriga complex (B. flavistriga McDunnough + B. phoebus McDunnough + B. rusticans McDunnough), B. intercalaris complex (B. intercalaris McDunnough), B. vernus complex (B. brunneicolor McDunnough + B. vernus Curtis), B. bicaudatus complex (B. bicaudatus Dodds), B. tricaudatus complex (B. tricaudatus Dodds), and B. piscatoris complex (B. piscatoris Traver + B. palisadi Mayo + B. persecutus McDunnough [=B. persecutor McCafferty n. obj. syn]). A new larval identification key incorporating the B. piscatoris complex is provided.}, } @article {pmid29690288, year = {2018}, author = {Burks, RA and Heraty, JM and Dominguez, C and Mottern, JL}, title = {Complex diversity in a mainly tropical group of ant parasitoids: Revision of the Orasema stramineipes species group (Hymenoptera: Chalcidoidea: Eucharitidae).}, journal = {Zootaxa}, volume = {4401}, number = {1}, pages = {1-107}, doi = {10.11646/zootaxa.4401.1.1}, pmid = {29690288}, issn = {1175-5334}, mesh = {Animals ; *Ants ; Argentina ; Caribbean Region ; Phylogeny ; West Indies ; }, abstract = {Twenty-nine species are recognized in the Orasema stramineipes species group, including 22 new species in what is now the most diverse species group of the New World ant-parasitoid genus Orasema Cameron. Orasema aenea Gahan syn. n. is synonymized with O. freychei (Gemignani), the holotype of which has been rediscovered. Orasema smithi Howard syn. n. is synonymized with Orasema minutissima Howard. Orasema violacea Gemignani syn. n. and its replacement name Orasema gemignanii De Santis syn. n. are synonymized with O. worcesteri (Girault). Twenty-two species are described as new: O. arimbome Dominguez, Heraty Burks n. sp., O. carchi Heraty, Burks Dominguez n. sp., and the following 20 species by Burks, Heraty Dominguez: O. chunpi n. sp., O. cozamalotl n. sp., O. evansi n. sp., O. hyarimai n. sp., O. kaspi n. sp., O. kulli n. sp., O. llanthu n. sp., O. llika n. sp., O. mati n. sp., O. nyamo n. sp., O. pirca n. sp., O. pisi n. sp., O. qillu n. sp., O. qincha n. sp., O. rikra n. sp., O. taku n. sp., O. tapi n. sp., O. torrensi n. sp., O. woolleyi n. sp., and O. yaax n. sp. The stramineipes-group has much greater diversity in tropical America than outside the tropics, and is much more diverse than its sister-group, the susanae-group, which is mainly present in temperate regions of Argentina. A hypothesis of phylogenetic relationships is proposed based on an analysis of 28S-D2 rDNA and cytochrome oxidase I (COI) for 14 stramineipes-group species. Species concepts were established using both morphological and molecular data. Most species in the stramineipes-group have a tropical distribution, with only a few species in temperate regions. Ant hosts for the group include Pheidole Westwood, Wasmannia Forel, and possibly Solenopsis Westwood (Formicidae: Myrmicinae). Orasema minutissima is a common parasitoid of Wasmannia auropunctata Roger in the Caribbean and has the potential to be a biological control agent in other areas of the world. Two distinct size morphs are recognized for O. minutissima, which are correlated with attacking either Wasmannia (small morph) or different castes of Pheidole (medium to large size morphs). Some species of Orasema have been regarded as pests due to scarring or secondary infections of leaves or fruit of banana, yerba mate or blueberry, but outbreaks are rare and the threat is usually temporary.}, } @article {pmid29690132, year = {2018}, author = {Tippelt, L and Schwentner, M}, title = {Taxonomic assessment of Australian Eocyzicus species (Crustacea: Branchiopoda: Spinicaudata).}, journal = {Zootaxa}, volume = {4410}, number = {3}, pages = {401-452}, doi = {10.11646/Zootaxa.4410.3.1}, pmid = {29690132}, issn = {1175-5334}, mesh = {Animal Shells ; Animals ; Australia ; *Crustacea ; Phylogeny ; }, abstract = {Herein we describe nine species of Eocyzicus from Australia and re-describe the morphological variability of Eocyzicus parooensis Richter Timms, 2005 and Eocyzicus argillaquus Timms Richter, 2009. All species were previously delimited by molecular phylogenetic analyses and the species descriptions are based on the same individuals. Characters were scored with the aid of the taxonomic software DELTA. The morphological analyses largely corroborated the previously delimited species despite high levels of intraspecific variability that overlapped with interspecific variation in many instances. Morphological species delimitation was generally supported by principal component and canonical variate analyses. Characters best suited for morphological species identification were the numbers of growth lines on the carapace, the number of telsonic spines and the number of setae on the furca.}, } @article {pmid29690053, year = {2018}, author = {Battiston, R and Correas, J and Lombardo, F and Mouna, M and Payne, K and SchÜtte, K}, title = {Morphological convergences in Ameles Burmeister and Pseudoyersinia Kirby: Taxonomic implications of wing reduction and flight predisposition in some West-Mediterranean Amelini (Insecta: Mantodea).}, journal = {Zootaxa}, volume = {4377}, number = {1}, pages = {21-38}, doi = {10.11646/zootaxa.4377.1.2}, pmid = {29690053}, issn = {1175-5334}, mesh = {Animals ; Insecta ; Italy ; Male ; *Mantodea ; Morocco ; Spain ; }, abstract = {Species in the genus Ameles Burmeister and Pseudoyersinia Kirby (Amelini) are traditionally defined as small-sized, ground-dwelling mantids whose males are distinct for being, respectively, macropterous and brachypterous. However, comparative morphological studies across Amelini confirmed the existence of short-winged males in Ameles, suggesting that this traditional diagnostic concept does not apply to all species. Our analyses of several species from West Mediterranean localities (Canary Islands, Spain, Italy, and Morocco) resulted in the relocation of Pseudoyersinia andreae Galvagni, 1976 to Ameles as Ameles andreae (Galvagni, 1976) (n. comb.) with Ameles insularis Agabiti, Ippolito Lombardo, 2010 as its new synonym (n. syn.), the clarification of the taxonomic identity of A. gracilis (Brullé, 1838) and A. maroccana Uvarov, 1931, including diagnoses of their males, and the description of Ameles spallanzania obscura (n. ssp.) (from Spain). We also take the opportunity to describe Pseudoyersinia maroccana (n. sp.) (from Morocco) based on museum specimens separating it from Ameles maroccana Uvarov, 1931. We also found that wing length is positively correlated to ocelli size. We discuss this trend from an ecological, evolutionary, and biogeographic perspectives to both facilitate species circumscription and justify the taxonomic modifications herein introduced.}, } @article {pmid29689812, year = {2018}, author = {VujiĆ, A and StÅhls, G and AČanski, J and Rojo, S and PÉrez-baÑÓn, C and RadenkoviĆ, S}, title = {Review of the Merodon albifasciatus Macquart species complex (Diptera: Syrphidae): the nomenclatural type located and its provenance discussed.}, journal = {Zootaxa}, volume = {4374}, number = {1}, pages = {25-48}, doi = {10.11646/zootaxa.4374.1.2}, pmid = {29689812}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; *Diptera ; Female ; Greece ; Male ; Plants ; }, abstract = {The Palaearctic Merodon geniculatus species group (Diptera, Syrphidae: Merodontini) currently comprises six Western Mediterranean species and four species with Eastern Mediterranean distribution. One of this group species, Merodon albifasciatus Macquart, 1842, is the only Merodon species listed from the Oriental Region. We discovered the lost holotype, which fit morphologically with European Merodon females of the M. albifasciatus species complex confirmed here and that occurs in the Palaearctic region. An integrative approach to the taxonomy of M. albifasciatus based on morphological and molecular evidences revealed the existence of two additional closely-related species in the Eastern Mediterranean area, M. luteofasciatus Vujić, Radenković Ståhls sp. nov. and M. neofasciatus Ståhls Vujić sp. nov.. The females of these three species can only be separated by molecular and distributional data. With the aim of stabilising species concepts within the complex, the taxon distributed in mainland Greece, including the Peloponnese was associated to the old female holotype of M. albifasciatus. The identity of Merodon fractipes Paramonov, described from Rhodes Island (Greece) as subspecies of M. geniculatus Strobl in Czerny Strobl, could not be resolved as the type specimen is lost. Thus the name M. fractipes is suppressed as nomen dubium. We discuss the distribution of the species of M. albifasciatus complex, identify host plants of M. neofasciatus, and provide an identification key to males of Eastern Mediterranean species of Merodon geniculatus group.}, } @article {pmid29686507, year = {2018}, author = {Aldhebiani, AY}, title = {Species concept and speciation.}, journal = {Saudi journal of biological sciences}, volume = {25}, number = {3}, pages = {437-440}, pmid = {29686507}, issn = {1319-562X}, abstract = {Defining and recognizing a species has been a controversial issue for a long time. To determine the variation and the limitation between species, many concepts have been proposed. When a taxonomist study a particular taxa, he/she must adopted a species concept and provide a species limitation to define this taxa. In this paper some of species concepts are discussed starting from the typological species concepts to the phylogenetic concept. Positive and negative aspects of these concepts are represented in addition to their application.}, } @article {pmid29676994, year = {2018}, author = {Zhang, F and Meier-Schellersheim, M}, title = {SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 1.}, journal = {Journal of integrative bioinformatics}, volume = {15}, number = {1}, pages = {}, doi = {10.1515/jib-2017-0077}, pmid = {29676994}, issn = {1613-4516}, mesh = {Animals ; Cell Physiological Phenomena ; *Computer Graphics ; Documentation ; Humans ; *Models, Biological ; Programming Languages ; Signal Transduction ; *Software ; Systems Biology/*standards ; }, abstract = {Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains (components) and the states such as phosphorylation and binding status of the involved components. Fine-grained spatial information such as the locations of the molecular components relative to a membrane (e.g. whether a modeled molecular domain is embedded into the inner leaflet of the cellular plasma membrane) can also be provided. Through wildcards representing component states entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states and multiple compartments. The SBML Level 3 Multi Package (Multistate, Multicomponent and Multicompartment Species Package for SBML Level 3) extends the SBML Level 3 core with the "type" concept in the Species and Compartment classes and therefore reaction rules may contain species that can be patterns and be in multiple locations in reaction rules. Multiple software tools such as Simmune and BioNetGen support the SBML Level 3 Multi package that thus also becomes a medium for exchanging rule-based models.}, } @article {pmid29672539, year = {2018}, author = {Vaidya, G and Lepage, D and Guralnick, R}, title = {The tempo and mode of the taxonomic correction process: How taxonomists have corrected and recorrected North American bird species over the last 127 years.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0195736}, pmid = {29672539}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Birds/*classification ; North America ; }, abstract = {While studies of taxonomy usually focus on species description, there is also a taxonomic correction process that retests and updates existing species circumscriptions on the basis of new evidence. These corrections may themselves be subsequently retested and recorrected. We studied this correction process by using the Check-List of North and Middle American Birds, a well-known taxonomic checklist that spans 130 years. We identified 142 lumps and 95 splits across sixty-three versions of the Check-List and found that while lumping rates have markedly decreased since the 1970s, splitting rates are accelerating. We found that 74% of North American bird species recognized today have never been corrected (i.e., lumped or split) over the period of the checklist, while 16% have been corrected exactly once and 10% have been corrected twice or more. Since North American bird species are known to have been extensively lumped in the first half of the 20th century with the advent of the biological species concept, we determined whether most splits seen today were the result of those lumps being recorrected. We found that 5% of lumps and 23% of splits fully reverted previous corrections, while a further 3% of lumps and 13% of splits are partial reversions. These results show a taxonomic correction process with moderate levels of recorrection, particularly of previous lumps. However, 81% of corrections do not revert any previous corrections, suggesting that the majority result in novel circumscriptions not previously recognized by the Check-List. We could find no order or family with a significantly higher rate of correction than any other, but twenty-two genera as currently recognized by the AOU do have significantly higher rates than others. Given the currently accelerating rate of splitting, prediction of the end-point of the taxonomic recorrection process is difficult, and many entirely new taxonomic concepts are still being, and likely will continue to be, proposed and further tested.}, } @article {pmid29657396, year = {2018}, author = {Narladkar, BW}, title = {Projected economic losses due to vector and vector-borne parasitic diseases in livestock of India and its significance in implementing the concept of integrated practices for vector management.}, journal = {Veterinary world}, volume = {11}, number = {2}, pages = {151-160}, pmid = {29657396}, issn = {0972-8988}, abstract = {Broadly, species of arthropods infesting livestock are grouped into flies (biting and non-biting), fleas, lice (biting and sucking), ticks (soft and hard), and mites (burrowing, non-burrowing, and follicular). Among which, biting and non-biting flies and ticks are the potent vectors for many bacterial, viral, rickettsial, and protozoan diseases. Vectors of livestock are having economic significance on three points (1) direct losses from their bite and annoyance, worries, and psychological disturbances produced during the act of biting and feeding, (2) diseases they transmit, and (3) expenditure incurred for their control. Flies such as Culicoides spp. and Musca spp. and various species of hard ticks play important role in disease transmission in addition to their direct effects. For control of vectors, recent concept of integrated pest management (IPM) provides the best solution and also addresses the problems related to acaricide resistance and environmental protection from hazardous chemicals. However, to successfully implement the concept of IPM, for each vector species, estimation of two monitory benchmarks, i.e., economic injury level (EIL) and economic threshold level (ETL) is essential prerequisite. For many vector species and under several circumstances, estimation of EIL and ETL appears to be difficult. Under such scenario, although may not be exact, an approximate estimate can be accrued by taking into account several criteria such as percent prevalence of vectors in a geographical area, percent losses produced, total livestock population, and current prices of livestock products such as milk, meat, and wool. Method for approximate estimation is first time described and elaborated in the present review article.}, } @article {pmid29648541, year = {2018}, author = {Citti, C and Dordet-Frisoni, E and Nouvel, LX and Kuo, CH and Baranowski, E}, title = {Horizontal Gene Transfers in Mycoplasmas (Mollicutes).}, journal = {Current issues in molecular biology}, volume = {29}, number = {}, pages = {3-22}, doi = {10.21775/cimb.029.003}, pmid = {29648541}, issn = {1467-3045}, mesh = {Chromosomes, Bacterial ; Conjugation, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Mycoplasma/classification/*physiology ; Response Elements ; Tenericutes/classification/*physiology ; }, abstract = {The class Mollicutes (trivial name "mycoplasma") is composed of wall-less bacteria with reduced genomes whose evolution was long thought to be only driven by gene losses. Recent evidences of massive horizontal gene transfer (HGT) within and across species provided a new frame to understand the successful adaptation of these minimal bacteria to a broad range of hosts. Mobile genetic elements are being identified in a growing number of mycoplasma species, but integrative and conjugative elements (ICEs) are emerging as pivotal in HGT. While sharing common traits with other bacterial ICEs, such as their chromosomal integration and the use of a type IV secretion system to mediate horizontal dissemination, mycoplasma ICEs (MICEs) revealed unique features: their chromosomal integration is totally random and driven by a DDE recombinase related to the Mutator-like superfamily. Mycoplasma conjugation is not restricted to ICE transmission, but also involves the transfer of large chromosomal fragments that generates progenies with mosaic genomes, nearly every position of chromosome being mobile. Mycoplasmas have thus developed efficient ways to gain access to a considerable reservoir of genetic resources distributed among a vast number of species expanding the concept of minimal cell to the broader context of flowing information.}, } @article {pmid29635015, year = {2018}, author = {Seethapathy, GS and Ravikumar, K and Paulsen, BS and de Boer, HJ and Wangensteen, H}, title = {Ethnobotany of dioecious species: Traditional knowledge on dioecious plants in India.}, journal = {Journal of ethnopharmacology}, volume = {221}, number = {}, pages = {56-64}, doi = {10.1016/j.jep.2018.04.011}, pmid = {29635015}, issn = {1872-7573}, mesh = {Adult ; Aged ; Aged, 80 and over ; Ethnobotany ; Female ; *Health Knowledge, Attitudes, Practice ; Humans ; India ; Male ; Medicine, Traditional ; Middle Aged ; *Plants, Medicinal ; Surveys and Questionnaires ; }, abstract = {More than 15,000 angiosperm species are dioecious, i.e., having distinct male and female individual plants. The allocation of resources between male and female plants is different, and also variation in secondary metabolites and sex-biased herbivory is reported among dioecious plants. However, little is known about the ethnobotany of dioecious species and whether preferences exist for a specific gender, e.g., in food, medicine or timber.

AIM OF THE STUDY: The aim of this study was: 1) to study whether Indian folk healers have preference for plant genders, and to document their knowledge and use of dioecious species; 2) to understand the concept of plant gender in Indian systems of medicine and folk medicine, and whether Ayurvedic literature includes any references to gender preference.

MATERIALS AND METHODS: Lists of dioecious plants used in Indian systems of medicine and folk medicine were compiled. Ethnobotanical data was collected on perceptions and awareness of dioecious plants, and preferences of use for specific genders of dioecious species using semi-structured interviews with folk healers in Tamil Nadu, India. In addition, twenty Ayurvedic doctors were interviewed to gain insight into the concept of plant gender in Ayurveda.

RESULTS: Indian systems of medicine contain 5-7% dioecious species, and this estimate is congruent with the number of dioecious species in flowering plants in general. Informants recognized the phenomenon of dioecy in 31 out of 40 species, and reported gender preferences for 13 species with respect to uses as timber, food and medicine. Among informants different plant traits such as plant size, fruit size, and visibility of fruits determines the perception of a plant being a male or female. Ayurvedic classical literature provides no straightforward evidence on gender preferences in preparation of medicines or treatment of illness, however it contains details about reproductive morphology and sexual differentiation of plants.

CONCLUSIONS: A knowledge gap exists in ethnobotanical and ethnopharmacological literature on traditional knowledge of dioecious plants. From this explorative study it is evident that people have traditional knowledge on plant gender and preferential usages towards one gender. Based on this, we propose that researchers conducting ethnobotanical and ethnopharmacological studies should consider documenting traditional knowledge on sexual systems of plants, and test the existence of gender specific usages in their conceptual framework and hypothesis testing. Incorporating such concepts could provide new dimensions of scientific knowledge with potential implications to conservation biology, chemical ecology, ethnoecology and drug discovery.}, } @article {pmid29631052, year = {2018}, author = {Zhou, W and Ji, X and Obata, S and Pais, A and Dong, Y and Peet, R and Xiang, QJ}, title = {Resolving relationships and phylogeographic history of the Nyssa sylvatica complex using data from RAD-seq and species distribution modeling.}, journal = {Molecular phylogenetics and evolution}, volume = {126}, number = {}, pages = {1-16}, doi = {10.1016/j.ympev.2018.04.001}, pmid = {29631052}, issn = {1095-9513}, mesh = {Bayes Theorem ; Genetic Loci ; *Models, Theoretical ; Nyssa/*classification/*genetics ; Phylogeny ; *Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA/*methods ; Species Specificity ; Time Factors ; }, abstract = {Nyssa sylvatica complex consists of several woody taxa occurring in eastern North America. These taxa were recognized as two or three species including three or four varieties by different authors. Due to high morphological similarities and complexity of morphological variation, classification and delineation of taxa in the group have been difficult and controversial. Here we employ data from RAD-seq to elucidate the genetic structure and phylogenetic relationships within the group. Using the genetic evidence, we evaluate previous classifications and delineate species. We also employ Species Distribution Modeling (SDM) to evaluate impacts of climatic changes on the ranges of the taxa and to gain insights into the relevant refugia in eastern North America. Results from Molecular Variance Analysis (AMOVA), STRUCTURE, phylogenetic analyses using Maximum likelihood, Bayesian Inference, and Splittree methods of RAD-seq data strongly support a two-clade pattern, largely separating samples of N. sylvatica from those of N. biflora-N. ursina mix. Divergence time analysis with BEAST suggests the two clades diverged in the mid Miocene. The ancestor of the present trees of N. sylvatica was suggested to be in the Pliocene and that of N. biflora-N. ursina mix in the end of the Miocene. Results from SDM predicted a smaller range in the southern part of the species present range of each clade during the Last Glacial Maximum (LGM). A northward expansion of the ranges during interglacial period and a northward shift of the ranges in the future under a model of global warming were also predicted. Our results support the recognition of two species in the complex, N. sylvatica and N. biflora, following the phylogenetic species concept. We found no genetic evidence supporting recognitions of intraspecific taxa. However, we propose subsp. ursina and subsp. biflora within N. biflora due to their distinction in habits, distributions, and habitats. Our results further support movements of trees in eastern North America in response to climatic changes. Finally, our study demonstrates that RAD-seq data and a combination of population genomics and SDM are valuable in resolving relationship and biogeographic history of closely related species that are taxonomically difficult.}, } @article {pmid29630628, year = {2018}, author = {Klishko, OK and Lopes-Lima, M and Bogan, AE and Matafonov, DV and Froufe, E}, title = {Morphological and molecular analyses of Anodontinae species (Bivalvia, Unionidae) of Lake Baikal and Transbaikalia.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0194944}, pmid = {29630628}, issn = {1932-6203}, mesh = {Animals ; Anodonta/*anatomy & histology/classification/*genetics ; *DNA, Mitochondrial ; *Genome, Mitochondrial ; Lakes ; }, abstract = {The diversity and taxonomy of anodontine species in Lake Baikal and Transbaikalia region has been contentious since it is based on a typological species concept, the so called "Comparatory Method". Using this method, six Comparatory anodontine species have been described for the study area as belonging to the genus Colletopterum. This genus was separated from Anodonta based on shell characteristics and further split into two subgenera, i.e. Colletopterum sensu stricto and Colletopterum (Piscinaliana). However, many authors do not recognize this separation maintaining all Colletopterum forms within Anodonta. The current study clarifies the taxonomy and systematics of Anodontinae in this region, using a combination of molecular, morphological and anatomical data. All previously recognized Comparatory forms are here recognized as a single species, i.e. Anodonta anatina.}, } @article {pmid29615879, year = {2018}, author = {Beery, AK and Christensen, JD and Lee, NS and Blandino, KL}, title = {Specificity in Sociality: Mice and Prairie Voles Exhibit Different Patterns of Peer Affiliation.}, journal = {Frontiers in behavioral neuroscience}, volume = {12}, number = {}, pages = {50}, pmid = {29615879}, issn = {1662-5153}, support = {R15 MH113085/MH/NIMH NIH HHS/United States ; }, abstract = {Social behavior is often described as a unified concept, but highly social (group-living) species exhibit distinct social structures and may make different social decisions. Prairie voles (Microtus ochrogaster) are socially monogamous rodents that often reside in extended family groups, and exhibit robust preferences for familiar social partners (same- and opposite-sex) during extended choice tests, although short-term preferences are not known. Mice (Mus musculus) are gregarious and colonial, but in brief laboratory tests of social preference they typically prefer social novelty. This preference for novel vs. familiar peers may represent a species-specific difference in social decision-making between mice and prairie voles. However, the tests used to measure preferences in each species differ markedly in duration and degree of contact, such that the behaviors cannot be directly compared. We assessed whether social preferences for novelty or familiarity differed between mice and prairie voles of both sexes when assessed with matching protocols: the sociability/social preference test (SPT) typically used in mice (short, no direct contact), and the partner preference test (PPT) used in voles (long, direct contact). A subset of voles also underwent a PPT using barriers (long, no direct contact). In the short SPT, behavior did not differ between species. In the longer test, pronounced partner preferences emerged in prairie voles, but mice exhibited no social preferences and rarely huddled. No sex differences were evident in either test. Direct physical contact was required for partner preferences in huddling time in voles, but preference for the partner chamber was evident with or without contact. Both prairie voles and mice are social, but they exhibit important differences in the specificity and extent of their social behavior. While mice are often used to study social approach and other behaviors, voles are a more suitable species for the study of selective social relationships. Consideration of these differences will be important for studies examining the neural mechanisms supporting different kinds of peer social behavior.}, } @article {pmid29606595, year = {2018}, author = {Lherminier, P}, title = {[Informative predation: Towards a new species concept].}, journal = {Comptes rendus biologies}, volume = {341}, number = {4}, pages = {209-218}, doi = {10.1016/j.crvi.2018.02.004}, pmid = {29606595}, issn = {1768-3238}, mesh = {*Adaptation, Physiological ; Animals ; Biological Evolution ; Child ; Courtship ; Diploidy ; Female ; Fertility ; Genome ; Humans ; Male ; *Predatory Behavior ; Pregnancy ; Reproduction/genetics ; *Selection, Genetic ; }, abstract = {We distinguish two types of predations: the predation of matter-energy equals the food chain, and the informative predation is the capture of the information brought by the sexual partners. The cell or parent consumes energy and matter to grow, multiply and produce offspring. A fixed amount of resources is divided by the number of organisms, so individual growth and numerical multiplication are limited by depletion resources of the environment. Inversely, fertilization does not destroy information, but instead produces news. The information is multiplied by the number of partners and children, since each fertilization gives rise to a new genome following a combinatorial process that continues without exhaustion. The egg does not swallow the sperm to feed, but exchange good food for quality information. With the discovery of sex, that is, 1.5 Ga ago, life added soft predation to hard predation, i.e. information production within each species to matter-energy flow between species. Replicative and informative structures are subject to two competing biological constraints: replicative fidelity promotes proliferation, but limits adaptive evolution. On the contrary, the offspring of a couple obviously cannot be a copy of both partners, they are a new production, a re-production. Sexual recombination allows the exponential enrichment of the genetic diversity, thus promoting indefinite adaptive and evolutionary capacities. Evolutionary history illustrates this: the bacteria proliferate but have remained at the first purely nutritive stage in which most of the sensory functions, mobility, defense, and feeding have experienced almost no significant novelty in three billion years. Another world appeared with the sexual management of information. Sexual reproduction actually combines two functions: multiplicative by "vertical transfer" and informative by "horizontal transfer". This distinction is very common: polypus - medusa alternations, parasite multiplication cycles, the lytochal and deuterotochal parthenogenesis of aphids, and the innumerable para- and pseudo-sexual strategies of plants opportunistically combine the two modes of asexual replication and sexual combination. However, for the majority of animals and multicellular plants that produce many gametes, numerical proliferation by descendants and informative diversity by sexuality are mutually implicated, for example in the seed. The true discovery of eukaryotes may not be the "true nucleus", as their name implies, but an orderly informative function. The field of recombinations circumscribes a class of partners genetically compatible with each other, each simultaneously prey and predator of the DNA of the other. The mythical Maxwell demon capable of tracing entropy by sorting molecules according to their state does exist: each mate is the other's Maxwell's demon. While a sexless bacterium is simply divided into two cells, two sexual parents work together to produce a single offspring a time. Added to this are the burdens involved in meiosis and crossing-over, cellular diploidy, and mating. Sex produces an information gain that is paid for by a cost of energy-material, and this barter must be fair to survive. The domains of sexual intercourse are very diverse: uniparental reproduction, alternation of asexual proliferation and sexual information, self-fertilization, endogamy, exogamy, panmixis, diffuse or structured polymorphism, fertile or sterile hybridization, horizontal transfers. Each species is a recombination field between two domains, cloning and hybridization. Multiplicative descent and informative fertilization are organically distinct, but selectively associated: the information produced by the parents' sexuality favors the predation of matter-energy and therefore the proliferation of offspring, and this proliferation in turn favors the sexed producers of information. The equation specific to each species is: enough energy to proliferate, enough information to diversify. Alternatively, two other reproductive modes obtain or transmit less information at lower cost: not enough recombinations=repetitive clonal proliferation, and too many recombinations=disordered hybridization. But these marginal modes have poor prospects, as the model of the species is successfully attractive. Better discriminate to better inform. In bacteria, the exchanged and incorporated DNA segments are directly identified by the parity of the complementary strands, which determines simultaneously the similarity, the offspring, and the pairing. In eukaryotes, on the contrary, somatic growth and germinal information are segregated. During speciation, adaptive information is compacted, delocalized, codified and published to inform the species about its own state: the prezygotic relationship governs viable mating. Under the effect of sexual selection, the runaway and the reinforcement of the characters related to courtship testifies to their identifying function, which explains the paradox of the singularity and luxuriance of the sexual hypertrophies. The speciation discretizes a balanced recombination field and validates the informative relations. The species is without degree. Mates of a species recognize each other quickly and well because the logic of coding disengages from the ecological game of adaptations. The system of mate recognition has a function of cohesion and its regularity allows the adaptations of the less regular being, it is neither elitist nor normative, it is subjected neither to a level of aptitudes, nor to sexual performances, but permissive; it protects the variability and polymorphism. Two mutually irreducible relationships triggered the debate between the taxonomists who support the phyletic definition of the species by the descendance, and the proponents of the definition by interfertility. Such a taxonomic disagreement is not insurmountable, but the issue is deeper than taxonomic concepts, because these concepts relate to two different modes of evolution. According to the phyletic model, each species is a lineage passively isolated by external circumstances; on the contrary, in the sexual model each species is actively produced by an internal process of adjustment between replicative costs and informative gains. Each species develops a solution of the equation that matches material-energy expenditures with informative gains. A species concept based on a lasting relationship between these two quantities or on the limits of certain values or their equilibrium is therefore legitimate. It is this equilibrium that all couples resolve, without our formulation being as clearly as biology desires and as physics demands. Energy expenditures and informative gains in sexuality are almost impossible to measure, yet observation and experience allow an approximate ranking of the energy/information ratio. For example, endogamy is more economical, but less diversifying than exogamy, polymorphism increases information, the reinforcement of sexual isolation limits the rate of unproductive fertilization, between neighboring species hybridization allows certain genetic contributions, etc. A closed species evolves naturally towards another just as closed. On the contrary, the artificial transfer of DNA opens the species. The natural boundaries that isolate the species are easily trespassed as energy costs and constraints of sexual recognition are easily controlled; and the perspectives of manipulations are visible, whereas natural selection never anticipates and thus works blindly. Informative, artificially directed predation stimulates the evolution of species.}, } @article {pmid29577296, year = {2018}, author = {Slomka, V and Herrero, ER and Boon, N and Bernaerts, K and Trivedi, HM and Daep, C and Quirynen, M and Teughels, W}, title = {Oral prebiotics and the influence of environmental conditions in vitro.}, journal = {Journal of periodontology}, volume = {89}, number = {6}, pages = {708-717}, doi = {10.1002/JPER.17-0437}, pmid = {29577296}, issn = {1943-3670}, mesh = {Bacteria ; *Microbiota ; Prebiotics ; *Probiotics ; }, abstract = {BACKGROUND: Only recently the concept of prebiotics has been introduced in oral health. Few potential oral prebiotics have already been identified in dual species competition assays, showing a stimulatory effect on beneficial bacteria and by this suppressing the outgrowth of pathogenic species. This study aimed to validate the effect of previously identified potential prebiotic substrates on multispecies cultures by shifting the biofilm composition towards a more beneficial species dominated microbiota.

METHODS: A chemostat culture containing 14 model oral bacterial species was used to grow biofilms for 24 hours which subsequently were treated with prebiotic solutions three times a day for 3 consecutive days. Further the influence of environmental factors such as pH, nutrient availability, oxygen concentration and prebiotic dose on the efficacy of the prebiotic substances was investigated.

RESULTS: Three potential prebiotic substrates N-acetyl-D-mannosamine, succinic acid and Met-Pro were able to bring the beneficial proportion to > 95%. While the pH of the prebiotic solution did not have an influence on the prebiotic effect, the interplay of nutrient availability, oxygen concentration and prebiotic treatment resulted in significant changes of the microbial composition identifying N-acetyl-D-mannosamine as the most promising oral prebiotic substrate. Showing a clear dose dependent effect, concentrations of N-acetyl-D-mannosamine of 1.0 and 1.5 M resulted in a biofilm composition of 97% beneficial species.

CONCLUSION: Introducing the prebiotic concept in oral health might reveal a valid approach for treatment and prevention of oral diseases and promote oral health.}, } @article {pmid29576952, year = {2018}, author = {McGuire, JA and Cotoras, DD and O'Connell, B and Lawalata, SZS and Wang-Claypool, CY and Stubbs, A and Huang, X and Wogan, GOU and Hykin, SM and Reilly, SB and Bi, K and Riyanto, A and Arida, E and Smith, LL and Milne, H and Streicher, JW and Iskandar, DT}, title = {Squeezing water from a stone: high-throughput sequencing from a 145-year old holotype resolves (barely) a cryptic species problem in flying lizards.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4470}, pmid = {29576952}, issn = {2167-8359}, abstract = {We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco species that cannot otherwise be distinguished from one another on the basis of museum specimens. Initial analyses suggested that the DNA present in the holotype sample was so degraded as to be unusable for sequencing. However, we used a specialized extraction procedure developed for highly degraded ancient DNA samples and MiSeq shotgun sequencing to obtain just enough low-coverage mitochondrial DNA (721 base pairs) to conclusively resolve the species status of the holotype as well as a second known specimen of this species. The holotype was prepared before the advent of formalin-fixation and therefore was most likely originally fixed with ethanol and never exposed to formalin. Whereas conventional wisdom suggests that formalin-fixed samples should be the most challenging for DNA sequencing, we propose that evaporation during long-term alcohol storage and consequent water-exposure may subject older ethanol-fixed museum specimens to hydrolytic damage. If so, this may pose an even greater challenge for sequencing efforts involving historical samples.}, } @article {pmid29569239, year = {2018}, author = {Spasojevic, MJ and Catano, CP and LaManna, JA and Myers, JA}, title = {Integrating species traits into species pools.}, journal = {Ecology}, volume = {99}, number = {6}, pages = {1265-1276}, doi = {10.1002/ecy.2220}, pmid = {29569239}, issn = {0012-9658}, mesh = {Biodiversity ; Biological Evolution ; Ecology ; *Ecosystem ; *Models, Biological ; }, abstract = {Despite decades of research on the species-pool concept and the recent explosion of interest in trait-based frameworks in ecology and biogeography, surprisingly little is known about how spatial and temporal changes in species-pool functional diversity (SPFD) influence biodiversity and the processes underlying community assembly. Current trait-based frameworks focus primarily on community assembly from a static regional species pool, without considering how spatial or temporal variation in SPFD alters the relative importance of deterministic and stochastic assembly processes. Likewise, species-pool concepts primarily focus on how the number of species in the species pool influences local biodiversity. However, species pools with similar richness can vary substantially in functional-trait diversity, which can strongly influence community assembly and biodiversity responses to environmental change. Here, we integrate recent advances in community ecology, trait-based ecology, and biogeography to provide a more comprehensive framework that explicitly considers how variation in SPFD, among regions and within regions through time, influences the relative importance of community assembly processes and patterns of biodiversity. First, we provide a brief overview of the primary ecological and evolutionary processes that create differences in SPFD among regions and within regions through time. We then illustrate how SPFD may influence fundamental processes of local community assembly (dispersal, ecological drift, niche selection). Higher SPFD may increase the relative importance of deterministic community assembly when greater functional diversity in the species pool increases niche selection across environmental gradients. In contrast, lower SPFD may increase the relative importance of stochastic community assembly when high functional redundancy in the species pool increases the influence of dispersal history or ecological drift. Next, we outline experimental and observational approaches for testing the influence of SPFD on assembly processes and biodiversity. Finally, we highlight applications of this framework for restoration and conservation. This species-pool functional diversity framework has the potential to advance our understanding of how local- and regional-scale processes jointly influence patterns of biodiversity across biogeographic regions, changes in biodiversity within regions over time, and restoration outcomes and conservation efforts in ecosystems altered by environmental change.}, } @article {pmid29555180, year = {2018}, author = {Rodríguez-Sevilla, G and García-Coca, M and Romera-García, D and Aguilera-Correa, JJ and Mahíllo-Fernández, I and Esteban, J and Pérez-Jorge, C}, title = {Non-Tuberculous Mycobacteria multispecies biofilms in cystic fibrosis: development of an in vitro Mycobacterium abscessus and Pseudomonas aeruginosa dual species biofilm model.}, journal = {International journal of medical microbiology : IJMM}, volume = {308}, number = {3}, pages = {413-423}, doi = {10.1016/j.ijmm.2018.03.003}, pmid = {29555180}, issn = {1618-0607}, mesh = {Anti-Bacterial Agents ; Biofilms/drug effects/*growth & development ; Clarithromycin/pharmacology ; Cystic Fibrosis/*microbiology ; Humans ; In Vitro Techniques ; Models, Biological ; Mycobacterium abscessus/growth & development/*physiology/ultrastructure ; Nontuberculous Mycobacteria/growth & development/*physiology ; Pseudomonas Infections/microbiology ; Pseudomonas aeruginosa/growth & development/*physiology/ultrastructure ; }, abstract = {Lung disease in cystic fibrosis (CF) is characterized by the progressive colonization of the respiratory tract by different bacteria, which develop polymicrobial biofilms. In the past decades, there has been an increase in the number of CF patients infected with Non-Tuberculous Mycobacteria (NTM). Although Mycobacterium abscessus is the main NTM isolated globally, little is known about M. abscessus multispecies biofilm formation. In the present study we developed an in vitro model to study the phenotypic characteristics of biofilms formed by M. abscessus and Pseudomonas aeruginosa, a major pathogen in CF. For that purpose, dual species biofilms were grown on polycarbonate membranes with a fixed concentration of P. aeruginosa and different inoculums of M. abscessus. The biofilms were sampled at 24, 48, and 72 h and bacteria were quantified in specific media. The results revealed that the increasing initial concentration of M. abscessus in dual species biofilms had an effect on its population only at 24 and 48 h, whereas P. aeruginosa was not affected by the different concentrations used of M. abscessus. Time elapsed increased biofilm formation of both species, specially between 24 and 48 h. According to the results, the conditions to produce a mature dual species biofilm in which the relative species distribution remained stable were 72 h growth of the mixed microbial culture at a 1:1 ratio. A significant decrease in mycobacterial population in dual compared to single species biofilms was found, suggesting that P. aeruginosa has a negative influence on M. abscessus. Finally, in a proof of concept experiment, young and mature dual species biofilms were exposed to clarithromycin.}, } @article {pmid29551763, year = {2018}, author = {Gutiérrez, EE and Garbino, GST}, title = {Species delimitation based on diagnosis and monophyly, and its importance for advancing mammalian taxonomy.}, journal = {Zoological research}, volume = {39}, number = {5}, pages = {301-308}, pmid = {29551763}, issn = {2095-8137}, mesh = {Animals ; Extinction, Biological ; Mammals/*classification/genetics ; Phylogeny ; Species Specificity ; }, abstract = {A recently proposed taxonomic classification of extant ungulates sparked a series of publications that criticize the Phylogenetic Species Concept (PSC) claiming it to be a particularly poor species concept. These opinions reiteratively stated that (1) the two fundamental elements of the "PSC", i.e., monophyly and diagnosability, do not offer objective criteria as to where the line between species should be drawn; and (2) that extirpation of populations can lead to artificial diagnosability and spurious recognitions of species. This sudden eruption of criticism against the PSC is misleading. Problems attributed to the PSC are common to most approaches and concepts that modern systematists employ to establish species boundaries. The controversial taxonomic propositions that sparked criticism against the PSC are indeed highly problematic, not because of the species concept upon which they are based, but because no evidence (whatsoever) has become public to support a substantial portion of the proposed classification. We herein discuss these topics using examples from mammals. Numerous areas of biological research rest upon taxonomic accuracy (including conservation biology and biomedical research); hence, it is necessary to clarify what are (and what are not) the real sources of taxonomic inaccuracy.}, } @article {pmid29551132, year = {2018}, author = {Van Regenmortel, MHV}, title = {The Species Problem in Virology.}, journal = {Advances in virus research}, volume = {100}, number = {}, pages = {1-18}, doi = {10.1016/bs.aivir.2017.10.008}, pmid = {29551132}, issn = {1557-8399}, mesh = {Classification ; Genome, Viral/genetics ; Species Specificity ; *Virology ; Viruses/chemistry/*classification/genetics ; }, abstract = {Virus classification deals with conceptual species classes that have viruses as their members. A virus species cannot be described but can only be defined by listing certain species-defining properties of its member. However, it is not possible to define a virus species by using a single species-defining property. The new 2013 official definition of virus species is not appropriate because it applies equally to virus genera. A nucleotide motif is a chemical part of a viral genome and is not a species-defining property that could be used for establishing new virus species. A virus classification based solely on nucleotide sequences is a classification of viral genomes and not of viruses. The variable distribution of species-defining properties of a polythetic species class is not itself a single common property of all the members of the class, since this would lead to the paradox that every polythetic class is also a monothetic one.}, } @article {pmid29500562, year = {2018}, author = {Gan, HM and Savka, MA}, title = {One More Decade of Agrobacterium Taxonomy.}, journal = {Current topics in microbiology and immunology}, volume = {418}, number = {}, pages = {1-14}, doi = {10.1007/82_2018_81}, pmid = {29500562}, issn = {0070-217X}, mesh = {Agrobacterium/*classification/genetics ; DNA, Bacterial/genetics ; Genes, Bacterial/genetics ; Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This chapter presents a historical overview of the development and changes in scientific approaches to classifying members of the Agrobacterium genus. We also describe the changes in the inference of evolutionary relationships among Agrobacterium biovars and Agrobacterium strains from using the 16S rRNA marker to recA genes and to the use of multilocus sequence analysis (MLSA). Further, the impacts of the genomic era enabling low cost and rapid whole genome sequencing on Agrobacterium phylogeny are reviewed with a focus on the use of new and sophisticated bioinformatics approaches to refine phylogenetic inferences. An updated genome-based phylogeny of ninety-seven Agrobacterium tumefaciens complex isolates representing ten known genomic species is presented, providing additional support to the monophyly of the Agrobacterium clade. Additional taxon sampling within Agrobacterium genomovar G3 indicates potential exceptions to interpretation of the concept of bacterial genomics species as ecological species because the genomovar G3 genomic cluster, which initially includes clinical strains, now also includes plant-associated and cave isolates.}, } @article {pmid29492785, year = {2018}, author = {Wright, AA and Kelly, DM and Katz, JS}, title = {Comparing cognition by integrating concept learning, proactive interference, and list memory.}, journal = {Learning & behavior}, volume = {46}, number = {2}, pages = {107-123}, pmid = {29492785}, issn = {1543-4508}, mesh = {Animals ; Birds ; Cognition/*physiology ; Concept Formation/*physiology ; Discrimination Learning/physiology ; Haplorhini ; Learning/*physiology ; Memory/physiology ; Species Specificity ; }, abstract = {This article describes an approach for training a variety of species to learn the abstract concept of same/different, which in turn forms the basis for testing proactive interference and list memory. The stimulus set for concept-learning training was progressively doubled from 8, 16, 32, 64, 128 . . . to 1,024 different pictures with novel-stimulus transfer following learning. All species fully learned the same/different abstract concept: capuchin and rhesus monkeys learned more readily than pigeons; nutcrackers and magpies were at least equivalent to monkeys and transferred somewhat better following initial training sets. A similar task using the 1,024-picture set plus delays was used to test proactive interference on occasional trials. Pigeons revealed greater interference with 10-s than with 1-s delays, whereas delay time had no effect on rhesus monkeys, suggesting that the monkeys' interference was event based. This same single-item same/different task was expanded to a 4-item list memory task to test animal list memory. Humans were tested similarly with lists of kaleidoscope pictures. Delays between the list and test were manipulated, resulting in strong initial recency effects (i.e., strong 4th-item memory) at short delays and changing to a strong primacy effect (i.e., strong 1st-item memory) at long delays (pigeons 0-s to 10-s delays; monkeys 0-s to 30-s delays; humans 0-s to 100-s delays). Results and findings are discussed in terms of these species' cognition and memory comparisons, evolutionary implications, and future directions for testing other species in these synergistically related tasks.}, } @article {pmid29480295, year = {2018}, author = {Kadiyala, U and Turali-Emre, ES and Bahng, JH and Kotov, NA and VanEpps, JS}, title = {Unexpected insights into antibacterial activity of zinc oxide nanoparticles against methicillin resistant Staphylococcus aureus (MRSA).}, journal = {Nanoscale}, volume = {10}, number = {10}, pages = {4927-4939}, pmid = {29480295}, issn = {2040-3372}, support = {K08 AI128006/AI/NIAID NIH HHS/United States ; R01 GM081702/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Hydrogen Peroxide ; *Metal Nanoparticles ; Methicillin-Resistant Staphylococcus aureus/*drug effects ; Zinc Oxide/*pharmacology ; }, abstract = {Zinc oxide nanoparticles (ZnO-NPs) are attractive as broad-spectrum antibiotics, however, their further engineering as antimicrobial agents and clinical translation is impeded by controversial data about their mechanism of activity. It is commonly reported that ZnO-NP's antimicrobial activity is associated with the production of reactive oxygen species (ROS). Here we disprove this concept by comparing the antibacterial potency of ZnO-NPs and their capacity to generate ROS with hydrogen peroxide (H2O2). Then, using gene transcription microarray analysis, we provide evidence for a novel toxicity mechanism. Exposure to ZnO-NPs resulted in over three-log reduction in colonies of methicillin resistant S. aureus with minimal increase in ROS or lipid peroxidation. The amount of ROS required for the same amount of killing by H2O2 was much greater than that generated by ZnO-NPs. In contrast to H2O2, ZnO-NP mediated killing was not mitigated by the antioxidant, N-acetylcysteine. ZnO-NPs caused significant up-regulation of pyrimidine biosynthesis and carbohydrate degradation. Simultaneously, amino acid synthesis in S. aureus was significantly down-regulated indicating a complex mechanism of antimicrobial action involving multiple metabolic pathways. The results of this study point to the importance of specific experimental controls in the interpretation of antimicrobial mechanistic studies and the need for targeted molecular mechanism studies. Continued investigation on the antibacterial mechanisms of biomimetic ZnO-NPs is essential for future clinical translation.}, } @article {pmid29461510, year = {2018}, author = {Heenan, P and Mitchell, C and Houliston, G}, title = {Genetic Variation and Hybridisation among Eight Species of kōwhai (Sophora: Fabaceae) from New Zealand Revealed by Microsatellite Markers.}, journal = {Genes}, volume = {9}, number = {2}, pages = {}, pmid = {29461510}, issn = {2073-4425}, abstract = {We analysed nine microsatellite markers for 626 individuals representing the geographic range of eight closely related endemic New Zealand species of Sophora. Structure analysis identified the optimal K value as seven, with samples identified as Sophorachathamica, Sophorafulvida, Sophoralongicarinata, and Sophoraprostrata retrieved as well-defined groups. The remaining samples formed less resolved groups referable to Sophoratetraptera and Sophoragodleyi, with Sophoramicrophylla and Sophoramolloyi forming the seventh group. Our data suggest that considerable admixture occurs and this is most likely the result of hybridisation or introgression. S.fulvida shows admixture with the sympatric S.chathamica, and the widespread S.microphylla exhibits admixture with the sympatric S.godleyi, S.molloyi, and S.tetraptera.}, } @article {pmid29458472, year = {2018}, author = {Hubka, V and Nováková, A and Jurjević, Ž and Sklenář, F and Frisvad, JC and Houbraken, J and Arendrup, MC and Jørgensen, KM and Siqueira, JPZ and Gené, J and Kolařík, M}, title = {Polyphasic data support the splitting of Aspergillus candidus into two species; proposal of Aspergillus dobrogensis sp. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {68}, number = {4}, pages = {995-1011}, doi = {10.1099/ijsem.0.002583}, pmid = {29458472}, issn = {1466-5034}, mesh = {Antifungal Agents/pharmacology ; Aspergillus/*classification/drug effects ; Bayes Theorem ; DNA, Fungal/genetics ; Microbial Sensitivity Tests ; Mycological Typing Techniques ; Phenotype ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Aspergillus candidus is a species frequently isolated from stored grain, food, indoor environments, soil and occasionally also from clinical material. Recent bioprospecting studies highlighted the potential of using A. candidus and its relatives in various industrial sectors as a result of their significant production of enzymes and bioactive compounds. A high genetic variability was observed among A. candidus isolates originating from various European countries and the USA, that were mostly isolated from indoor environments, caves and clinical material. The A. candidus sensu lato isolates were characterized by DNA sequencing of four genetic loci, and agreement between molecular species delimitation results, morphological characters and exometabolite spectra were studied. Classical phylogenetic methods (maximum likelihood, Bayesian inference) and species delimitation methods based on the multispecies coalescent model supported recognition of up to three species in A. candidus sensu lato. After evaluation of phenotypic data, a broader species concept was adopted, and only one new species, Aspergillus dobrogensis, was proposed. This species is represented by 22 strains originating from seven countries (ex-type strain CCF 4651[T]=NRRL 62821[T]=IBT 32697[T]=CBS 143370[T]) and its differentiation from A. candidus is relevant for bioprospecting studies because these species have different exometabolite profiles. Evaluation of the antifungal susceptibility of section Candidi members to six antifungals using the reference EUCAST method showed that all species have low minimum inhibitory concentrations for all tested antifungals. These results suggest applicability of a wide spectrum of antifungal agents for treatment of infections caused by species from section Candidi.}, } @article {pmid29442492, year = {2018}, author = {Stock, D and Dongmo, S and Walther, F and Sann, J and Janek, J and Schröder, D}, title = {Homogeneous Coating with an Anion-Exchange Ionomer Improves the Cycling Stability of Secondary Batteries with Zinc Anodes.}, journal = {ACS applied materials & interfaces}, volume = {10}, number = {10}, pages = {8640-8648}, doi = {10.1021/acsami.7b18623}, pmid = {29442492}, issn = {1944-8252}, abstract = {Limited cycling stability of secondary cells with zinc anodes arises mainly from the high solubility of oxidized zinc species in the alkaline electrolyte resulting in electrode shape change and loss of active material during repeated discharge and charge. We propose and successfully employ a homogeneous coating with an anion-exchange ionomer (AEI) on model electrodes with electron-conductive host structures to confine the oxidized zinc species. Ideally, the confinement of oxidized zinc species reduces the shape change of the electrode and keeps the active material as close as possible at its place of origin. In this work, the confinement concept for the oxidized zinc species is elucidated by means of electrochemical studies and X-ray photoelectron spectroscopy: as intended, an interlayer of zinc oxide forms between the AEI and the surface of the zinc electrode. This interlayer implies that the hydroxide ions are able to pass and react as intended, whereas the migration of oxidized zinc species into the bulk electrolyte is hindered. The coating with an AEI yields a higher amount of restored zinc during electrodeposition in comparison to an uncoated zinc electrode-applying an AEI coating increases the achievable cycle number by up to six times. We investigate the morphology of the cycled electrodes and derive thereby the needs for further material classes that might be employed in the confinement concept. This approach demonstrates the benefit of ion-selective coatings, allowing for the permeation of hydroxide ions but not of oxidized zinc species, a concept which improves rechargeable batteries with zinc anodes, such as zinc-oxygen batteries.}, } @article {pmid29440519, year = {2018}, author = {Arbilly, M}, title = {High-magnitude innovators as keystone individuals in the evolution of culture.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {373}, number = {1743}, pages = {}, pmid = {29440519}, issn = {1471-2970}, mesh = {Animals ; *Behavior, Animal ; Computer Simulation ; Creativity ; *Cultural Evolution ; *Diffusion of Innovation ; Models, Psychological ; }, abstract = {Borrowing from the concept of keystone species in ecological food webs, a recent focus in the field of animal behaviour has been keystone individuals: individuals whose impact on population dynamics is disproportionally larger than their frequency in the population. In populations evolving culture, such may be the role of high-magnitude innovators: individuals whose innovations are a major departure from the population's existing behavioural repertoire. Their effect on cultural evolution is twofold: they produce innovations that constitute a 'cultural leap' and, once copied, their innovations may induce further innovations by conspecifics (socially induced innovations) as they explore the new behaviour themselves. I use computer simulations to study the coevolution of independent innovations, socially induced innovations and innovation magnitude, and show that while socially induced innovation is assumed here to be less costly than independent innovation, it does not readily evolve. When it evolves, it may in some conditions select against independent innovation and lower its frequency, despite it requiring independent innovation in order to operate; at the same time, however, it leads to much faster cultural evolution. These results confirm the role of high-magnitude innovators as keystones, and suggest a novel explanation for the low frequency of independent innovation.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'.}, } @article {pmid29422770, year = {2017}, author = {Johnson, LA and Gowen, D}, title = {Ex uno, multis: taxonomic revision in Navarretia divaricata (Polemoniaceae) and the recognition of four additional cryptic or near-cryptic species.}, journal = {PhytoKeys}, volume = {}, number = {91}, pages = {39-83}, pmid = {29422770}, issn = {1314-2011}, abstract = {Navarretia divaricata, endemic to western North America and most recently considered a single species with two subspecies, was re-examined in light of field work, DNA sequences, comparative morphology, and a review of herbarium specimens including types. From these studies, we lectotypify the material on which N. divaricata is based, elevate N. divaricata subsp. vividior, which is an allotetraploid, to species rank (as N. vividiorcomb. et stat. nov.), and recognize three additional species: N. modocensissp. nov., N. aeroidessp. nov., and N. torreyellasp. nov.Navarretia modocensis, the diploid paternal progenitor of N. vividior, is morphologically cryptic with respect to its allotetraploid offspring and difficult to distinguish on herbarium sheets. Navarretia aeroides, the diploid maternal progenitor of N. vividior, is nearly cryptic, but more easily distinguished from both N. modocensis and N. vividior by its smaller, more glandular inflorescences. Navarretia torreyella is readily distinguished from all of these species, but has been generally mistaken for N. divaricata subsp. vividior given its colored corolla tube and rare co-occurrence with the other vividior-like species. Conservation assessments, an identification key, and table of comparative morphological features are provided for each species, emended descriptions for N. divaricata and N. vividior, and a discussion of the syntypes for Gilia divaricata Torr. ex A.Gray.}, } @article {pmid29408799, year = {2018}, author = {Ashrafian, H}, title = {The case for a distinctive philosophy of physiology and pathophysiology.}, journal = {Journal of basic and clinical physiology and pharmacology}, volume = {29}, number = {3}, pages = {237-240}, doi = {10.1515/jbcpp-2017-0143}, pmid = {29408799}, issn = {2191-0286}, mesh = {Animals ; Humans ; *Models, Biological ; *Philosophy ; Physiology ; *Systems Biology ; }, abstract = {What is an organ and what is an organ system? According to the 'standard' hierarchical model of physiology, each living organism comprises of organ systems including those that offer sensory and control functions (nervous system), energy accumulation (gastrointestinal system), internal dissipation (circulatory system) and mobility (musculoskeletal system). Each organ system in turn is comprised of individual organs. This taxonomy has conceptual flaws as not every organ has a single organ system function but may participate in a myriad of physiological functions. To answer this philosophical question, several principles are applied. At one level, the assessment of physiological function and organ system can be considered to have some relation to the broader issue of the species problem in the philosophy of biology. Additionally, however, there is a relationship to the more fundamental issue of the biochemistry of each organ that can be considered through the philosophy of chemistry. The philosophy of physiology can therefore be considered to occupy a position somewhere between these two strata of thought on the path of science reductionism. A distinctive philosophy of physiology and pathophysiology may ultimately offer a myriad of new pathways through which to better explore the metaphysical elements of medicine and science.}, } @article {pmid29380888, year = {2018}, author = {Génin, F and Masters, JC}, title = {Sharing the burden: A neutral approach to socioecological theory.}, journal = {American journal of physical anthropology}, volume = {165 Suppl 65}, number = {}, pages = {90-103}, doi = {10.1002/ajpa.23383}, pmid = {29380888}, issn = {1096-8644}, mesh = {Animals ; *Anthropology ; Bayes Theorem ; Biological Evolution ; Ecology ; Female ; Genetic Fitness ; Humans ; Male ; Marriage ; Mating Preference, Animal/*physiology ; Models, Theoretical ; Primates/*physiology ; Sociology ; }, abstract = {OBJECTIVE: The socioecological model (SEM) is a popular collection of controversial models purporting to explain mating systems in terms of ecological and social parameters. Despite its guise of objectivity, several of its hypotheses assume Victorian gender stereotypes of active, competing males heedlessly sowing their seeds, and cautious, passive females, imprisoned by greater costs of reproduction and their consequent resourceߚdependence.

METHODS: We enter this debate by taking a previously neglected explanatory approach borrowed from species theory. According to the Recognition Concept of sexual species, the unit of reproductive success/fitness is irreducible to fewer than two integrated subparts (minimally a male and a female). Phyletic changes in mating systems logically effect changes in fertilization systems, leading to reproductive isolation. We take our primary assumption of the average equivalence of female and male contributions to successful reproduction from the writings of the natural philosopher, Antoinette Blackwell.

RESULTS: We revisit the SEM with its contradictions and extrapolations, and develop a genderߚneutral alternative hypothesis termed SpecificߚMate Contact (SMC), centered on two fundamental mating strategies: sexual animals may behave as synchronous mateߚattractors or asynchronous mateߚseekers, generating four possible mating system combinations (monogamy: two attractors; promiscuity: two seekers; polygyny: male attractor and female seeker; polyandry: female attractor and male seeker).

CONCLUSIONS: Our approach predicts all known primate mating systems using a neutral (nonߚsexist) principle. The approach is also neutral in the sense that it does not invoke either competition or cooperation: fertilization success is considered a posteriori and males and females are coߚadapted to this end rather than cognitively cooperative.}, } @article {pmid29360839, year = {2018}, author = {Petkevičiūtė, R and Stunžėnas, V and Stanevičiūtė, G}, title = {Comments on species divergence in the genus Sphaerium (Bivalvia) and phylogenetic affinities of Sphaerium nucleus and S. corneum var. mamillanum based on karyotypes and sequences of 16S and ITS1 rDNA.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0191427}, pmid = {29360839}, issn = {1932-6203}, mesh = {Animals ; Bivalvia/*classification/*genetics ; DNA, Ribosomal Spacer/genetics ; Europe, Eastern ; Evolution, Molecular ; Genetic Speciation ; Genetics, Population ; Karyotyping ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {Chromosome, 16S and ITS1 rDNA sequence analyses were used to obtain reliable diagnostic characters and to clarify phylogenetic relationships of sphaeriid bivalves of the genus Sphaerium. The species studied were found to be diploid, with modal number 2n = 28 in S. nucleus and 2n = 30 in S. corneum var. mamillanum. Small, biarmed, C- negative B chromosomes were found in all studied populations of both species. Karyological and molecular markers revealed no differences between S. corneum s. str. and S. corneum var. mamillanum. No intraspecific differences were found in the basic karyotype of S. nucleus. Molecular analyses, however, uncovered three genetically distinct ITS1 lineages: one comprised of samples from Lithuania, Slovakia, and Russia, another from Czech, and a third from Ukraine. Additionally to known 16S haplotype from Ukraine, three new 16S haplotypes of S. nucleus were detected: one in the samples from Lithuania and Russia, one in Slovakian and one in Czech population. In the ITS1 phylogenetic tree, all branches of S. nucleus clustered in one clade. In the 16S phylogenetic tree, however, the haplotype of Czech S. nucleus formed a separate branch, distant from three other haplotypes of S. nucleus. Molecular results indicate that in the context of the Evolutionary Species Concept the S. nucleus morphospecies may represent a complex of separate taxa, however referring on the Biological Species Concept the genetic lineages could represent the intraspecific variability.}, } @article {pmid29352303, year = {2018}, author = {Gerli, MFM and Guyette, JP and Evangelista-Leite, D and Ghoshhajra, BB and Ott, HC}, title = {Perfusion decellularization of a human limb: A novel platform for composite tissue engineering and reconstructive surgery.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0191497}, pmid = {29352303}, issn = {1932-6203}, support = {P30 AR066261/AR/NIAMS NIH HHS/United States ; U42 OD011158/OD/NIH HHS/United States ; }, mesh = {Animals ; Arm/anatomy & histology/blood supply/*surgery ; Bioreactors ; Cadaver ; Extracellular Matrix/chemistry ; Humans ; Imaging, Three-Dimensional ; Male ; Middle Aged ; Perfusion ; Rats ; Reconstructive Surgical Procedures/*methods ; Tissue Engineering/instrumentation/*methods ; *Tissue Scaffolds/chemistry ; X-Ray Microtomography ; }, abstract = {Muscle and fasciocutaneous flaps taken from autologous donor sites are currently the most utilized approach for trauma repair, accounting annually for 4.5 million procedures in the US alone. However, the donor tissue size is limited and the complications related to these surgical techniques lead to morbidities, often involving the donor sites. Alternatively, recent reports indicated that extracellular matrix (ECM) scaffolds boost the regenerative potential of the injured site, as shown in a small cohort of volumetric muscle loss patients. Perfusion decellularization is a bioengineering technology that allows the generation of clinical-scale ECM scaffolds with preserved complex architecture and with an intact vascular template, from a variety of donor organs and tissues. We recently reported that this technology is amenable to generate full composite tissue scaffolds from rat and non-human primate limbs. Translating this platform to human extremities could substantially benefit soft tissue and volumetric muscle loss patients providing tissue- and species-specific grafts. In this proof-of-concept study, we show the successful generation a large-scale, acellular composite tissue scaffold from a full cadaveric human upper extremity. This construct retained its morphological architecture and perfusable vascular conduits. Histological and biochemical validation confirmed the successful removal of nuclear and cellular components, and highlighted the preservation of the native extracellular matrix components. Our results indicate that perfusion decellularization can be applied to produce human composite tissue acellular scaffolds. With its preserved structure and vascular template, these biocompatible constructs, could have significant advantages over the currently implanted matrices by means of nutrient distribution, size-scalability and immunological response.}, } @article {pmid29346992, year = {2017}, author = {Haerter, JO and Mitarai, N and Sneppen, K}, title = {Existence and construction of large stable food webs.}, journal = {Physical review. E}, volume = {96}, number = {3-1}, pages = {032406}, doi = {10.1103/PhysRevE.96.032406}, pmid = {29346992}, issn = {2470-0053}, mesh = {Biodiversity ; *Food Chain ; *Models, Biological ; }, abstract = {Ecological diversity is ubiquitous despite the restrictions imposed by competitive exclusion and apparent competition. To explain the observed richness of species in a given habitat, food-web theory has explored nonlinear functional responses, self-interaction, or spatial structure and dispersal-model ingredients that have proven to promote stability and diversity. We return instead here to classical Lotka-Volterra equations, where species-species interaction is characterized by a simple product and spatial restrictions are ignored. We quantify how this idealization imposes constraints on coexistence and diversity for many species. To this end, we introduce the concept of free and controlled species and use this to demonstrate how stable food webs can be constructed by the sequential addition of species. The resulting food webs can reach dozens of species and generally yield nonrandom degree distributions in accordance with the constraints imposed through the assembly process. Our model thus serves as a formal starting point for the study of sustainable interaction patterns between species.}, } @article {pmid29346885, year = {2017}, author = {Tikhonov, M}, title = {Theoretical microbial ecology without species.}, journal = {Physical review. E}, volume = {96}, number = {3-1}, pages = {032410}, doi = {10.1103/PhysRevE.96.032410}, pmid = {29346885}, issn = {2470-0053}, mesh = {Bacteria ; *Ecosystem ; *Models, Biological ; }, abstract = {Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic and mounting experimental evidence raises the intriguing question whether this perspective is appropriate for the microbial world. Here an alternative formalism is proposed that does not require postulating the existence of species as fundamental ecological variables and provides a naturally hierarchical description of community dynamics. This formalism allows approaching the species problem from the opposite direction. While the classical models treat a world of imperfectly clustered organism types as a perturbation around well-clustered species, the presented approach allows gradually adding structure to a fully disordered background. The relevance of this theoretical construct for describing highly diverse natural ecosystems is discussed.}, } @article {pmid29334414, year = {2018}, author = {Fišer, C and Robinson, CT and Malard, F}, title = {Cryptic species as a window into the paradigm shift of the species concept.}, journal = {Molecular ecology}, volume = {27}, number = {3}, pages = {613-635}, doi = {10.1111/mec.14486}, pmid = {29334414}, issn = {1365-294X}, mesh = {Amphipoda/physiology ; Animals ; Biodiversity ; Databases as Topic ; *Genetic Speciation ; Phylogeny ; Species Specificity ; }, abstract = {The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.}, } @article {pmid31089674, year = {2018}, author = {Master, JC and Génin, F}, title = {The recognition concept of species, decades on.}, journal = {Theoretical biology forum}, volume = {111}, number = {1-2}, pages = {93-97}, doi = {10.19272/201811402010}, pmid = {31089674}, issn = {2282-2593}, mesh = {*Classification ; }, } @article {pmid29277862, year = {2018}, author = {Zekic, T and Holley, G and Stoye, J}, title = {Pan-Genome Storage and Analysis Techniques.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1704}, number = {}, pages = {29-53}, doi = {10.1007/978-1-4939-7463-4_2}, pmid = {29277862}, issn = {1940-6029}, mesh = {*Algorithms ; Cluster Analysis ; Computational Biology/methods ; Databases, Genetic ; *Genome, Microbial ; Genomics/*methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Computational pan-genome analysis has emerged from the rapid increase of available genome sequencing data. Starting from a microbial pan-genome, the concept has spread to a variety of species, such as plants or viruses. Characterizing a pan-genome provides insights into intra-species evolution, functions, and diversity. However, researchers face challenges such as processing and maintaining large datasets while providing accurate and efficient analysis approaches. Comparative genomics methods are required for detecting conserved and unique regions between a set of genomes. This chapter gives an overview of tools available for indexing pan-genomes, identifying the sub-regions of a pan-genome and offering a variety of downstream analysis methods. These tools are categorized into two groups, gene-based and sequence-based, according to the pan-genome identification method. We highlight the differences, advantages, and disadvantages between the tools, and provide information about the general workflow, methodology of pan-genome identification, covered functionalities, usability and availability of the tools.}, } @article {pmid29273049, year = {2017}, author = {Shen, TJ and Chen, Y and Chen, YF}, title = {Estimating species pools for a single ecological assemblage.}, journal = {BMC ecology}, volume = {17}, number = {1}, pages = {45}, pmid = {29273049}, issn = {1472-6785}, mesh = {Ecology ; *Ecosystem ; Forests ; Models, Biological ; Panama ; Population Dynamics ; Trees/*classification ; }, abstract = {BACKGROUND: The species pool concept was formulated over the past several decades and has since played an important role in explaining multi-scale ecological patterns. Previous statistical methods were developed to identify species pools based on broad-scale species range maps or community similarity computed from data collected from many areas. No statistical method is available for estimating species pools for a single local community (sampling area size may be very small as ≤ 1 km[2]). In this study, based on limited local abundance information, we developed a simple method to estimate the area size and richness of a species pool for a local ecological community. The method involves two steps. In the first step, parameters from a truncated negative trinomial model characterizing the distributional aggregation of all species (i.e., non-random species distribution) in the local community were estimated. In the second step, we assume that the unseen species in the local community are most likely the rare species, only found in the remaining part of the species pool, and vice versa, if the remaining portion of the pool was surveyed and was contrasted with the sampled area. Therefore, we can estimate the area size of the pool, as long as an abundance threshold for defining rare species is given. Since the size of the pool is dependent on the rarity threshold, to unanimously determine the pool size, we developed an optimal method to delineate the rarity threshold based on the balance of the changing rates of species absence probabilities in the sampled and unsampled areas of the pool.

RESULTS: For a 50 ha (0.5 km[2]) forest plot in the Barro Colorado Island of central Panama, our model predicted that the local, if not regional, species pool for the 0.5 km[2] forest plot was nearly the entire island. Accordingly, tree species richness in this pool was estimated as around 360. When the sampling size was smaller, the upper bound of the 95% confidence interval could reach 418, which was very close to the flora record of tree richness for the island. A numerical test further demonstrated the power and reliability of the proposed method, as the true values of area size and species richness for the hypothetical species pool have been well covered by the 95% confidence intervals of the true values.

CONCLUSIONS: Our method fills the knowledge gap on estimating species pools for a single local ecological assemblage with little information. The method is statistically robust and independent of sampling size, as proved by both empirical and numerical tests.}, } @article {pmid29245404, year = {2017}, author = {Jendek, E}, title = {Revision of the Agrilus humilis species-group (Coleoptera: Buprestidae: Agrilini) with description of thirteen new species from Southeastern Asia.}, journal = {Zootaxa}, volume = {4363}, number = {2}, pages = {249-271}, doi = {10.11646/zootaxa.4363.2.5}, pmid = {29245404}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures ; Animals ; Asia, Southeastern ; Body Size ; *Coleoptera ; Organ Size ; }, abstract = {The newly defined Agrilus humilis species-group comprising twenty taxa of Indo-Malayan and Australasian region is revised based on the examination of type specimens. The taxonomic concept and distribution of all known species is critically revised for the first time since they were described. The complete commented bibliographic data are given for each name. The key to species is provided and complemented with illustration of habitus and genitalia. Images of all primary types are also included. The following thirteen new species are described: Agrilus aruensis sp. nov.; A. ateles sp. nov.; A. bicoloripennis sp. nov.; A. chloros sp. nov.; A. duffelsorum sp. nov.; A. ecalcaratus sp. nov.; A. incrassatus sp. nov.; A. korbicola sp. nov.; A. oidema sp. nov.; A. sphenopterus sp. nov.; A. suturistriatus sp. nov.; A. thailandicus sp. nov. and A. vogti sp. nov.}, } @article {pmid29212391, year = {2017}, author = {Schön, C and Sothilingam, V and Mühlfriedel, R and Garcia Garrido, M and Beck, SC and Tanimoto, N and Wissinger, B and Paquet-Durand, F and Biel, M and Michalakis, S and Seeliger, MW}, title = {Gene Therapy Successfully Delays Degeneration in a Mouse Model of PDE6A-Linked Retinitis Pigmentosa (RP43).}, journal = {Human gene therapy}, volume = {28}, number = {12}, pages = {1180-1188}, doi = {10.1089/hum.2017.156}, pmid = {29212391}, issn = {1557-7422}, abstract = {Retinitis pigmentosa type 43 (RP43) is a blinding disease caused by mutations in the gene for rod phosphodiesterase 6 alpha (PDE6A). The disease process begins with a dysfunction of rod photoreceptors, subsequently followed by a currently untreatable progressive degeneration of the entire outer retina. Aiming at a curative approach via PDE6A gene supplementation, a novel adeno-associated viral (AAV) vector was developed for expression of the human PDE6A cDNA under control of the human rhodopsin promotor (rAAV8.PDE6A). This study assessed the therapeutic efficacy of rAAV8.PDE6A in the Pde6a[nmf363/nmf363]-mutant mouse model of RP43. All mice included in this study were treated with sub-retinal injections of the vector at 2 weeks after birth. The therapeutic effect was monitored at 1 month and 6 months post injection. Biological function of the transgene was assessed in vivo by means of electroretinography. The degree of morphological rescue was investigated both in vivo using optical coherence tomography and ex vivo by immunohistological staining. It was found that the novel rAAV8.PDE6A vector resulted in a stable and efficient expression of PDE6A protein in rod photoreceptors of Pde6a[nmf363/nmf363] mice following treatment at both the short- and long-term time points. The treatment led to a substantial morphological preservation of outer nuclear layer thickness, rod outer segment structure, and prolonged survival of cone photoreceptors for at least 6 months. Additionally, the ERG analysis confirmed a restoration of retinal function in a group of treated mice. Taken together, this study provides successful proof-of-concept for the cross-species efficacy of the rAAV8.PDE6A vector developed for use in human patients. Importantly, the data show stable expression and rescue effects for a prolonged period of time, raising hope for future translational studies based on this approach.}, } @article {pmid29208741, year = {2017}, author = {Sepúlveda, VE and Márquez, R and Turissini, DA and Goldman, WE and Matute, DR}, title = {Genome Sequences Reveal Cryptic Speciation in the Human Pathogen Histoplasma capsulatum.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, pmid = {29208741}, issn = {2150-7511}, mesh = {*Genetic Speciation ; Genetic Variation ; Genome, Fungal/*genetics ; Histoplasma/*classification/*genetics/isolation & purification ; Histoplasmosis/microbiology ; Humans ; *Phylogeny ; }, abstract = {Histoplasma capsulatum is a pathogenic fungus that causes life-threatening lung infections. About 500,000 people are exposed to H. capsulatum each year in the United States, and over 60% of the U.S. population has been exposed to the fungus at some point in their life. We performed genome-wide population genetics and phylogenetic analyses with 30 Histoplasma isolates representing four recognized areas where histoplasmosis is endemic and show that the Histoplasma genus is composed of at least four species that are genetically isolated and rarely interbreed. Therefore, we propose a taxonomic rearrangement of the genus.IMPORTANCE The evolutionary processes that give rise to new pathogen lineages are critical to our understanding of how they adapt to new environments and how frequently they exchange genes with each other. The fungal pathogen Histoplasma capsulatum provides opportunities to precisely test hypotheses about the origin of new genetic variation. We find that H. capsulatum is composed of at least four different cryptic species that differ genetically and also in virulence. These results have implications for the epidemiology of histoplasmosis because not all Histoplasma species are equivalent in their geographic range and ability to cause disease.}, } @article {pmid29190130, year = {2018}, author = {Luo, X and Tinker, NA and Zhou, Y and Wight, CP and Liu, J and Wan, W and Chen, L and Peng, Y}, title = {Genomic relationships among sixteen species of Avena based on (ACT)6 trinucleotide repeat FISH.}, journal = {Genome}, volume = {61}, number = {1}, pages = {63-70}, doi = {10.1139/gen-2017-0132}, pmid = {29190130}, issn = {1480-3321}, mesh = {Avena/classification/*genetics ; *Chromosomes, Plant ; Genome, Plant ; In Situ Hybridization, Fluorescence ; Metaphase/genetics ; Mitosis/genetics ; *Trinucleotide Repeats ; }, abstract = {Knowledge of the locations of repeat elements could be very important in the assembly of genome sequences and their assignment to physical chromosomes. Genomic and species relationships among 16 species were investigated using fluorescence in situ hybridization (FISH) with the Am1 and (ACT)6 probes. The Am1 oligonucleotide probe was particularly enriched in the C genomes, whereas the (ACT)6 trinucleotide repeat probe showed a diverse distribution of hybridization patterns in the A, AB, C, AC, and ACD genomes but might not be present in the B and D genomes. The hybridization pattern of Avena sativa was very similar to that of A. insularis, indicating that this species most likely originated from A. insularis as a tetraploid ancestor. Although the two FISH probes failed to identify relationships of more species, this proof-of-concept approach opens the way to the use of FISH probes in assigning other signature elements from genomic sequence to physical chromosomes.}, } @article {pmid29187784, year = {2017}, author = {Wallin, H and Kvamme, T and Bergsten, J}, title = {To be or not to be a subspecies: description of Saperda populnea lapponica ssp. n. (Coleoptera, Cerambycidae) developing in downy willow (Salix lapponum L.).}, journal = {ZooKeys}, volume = {}, number = {691}, pages = {103-148}, pmid = {29187784}, issn = {1313-2989}, abstract = {A new subspecies of the European cerambycid Saperda populnea (Linnaeus, 1758) is described: Saperda populnea lapponicassp. n. based on specimens from Scandinavia. The male genitalia characters were examined and found to provide support for this separation, as well as differences in morphology, geographical distribution and bionomy. The preferred host tree for the nominate subspecies S. populnea populnea is Populus tremula L., whereas S. populnea lapponicassp. n. is considered to be monophagous on Salix lapponum L. DNA sequence data of mitochondrial cytochrome oxidase subunit I (COI) was generated from Scandinavian specimens of S. populnea populnea and specimens representing S. populnea lapponicassp. n. The two subspecies were not reciprocally monophyletic and genetic distances in COI were small. All synonyms of S. populnea populnea have been considered, and species similar to S. populnea populnea have been examined, and not found to be related to S. populnea lapponicassp. n. A male lectotype has been designated for each of the two following synonyms: Cerambyx decempunctatus De Geer, 1775, and Saperda salicis Zetterstedt, 1818. The synonymised species from Asia, S. balsamifera (Motshulsky, 1860), is elevated to subspecies: S. populnea balsamiferastat. n. We end with a discussion on the definition of subspecies under the unified species concept.}, } @article {pmid29187208, year = {2017}, author = {Segatto, ALA and Reck-Kortmann, M and Turchetto, C and Freitas, LB}, title = {Multiple markers, niche modelling, and bioregions analyses to evaluate the genetic diversity of a plant species complex.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {234}, pmid = {29187208}, issn = {1471-2148}, mesh = {Amplified Fragment Length Polymorphism Analysis ; DNA, Chloroplast/genetics ; *Ecosystem ; Genetic Markers ; *Genetic Variation ; *Geography ; Haplotypes/genetics ; Microsatellite Repeats/genetics ; Petunia/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: The classification of closely related plants is not straightforward. These morphologically similar taxa frequently maintain their inter-hybridization potential and share ancestral polymorphisms as a consequence of their recent divergence. Under the biological species concept, they may thus not be considered separate species. The Petunia integrifolia complex is especially interesting because, in addition to the features mentioned above, its taxa share a pollinator, and their geographical ranges show multiple overlaps. Here, we combined plastid genome sequences, nuclear microsatellites, AFLP markers, ecological niche modelling, and bioregions analysis to investigate the genetic variability between the different taxa of the P. integrifolia complex in a comprehensive sample covering the entire geographical range of the complex.

RESULTS: Results from molecular markers did not fully align with the current taxonomic classification. Niche modelling and bioregions analyses revealed that taxa were associated with different ecological constraints, indicating that the habitat plays an important role in preserving species boundaries. For three taxa, our analyses showed a mostly conserved, non-overlapping geographical distribution over time. However, for two taxa, niche modelling found an overlapping distribution over time; these taxa were also associated with the same bioregions.

CONCLUSIONS: cpDNA markers were better able to discriminate between Petunia taxa than SSRs and AFLPs. Overall, our results suggest that the P. integrifolia complex represents a continuum of individuals from distant and historically isolated populations, which share some morphological traits, but are established in four different evolutionary lineages.}, } @article {pmid29181275, year = {2017}, author = {Florentín, JE and Cabaña Fader, AA and Salas, RM and Janssens, S and Dessein, S and Cabral, EL}, title = {Morphological and molecular data confirm the transfer of homostylous species in the typically distylous genus Galianthe (Rubiaceae), and the description of the new species Galianthe vasquezii from Peru and Colombia.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4012}, pmid = {29181275}, issn = {2167-8359}, abstract = {Galianthe (Rubiaceae) is a neotropical genus comprising 50 species divided into two subgenera, Galianthe subgen. Galianthe, with 39 species and Galianthe subgen. Ebelia, with 11 species. The diagnostic features of the genus are: usually erect habit with xylopodium, distylous flowers arranged in lax thyrsoid inflorescences, bifid stigmas, 2-carpellate and longitudinally dehiscent fruits, with dehiscent valves or indehiscent mericarps, plump seeds or complanate with a wing-like strophiole, and pollen with double reticulum, rarely with a simple reticulum. This study focused on two species that were originally described under Diodia due to the occurrence of fruits indehiscent mericarps: Diodia palustris and D. spicata. In the present study, classical taxonomy is combined with molecular analyses. As a result, we propose that both Diodia species belong to Galianthe subgen. Ebelia. The molecular position within Galianthe, based on ITS and ETS sequences, has been supported by the following morphological characters: thyrsoid, spiciform or cymoidal inflorescences, bifid stigmas, pollen grains with a double reticulum, and indehiscent mericarps. However, both species, unlike the remainder of the genus Galianthe, have homostylous flowers, so the presence of this type of flower significantly modifies the generic concept. In this framework, a third homostylous species, Galianthe vasquezii, from the Andean region is also described. Until now, this species remained cryptic under specimens of Galianthe palustris It differs however from the latter by having longer calyx lobes, the presence of dispersed trichomes inside the corolla lobes (vs. glabrous), fruits that are acropetally dehiscent (vs. basipetally dehiscent), and its Andean geographical distribution (vs. Paranaense). Additionally, a lectotype has been chosen for Diodia palustris, Borreria pterophora has been placed under synonymy of Galianthe palustris, and Galianthe boliviana is reported for the first time from Peru. A key of all Galianthe species with indehiscent mericarps is also provided.}, } @article {pmid29167517, year = {2017}, author = {Datla, US and Mather, WH and Chen, S and Shoultz, IW and Täuber, UC and Jones, CN and Butzin, NC}, title = {The spatiotemporal system dynamics of acquired resistance in an engineered microecology.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16071}, pmid = {29167517}, issn = {2045-2322}, mesh = {Computer Simulation ; *Ecosystem ; Escherichia coli/*physiology ; Models, Biological ; Monte Carlo Method ; *Spatio-Temporal Analysis ; }, abstract = {Great strides have been made in the understanding of complex networks; however, our understanding of natural microecologies is limited. Modelling of complex natural ecological systems has allowed for new findings, but these models typically ignore the constant evolution of species. Due to the complexity of natural systems, unanticipated interactions may lead to erroneous conclusions concerning the role of specific molecular components. To address this, we use a synthetic system to understand the spatiotemporal dynamics of growth and to study acquired resistance in vivo. Our system differs from earlier synthetic systems in that it focuses on the evolution of a microecology from a killer-prey relationship to coexistence using two different non-motile Escherichia coli strains. Using empirical data, we developed the first ecological model emphasising the concept of the constant evolution of species, where the survival of the prey species is dependent on location (distance from the killer) or the evolution of resistance. Our simple model, when expanded to complex microecological association studies under varied spatial and nutrient backgrounds may help to understand the complex relationships between multiple species in intricate natural ecological networks. This type of microecological study has become increasingly important, especially with the emergence of antibiotic-resistant pathogens.}, } @article {pmid29166166, year = {2017}, author = {Nelson, PG and May, G}, title = {Coevolution between Mutualists and Parasites in Symbiotic Communities May Lead to the Evolution of Lower Virulence.}, journal = {The American naturalist}, volume = {190}, number = {6}, pages = {803-817}, doi = {10.1086/694334}, pmid = {29166166}, issn = {1537-5323}, mesh = {Animals ; *Biological Evolution ; Host-Pathogen Interactions ; Models, Biological ; Plant Diseases/*microbiology ; Plants/*microbiology ; Symbiosis/*physiology ; Virulence ; }, abstract = {Most eukaryotes harbor a diverse community of parasitic, mutualistic, and commensal microbial symbionts. Although the diversity of these microbial symbiotic communities has recently drawn considerable attention, theory regarding the evolution of interactions among symbionts and with the host is still in its nascent stages. Here we evaluate the role of interactions among coinfecting symbionts in the evolution of symbiont virulence toward the host. To do so, we place the virulence-transmission trade-off into a community context and model the evolution of symbiont trophic modes along the continuum from parasitism (virulence) to mutualism (negative virulence). We establish a framework for studying multiple infections of a host by the same symbiont species and coinfection by multiple species, using a concept of shared costs, wherein the negative consequences of virulence (or harm) toward the host are shared among symbionts. Our results show that mutualism can be maintained under infection by multiple symbionts when shared costs are sufficiently low, while greater virulence and parasitism toward the host are more likely when shared costs are high. Last, for coinfection by more than one species, we show that if the presence of a mutualist ameliorates some of the costs of pathogen virulence, then the symbiotic community may more often evolve to a more commensal state and maintain mutualisms.}, } @article {pmid29165821, year = {2018}, author = {Bruns, TD and Corradi, N and Redecker, D and Taylor, JW and Öpik, M}, title = {Glomeromycotina: what is a species and why should we care?.}, journal = {The New phytologist}, volume = {220}, number = {4}, pages = {963-967}, doi = {10.1111/nph.14913}, pmid = {29165821}, issn = {1469-8137}, support = {DE-SC0016365//US DOE/International ; DE-SC0014081//US DOE/International ; IUT20-28//Estonian Research Council/International ; //European Regional Development Fund/International ; //ERA-NET Cofund BiodivERsA3/International ; //Natural Sciences and Engineering Research Council of Canada/International ; ER13-09-190//Ontario Ministry of Research and Innovation/International ; }, mesh = {Glomeromycota/classification/genetics/*physiology ; Phylogeny ; Species Specificity ; }, abstract = {A workshop at the recent International Conference on Mycorrhiza was focused on species recognition in Glomeromycotina and parts of their basic biology that define species. The workshop was motivated by the paradigm-shifting evidence derived from genomic data for sex and for the lack of heterokaryosis, and by published exchanges in Science that were based on different species concepts and have led to differing views of dispersal and endemism in these fungi. Although a lively discussion ensued, there was general agreement that species recognition in the group is in need of more attention, and that many basic assumptions about the biology of these important fungi including sexual or clonal reproduction, similarity or dissimilarity of nuclei within an individual, and species boundaries need to be re-examined and scrutinized with current techniques.}, } @article {pmid29157065, year = {2018}, author = {Ruiz-García, M and Pinedo-Castro, M and Shostell, JM}, title = {Small spotted bodies with multiple specific mitochondrial DNAs: existence of diverse and differentiated tigrina lineages or species (Leopardus spp: Felidae, Mammalia) throughout Latin America.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {7}, pages = {993-1014}, doi = {10.1080/24701394.2017.1404041}, pmid = {29157065}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Felidae/anatomy & histology/classification/*genetics ; *Genetic Speciation ; Haplotypes ; Latin America ; Phylogeny ; Pigmentation ; *Polymorphism, Genetic ; }, abstract = {We analysed two sets of mitochondrial (mt) DNA data from tigrinas (traditionally, Leopardus tigrinus) we sampled in Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, northwestern and northeastern Argentina and southern Brazil. Additionally, the analysis included some GenBank sequences from southern, central and northeastern Brazil. The first mt set (mt ATP8+mt 16S rRNA with 41 tigrina) revealed the existence of seven different tigrina-like haplogroups. They could represent, at least, 4-6 different tigrina species following the Phylogenetic Species Concept (PSC). In the second mt set (mitogenomics with 18 tigrinas), we detected six different tigrina-like haplogroups. They could represent 4-5 different tigrina species - including a possible full new species, which has gone previously unnoticed to the world of science both morphologic and molecularly. Coat patterns of several of these different tigrinas support the molecular differences. We also detected intense hybridization in many Andean tigrina with margays (Leopardus wiedii) and ocelots (Leopardus pardalis) as well as hybridization of one Bolivian tigrina with Leopardus geoffroyi. Similar hybridization was found for many of the southern Brazilian tigrina (Leopardus guttulus). All of the temporal split estimates for these tigrina haplogroups, together with those of the Leopardus species recognized to date, began in the late Pliocene but mostly occurred during the Pleistocene. In agreement with the existence of multiple species within the traditional L. tigrinus species, we detected strong and significant spatial structure in the two mt data sets. There were clear circular clines. A major part of the analyses detected more genetic resemblance between the Central American + trans Andean Colombian and Ecuadorian tigrina (L. oncilla) with the most geographically distant tigrina from central and southern Brazil (L. guttulus; pure individuals not hybridized with L. geoffroyi). In comparison, the Andean tigrina taxa had intermediate geographical origins but were highly genetically differentiated both from the Central American + trans Andean Colombian-Ecuadorian tigrina and from the central and southern Brazilian tigrina.}, } @article {pmid29136647, year = {2017}, author = {Dunleavy, JEM and Okuda, H and O'Connor, AE and Merriner, DJ and O'Donnell, L and Jamsai, D and Bergmann, M and O'Bryan, MK}, title = {Katanin-like 2 (KATNAL2) functions in multiple aspects of haploid male germ cell development in the mouse.}, journal = {PLoS genetics}, volume = {13}, number = {11}, pages = {e1007078}, pmid = {29136647}, issn = {1553-7404}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Amino Acid Sequence/genetics ; Animals ; Germ Cells/metabolism ; Haploidy ; Infertility, Male/metabolism ; Katanin/genetics/*metabolism ; Male ; Mice ; Microtubules/metabolism ; Protein Isoforms ; Seminiferous Epithelium/metabolism ; Spermatogenesis/genetics ; Spermatozoa/metabolism ; Testis/metabolism ; Tubulin/metabolism ; }, abstract = {The katanin microtubule-severing proteins are essential regulators of microtubule dynamics in a diverse range of species. Here we have defined critical roles for the poorly characterised katanin protein KATNAL2 in multiple aspects of spermatogenesis: the initiation of sperm tail growth from the basal body, sperm head shaping via the manchette, acrosome attachment, and ultimately sperm release. We present data suggesting that depending on context, KATNAL2 can partner with the regulatory protein KATNB1 or act autonomously. Moreover, our data indicate KATNAL2 may regulate δ- and ε-tubulin rather than classical α-β-tubulin microtubule polymers, suggesting the katanin family has a greater diversity of function than previously realised. Together with our previous research, showing the essential requirement of katanin proteins KATNAL1 and KATNB1 during spermatogenesis, our data supports the concept that in higher order species the presence of multiple katanins has allowed for subspecialisation of function within complex cellular settings such as the seminiferous epithelium.}, } @article {pmid29104436, year = {2017}, author = {Suprayitno, N and Narakusumo, RP and von Rintelen, T and Hendrich, L and Balke, M}, title = {Taxonomy and Biogeography without frontiers - WhatsApp, Facebook and smartphone digital photography let citizen scientists in more remote localities step out of the dark.}, journal = {Biodiversity data journal}, volume = {}, number = {5}, pages = {e19938}, pmid = {29104436}, issn = {1314-2828}, abstract = {BACKGROUND: Taxonomy and biogeography can benefit from citizen scientists. The use of social networking and open access cooperative publishing can easily connect naturalists even in more remote areas with in-country scientists and institutions, as well as those abroad. This enables taxonomic efforts without frontiers and at the same time adequate benefit sharing measures.

NEW INFORMATION: We present new distribution and habitat data for diving beetles of Bali island, Indonesia, as a proof of concept. The species Hydaticus luczonicus Aubé, 1838 and Eretes griseus (Fabricius, 1781) are reported from Bali for the first time. The total number of Dytiscidae species known from Bali is now 34.}, } @article {pmid29104300, year = {2017}, author = {Falzone, G and Balonis, M and Bentz, D and Jones, S and Sant, G}, title = {Anion Capture and Exchange by Functional Coatings: New Routes to Mitigate Steel Corrosion in Concrete Infrastructure.}, journal = {Cement and concrete research}, volume = {101}, number = {}, pages = {82-92}, pmid = {29104300}, issn = {0008-8846}, support = {9999-NIST//Intramural NIST DOC/United States ; }, abstract = {Chloride-induced corrosion is a major cause of degradation of reinforced concrete infrastructure. While the binding of chloride ions (Cl[-]) by cementitious phases is known to delay corrosion, this approach has not been systematically exploited as a mechanism to increase structural service life. Recently, Falzone et al. [Cement and Concrete Research72, 54-68 (2015)] proposed calcium aluminate cement (CAC) formulations containing NO3-AFm to serve as anion exchange coatings that are capable of binding large quantities of Cl[-] ions, while simultaneously releasing corrosion-inhibiting NO3[-] species. To examine the viability of this concept, Cl[-] binding isotherms and ion-diffusion coefficients of a series of hydrated CAC formulations containing admixed Ca(NO3)2 (CN) are quantified. This data is input into a multi-species Nernst-Planck (NP) formulation, which is solved for a typical bridge-deck geometry using the finite element method (FEM). For exposure conditions corresponding to seawater, the results indicate that Cl[-] scavenging CAC coatings (i.e., top-layers) can significantly delay the time to corrosion (e.g., 5 ≤ df ≤ 10, where df is the steel corrosion initiation delay factor [unitless]) as compared to traditional OPC-based systems for the same cover thickness; as identified by thresholds of Cl[-]/OH[-] or Cl[-]/NO3[-] (molar) ratios in solution. The roles of hindered ionic diffusion, and the passivation of the reinforcing steel rendered by NO3[-] are also discussed.}, } @article {pmid31457297, year = {2017}, author = {Xu, H and Xu, DC and Wang, Y}, title = {Natural Indices for the Chemical Hardness/Softness of Metal Cations and Ligands.}, journal = {ACS omega}, volume = {2}, number = {10}, pages = {7185-7193}, pmid = {31457297}, issn = {2470-1343}, abstract = {Quantitative understanding of reactivity and stability for a chemical species is fundamental to chemistry. The concept has undergone many changes and additions throughout the history of chemistry, stemming from the ideas such as Lewis acids and bases. For a given complexing ligand (Lewis base) and a group of isovalent metal cations (Lewis acids), the stability constants of metal-ligand (ML) complexes can simply correlate to the known properties of metal ions [ionic radii (r M [n+]), Gibbs free energy of formation (ΔG°f,M [n+]), and solvation energy (ΔG°s,M [n+])] by 2.303RT log K ML = (α*MLΔG°f,M [n+] - β*ML r M [n+] + γ*MLΔG°s,M [n+] - δ*ML), where the coefficients (α*ML, β*ML, γ*ML, and intercept δ*ML) are determined by fitting the equation to the existing experimental data. Coefficients β*ML and γ*ML have the same sign and are in a linear relationship through the origin. Gibbs free energies of formation of cations (ΔG°f,M [n+]) are found to be natural indices for the softness or hardness of metal cations, with positive values corresponding to soft acids and negative values to hard acids. The coefficient α*ML is an index for the softness or hardness of a complexing ligand. Proton (H[+]) with the softness index of zero is a unique acid that has strong interactions with both soft and hard bases. The stability energy resulting from the acid-base interactions is determined by the term α*MLΔG°f,M [n+] ; a positive product of α*ML and ΔG°f,M [n+] indicates that the acid-base interaction between the metal cation and the complexing ligand stabilizes the complex. The terms β*ML r M [n+] and γ*MLΔG°s,M [n+] , which are related to ionic radii of metal cations, represent the steric and solvation effects of the cations. The new softness indices proposed here will help to understand the interactions of ligands (Lewis bases) with metal cations (Lewis acids) and provide guidelines for engineering materials with desired chemical reactivity and selectivity. The new correlation can also enhance our ability for predicting the speciation, mobility, and toxicity of heavy metals in the earth environments and biological systems.}, } @article {pmid29064843, year = {2017}, author = {Kangas, BD and Bergman, J}, title = {Touchscreen technology in the study of cognition-related behavior.}, journal = {Behavioural pharmacology}, volume = {28}, number = {8}, pages = {623-629}, pmid = {29064843}, issn = {1473-5849}, support = {K01 DA035974/DA/NIDA NIH HHS/United States ; R01 DA035857/DA/NIDA NIH HHS/United States ; }, mesh = {Animals ; *Behavior, Animal ; *Cognition ; *Computers, Handheld ; Diagnosis, Computer-Assisted/instrumentation/methods ; Motor Activity ; *Neuropsychological Tests ; Touch ; }, abstract = {There is a growing need for new translational animal models designed to capture complex behavioral phenotypes implicated in addiction and other neuropsychiatric conditions. For example, a complete understanding of the effects of commonly abused drugs, as well as candidate medications, requires assessments of their effects on learning, memory, attention, and other cognition-related behavior. Modern touch-sensitive technology provides an extremely flexible means to expose an experimental subject to a variety of complex behavioral tasks designed to assay dimensions of cognitive function before, during, and after drug administration. In addition to tailored variants of gold-standard cognitive assessments, touchscreen chambers offer the ability to develop novel tasks based upon the researcher's needs. This methods perspective presents (i) a brief review of previous touchscreen-based animal studies, (ii) a primer on the construction of a touch-sensitive experimental chamber, and (iii) data from a proof-of-concept study examining cross-species continuity in performance across a diverse assortment of animal subjects (rats, marmosets, squirrel monkeys, and rhesus macaques) using the repeated acquisition task - a modern variant of a traditional animal model of learning. Taken together, the procedures and data discussed in this review illustrate the point that contemporary touchscreen methodology can be tailored to desired experimental goals and adapted to provide formal similarity in cognition-related tasks across experimental species. Moreover, touchscreen methodology allows for the development of new translational models that emerge through laboratory and clinical discovery to capture important dimensions of complex behavior and cognitive function.}, } @article {pmid29053357, year = {2017}, author = {Cotto, O and Servedio, MR}, title = {The Roles of Sexual and Viability Selection in the Evolution of Incomplete Reproductive Isolation: From Allopatry to Sympatry.}, journal = {The American naturalist}, volume = {190}, number = {5}, pages = {680-693}, doi = {10.1086/693855}, pmid = {29053357}, issn = {1537-5323}, mesh = {Animals ; *Hybridization, Genetic ; *Mating Preference, Animal ; Models, Biological ; *Reproductive Isolation ; *Selection, Genetic ; Sympatry ; }, abstract = {In recent years, theoretical models have introduced the concept that ongoing hybridization between "good" species can occur because incomplete reproductive isolation can be a selected optimum. They furthermore show that positive frequency-dependent sexual selection, which is naturally generated by some of the underlying processes that lead to assortative mating, plays a key role in the evolution of incomplete reproductive isolation. This occurs, however, through different mechanisms in sympatric versus allopatric scenarios. We investigate the evolution of incomplete reproductive isolation by sexual selection in scenarios ranging from sympatry to allopatry, to examine how these mechanisms interact. We consider an ecological scenario in which there are two habitats used during foraging and individuals can breed either within a habitat or in a common mating pool. We find that when trait divergence is maintained, sexual selection drives the evolution of choosiness in opposite ways in the common mating pool versus within each habitat. Specifically, strong choosiness is favored in the common mating pool, whereas intermediate choosiness is favored within habitat; the interaction of these forces determines whether intermediate reproductive isolation ultimately evolves in the system. We further find cases where the evolution of stronger choosiness occurs but leads to the loss of divergence. Overall, our study shows that contrasting forces on the evolution of reproductive isolation can occur in different mating areas, and we propose a new avenue for understanding the diversity in levels of reproductive isolation within and across species.}, } @article {pmid29044743, year = {2018}, author = {Shadwick, JDL and Silberman, JD and Spiegel, FW}, title = {Variation in the SSUrDNA of the Genus Protostelium Leads to a New Phylogenetic Understanding of the Genus and of the Species Concept for Protostelium mycophaga (Protosteliida, Amoebozoa).}, journal = {The Journal of eukaryotic microbiology}, volume = {65}, number = {3}, pages = {331-344}, doi = {10.1111/jeu.12476}, pmid = {29044743}, issn = {1550-7408}, mesh = {DNA, Ribosomal/*genetics ; Flagella/physiology ; Fruiting Bodies, Fungal/classification ; *Mycetozoa/classification/genetics/isolation & purification ; Phylogeny ; Plants/microbiology ; }, abstract = {Members of the genus Protostelium (including P. mycophaga, P. nocturnum, and P. okumukumu) are protosteloid amoebae commonly found in terrestrial habitats on dead plant matter. They, along with the closely allied nominal genus Planoprotostelium, containing the single species Pl. aurantium, all have an amoeboid trophic stage with acutely pointed subpseudopodia and orange lipid droplets in the granuloplasm. These amoebae form stalked fruiting bodies topped with a single, usually deciduous spore. The species are identified based on their fruiting body morphologies except for Pl. aurantium which looks similar to P. mycophaga in fruiting morphology, but has amoebae that can make flagella in liquid medium. We built phylogenetic trees using nuclear small subunit ribosomal DNA sequences of 35 isolates from the genera Protostelium and Planoprotostelium and found that (1) the nonflagellated P. nocturnum and P. okumukumu branch basally in the genus Protostelium, (2) the flagellate, Pl. aurantium falls within the genus Protostelium in a monophyletic clade with the nominal variety, P. mycophaga var. crassipes, (3) the cultures initially identified as Protostelium mycophaga can be divided into at least three morphologically recognizable taxa, P. aurantium n. comb., P. apiculatum n. sp., and P. m. rodmani n. subsp., as well as a paraphyletic assemblage that includes the remainder of the P. mycophaga morphotype. These findings have implications for understanding the ecology, evolution, and diversity of these amoeboid organisms and for using these amoebae as models for other amoeboid groups.}, } @article {pmid29043106, year = {2017}, author = {Pavloudi, C and Kristoffersen, JB and Oulas, A and De Troch, M and Arvanitidis, C}, title = {Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane's "species minimum" concept.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3687}, pmid = {29043106}, issn = {2167-8359}, abstract = {Several models have been developed for the description of diversity in estuaries and other brackish habitats, with the most recognized being Remane's Artenminimum ("species minimum") concept. It was developed for the Baltic Sea, one of the world's largest semi-enclosed brackish water body with a unique permanent salinity gradient, and it argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum (5 to 8 psu). The aim of the present study was to investigate the relationship between salinity and sediment microbial diversity at a freshwater-marine transect in Amvrakikos Gulf (Ionian Sea, Western Greece) and assess whether species composition and community function follow a generalized concept such as Remane's. DNA was extracted from sediment samples from six stations along the aforementioned transect and sequenced for the 16S rRNA gene using high-throughput sequencing. The metabolic functions of the OTUs were predicted and the most abundant metabolic pathways were extracted. Key abiotic variables, i.e., salinity, temperature, chlorophyll-a and oxygen concentration etc., were measured and their relation with diversity and functional patterns was explored. Microbial communities were found to differ in the three habitats examined (river, lagoon and sea) with certain taxonomic groups being more abundant in the freshwater and less in the marine environment, and vice versa. Salinity was the environmental factor with the highest correlation to the microbial community pattern, while oxygen concentration was highly correlated to the metabolic functional pattern. The total number of OTUs showed a negative relationship with increasing salinity, thus the sediment microbial OTUs in this study area do not follow Remane's concept.}, } @article {pmid29043053, year = {2017}, author = {Gama, R and Aguirre-Gutiérrez, J and Stech, M}, title = {Ecological niche comparison and molecular phylogeny segregate the invasive moss species Campylopus introflexus (Leucobryaceae, Bryophyta) from its closest relatives.}, journal = {Ecology and evolution}, volume = {7}, number = {19}, pages = {8017-8031}, pmid = {29043053}, issn = {2045-7758}, abstract = {The delimitation of the invasive moss species Campylopus introflexus from its closest relative, Campylopus pilifer, has been long debated based on morphology. Previous molecular phylogenetic reconstructions based on the nuclear ribosomal internal transcribed spacers (ITS) 1 and 2 showed that C. pilifer is split into an Old World and a New World lineage, but remained partly inconclusive concerning the relationships between these two clades and C. introflexus. Analyses of an extended ITS dataset displayed statistically supported incongruence between ITS1 and ITS2. ITS1 separates the New World clade of C. pilifer from a clade comprising C. introflexus and the Old World C. pilifer. Ancestral state reconstruction showed that this topology is morphologically supported by differences in the height of the dorsal costal lamellae in leaf cross-section (despite some overlap). ITS2, in contrast, supports the current morphological species concept, i.e., separating C. introflexus from C. pilifer, which is morphologically supported by the orientation of the hyaline hair point at leaf apex as well as costal lamellae height. Re-analysis of published and newly generated plastid atpB-rbcL spacer sequences supported the three ITS lineages. Ecological niche modeling proved a useful approach and showed that all three molecular lineages occupy distinct environmental spaces that are similar, but undoubtedly not equivalent. In line with the ITS1 topology, the C. pilifer lineage from the New World occupies the most distinct environmental niche, whereas the niches of Old World C. pilifer and C. introflexus are very similar. Taking the inferences from ecological niche comparisons, phylogenetics, and morphology together, we conclude that all three molecular lineages represent different taxa that should be recognized as independent species, viz. C. introflexus, C. pilifer (Old World clade), and the reinstated C. lamellatus Mont. (New World clade).}, } @article {pmid29037158, year = {2017}, author = {Hoetzinger, M and Hahn, MW}, title = {Genomic divergence and cohesion in a species of pelagic freshwater bacteria.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {794}, pmid = {29037158}, issn = {1471-2164}, support = {I 482/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Burkholderiaceae/*genetics ; DNA Mismatch Repair/genetics ; Evolution, Molecular ; Genome, Bacterial/genetics ; Genomic Islands/genetics ; *Genomics ; Homologous Recombination ; Multilocus Sequence Typing ; }, abstract = {BACKGROUND: In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity - i.e. elevated geographic barriers to gene flow - is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P. asymbioticus.

RESULTS: Comparisons among 20 PnecC genomes revealed a clearly discontinuous distribution of nucleotide sequence similarities. Among the nine conspecific individuals (P. asymbioticus) all average nucleotide identity (ANI) values were greater than 97%, whereas all other comparisons exhibited ANI values lower than 85%. The reconstruction of recombination and mutation events for the P. asymbioticus core genomes yielded an r/m ratio of 7.4, which is clearly above estimated thresholds for recombination to act as a cohesive force. Hotspots of recombination were found to be located in the flanking regions of genomic islands. Even between geographically separated habitats a high flux of recombination was evident. While a biogeographic population structure was suggested from MLST data targeting rather conserved loci, such a structure was barely visible when whole genome data was considered. However, both MLST and whole genome data showed evidence of differentiation between two lineages of P. asymbioticus. The ratios of non-synonymous to synonymous substitution rates as well as growth rates in transplantation experiments suggested that this divergence was not selectively neutral.

CONCLUSIONS: The high extent of homologous recombination among P. asymbioticus bacteria can act as a cohesive force that effectively counteracts genetic divergence. At least on a regional scale, homologous recombination can act across geographically separated ecosystems and therefore plays an important role in the evolution and consistency of bacterial freshwater species. A species model akin to the biological species concept may be applicable for P. asymbioticus. Nonetheless, two genetically distinct lineages have emerged and further research may clarify if their divergence has been initiated by reinforced geographical barriers or has been evolving in sympatry.}, } @article {pmid29024429, year = {2018}, author = {Borg Dahl, M and Brejnrod, AD and Unterseher, M and Hoppe, T and Feng, Y and Novozhilov, Y and Sørensen, SJ and Schnittler, M}, title = {Genetic barcoding of dark-spored myxomycetes (Amoebozoa)-Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies.}, journal = {Molecular ecology resources}, volume = {18}, number = {2}, pages = {306-318}, doi = {10.1111/1755-0998.12725}, pmid = {29024429}, issn = {1755-0998}, mesh = {Cluster Analysis ; DNA Barcoding, Taxonomic/*methods ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Myxomycetes/*classification/*genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.}, } @article {pmid29021178, year = {2017}, author = {Hiltunen, T and Kaitala, V and Laakso, J and Becks, L}, title = {Evolutionary contribution to coexistence of competitors in microbial food webs.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1864}, pages = {}, pmid = {29021178}, issn = {1471-2954}, mesh = {Bacteriophage T4/*physiology ; Bacteriophages/physiology ; Biological Evolution ; Escherichia coli/*physiology ; *Food Chain ; Microbial Interactions ; Population Density ; Pseudomonas fluorescens/*physiology/virology ; Tetrahymena thermophila/*physiology ; }, abstract = {The theory of species coexistence is a key concept in ecology that has received much attention. The role of rapid evolution for determining species coexistence is still poorly understood although evolutionary change on ecological time-scales has the potential to change almost any ecological process. The influence of evolution on coexistence can be especially pronounced in microbial communities where organisms often have large population sizes and short generation times. Previous work on coexistence has assumed that traits involved in resource use and species interactions are constant or change very slowly in terms of ecological time-scales. However, recent work suggests that these traits can evolve rapidly. Nevertheless, the importance of rapid evolution to coexistence has not been tested experimentally. Here, we show how rapid evolution alters the frequency of two bacterial competitors over time when grown together with specialist consumers (bacteriophages), a generalist consumer (protozoan) and all in combination. We find that consumers facilitate coexistence in a manner consistent with classic ecological theory. However, through disentangling the relative contributions of ecology (changes in consumer abundance) and evolution (changes in traits mediating species interactions) on the frequency of the two competitors over time, we find differences between the consumer types and combinations. Overall, our results indicate that the influence of evolution on species coexistence strongly depends on the traits and species interactions considered.}, } @article {pmid28904389, year = {2017}, author = {Kurosaki, K and Suzuki, M and Uno, M and Ishii, H and Kumagai, M and Anada, K and Murakami, Y and Ohishi, Y and Muta, H and Tanaka, T and Yamanaka, S}, title = {High wettability of liquid caesium iodine with solid uranium dioxide.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11449}, pmid = {28904389}, issn = {2045-2322}, abstract = {In March 2011, the Fukushima Daiichi Nuclear Power Plant accident caused nuclear fuel to melt and the release of high-volatility fission products into the environment. Caesium and iodine caused environmental contamination and public exposure. Certain fission-product behaviours remain unclear. We found experimentally that liquid CsI disperses extremely favourably toward solid UO2, exhibiting a contact angle approaching zero. We further observed the presence of CsI several tens of micrometres below the surface of the solid UO2 sample, which would be caused by the infiltration of pores network by liquid CsI. Thus, volatile fission products released from molten nuclear fuels with complex internal composition and external structure migrate or evaporate to varying extents, depending on the nature of the solid-liquid interface and the fuel material surface, which becomes the pathway for the released fission products. Introducing the concept of the wettability of liquid chemical species of fission products in contact with solid fuels enabled developing accurate behavioural assessments of volatile fission products released by nuclear fuel.}, } @article {pmid28895293, year = {2017}, author = {Zhang, G and Wu, Z and Liu, H and Ji, Q and Qu, J and Li, J}, title = {Photoactuation Healing of α-FeOOH@g-C3 N4 Catalyst for Efficient and Stable Activation of Persulfate.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {13}, number = {41}, pages = {}, doi = {10.1002/smll.201702225}, pmid = {28895293}, issn = {1613-6829}, abstract = {Inspired by living systems, the construction of smart devices that can self-heal in response to structural damage is a promising technology for maintaining the high activity and stability of catalysts during heterocatalytic reactions. Here this study demonstrates an ingenious platform that enabled efficient persulfate (PS) activation for contaminant degradation via integrating a catalyst with photoactuation regeneration. Under irradiation, it is unambiguously confirmed that the collective properties of a tailored FeOOH@C3 N4 catalyst permit interfacial photoexcited electron transport from the photocatalyst substrate to needle-shaped FeOOH. This results in the simultaneous recovery of Fe(III) and optimization of the Fe(II)/Fe(III) ratio on FeOOH surface during PS activation process, so that the healed chemical structure ensures that subsequent PS activation remains unimpaired. Aqueous organic contaminant (bisphenol A) oxidation efficacy in this system is almost 20 times higher than for photo- or Fenton-oxidation alone. This work highlights the concept of catalyst regeneration for stable reactive species generation in solution, which represents alternative application of photocatalysis for practical environmental remediation. Further, the photoactuation healing approach can be expanded into various domains, such as material fabrication or chemical synthesis.}, } @article {pmid28892160, year = {2017}, author = {Cornelissen, JHC and Grootemaat, S and Verheijen, LM and Cornwell, WK and van Bodegom, PM and van der Wal, R and Aerts, R}, title = {Are litter decomposition and fire linked through plant species traits?.}, journal = {The New phytologist}, volume = {216}, number = {3}, pages = {653-669}, doi = {10.1111/nph.14766}, pmid = {28892160}, issn = {1469-8137}, mesh = {*Fires ; Plant Leaves/physiology ; *Plant Physiological Phenomena ; Plants/anatomy & histology ; }, abstract = {Contents 653 I. 654 II. 657 III. 659 IV. 661 V. 662 VI. 663 VII. 665 665 References 665 SUMMARY: Biological decomposition and wildfire are connected carbon release pathways for dead plant material: slower litter decomposition leads to fuel accumulation. Are decomposition and surface fires also connected through plant community composition, via the species' traits? Our central concept involves two axes of trait variation related to decomposition and fire. The 'plant economics spectrum' (PES) links biochemistry traits to the litter decomposability of different fine organs. The 'size and shape spectrum' (SSS) includes litter particle size and shape and their consequent effect on fuel bed structure, ventilation and flammability. Our literature synthesis revealed that PES-driven decomposability is largely decoupled from predominantly SSS-driven surface litter flammability across species; this finding needs empirical testing in various environmental settings. Under certain conditions, carbon release will be dominated by decomposition, while under other conditions litter fuel will accumulate and fire may dominate carbon release. Ecosystem-level feedbacks between decomposition and fire, for example via litter amounts, litter decomposition stage, community-level biotic interactions and altered environment, will influence the trait-driven effects on decomposition and fire. Yet, our conceptual framework, explicitly comparing the effects of two plant trait spectra on litter decomposition vs fire, provides a promising new research direction for better understanding and predicting Earth surface carbon dynamics.}, } @article {pmid28889912, year = {2017}, author = {Kuhar, F and Smith, ME and Mujic, A and Truong, C and Nouhra, E}, title = {A systematic overview of Descolea (Agaricales) in the Nothofagaceae forests of Patagonia.}, journal = {Fungal biology}, volume = {121}, number = {10}, pages = {876-889}, doi = {10.1016/j.funbio.2017.06.006}, pmid = {28889912}, issn = {1878-6146}, mesh = {Agaricales/*classification/genetics/growth & development ; Argentina ; Cortinarius/classification/genetics/growth & development ; DNA, Fungal/chemistry/isolation & purification ; DNA, Ribosomal Spacer/chemistry/isolation & purification ; Fagales/*microbiology ; Phylogeny ; Sequence Alignment ; }, abstract = {The descolea clade includes species of ectomycorrhizal basidiomycetes in the genera Descolea, Setchelliogaster, Descomyces, and Timgrovea that are known primarily from the Southern Hemisphere. Taxa in this group produce basidiomes that range in morphology from typical epigeous mushrooms (Descolea) and secotioid taxa (Setchelliogaster) to fully gasteroid species (Descomyces and Timgrovea). High intraspecific morphological variation has been reported in several species within this clade, suggesting that careful morphological and molecular studies are needed to refine species concepts. Molecular analyses of fresh Patagonian collections in conjunction with taxonomic studies have confirmed high variability in key morphological features, including overall sporocarp form, spore shape and dimensions, universal veil remnants, and cuticle configuration. Based on our synthesis, we emend the genus Descolea to include sequestrate species. We describe the new sequestrate taxon Descolea inferna sp. nov. from Nothofagaceae forests in Patagonia and we propose Cortinarius squamatus as a synonym of our new combination Descolea brunnea. We also formalize the identity of Descolea pallida as a synonym of Descolea antarctica and provide new specimens of Cortinarius archeuretus, a species that has not been encountered since the original discovery during the expeditions of Roland Thaxter in 1905-1906. Here we re-describe and transfer this species to Descolea as D. archeureta. We also discuss diagnostic features that can be used to delimitate the four known South American taxa in the descolea clade.}, } @article {pmid28866753, year = {2017}, author = {Wee, NQ and Cutmore, SC and Yong, RQ and Cribb, TH}, title = {Two new and one known species of Tergestia Stossich, 1899 (Trematoda: Fellodistomidae) with novel molecular characterisation for the genus.}, journal = {Systematic parasitology}, volume = {94}, number = {8}, pages = {861-874}, pmid = {28866753}, issn = {1573-5192}, support = {RF215-40//Australian Biological Resources Study/International ; }, mesh = {Animals ; Beloniformes/parasitology ; DNA, Ribosomal Spacer/genetics ; *Phylogeny ; Queensland ; RNA, Ribosomal, 28S/genetics ; Species Specificity ; Trematoda/anatomy & histology/*classification/*genetics ; }, abstract = {Combined morphological and molecular analyses are employed to characterise three species of Tergestia Stossich, 1899 (Digenea: Fellodistomidae) from fishes of Moreton Bay, Queensland, Australia. Tergestia clonacantha Manter, 1963 is reported here for the first time from the halfbeak (Beloniformes: Hemiramphidae) species Arrhamphus sclerolepis krefftii (Steindachner), Hyporhamphus australis (Steindachner), H. quoyi (Valenciennes) and H. regularis ardelio (Whitley). Two new species, both infecting trevally (Perciformes: Carangidae) species, are described: T. maryae n. sp. from Alepes apercna Grant and T. henryi n. sp. from Pantolabus radiatus (MacLeay). Complete ITS2 and partial 28S ribosomal DNA data were generated for each of the new taxa. The three species differ from each other by 47-58 base pairs (bp) in the ITS2 rDNA region. Phylogenetic analysis of 28S rDNA supports Tergestia as a reliable generic concept, with our analyses showing that some species of the genus form a well-supported clade to the exclusion of all other fellodistomids for which sequence data are available.}, } @article {pmid28854567, year = {2017}, author = {Alix, K and Gérard, PR and Schwarzacher, T and Heslop-Harrison, JSP}, title = {Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants.}, journal = {Annals of botany}, volume = {120}, number = {2}, pages = {183-194}, pmid = {28854567}, issn = {1095-8290}, mesh = {Adaptation, Biological ; *Genetic Speciation ; Genome, Plant ; *Hybridization, Genetic ; Phylogeny ; Plants/*genetics ; *Polyploidy ; }, abstract = {BACKGROUND: Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy.

APPROACHES: Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical.

CONCLUSIONS: The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.}, } @article {pmid28854121, year = {2017}, author = {Rooney-Latham, S and Lutz, M and Blomquist, CL and Romberg, MK and Scheck, HJ and Piątek, M}, title = {Entyloma helianthi: identification and characterization of the causal agent of sunflower white leaf smut.}, journal = {Mycologia}, volume = {109}, number = {3}, pages = {520-528}, doi = {10.1080/00275514.2017.1362314}, pmid = {28854121}, issn = {0027-5514}, mesh = {Basidiomycota/*classification/cytology/genetics/*isolation & purification ; California ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Helianthus/*microbiology ; Microscopy ; Phylogeny ; Plant Diseases/*microbiology ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; Spores, Fungal/cytology ; }, abstract = {White leaf smut is a minor foliar disease of sunflower (Helianthus annuus) in the United States. The disease occurs primarily in greenhouse-grown sunflowers in California and causes leaf spot, defoliation, and a reduction in yield and crop value. Historically, many Entyloma specimens with similar morphological characters, but infecting diverse plant genera including Helianthus, were called Entyloma polysporum. Recent comparative morphological and molecular work has shown that Entyloma species infect hosts within a single genus or species, suggesting that the sunflower Entyloma species may not be E. polysporum. In 2015, sunflower leaf smut material was collected from ornamental sunflowers in a greenhouse in Santa Barbara County, California. Morphologically, this species differed from E. polysporum in having smaller, more regular-shaped teliospores and prominently developed conidiophores with cylindrical conidia. The rDNA ITS1-5.8S-ITS2 (internal transcribed spacer [ITS]) region of the sunflower leaf smut was phylogenetically distinct from all previously sequenced Entyloma species and found only on H. annuus. This study confirms that the sunflower leaf smut pathogen represents a novel species, Entyloma helianthi. Possible misidentification of the anamorphic stage of Entyloma helianthi as another leaf spot pathogen, Ramularia helianthi, is also discussed.}, } @article {pmid28850628, year = {2017}, author = {Lu, Y and Aitken, RJ and Lin, M}, title = {Ultrastructural investigation and in vitro recapitulation of spermatid differentiation in a potential bio-indicator species - The marine invertebrate Galeolaria gemineoa (Polychaeta: Serpulidae).}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0183986}, pmid = {28850628}, issn = {1932-6203}, mesh = {Acrosome/ultrastructure ; Animals ; Cell Membrane/*ultrastructure ; Cell Nucleus/ultrastructure ; Cytoplasm/ultrastructure ; Male ; Polychaeta/*ultrastructure ; Spermatids/*ultrastructure ; Spermatogenesis/*physiology ; }, abstract = {Galeolaria gemineoa is a sessile broadcast-spawning marine invertebrate, whose spermatozoa have been regarded as a sensitive indicator for water quality monitoring. In this study, 10 steps of spermiogenesis have been identified at the ultrastructural level and this differentiation process has been recapitulated in vitro up to the point of spermiogenesis (step 7-9 spermatids). On completion of the second meiosis, newly formed spermatids were detached from the seminiferous epithelium and released to the lumen of each germinal chamber. These spermatids were present in pairs and interconnected by a cytoplasmic bridge throughout the entire spermiogenic process. On the basis of morphological events such as formation of the acrosome, elongation of the flagellum, and condensation of the nucleus, spermiogenesis has been temporally divided into Golgi phase, acrosomal phase and maturation phase. During the Golgi phase, proacrosomal vesicles appeared at the posterior pole of the spermatids and gradually fused into a proacrosomal vacuole. Simultaneously, the distal centriole docked onto the plasma membrane and gave rise to a formative flagellum. The acrosomal phase was characterised by differentiation of the acrosome, condensation of the chromatin and formation of a mitochondrial sheath surrounding the initial portion of the flagellum. During the maturation phase, the fully differentiated acrosome migrated to the anterior pole and excess cytoplasm was extruded from the spermatids in the form of residual bodies. In addition, we successfully induced step 1-3 spermatids to differentiate into the step 7-9 spermatids in both male germinal fluid and 10% foetal bovine serum in RPMI 1640 medium, but failed to replicate this process in female or boiled male germinal fluids. This finding supports our concept that spermatid differentiation in this species is dependent on intrinsic developmental programming and does not require input from accompanying nurse cells.}, } @article {pmid28836869, year = {2017}, author = {Perez-Lloret, S and Otero-Losada, M and Toblli, JE and Capani, F}, title = {Renin-angiotensin system as a potential target for new therapeutic approaches in Parkinson's disease.}, journal = {Expert opinion on investigational drugs}, volume = {26}, number = {10}, pages = {1163-1173}, doi = {10.1080/13543784.2017.1371133}, pmid = {28836869}, issn = {1744-7658}, mesh = {Angiotensin II Type 1 Receptor Blockers/pharmacology/therapeutic use ; Angiotensin-Converting Enzyme Inhibitors/pharmacology/therapeutic use ; Animals ; Antiparkinson Agents/adverse effects/pharmacology/*therapeutic use ; Dopamine/metabolism ; Drug Design ; Humans ; Molecular Targeted Therapy ; Neuroprotective Agents/adverse effects/pharmacology/*therapeutic use ; Parkinson Disease/*drug therapy/physiopathology ; Randomized Controlled Trials as Topic ; Reactive Oxygen Species/metabolism ; Renin-Angiotensin System/drug effects ; }, abstract = {Currently, available therapies for Parkinson's disease (PD) are symptomatic. Therefore, the search for neuroprotective drugs remains a top priority. Areas covered: In this review, the potential symptomatic or disease-modifying effect of drugs targeting the Renin-Angiotensin System (RAS) in PD will be explored. Expert opinion: The importance of nigrostriatal local RAS has only begun to be unraveled in the last decades. On one hand, there is a complex feedback cycle between RAS and dopamine (DA). On the other hand, RAS affects dopaminergic neurons vulnerability. Neuroprotective effects in animal PD models have been shown for the angiotensin-converting enzyme (ACE) inhibitors captopril and perindopril, and the AT1 receptor antagonists losartan, candesartan and telmisartan. These effects appear to be mediated by a reduction in the overproduction of reactive oxygen species. In a proof-of-concept, randomized, double-blind, crossover study in PD patients, perindopril enhanced the effect of levodopa without inducing dyskinesias. There has not been any clinical trial exploring the neuroprotective effect of RAS drugs, but one cohort study in hypertensive patients suggested a protective effect of ACE inhibitors on PD risk. RAS is a promising target for symptomatic and neuroprotective therapies in PD. Further studies in PD animal models and patients are warranted.}, } @article {pmid28824843, year = {2017}, author = {Smith, PA and Lutz, M and Ziegler, R and Piątek, M}, title = {Anther smuts of Silene acaulis and S. uniflora in the Outer Hebrides, including an assessment of ITS genotypes of Microbotryum silenes-acaulis.}, journal = {IMA fungus}, volume = {8}, number = {1}, pages = {107-116}, pmid = {28824843}, issn = {2210-6340}, abstract = {Anther smuts on Silene acaulis and S. uniflora from the Outer Hebrides, Scotland, UK), are analysed using morphological and molecular techniques, and found to represent Microbotryum silenes-acaulis and M. silenes-inflatae, respectively. This is the first identification of caryophyllaceous anther smuts in the Outer Hebrides according to modern species concepts and the first report of Microbotryum silenes-acaulis confirmed by molecular analysis from the British Isles. Additionally, the genetic structure of Microbotryum silenes-acaulis, based on all currently available ITS sequences, is analysed and discussed. Seven ITS genotypes are determined for Microbotryum silenes-acaulis, including three genotypes in North America and four genotypes in Europe. Compared to European accessions, all North American accessions share specific nucleotides and are genetically divergent.}, } @article {pmid30363390, year = {2017}, author = {Nagai, T}, title = {Studies on ecological risk assessment of pesticide using species sensitivity distribution.}, journal = {Journal of pesticide science}, volume = {42}, number = {3}, pages = {124-131}, pmid = {30363390}, issn = {1348-589X}, abstract = {Species sensitivity distribution (SSD) is a key concept of probabilistic analysis for quantifying ecological risk. I developed a method of probabilistic ecological risk assessment in Japan with a case study of the herbicide simetryn. Then, risk comparison among eleven herbicides was conducted using the developed method. However, one of the most important limitations of SSD application is the lack of sufficient toxicity data for SSD analysis. Thus, an ecotoxicity database was developed for the application of SSD to a wide range of pesticides. After that, I proposed that species batteries of the five species should be the standardized dataset for the SSD analysis of insecticides and herbicides. Finally, I have published a technical guidance document for SSD analysis written in Japanese to promote the application of SSDs in Japan. The remarkable point is that the supplemental Excel-based tool makes it easy to analyze SSDs and conduct ecological risk assessments.}, } @article {pmid28812688, year = {2017}, author = {Österblom, H}, title = {Reimagining ocean governance using the keystone species concept.}, journal = {Nature ecology & evolution}, volume = {1}, number = {5}, pages = {133}, doi = {10.1038/s41559-017-0133}, pmid = {28812688}, issn = {2397-334X}, } @article {pmid28802073, year = {2017}, author = {Chan, KO and Alexander, AM and Grismer, LL and Su, YC and Grismer, JL and Quah, ESH and Brown, RM}, title = {Species delimitation with gene flow: A methodological comparison and population genomics approach to elucidate cryptic species boundaries in Malaysian Torrent Frogs.}, journal = {Molecular ecology}, volume = {26}, number = {20}, pages = {5435-5450}, doi = {10.1111/mec.14296}, pmid = {28802073}, issn = {1365-294X}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Gene Flow ; *Genetic Speciation ; Genetics, Population/*methods ; Malaysia ; Models, Genetic ; Phylogeny ; Polymorphism, Single Nucleotide ; Ranidae/classification/*genetics ; }, abstract = {Accurately delimiting species boundaries is a nontrivial undertaking that can have significant effects on downstream inferences. We compared the efficacy of commonly used species delimitation methods (SDMs) and a population genomics approach based on genomewide single-nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genomewide SNPs to identify putative species boundaries by implementing noncoalescent and coalescent-based SDMs (mPTP, iBPP, BFD*). We then tested the validity of putative boundaries by estimating spatiotemporal gene flow (fastsimcoal2, ABBA-BABA) to assess the extent of genetic isolation among putative species. Our results show that the A. larutensis complex runs the gamut of the speciation continuum from highly divergent, genetically isolated lineages (mean Fst = 0.9) to differentiating populations involving recent gene flow (mean Fst = 0.05; Nm > 5). As expected, SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. This study does not discount the utility of SDMs but highlights the danger of violating model assumptions and the importance of carefully considering methods that appropriately fit the diversification history of a particular system.}, } @article {pmid28761006, year = {2017}, author = {Shanker, K and Vijayakumar, SP and Ganeshaiah, KN}, title = {Unpacking the species conundrum: philosophy, practice and a way forward.}, journal = {Journal of genetics}, volume = {96}, number = {3}, pages = {413-430}, pmid = {28761006}, issn = {0973-7731}, mesh = {Animals ; DNA, Mitochondrial/classification/*genetics ; Genes, Mitochondrial/*genetics ; Genetic Variation ; *Haplotypes ; Humans ; Phenotype ; *Phylogeny ; Reproduction/genetics ; Species Specificity ; }, abstract = {The history of ecology and evolutionary biology is rife with attempts to define and delimit species. However, there has been confusion between concepts and criteria, which has led to discussion, debate, and conflict, eventually leading to lack of consistency in delimitation. Here, we provide a broad review of species concepts, a clarification of category versus concept, an account of the general lineage concept (GLC), and finally a way forward for species discovery and delimitation. Historically, species were considered as varieties bound together by reproduction. After over 200 years of uncertainty, Mayr attempted to bring coherence to the definition of species through the biological species concept (BSC). This has, however, received much criticism, and the last half century has spawned at least 20 other concepts. A central philosophical problem is that concepts treat species as 'individuals' while the criteria for categorization treats them as 'classes'. While not getting away from this problem entirely, the GLC attempts to provide a framework where lineage divergence is influenced by a number of different factors (and correlated to different traits) which relate to the different species concepts. We also introduce an 'inclusive' probabilistic approach for understanding and delimiting species. Finally, we provide aWallacean (geography related) approach to the Linnaean problem of identifying and delimiting species, particularly for cases of allopatric divergence, and map this to the GLC. Going one step further, we take a morphometric terrain approach to visualizing and understanding differences between lineages. In summary, we argue that while generalized frameworks may work well for concepts of what species are, plurality and 'inclusive' probabilistic approaches may work best for delimitation.}, } @article {pmid28729560, year = {2017}, author = {Lorenc, D and Jerigova, M and Stupavska, M and Velic, D}, title = {Adaptive Control of Ion Yield in Femtosecond Laser Post-ionization for Secondary Ion Mass Spectrometry.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5953}, pmid = {28729560}, issn = {2045-2322}, abstract = {Secondary ion mass spectrometry is an excellent technique of analytical chemistry, where primary ions sputter a solid sample generating the secondary ions which are determined. Although the ion yield is inherently low, it can be enhanced by using a post-ionization of sputtered neutral species. Our novel approach integrates this technique with a near infrared femtosecond laser post-ionization based on an adaptive control through a laser pulse shaper. The shaping of the laser pulse provides adaptive control to select a mass peak of interest and to enhance this peak intensity. Versatility is confirmed by optimizing the ion yield for different molecules (tryptophan, anthracene, polyethylene, and oxalic acid) with focus on parent ion enhancement, fragmentation process, sublimation effect, and excited secondary species. This proof-of-concept experiment provides not only a nonspecific increase of the overall ion yield, but also the selection of specific secondary species and the adaptive enhancement of their intensities on the order of 100, potentially simplifying data interpretation. Such tailored spectra might advance the (secondary ion) mass spectrometry to new capabilities.}, } @article {pmid28722181, year = {2017}, author = {Pärtel, M and Öpik, M and Moora, M and Tedersoo, L and Szava-Kovats, R and Rosendahl, S and Rillig, MC and Lekberg, Y and Kreft, H and Helgason, T and Eriksson, O and Davison, J and de Bello, F and Caruso, T and Zobel, M}, title = {Historical biome distribution and recent human disturbance shape the diversity of arbuscular mycorrhizal fungi.}, journal = {The New phytologist}, volume = {216}, number = {1}, pages = {227-238}, doi = {10.1111/nph.14695}, pmid = {28722181}, issn = {1469-8137}, mesh = {*Biodiversity ; Ecosystem ; Geography ; *Human Activities ; Humans ; Mycorrhizae/*physiology ; }, abstract = {The availability of global microbial diversity data, collected using standardized metabarcoding techniques, makes microorganisms promising models for investigating the role of regional and local factors in driving biodiversity. Here we modelled the global diversity of symbiotic arbuscular mycorrhizal (AM) fungi using currently available data on AM fungal molecular diversity (small subunit (SSU) ribosomal RNA (rRNA) gene sequences) in field samples. To differentiate between regional and local effects, we estimated species pools (sets of potentially suitable taxa) for each site, which are expected to reflect regional processes. We then calculated community completeness, an index showing the fraction of the species pool present, which is expected to reflect local processes. We found significant spatial variation, globally in species pool size, as well as in local and dark diversity (absent members of the species pool). Species pool size was larger close to areas containing tropical grasslands during the last glacial maximum, which are possible centres of diversification. Community completeness was greater in regions of high wilderness (remoteness from human disturbance). Local diversity was correlated with wilderness and current connectivity to mountain grasslands. Applying the species pool concept to symbiotic fungi facilitated a better understanding of how biodiversity can be jointly shaped by large-scale historical processes and recent human disturbance.}, } @article {pmid28705397, year = {2017}, author = {Malysheva, V and Spirin, V}, title = {Taxonomy and phylogeny of the Auriculariales (Agaricomycetes, Basidiomycota) with stereoid basidiocarps.}, journal = {Fungal biology}, volume = {121}, number = {8}, pages = {689-715}, doi = {10.1016/j.funbio.2017.05.001}, pmid = {28705397}, issn = {1878-6146}, mesh = {Basidiomycota/*classification/genetics/*growth & development ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Fruiting Bodies, Fungal/*growth & development ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {In the present study, we investigate taxonomy of the Auriculariales with effused or cupulate, persistent basidiocarps; generic and species concepts are revised based on morphological and DNA evidences. The genus Eichleriella is reinstated to embrace ten closely related species with ellipsoid-ovoid basidia, and the genus type, Eichleriella incarnata, is placed to the synonyms of Eichleriella leucophaea. Eichleriella bactriana, Eichleriella desertorum and Eichleriella sicca are described as new to science. In addition, four species earlier treated as members of Exidiopsis or Heterochaete are combined to the genus. The genus name Heteroradulum (type Radulum kmetii) is introduced for seven species with large, obconical, stipitate basidia. Of them, Heteroradulum adnatum and Heteroradulum semis are described as new. Two new genera, Amphistereum (with two species, type Eichleriella schrenkii) and Sclerotrema (monotypic, type Exidiopsis griseobrunnea), are proposed; Hirneolina (monotypic, type H. hirneoloides) and Tremellochaete (with two species, type Exidia japonica) are restored as good genera. The type species of Heterochaete, H. andina, is congeneric with Exidiopsis (type E. effusa).}, } @article {pmid28694506, year = {2017}, author = {Tomura, T and Molli, SD and Murata, R and Ojika, M}, title = {Universality of the Phytophthora mating hormones and diversity of their production profile.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5007}, pmid = {28694506}, issn = {2045-2322}, mesh = {Diterpenes/metabolism ; Mating Factor/*metabolism ; Phytophthora/classification/metabolism/*physiology ; Reproduction ; Stereoisomerism ; }, abstract = {Sexual reproduction of the plant pest Phytophthora is regulated by two mating hormones α1 and α2, which are acyclic oxygenated diterpenes first isolated from P. nicotianae A1 and A2 mating types, respectively. A previous report suggested the universality of these factors within this genus. To confirm this concept, we investigated 80 strains (19 species) of Phytophthora and a related genus, not only for the responsiveness to mating hormones but also for their productivity. The results indicated that among the 55 heterothallic strains, 24 (44%) responded to a mating hormone and 40 (73%) produced one or both hormones. These findings demonstrate the interspecies universality of mating hormones within the genus Phytophthora. Hormone productivity was found to be highly diverse and dependent on the strains used. Although the A2 mating type has been regarded as the α2 producer, 19 (59%) of the 32 A2-type strains produced both the hormones and two A2-type strains exclusively produced α1 in high yields. These results indicate that hormone biosynthesis in Phytophthora is universal but highly diverse and complex, and varies with culture conditions, providing us valuable information for future studies on the mechanism of mating hormone biosynthesis of Phytophthora.}, } @article {pmid28686672, year = {2017}, author = {Bai, Y and Li, X}, title = {Late Miocene Pseudolarix amabilis bract-scale complex from Zhejiang, East China.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180979}, pmid = {28686672}, issn = {1932-6203}, mesh = {Biological Evolution ; China ; Forests ; Fossils/history/*ultrastructure ; History, Ancient ; Phylogeny ; Phylogeography ; Pinaceae/*anatomy & histology/classification/physiology ; Plant Leaves/*anatomy & histology/physiology ; Seeds/*anatomy & histology/physiology ; }, abstract = {Previously, the identification of fossil Pseudolarix at the species level has been based on the morphology of the bract-scale complex of the seed cone. The morphological consistence of fossils through most of the Cenozoic with extant P. amabilis has led them to be considered conspecific, suggesting that P. amabilis is an extraordinary example of morphological stasis. However, the lack of cuticular evidence, especially for the leaf-homologous bract, reduces the accuracy of fossil identification based on morphology, thus weakening the evidence for morphological stasis in P. amabilis. For the first time, we provide cuticular evidence of the bract-scale of fossil P. amabilis based on the bract-scale complex from the late Miocene Shengxian Formation, Zhejiang, East China, which improves the identification accuracy and reinforces the concept of morphological stasis in this species. Second, we preliminarily reveal the niche stability of P. amabilis, which corresponds to its morphological stasis. Finally, we infer that the late Miocene forest containing P. amabilis in Zhejiang was an evergreen sclerophyllous broad-leaved or mixed mesophytic forest, which combined with the evergreen broad-leaved forest suggested by previous megafossil studies, indicates the occurrence of vertical vegetation zonation.}, } @article {pmid28683715, year = {2017}, author = {Schmidt, M and Van Bel, M and Woloszynska, M and Slabbinck, B and Martens, C and De Block, M and Coppens, F and Van Lijsebettens, M}, title = {Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions.}, journal = {BMC plant biology}, volume = {17}, number = {1}, pages = {115}, pmid = {28683715}, issn = {1471-2229}, mesh = {Cytosine/metabolism ; *DNA Methylation ; DNA Restriction Enzymes ; *Genetic Techniques ; *Genome, Plant ; Oryza ; Sulfites ; }, abstract = {BACKGROUND: Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hydrogen sulfite (bisulfite)-conversion and next-generation sequencing (NGS) provide genome-wide information on cytosine methylation. However, a profiling method that detects cytosine methylation state dispersed over the genome would allow high-throughput analysis of multiple plant samples with distinct epigenetic signatures. We use specific restriction endonucleases to enrich for cytosine coverage in a bisulfite and NGS-based profiling method, which was compared to whole-genome bisulfite sequencing of the same plant material.

METHODS: We established an effective methylome profiling method in plants, termed plant-reduced representation bisulfite sequencing (plant-RRBS), using optimized double restriction endonuclease digestion, fragment end repair, adapter ligation, followed by bisulfite conversion, PCR amplification and NGS. We report a performant laboratory protocol and a straightforward bioinformatics data analysis pipeline for plant-RRBS, applicable for any reference-sequenced plant species.

RESULTS: As a proof of concept, methylome profiling was performed using an Oryza sativa ssp. indica pure breeding line and a derived epigenetically altered line (epiline). Plant-RRBS detects methylation levels at tens of millions of cytosine positions deduced from bisulfite conversion in multiple samples. To evaluate the method, the coverage of cytosine positions, the intra-line similarity and the differential cytosine methylation levels between the pure breeding line and the epiline were determined. Plant-RRBS reproducibly covers commonly up to one fourth of the cytosine positions in the rice genome when using MspI-DpnII within a group of five biological replicates of a line. The method predominantly detects cytosine methylation in putative promoter regions and not-annotated regions in rice.

CONCLUSIONS: Plant-RRBS offers high-throughput and broad, genome-dispersed methylation detection by effective read number generation obtained from reproducibly covered genome fractions using optimized endonuclease combinations, facilitating comparative analyses of multi-sample studies for cytosine methylation and transgenerational stability in experimental material and plant breeding populations.}, } @article {pmid28610323, year = {2017}, author = {Paulsen, MJ}, title = {Correction of existing generic and species concepts in Platyceroidini (Coleoptera: Lucanidae: Lucaninae) and the description of four new species of Platyceroides Benesh.}, journal = {Zootaxa}, volume = {4269}, number = {3}, pages = {346-378}, doi = {10.11646/zootaxa.4269.3.2}, pmid = {28610323}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; California ; *Coleoptera ; Male ; Oregon ; }, abstract = {The endemic North American stag beetle tribe Platyceroidini Paulsen & Hawks (Coleoptera: Lucanidae: Lucaninae) is reviewed. All primary types were studied and the existing generic and species concepts are subsequently corrected. Based on study of the male genitalia and external morphology, the previously monotypic genus Platyceropsis Benesh is reduced to subgeneric status under Platyceroides Benesh, new status, and the species Platyceroides laticollis (Casey) and Platyceroides keeni (Casey) new combination are transferred to this subgenus. Praocerus, new subgenus, is created to contain the species Platyceroides latus (Fall), and P. viriditinctus (Benesh). In the nominal subgenus, confusion has resulted from the historic misapplication of the oldest available name, Platyceroides agassii (LeConte), resulting in significant underestimation of the number of extant taxa. Lectotypes are designated for four species-group names (listed in their original combinations): Platycerus latus Fall, Platycerus opacus Fall, Platycerus pacificus Casey, and Platycerus parvicollis Casey. Four new species (Platyceroides barrae, P. infernus, P. pampinatus, and P. umpquus) are described from California and Oregon, United States of America. The following species are valid and are removed from synonymy with P. agassii: P. pacificus (Casey), revised status, and P. californicus (Casey), revised status. The synonym Platycerus parvicollis Casey is transferred from Platyceroides agassii to P. californicus, new synonymy. With the addition of four new species and the correction of the mistaken synonymies the total number of species in the tribe Platyceroidini is now 16.}, } @article {pmid28610313, year = {2017}, author = {Loughman, ZJ and Henkanaththegedara, SM and Fetzner, JW and Thoma, RF}, title = {A case of Appalachian endemism: Revision of the Cambarus robustus complex (Decapoda: Cambaridae) in the Kentucky and Licking River basins of Kentucky, USA, with the description of three new species.}, journal = {Zootaxa}, volume = {4269}, number = {4}, pages = {460-494}, doi = {10.11646/zootaxa.4269.4.4}, pmid = {28610313}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; Appalachian Region ; *Astacoidea ; Kentucky ; Rivers ; }, abstract = {The amazing levels of freshwater biodiversity found in the Appalachian Mountains of the eastern United States are among the highest recorded globally. Localized endemics make up much of this diversity, with numerous fish, freshwater mussels, salamanders and crayfish often being restricted to a single watershed, and in some instances, subwatersheds. Much of this diversity is the product of the processes of vicariance and historical stream drainage patterns. Herein, we describe three new crayfish species, all previously members of the Cambarus robustus complex, which occur in the Appalachian portion of the Kentucky and Licking river basins in Kentucky, USA. All three species differ from each other morphologically, genetically, and zoogeographically, fulfilling the requirements of the integrated species concept. Cambarus guenteri occurs in the southern tributaries of the Kentucky River mainstem as well as throughout the South Fork Kentucky River. Cambarus taylori is a narrow endemic, which only occurs in the Middle Fork Kentucky River. Cambarus hazardi, which has the widest distribution of the three new species, occurs in the North Fork Kentucky River, Red River, and upper reaches of the Licking River basin. Stream piracy events between the Cumberland and South Fork Kentucky River, as well as the Licking, Red and North Fork Kentucky rivers, are theorized to be important in the evolution of this complex. Cambarus guenteri is proposed as currently stable, though both C. taylori and C. hazardi are considered imperiled at this time due to habitat destruction throughout both of their respective ranges.}, } @article {pmid28610172, year = {2017}, author = {Molinari, J and Bustos, XE and Burneo, SF and Camacho, MA and Moreno, SA and Fermín, G}, title = {A new polytypic species of yellow-shouldered bats, genus Sturnira (Mammalia: Chiroptera: Phyllostomidae), from the Andean and coastal mountain systems of Venezuela and Colombia.}, journal = {Zootaxa}, volume = {4243}, number = {1}, pages = {75-96}, doi = {10.11646/zootaxa.4243.1.3}, pmid = {28610172}, issn = {1175-5334}, mesh = {Animals ; *Chiroptera ; Colombia ; Conservation of Natural Resources ; Forests ; Venezuela ; }, abstract = {Sturnira is the most speciose genus of New World leaf-nosed bats (Phyllostomidae). We name Sturnira adrianae, new species. This taxon is born polytypic, divided into a larger subspecies (S. a. adrianae) widespread in the mountains of northern and western Venezuela, and northern Colombia, and a smaller subspecies (S. a. caripana) endemic to the mountains of northeastern Venezuela. The new species inhabits evergreen, deciduous, and cloud forests at mainly medium (1000-2000 m) elevations. It has long been confused with S. ludovici, but it is more closely related to S. oporaphilum. It can be distinguished from other species of Sturnira by genetic data, and based on discrete and continuously varying characters. Within the genus, the new species belongs to a clade that also includes S. oporaphilum, S. ludovici, S. hondurensis, and S. burtonlimi. The larger new subspecies is the largest member of this clade. The two new subspecies are the most sexually dimorphic members of this clade. The smaller new subspecies is restricted to small mountain systems undergoing severe deforestation processes, therefore can be assigned to the Vulnerable (VU) conservation category of the International Union for Conservation of Nature (IUCN).}, } @article {pmid28610076, year = {2017}, author = {Zoysa, HKS and Ukuwela, KDB and Wickramasinghe, S and Nguyen, AD and Hollier, J}, title = {Reinstatement of Spirostreptus kandyanus Humbert, 1865 and deletion of Thyropygus allevatus (Karsch, 1881) and Sphaeropoeus hercules (Brandt, 1833) in the checklist of Sri Lankan Diplopoda.}, journal = {Zootaxa}, volume = {4247}, number = {3}, pages = {333-335}, doi = {10.11646/zootaxa.4247.3.8}, pmid = {28610076}, issn = {1175-5334}, mesh = {Animals ; *Arthropods ; Europe ; }, abstract = {The Diplopoda have been studied for some 250 years, but until the later part of the nineteenth century most descriptions were rather cursory and neither the species concept nor type concept were well established (Hoffman 2009). Even for well-explored regions like Europe, the description of the Diplopoda saw a proliferation of synonyms (Enghoff 1976) while the complexity of Diplopoda systematics was severely underestimated until very recently (Brewer et al. 2012).}, } @article {pmid28603246, year = {2017}, author = {Cao, HX and Salle, J and Zhu, CD}, title = {Chinese species of Pediobius Walker (Hymenoptera: Eulophidae).}, journal = {Zootaxa}, volume = {4240}, number = {1}, pages = {1-71}, doi = {10.11646/zootaxa.4240.1.1}, pmid = {28603246}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; China ; Female ; *Hymenoptera ; Male ; }, abstract = {The Chinese species of Pediobius Walker, 1846 are treated in this paper, resulting in 34 species, of which 5 are newly described: P. bisulcatus Cao & Zhu sp. n., P. elongatus Cao & Zhu sp. n., P.petiolapilus Cao & Zhu sp. n., P. prominentis Cao & Zhu, sp. n., and P. tortricida Cao & Zhu, sp. n. Nine species are also newly recorded from China: P. anomalus (Gahan, 1920), P. bethylicidus Kerrich, 1973, P. bruchicida (Rondani, 1872), P. cassidae Erdös, 1958, P. claviger (Thomson, 1878), P. erionotae Kerrich, 1973, P. phragmitis Bouček, 1965, P. saulius (Walker, 1839), and P. tetratomus (Thomson, 1878). Four new synonyms are proposed: P. illiberidis Liao, 1987 under P. pyrgo (Walker, 1839) syn. n., P. planiceps Sheng & Kamijo, 1992 under P. inexpectatus Kerrich, 1973 syn. n., P. sinensis Sheng & Wang, 1994 under P. facialis (Giraud, 1863) syn. n., and P. songshaominus Liao, 1987 under P. yunanensis Liao, 1987 syn. n. The species-group concept is used to compare similar species, of which eight are recognized in China including two newly recognized groups: the cassidae-group and the crassicornis-group. One species complex, the P. eubius complex, is also recognized. An updated checklist of the Chinese species of Pediobius is provided, with species-group placement. New host records for Pediobius species from China are summarized in a table and valid species possibly present in China but not included in this study in another table. A key to all known females and males of Chinese Pediobius is also provided.}, } @article {pmid28603037, year = {2017}, author = {Zimmers, JC and Thomas, M and Yang, L and Bombarely, A and Mancuso, MM and Wojciechowski, MF and Smith, JF}, title = {Species boundaries in the Astragalus cusickii complex delimited using molecular phylogenetic techniques.}, journal = {Molecular phylogenetics and evolution}, volume = {114}, number = {}, pages = {93-110}, doi = {10.1016/j.ympev.2017.06.004}, pmid = {28603037}, issn = {1095-9513}, mesh = {Bayes Theorem ; Chloroplasts/classification/genetics ; DNA, Plant/chemistry/isolation & purification/metabolism ; Fabaceae/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Understanding the source of phenotypic variability is a challenge in the biological sciences. Variation in phenotypes is the result of variation in the genetics and environment the organism experiences, but elucidating the relative contribution of these two parameters can pose problems, especially in the field of systematics. Systematists are challenged to classify biological diversity into groups that share common ancestry. Phenotypic variation can be useful to demonstrate common ancestry, but only when the primary contributor to the variation is under strong genetic control, and thus heritable. Cusick's milkvetch (Astragalus cusickii) is a perennial forb endemic to the northwestern intermountain region of the United States. The species currently comprises four varieties based on subtle morphological dissimilarities, such as leaf size and density, and the size and shape of the seed pods. The taxonomic organization of the varieties of A. cusickii and related species of Astragalus were reexamined through phylogenetic analysis of low copy nuclear, nuclear-ribosomal, and chloroplast gene regions. Maximum parsimony, maximum likelihood, Bayesian inference, the genealogical sorting index, and an approximately unbiased test were used to determine appropriate species boundaries under the phylogenetic species concept. The results support reclassification of A. cusickii var. packardiae and A. cusickii var. sterilis as separate species. Additionally, evidence suggests a chloroplast capture event may have occurred in one population of A. cusickii var. packardiae.}, } @article {pmid28599072, year = {2017}, author = {Xiong, W and Ni, P and Chen, Y and Gao, Y and Shan, B and Zhan, A}, title = {Zooplankton community structure along a pollution gradient at fine geographical scales in river ecosystems: The importance of species sorting over dispersal.}, journal = {Molecular ecology}, volume = {26}, number = {16}, pages = {4351-4360}, doi = {10.1111/mec.14199}, pmid = {28599072}, issn = {1365-294X}, mesh = {*Animal Distribution ; Animals ; China ; Ecosystem ; Geography ; *Rivers ; *Water Pollution ; Zooplankton/*classification ; }, abstract = {The release of anthropogenic pollution into freshwater ecosystems has largely transformed biodiversity and its geographical distribution patterns globally. However, for many communities including ecologically crucial ones such as zooplankton, it is largely unknown how different communities respond to environmental pollution. Collectively, dispersal and species sorting are two competing processes in determining the structure and geographical distribution of zooplankton communities in running water ecosystems such as rivers. At fine geographical scales, dispersal is usually considered as the dominant factor; however, the relative role of species sorting has not been evaluated well, mainly because significant environmental gradients rarely exist along continuously flowing rivers. The Chaobai River in northern China represents a rare system, where a significant environmental gradient exists at fine scales. Here, we employed high-throughput sequencing to characterize complex zooplankton communities collected from the Chaobai River, and tested the relative roles of dispersal and species sorting in determining zooplankton community structure along the pollution gradient. Our results showed distinct patterns of zooplankton communities along the environmental gradient, and chemical pollutant-related factors such as total phosphorus and chlorophyll-a were identified as the major drivers for the observed patterns. Further partial redundancy analyses showed that species sorting overrode the effect of dispersal to shape local zooplankton community structure. Thus, our results reject the dispersal hypothesis and support the concept that species sorting caused by local pollution can largely determine the zooplankton community structure when significant environmental gradients exist at fine geographical scales in highly polluted running water ecosystems.}, } @article {pmid28592249, year = {2017}, author = {Banag, CI and Mouly, A and Alejandro, GJD and Bremer, B and Meve, U and Grimm, GW and Liede-Schumann, S}, title = {Ixora (Rubiaceae) on the Philippines - crossroad or cradle?.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {131}, pmid = {28592249}, issn = {1471-2148}, mesh = {Animals ; Biological Evolution ; Chloroplasts/genetics ; DNA, Plant/genetics ; Genetic Variation ; Philippines ; Phylogeny ; Rubiaceae/*classification/cytology/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The Philippine archipelago is globally one of the most important model island systems for studying evolutionary processes. However, most plant species on this archipelago have not yet been studied in sufficient detail. The main aim of this study is to unravel the evolutionary history and biogeographic relationships of the Philippine members of the pantropical genus Ixora.

RESULTS: The complex plastid and nuclear divergence patterns in Philippine Ixora, documented using tree and network approaches, reveal a highly dynamic evolution in Ixora, involving several phases of radiation and recolonization. Philippine Ixora comprises at least five lineages, of which one is most closely related to species from Wallacea, and the remaining four to species from Asia.

CONCLUSIONS: Our study highlights the importance of Philippine species for understanding phytogeographic patterns in the Indomalayan-Australasian eco-region. The overall genetic differentiation, as well as the incongruence between genealogies based on the biparentally inherited nucleome and the maternally inherited plastome in Ixora, reflect the complex tectonic history of the Philippine archipelago. The Ixora lineage related to Wallacean species supports the delimitation of different ecozones along Huxley's line, because it is absent from Palawan. The remaining four lineages are all allied with Asian taxa, reflecting several waves of colonization. Close relationships between some widespread Philippine species and locally adapted narrow endemics suggest that the widespread, genetically diverse species act as pools for the formation of new species in a process of ongoing speciation. Our results suggest that the species concepts of some of the more widespread taxa need to be revised.}, } @article {pmid28588130, year = {2017}, author = {McDonald, BR and Currie, CR}, title = {Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces.}, journal = {mBio}, volume = {8}, number = {3}, pages = {}, pmid = {28588130}, issn = {2150-7511}, support = {T32 GM007215/GM/NIGMS NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/biosynthesis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Phylogeny ; Point Mutation ; Streptomyces/*genetics/metabolism ; }, abstract = {Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates. Calibrating LGT rate to this geologic time span, we find that on average only 10 genes per million years were acquired and subsequently maintained. Over that same time span, Streptomyces accumulated thousands of point mutations. By explicitly incorporating evolutionary timescale into our analyses, we provide a dramatically different view on the dynamics of LGT and its impact on bacterial evolution.IMPORTANCE Tree-based phylogenetics and the use of species as units of diversity lie at the foundation of modern biology. In bacteria, these pillars of evolutionary theory have been called into question due to the observation of thousands of lateral gene transfer (LGT) events within and between lineages. Here, we show that acquisition and retention of genes through LGT are exceedingly rare in the bacterial genus Streptomyces, with merely one gene acquired in Streptomyces lineages every 100,000 years. These findings stand in contrast to the current assumption of rampant genetic exchange, which has become the dominant hypothesis used to explain bacterial diversity. Our results support a more nuanced understanding of genetic exchange, with LGT impacting evolution over short timescales but playing a significant role over long timescales. Deeper understanding of LGT provides new insight into the evolutionary history of life on Earth, as the vast majority of this history is microbial.}, } @article {pmid28560106, year = {2017}, author = {Singh, SP and Groeneveld, JC and Al-Marzouqi, A and Willows-Munro, S}, title = {A molecular phylogeny of the spiny lobster Panulirus homarus highlights a separately evolving lineage from the Southwest Indian Ocean.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3356}, pmid = {28560106}, issn = {2167-8359}, abstract = {Accurate species description in the marine environment is critical for estimating biodiversity and identifying genetically distinct stocks. Analysis of molecular data can potentially improve species delimitations because they are easily generated and independent, and yield consistent results with high statistical power. We used classical phylogenetic (maximum likelihood and Bayesian inference) and coalescent-based methods (divergence dating with fossil calibrations and coalescent-based species delimitation) to resolve the phylogeny of the spiny lobster Panulirus homarus subspecies complex in the Indo-West Pacific. Analyses of mitochondrial data and combined nuclear and mitochondrial data recovered Panulirus homarus homarus and Panulirus homarus rubellus as separately evolving lineages, while the nuclear data trees were unresolved. Divergence dating analysis also identified Panulirus homarus homarus and Panulirus homarus rubellus as two distinct clades which diverged from a common ancestor during the Oligocene, approximately 26 million years ago. Species delimitation using coalescent-based methods corroborated these findings. A long pelagic larval life stage and the influence of ocean currents on post-larval settlement patterns suggest that a parapatric mode of speciation drives evolution in this subspecies complex. In combination, the results indicate that Panulirus homarus rubellus from the Southwest Indian Ocean is a separately evolving lineage and possibly a separate species.}, } @article {pmid28545257, year = {2017}, author = {Giles, GI and Nasim, MJ and Ali, W and Jacob, C}, title = {The Reactive Sulfur Species Concept: 15 Years On.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {6}, number = {2}, pages = {}, pmid = {28545257}, issn = {2076-3921}, abstract = {Fifteen years ago, in 2001, the concept of "Reactive Sulfur Species" or RSS was advocated as a working hypothesis. Since then various organic as well as inorganic RSS have attracted considerable interest and stimulated many new and often unexpected avenues in research and product development. During this time, it has become apparent that molecules with sulfur-containing functional groups are not just the passive "victims" of oxidative stress or simple conveyors of signals in cells, but can also be stressors in their own right, with pivotal roles in cellular function and homeostasis. Many "exotic" sulfur-based compounds, often of natural origin, have entered the fray in the context of nutrition, ageing, chemoprevention and therapy. In parallel, the field of inorganic RSS has come to the forefront of research, with short-lived yet metabolically important intermediates, such as various sulfur-nitrogen species and polysulfides (Sx[2-]), playing important roles. Between 2003 and 2005 several breath-taking discoveries emerged characterising unusual sulfur redox states in biology, and since then the truly unique role of sulfur-dependent redox systems has become apparent. Following these discoveries, over the last decade a "hunt" and, more recently, mining for such modifications has begun-and still continues-often in conjunction with new, innovative and complex labelling and analytical methods to capture the (entire) sulfur "redoxome". A key distinction for RSS is that, unlike oxygen or nitrogen, sulfur not only forms a plethora of specific reactive species, but sulfur also targets itself, as sulfur containing molecules, i.e., peptides, proteins and enzymes, preferentially react with RSS. Not surprisingly, today this sulfur-centred redox signalling and control inside the living cell is a burning issue, which has moved on from the predominantly thiol/disulfide biochemistry of the past to a complex labyrinth of interacting signalling and control pathways which involve various sulfur oxidation states, sulfur species and reactions. RSS are omnipresent and, in some instances, are even considered as the true bearers of redox control, perhaps being more important than the Reactive Oxygen Species (ROS) or Reactive Nitrogen Species (RNS) which for decades have dominated the redox field. In other(s) words, in 2017, sulfur redox is "on the rise", and the idea of RSS resonates throughout the Life Sciences. Still, the RSS story isn't over yet. Many RSS are at the heart of "mistaken identities" which urgently require clarification and may even provide the foundations for further scientific revolutions in the years to come. In light of these developments, it is therefore the perfect time to revisit the original hypotheses, to select highlights in the field and to question and eventually update our concept of "Reactive Sulfur Species".}, } @article {pmid28539524, year = {2017}, author = {Hedwig, B and Sarmiento-Ponce, EJ}, title = {Song pattern recognition in crickets based on a delay-line and coincidence-detector mechanism.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1855}, pages = {}, pmid = {28539524}, issn = {1471-2954}, mesh = {Acoustics ; Animals ; *Auditory Perception ; Female ; Gryllidae/*physiology ; Sound ; }, abstract = {Acoustic communication requires filter mechanisms to process and recognize key features of the perceived signals. We analysed such a filter mechanism in field crickets (Gryllus bimaculatus), which communicate with species-specific repetitive patterns of sound pulses and chirps. A delay-line and coincidence-detection mechanism, in which each sound pulse has an impact on the processing of the following pulse, is implicated to underlie the recognition of the species-specific pulse pattern. Based on this concept, we hypothesized that altering the duration of a single pulse or inter-pulse interval in three-pulse chirps will lead to different behavioural responses. Phonotaxis was tested in female crickets walking on a trackball exposed to different sound paradigms. Changing the duration of either the first, second or third pulse of the chirps led to three different characteristic tuning curves. Long first pulses decreased the phonotactic response whereas phonotaxis remained strong when the third pulse was long. Chirps with three pulses of increasing duration of 5, 20 and 50 ms elicited phonotaxis, but the chirps were not attractive when played in reverse order. This demonstrates specific, pulse duration-dependent effects while sequences of pulses are processed. The data are in agreement with a mechanism in which processing of a sound pulse has an effect on the processing of the subsequent pulse, as outlined in the flow of activity in a delay-line and coincidence-detector circuit. Additionally our data reveal a substantial increase in the gain of phonotaxis, when the number of pulses of a chirp is increased from two to three.}, } @article {pmid28501896, year = {2017}, author = {Pušić, B and Gregorić, P and Franjević, D}, title = {What do Biologists Make of the Species Problem?.}, journal = {Acta biotheoretica}, volume = {65}, number = {3}, pages = {179-209}, doi = {10.1007/s10441-017-9311-x}, pmid = {28501896}, issn = {1572-8358}, mesh = {*Biological Evolution ; Surveys and Questionnaires ; }, abstract = {The concept of species is one of the core concepts in biology and one of the cornerstones of evolutionary biology, yet it is rife with conceptual problems. Philosophers of biology have been discussing the concept of species for decades, and in doing so they sometimes appeal to the views of biologists. However, their statements as to what biologists think are seldom supported by empirical data. In order to investigate what biologists actually think about the key issues related to the problem of species, we have conducted a survey on the sample of 193 biologists from the population of biologists from over 150 biology departments at universities in the US and the EU. This article presents and discusses the results of the survey. Some results confirm and others falsify the reiterated statements of philosophers of biology as to what biologists think, but all results we obtained should be informative and relevant for future discussions of the problem of species.}, } @article {pmid28459805, year = {2017}, author = {Lin, YP and Edwards, RD and Kondo, T and Semple, TL and Cook, LG}, title = {Species delimitation in asexual insects of economic importance: The case of black scale (Parasaissetia nigra), a cosmopolitan parthenogenetic pest scale insect.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0175889}, pmid = {28459805}, issn = {1932-6203}, mesh = {Animals ; Australia ; Bayes Theorem ; Ecotype ; Hemiptera/*classification/*genetics ; Models, Genetic ; Polymerase Chain Reaction ; }, abstract = {Asexual lineages provide a challenge to species delimitation because species concepts either have little biological meaning for them or are arbitrary, since every individual is monophyletic and reproductively isolated from all other individuals. However, recognition and naming of asexual species is important to conservation and economic applications. Some scale insects are widespread and polyphagous pests of plants, and several species have been found to comprise cryptic species complexes. Parasaissetia nigra (Nietner, 1861) (Hemiptera: Coccidae) is a parthenogenetic, cosmopolitan and polyphagous pest that feeds on plant species from more than 80 families. Here, we implement multiple approaches to assess the species status of P. nigra, including coalescence-based analyses of mitochondrial and nuclear genes, and ecological niche modelling. Our results indicate that the sampled specimens of P. nigra should be considered to comprise at least two ecotypes (or "species") that are ecologically differentiated, particularly in relation to temperature and moisture. The presence of more than one ecotype under the current concept of P. nigra has implications for biosecurity because the geographic extent of each type is not fully known: some countries may currently have only one of the biotypes. Introduction of additional lineages could expand the geographic extent of damage by the pest in some countries.}, } @article {pmid28429851, year = {2018}, author = {Gippoliti, S and Cotterill, FPD and Zinner, D and Groves, CP}, title = {Impacts of taxonomic inertia for the conservation of African ungulate diversity: an overview.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {1}, pages = {115-130}, doi = {10.1111/brv.12335}, pmid = {28429851}, issn = {1469-185X}, mesh = {Africa ; Animals ; Artiodactyla/*classification/*physiology ; *Biodiversity ; *Conservation of Natural Resources ; }, abstract = {We review the state of African ungulate taxonomy over the last 120 years, with an emphasis on the introduction of the polytypic species concept and the discipline's general neglect since the middle of the 20th century. We single out negative consequences of 'orthodox' taxonomy, highlighting numerous cases of neglect of threatened lineages, unsound translocations that led to lineage introgression, and cases of maladaptation to local conditions including parasitic infections. Additionally, several captive breeding programmes have been hampered by chromosome rearrangements caused by involuntary lineage mixing. We advocate that specimen-based taxonomy should regain its keystone role in mammal research and conservation biology, with its scientific values augmented with genomic evidence. While integration with molecular biology, ecology and behaviour is needed for a full understanding of ungulate alpha diversity, we stress that morphological diversity has been neglected despite its tremendous practical importance for some groups of 'utilizers' such as trophy hunters, wildlife tourists and conservationists. We conclude that there is no evidence that purported 'taxonomic inflation' has adverse effects on ungulate conservation: rather, it is taxonomic inertia that has such adverse effects. We stress that sound science, founded on robust taxonomy, should underpin effective sustainable management (hunting, ranching, captive breeding and reintroduction programmes) of this unique African natural resource.}, } @article {pmid28398072, year = {2017}, author = {Cortese-Krott, MM and Koning, A and Kuhnle, GGC and Nagy, P and Bianco, CL and Pasch, A and Wink, DA and Fukuto, JM and Jackson, AA and van Goor, H and Olson, KR and Feelisch, M}, title = {The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine.}, journal = {Antioxidants & redox signaling}, volume = {27}, number = {10}, pages = {684-712}, pmid = {28398072}, issn = {1557-7716}, support = {R21 AG055022/AG/NIA NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Animals ; Humans ; Hydrogen Sulfide/*metabolism ; Metabolomics/*methods ; Oxidation-Reduction ; Precision Medicine ; Reactive Nitrogen Species/metabolism ; Reactive Oxygen Species/metabolism ; Sulfides/*metabolism ; }, abstract = {SIGNIFICANCE: Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level.

CRITICAL ISSUES: To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses.

FUTURE DIRECTIONS: Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox Signal. 00, 000-000.}, } @article {pmid28391326, year = {2017}, author = {Venton, D}, title = {Highlight: Applying the Biological Species Concept across All of Life.}, journal = {Genome biology and evolution}, volume = {9}, number = {3}, pages = {502-503}, pmid = {28391326}, issn = {1759-6653}, mesh = {Bacteria/*genetics ; Eukaryota/*genetics ; Gene Flow ; *Genetic Speciation ; *Genome ; Geography ; Homologous Recombination ; }, } @article {pmid28384166, year = {2017}, author = {Feckler, A and Schrimpf, A and Bundschuh, M and Bärlocher, F and Baudy, P and Cornut, J and Schulz, R}, title = {Quantitative real-time PCR as a promising tool for the detection and quantification of leaf-associated fungal species - A proof-of-concept using Alatospora pulchella.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0174634}, pmid = {28384166}, issn = {1932-6203}, mesh = {Ascomycota/*genetics ; *Genes, Fungal ; Limit of Detection ; Plant Leaves/*microbiology ; Real-Time Polymerase Chain Reaction/*methods ; }, abstract = {Traditional methods to identify aquatic hyphomycetes rely on the morphology of released conidia, which can lead to misidentifications or underestimates of species richness due to convergent morphological evolution and the presence of non-sporulating mycelia. Molecular methods allow fungal identification irrespective of the presence of conidia or their morphology. As a proof-of-concept, we established a quantitative real-time polymerase chain reaction (qPCR) assay to accurately quantify the amount of DNA as a proxy for the biomass of an aquatic hyphomycete species (Alatospora pulchella). Our study showed discrimination even among genetically closely-related species, with a high sensitivity and a reliable quantification down to 9.9 fg DNA (3 PCR forming units; LoD) and 155.0 fg DNA (47 PCR forming units; LoQ), respectively. The assay's specificity was validated for environmental samples that harboured diverse microbial communities and likely contained PCR-inhibiting substances. This makes qPCR a promising tool to gain deeper insights into the ecological roles of aquatic hyphomycetes and other microorganisms.}, } @article {pmid28374754, year = {2017}, author = {Pedrini, B and Menzel, A and Guzenko, VA and David, C and Abela, R and Gutt, C}, title = {Model-independent particle species disentanglement by X-ray cross-correlation scattering.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45618}, pmid = {28374754}, issn = {2045-2322}, abstract = {Mixtures of different particle species are often investigated using the angular averages of the scattered X-ray intensity. The number of species is deduced by singular value decomposition methods. The full disentanglement of the data into per-species contributions requires additional knowledge about the system under investigation. We propose to exploit higher-order angular X-ray intensity correlations with a new computational protocol, which we apply to synchrotron data from two-species mixtures of two-dimensional static test nanoparticles. Without any other information besides the correlations, we demonstrate the assessment of particle species concentrations in the measured data sets, as well as the full ab initio reconstruction of both particle structures. The concept extends straightforwardly to more species and to the three-dimensional case, whereby the practical application will require the measurements to be performed at an X-ray free electron laser.}, } @article {pmid28369873, year = {2017}, author = {Lefebvre, KE and Hamilton, PB and Pick, FR}, title = {A comparison of molecular markers and morphology for Neidium taxa (Bacillariophyta) from eastern North America.}, journal = {Journal of phycology}, volume = {53}, number = {3}, pages = {680-702}, doi = {10.1111/jpy.12537}, pmid = {28369873}, issn = {1529-8817}, mesh = {Algal Proteins/*genetics ; Canada ; Chloroplast Proteins/genetics ; Diatoms/*classification/cytology/genetics/ultrastructure ; Microscopy, Electron, Scanning ; New York ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Historically, a morphological species concept has applied shape subjectively in the delimitation of diatom species. This has led to confusion between taxa within the benthic diatom genus Neidium. Samples from Ontario, Quebec, Nova Scotia, Newfoundland (Canada) and New York (USA) were examined for Neidium taxa under LM and SEM. Fourier shape analysis showed that shape as a taxonomic character was not able to discern all species. Isolated individuals from the samples were amplified and sequenced for three chloroplast molecular markers (rbcL, psbC, and psbA) and one nuclear ribosomal molecular marker (18S). Phylogenetic reconstructions were completed with the concatenated chloroplast and 18S dataset using Maximum Likelihood and Bayesian analyses. The concatenated chloroplast dataset exhibited a species-level resolution phylogeny of Neidium taxa. The 18S dataset had a lower level of sequence divergence and was unable to differentiate between Neidium taxa. We present emended species descriptions and sequence data for four previously described species: Neidium sacoense, N. longiceps, N. fossum, and N. affine. We describe three novel species (Neidium lowei, N. promontorium, and N. potapovae) and identify two forms with unique molecular signatures. The distinguishing features of N. lowei are its size, valve shape, and longitudinal canal structure. Distinguishing features of N. promontorium are its valve shape, longitudinal canal and apex formation, and surface depression along the axial area. Neidium potapovae is distinguished by its size, formation of valve and apices and single longitudinal canal. This paper demonstrates how future phylogenetic treatments using single cell multigene sequencing can help resolve taxonomic confusion within diatoms.}, } @article {pmid28328079, year = {2017}, author = {Venuleo, M and Raven, JA and Giordano, M}, title = {Intraspecific chemical communication in microalgae.}, journal = {The New phytologist}, volume = {215}, number = {2}, pages = {516-530}, doi = {10.1111/nph.14524}, pmid = {28328079}, issn = {1469-8137}, mesh = {Biological Evolution ; Cell Communication/physiology ; Genetic Variation ; Microalgae/*chemistry/genetics/*metabolism ; Phenotype ; Reproduction/physiology ; Signal Transduction ; }, abstract = {Contents 516 I. 516 II. 518 III. 518 IV. 521 V. 523 VI. 523 VII. 526 526 References 526 SUMMARY: The relevance of infochemicals in the relationships between organisms is emerging as a fundamental aspect of aquatic ecology. Exchanges of chemical cues are likely to occur not only between organisms of different species, but also between conspecific individuals. Especially intriguing is the investigation of chemical communication in microalgae, because of the relevance of these organisms for global primary production and their key role in trophic webs. Intraspecific communication between algae has been investigated mostly in relation to sexuality and mating. The literature also contains information on other types of intraspecific chemical communication that have not always been explicitly tagged as ways to communicate to conspecifics. However, the proposed role of certain compounds as intraspecific infochemicals appears questionable. In this article, we make use of this plethora of information to describe the various instances of intraspecific chemical communication between conspecific microalgae and to identify the common traits and ecological significance of intraspecific communication. We also discuss the evolutionary implications of intraspecific chemical communication and the mechanisms by which it can be inherited. A special focus is the genetic diversity among conspecific algae, including the possibility that genetic diversity is an absolute requirement for intraspecific chemical communication.}, } @article {pmid28322330, year = {2017}, author = {Xiang, X and Wang, R and Wang, H and Gong, L and Man, B and Xu, Y}, title = {Distribution of Bathyarchaeota Communities Across Different Terrestrial Settings and Their Potential Ecological Functions.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {45028}, pmid = {28322330}, issn = {2045-2322}, mesh = {Archaea/*classification/*genetics ; *Biodiversity ; Computational Biology/methods ; *Ecosystem ; Environment ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {High abundance and widespread distribution of the archaeal phylum Bathyarchaeota in marine environment have been recognized recently, but knowledge about Bathyarchaeota in terrestrial settings and their correlation with environmental parameters is fairly limited. Here we reported the abundance of Bathyarchaeota members across different ecosystems and their correlation with environmental factors by constructing 16S rRNA clone libraries of peat from the Dajiuhu Peatland, coupling with bioinformatics analysis of 16S rRNA data available to date in NCBI database. In total, 1456 Bathyarchaeota sequences from 28 sites were subjected to UniFrac analysis based on phylogenetic distance and multivariate regression tree analysis of taxonomy. Both phylogenetic and taxon-based approaches showed that salinity, total organic carbon and temperature significantly influenced the distribution of Bathyarchaeota across different terrestrial habitats. By applying the ecological concept of 'indicator species', we identify 9 indicator groups among the 6 habitats with the most in the estuary sediments. Network analysis showed that members of Bathyarchaeota formed the "backbone" of archaeal community and often co-occurred with Methanomicrobia. These results suggest that Bathyarchaeota may play an important ecological role within archaeal communities via a potential symbiotic association with Methanomicrobia. Our results shed light on understanding of the biogeography, potential functions of Bathyarchaeota and environment conditions that influence Bathyarchaea distribution in terrestrial settings.}, } @article {pmid28319035, year = {2017}, author = {Lai, CC and Goyenola, C and Broitman, E and Näslund, LÅ and Högberg, H and Hultman, L and Gueorguiev, GK and Rosen, J}, title = {Synthesis and properties of CS x F y thin films deposited by reactive magnetron sputtering in an Ar/SF6 discharge.}, journal = {Journal of physics. Condensed matter : an Institute of Physics journal}, volume = {29}, number = {19}, pages = {195701}, doi = {10.1088/1361-648X/aa67d2}, pmid = {28319035}, issn = {1361-648X}, abstract = {A theoretical and experimental study on the growth and properties of a ternary carbon-based material, CS x F y , synthesized from SF6 and C as primary precursors is reported. The synthetic growth concept was applied to model the possible species resulting from the fragmentation of SF6 molecules and the recombination of S-F fragments with atomic C. The possible species were further evaluated for their contribution to the film growth. Corresponding solid CS x F y thin films were deposited by reactive direct current magnetron sputtering from a C target in a mixed Ar/SF6 discharge with different SF6 partial pressures ([Formula: see text]). Properties of the films were determined by x-ray photoelectron spectroscopy, x-ray reflectivity, and nanoindentation. A reduced mass density in the CS x F y films is predicted due to incorporation of precursor species with a more pronounced steric effect, which also agrees with the low density values observed for the films. Increased [Formula: see text] leads to decreasing deposition rate and increasing density, as explained by enhanced fluorination and etching on the deposited surface by a larger concentration of F/F2 species during the growth, as supported by an increment of the F relative content in the films. Mechanical properties indicating superelasticity were obtained from the film with lowest F content, implying a fullerene-like structure in CS x F y compounds.}, } @article {pmid28317543, year = {2017}, author = {Cruywagen, EM and Slippers, B and Roux, J and Wingfield, MJ}, title = {Phylogenetic species recognition and hybridisation in Lasiodiplodia: A case study on species from baobabs.}, journal = {Fungal biology}, volume = {121}, number = {4}, pages = {420-436}, doi = {10.1016/j.funbio.2016.07.014}, pmid = {28317543}, issn = {1878-6146}, mesh = {Adansonia/*microbiology ; Africa ; Ascomycota/*classification/genetics/*isolation & purification ; DNA, Fungal/*genetics ; *Phylogeny ; Plant Diseases/microbiology ; *Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Lasiodiplodia species (Botryosphaeriaceae, Ascomycota) infect a wide range of typically woody plants on which they are associated with many different disease symptoms. In this study, we determined the identity of Lasiodiplodia isolates obtained from baobab (Adansonia species) trees in Africa and reviewed the molecular markers used to describe Lasiodiplodia species. Publicly available and newly produced sequence data for some of the type strains of Lasiodiplodia species showed incongruence amongst phylogenies of five nuclear loci. We conclude that several of the previously described Lasiodiplodia species are hybrids of other species. Isolates from baobab trees in Africa included nine species of Lasiodiplodia and two hybrid species. Inoculation trials with the most common Lasiodiplodia species collected from these trees produced significant lesions on young baobab trees. There was also variation in aggressiveness amongst isolates from the same species. The apparently widespread tendency of Lasiodiplodia species to hybridise demands that phylogenies from multiple loci (more than two and preferably four or more) are compared for congruence prior to new species being described. This will avoid hybrids being incorrectly described as new taxa, as has clearly occurred in the past.}, } @article {pmid28279191, year = {2017}, author = {Unlu, I and Suman, DS and Wang, Y and Klingler, K and Faraji, A and Gaugler, R}, title = {Effectiveness of autodissemination stations containing pyriproxyfen in reducing immature Aedes albopictus populations.}, journal = {Parasites & vectors}, volume = {10}, number = {1}, pages = {139}, pmid = {28279191}, issn = {1756-3305}, support = {R43 AI096563/AI/NIAID NIH HHS/United States ; R44 AI096563/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/*drug effects ; Animals ; Female ; Insecticides/administration & dosage/*pharmacology ; Larva ; Male ; Mosquito Control/*methods ; Oviposition ; Ovum ; Powders ; Pupa ; Pyridines/administration & dosage/*pharmacology ; }, abstract = {BACKGROUND: Aedes albopictus, the Asian tiger mosquito, is an aggressive, highly anthropophilic, day-biting mosquito with an expanding geographic range. Suppression of Ae. albopictus is difficult because of the abundance and prevalence of larval habitats within peridomestic environments, particularly cryptic habitats such as corrugated extension spouts, fence post openings, discarded food containers, etc. Because of the challenges of eliminating or treating larval habitats of this species, we tested an autodissemination concept to contaminate these habitats with the insect growth regulator pyriproxyfen.

METHODS: Our study was conducted in the City of Trenton (Mercer County), New Jersey, USA (40°12'N, 74°44'W). We selected six hot spots, where five or more Ae. albopictus males or females were collected based on weekly trap surveillance. A trapping unit was a city block, approximately 0.8 ha (hot spot), where we deployed 26 to 28 autodissemination stations per treatment plot. To gauge efficacy, we deployed BGS traps, oviposition cups, and sentinel cups in treatment and control locations.

RESULTS: We found a significant reduction in eggs (P < 0.0001) and larval populations (P < 0.0001) as a result of treatment. Pupal mortality, as determined through bioassays, was also significantly higher in the treatment sites (P < 0.0001).

CONCLUSION: Our results clearly show the potential and unique use of the autodissemination stations to control immature Ae. albopictus in urban areas. Penetration of larvicides with existing methods are difficult to reach cryptic habitats, but the autodissemination approach, which exploits the oviposition behavior of the target pest, can be integrated into intervention programs. New tools are urgently needed to curb the expansion and public health implications of Ae. albopictus and other container-inhabiting species.}, } @article {pmid28264377, year = {2017}, author = {Plumari, M and Joharchi, O}, title = {Rediscovery and redescription of Laelaps lignicola G. & R. Canestrini, a remarkable myrmecophilous mite of the genus Cosmolaelaps Berlese (Acari: Mesostigmata: Laelapidae) from Italy.}, journal = {Zootaxa}, volume = {4232}, number = {1}, pages = {zootaxa.4232.1.2}, doi = {10.11646/zootaxa.4232.1.2}, pmid = {28264377}, issn = {1175-5334}, mesh = {Animal Structures ; Animals ; Ants ; Ecology ; Italy ; Male ; *Mites ; }, abstract = {Laelaps lignicola G. & R. Canestrini, 1882 is redescribed on the basis of numerous adults and deutonymphs, collected from Italy more than a century after its description. Despite its setiform setae without a discernible asymmetric swelling, this species fits the current concept of the genus Cosmolaelaps Berlese for all remaining diagnostic characters. Males of L. lignicola and Cosmolaelaps vacuus (Michael) share the presence of a basal process bearing seta av on telefemur II. This attribute is apparently not described in other laelapid mites. Also, males of L. lignicola are similar to those of some European species of Cosmolaelaps in having a distinct masticatory ridge on the fixed digit of chelicera. The ecological preference for decaying wood microhabitats, where L. lignicola is closely associated with Lasius emarginatus (Olivier) (Hymenoptera Formicidae), also suggests a close affinity with Cosmolaelaps species. Consequently, this species is provisionally placed in Cosmolaelaps and the new combination C. lignicolus (G. & R. Canestrini, 1882) comb. nov. is proposed.}, } @article {pmid28264319, year = {2017}, author = {Cole, JA}, title = {A new species of Megatibicen endemic to Mescalero-Monahans shinnery sands (Hemiptera: Auchenorrhyncha: Cicadidae).}, journal = {Zootaxa}, volume = {4236}, number = {3}, pages = {zootaxa.4236.3.9}, doi = {10.11646/zootaxa.4236.3.9}, pmid = {28264319}, issn = {1175-5334}, mesh = {Animals ; *Hemiptera ; Male ; Texas ; }, abstract = {Megatibicen harenosus sp. n. is described from the Mescalero-Monahans shinnery sands of New Mexico and Texas, U.S.A. The new species is diagnosed from similar species, especially M. tremulus which it resembles closely, by male genital morphology, color pattern, calling song, and ecology. Seven characters from the male calling song are described from analysis of field recordings, of which all four temporal song characters are significantly different from M. tremulus. With one of the most southwestern distribution of any Megatibicen species, M. harenosus is a new addition to the rich, endemic, and understudied Mescalero-Monahans shinnery sands biota. The possibility that M. harenosus and M. tremulus are sister species is raised. The ecological, biological, and evolutionary species concepts support species status for M. harenosus, and an hypothesis of peripatric speciation in peripheral isolation is advanced.}, } @article {pmid28261537, year = {2017}, author = {Dolezel, M and Miklau, M and Heissenberger, A and Reichenbecher, W}, title = {Are Limits of Concern a useful concept to improve the environmental risk assessment of GM plants?.}, journal = {Environmental sciences Europe}, volume = {29}, number = {1}, pages = {7}, pmid = {28261537}, issn = {2190-4707}, abstract = {BACKGROUND: The European Food Safety Authority (EFSA) has introduced a concept for the environmental risk assessment of genetically modified (GM) plants which foresees the definition of ecological threshold values defining acceptable adverse effects of the GM plant on the environment (Limits of Concern, LoC).

METHODS: We analysed the LoC concept by scrutinising its feasibility with regard to important aspects of the environmental risk assessment. We then considered its relationship with protection goals, the comparative safety assessment and the stepwise testing approach. We finally discussed its usefulness for assessing long-term effects, effects on non-target organisms and species of conservation concern.

RESULTS: The LoC concept is a possible approach to introduce ecological thresholds into environmental risk assessment in order to evaluate environmental harm. However, the concept leaves many important aspects open. Thresholds for environmental harm for protection goals need spatial and temporal differentiation from LoCs used for ERA indicators. Regionalisation of LoCs must be provided for as biodiversity levels and protection goals vary across the EU. Further guidance is needed with respect to the consequences, in case LoCs are exceeded and a link needs to be established between environmentally relevant results from the comparative safety assessment and the LoC concept. LoCs for long-term effects have to be evaluated by long-term monitoring. LoCs for non-target organisms need to be discriminated according to the species and parameters assessed.

CONCLUSIONS: The overall LoC concept is considered useful if LoCs are further specified and differentiated. Although LoCs will finally be determined by political decisions, they should be based on scientific grounds in order to increase confidence in the conclusions on the safety of GM plants.}, } @article {pmid28235635, year = {2017}, author = {Allan, RN and Kelso, MJ and Rineh, A and Yepuri, NR and Feelisch, M and Soren, O and Brito-Mutunayagam, S and Salib, RJ and Stoodley, P and Clarke, SC and Webb, JS and Hall-Stoodley, L and Faust, SN}, title = {Cephalosporin-NO-donor prodrug PYRRO-C3D shows β-lactam-mediated activity against Streptococcus pneumoniae biofilms.}, journal = {Nitric oxide : biology and chemistry}, volume = {65}, number = {}, pages = {43-49}, doi = {10.1016/j.niox.2017.02.006}, pmid = {28235635}, issn = {1089-8611}, mesh = {Amoxicillin/pharmacology ; Anti-Inflammatory Agents, Non-Steroidal/chemistry/*pharmacology ; Azithromycin/pharmacology ; Azo Compounds/chemistry/*pharmacology ; Biofilms/*drug effects ; Cephalosporins/chemistry/*pharmacology ; Nitric Oxide/analysis ; Nitric Oxide Donors/chemistry/*pharmacology ; Penicillinase/chemistry ; Plankton/microbiology ; Prodrugs/chemistry/*pharmacology ; Streptococcus pneumoniae/*drug effects ; }, abstract = {Bacterial biofilms show high tolerance towards antibiotics and are a significant problem in clinical settings where they are a primary cause of chronic infections. Novel therapeutic strategies are needed to improve anti-biofilm efficacy and support reduction in antibiotic use. Treatment with exogenous nitric oxide (NO) has been shown to modulate bacterial signaling and metabolic processes that render biofilms more susceptible to antibiotics. We previously reported on cephalosporin-3'-diazeniumdiolates (C3Ds) as NO-donor prodrugs designed to selectively deliver NO to bacterial infection sites following reaction with β-lactamases. With structures based on cephalosporins, C3Ds could, in principal, also be triggered to release NO following β-lactam cleavage mediated by transpeptidases/penicillin-binding proteins (PBPs), the antibacterial target of cephalosporin antibiotics. Transpeptidase-reactive C3Ds could potentially show both NO-mediated anti-biofilm properties and intrinsic (β-lactam-mediated) antibacterial effects. This dual-activity concept was explored using Streptococcus pneumoniae, a species that lacks β-lactamases but relies on transpeptidases for cell-wall synthesis. Treatment with PYRRO-C3D (a representative C3D containing the diazeniumdiolate NO donor PYRRO-NO) was found to significantly reduce viability of planktonic and biofilm pneumococci, demonstrating that C3Ds can elicit direct, cephalosporin-like antibacterial activity in the absence of β-lactamases. While NO release from PYRRO-C3D in the presence of pneumococci was confirmed, the anti-pneumococcal action of the compound was shown to arise exclusively from the β-lactam component and not through NO-mediated effects. The compound showed similar potency to amoxicillin against S. pneumoniae biofilms and greater efficacy than azithromycin, highlighting the potential of C3Ds as new agents for treating pneumococcal infections.}, } @article {pmid28235096, year = {2017}, author = {Willis, SC}, title = {One species or four? Yes!...and, no. Or, arbitrary assignment of lineages to species obscures the diversification processes of Neotropical fishes.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0172349}, pmid = {28235096}, issn = {1932-6203}, mesh = {Animals ; Cichlids/*classification/genetics ; *Classification ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; High-Throughput Nucleotide Sequencing ; Microsatellite Repeats/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Species are fundamental units in many biological disciplines, but there is continuing disagreement as to what species are, how to define them, and even whether the concept is useful. While some of this debate can be attributed to inadequate data and insufficient statistical frameworks in alpha taxonomy, an equal part results from the ambiguity over what species are expected to represent by the many who use them. Here, mtDNA data, microsatellite data, and sequence data from 17 nuclear loci are used in an integrated and quantitative manner to resolve the presence of evolutionary lineages, their contemporary and historical structure, and their correspondence to species, in a species complex of Amazonian peacock "bass" cichlids (Cichla pinima sensu lato). Results suggest that the historical narrative for these populations is more complex than can be portrayed by recognizing them as one, two, or four species: their history and contemporary dynamics cannot be unambiguously rendered as discrete units (taxa) at any level without both choosing the supremacy of one delimitation criterion and obscuring the very information that provides insight into the diversification process. This calls into question the utility of species as a rank, term, or concept, and suggests that while biologists may have a reasonable grasp of the structure of evolution, our methods of conveying these insights need updating. The lack of correspondence between evolutionary phenomena and discrete species should serve as a null hypothesis, and researchers should focus on quantifying the diversity in nature at whatever hierarchical level it occurs.}, } @article {pmid28232814, year = {2017}, author = {Marshall-Pescini, S and Virányi, Z and Kubinyi, E and Range, F}, title = {Motivational Factors Underlying Problem Solving: Comparing Wolf and Dog Puppies' Explorative and Neophobic Behaviors at 5, 6, and 8 Weeks of Age.}, journal = {Frontiers in psychology}, volume = {8}, number = {}, pages = {180}, pmid = {28232814}, issn = {1664-1078}, support = {311870/ERC_/European Research Council/International ; P 21244/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Background: Wolves have been shown to be better in independent problem-solving tasks than dogs, however it is unclear whether cognitive or motivational factors underlie such differences. In a number of species problem solving has been linked to both persistence in exploration and neophobia, suggesting both these aspects may underlie dog-wolf differences in problem solving. Indeed adult wolves have been shown to be more likely to approach a novel object and more persistent in their investigation of it, but also slower in making contact with it and more fearful of it than dogs. Methods: In the current study we investigated potential differences in equally-raised dogs' and wolves' explorative and neophobic behaviors in a novel environment and with novel objects at 5, 6, and 8 weeks of age. Results: Results showed that wolves were more persistent in exploring both the environment and the objects than dogs, and this was the case at all ages. There were no differences in the frequency of fear-related behaviors and time spent in proximity to humans. Stress-related behaviors were similarly expressed at 5 and 6 weeks, although wolves showed a higher frequency of such behaviors at 8 weeks. Discussion: Overall, results with puppies confirm those with adult animals: wolves appear to be more explorative than dogs. Such motivational differences need to be taken into account when comparing dogs and wolves in cognitive tasks.}, } @article {pmid28229261, year = {2017}, author = {Martin, SB and Cutmore, SC and Cribb, TH}, title = {Revision of Neolebouria Gibson, 1976 (Digenea: Opecoelidae), with Trilobovarium n. g., for species infecting tropical and subtropical shallow-water fishes.}, journal = {Systematic parasitology}, volume = {94}, number = {3}, pages = {307-338}, pmid = {28229261}, issn = {1573-5192}, mesh = {Animals ; Australia ; Fishes/*parasitology ; Pacific Ocean ; Phylogeny ; Species Specificity ; Trematoda/anatomy & histology/*classification ; }, abstract = {A new opecoelid trematode is reported from fishes of the Lethrinidae, Lutjanidae and Nemipteridae off Lizard Island on the northern Great Barrier Reef, Australia. The new species keys to Neolebouria Gibson, 1976 and shows strong similarity to several species of that genus, but is not consistent with the type-species, N. georgiensis Gibson, 1976, or others known from temperate/polar and/or deep-sea fishes. The new species is also phylogenetically distant from N. lanceolata (Price, 1934) Reimer, 1987, the only representative of the genus for which molecular data are available. A new genus, Trilobovarium n. g., is proposed for the new species, T. parvvatis n. sp. Eight morphologically similar species, previously recognised as belonging to Neolebouria, from shallow-water, mostly tropical/subtropical fishes, are transferred to Trilobovarium: T. diacopae (Nagaty & Abdel Aal, 1962) n. comb.; T. ira (Yamaguti, 1940) n. comb.; T. khalili (Ramadan, 1983) n. comb.; T. krusadaiense (Gupta, 1956) n. comb.; T. lineatum (Aken'Ova & Cribb, 2001) n. comb.; T. moretonense (Aken'Ova & Cribb, 2001) n. comb.; T. palauense (Machida, 2014) n. comb.; and T. truncatum (Linton, 1940) n. comb. Paramanteriella Li, Qiu & Zhang, 1988 is resurrected for five species of Neolebouria with a post-bifurcal genital pore: P. cantherini Li, Qiu & Zhang, 1988; P. capoori (Jaiswal, Upadhyay, Malhotra, Dronen & Malhotra, 2014) n. comb.; P. confusa (Overstreet, 1969) n. comb.; P. leiperi (Gupta, 1956) n. comb.; and P. pallenisca (Shipley & Hornell, 1905) n. comb. Neolebouria georgenascimentoi Bray, 2002, a species with an exceptionally long cirrus-sac, is transferred to Bentholebouria Andres, Pulis & Overstreet, 2004 as B. georgenascimentoi (Bray, 2002) n. comb., and N. maorum (Allison, 1966) Gibson 1976, an unusual species known from cephalopods, is designated a species incertae sedis. Eleven species are retained in a revised concept of Neolebouria.}, } @article {pmid28210871, year = {2017}, author = {Guo, Y and Wysoczynski, M and Nong, Y and Tomlin, A and Zhu, X and Gumpert, AM and Nasr, M and Muthusamy, S and Li, H and Book, M and Khan, A and Hong, KU and Li, Q and Bolli, R}, title = {Repeated doses of cardiac mesenchymal cells are therapeutically superior to a single dose in mice with old myocardial infarction.}, journal = {Basic research in cardiology}, volume = {112}, number = {2}, pages = {18}, pmid = {28210871}, issn = {1435-1803}, support = {P01 HL078825/HL/NHLBI NIH HHS/United States ; P20 GM103492/GM/NIGMS NIH HHS/United States ; P20 RR024489/RR/NCRR NIH HHS/United States ; UM1 HL113530/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Disease Models, Animal ; Echocardiography ; Female ; Immunohistochemistry ; Male ; Mesenchymal Stem Cell Transplantation/*methods ; Mesenchymal Stem Cells/cytology ; Mice ; Mice, Inbred C57BL ; *Myocardial Infarction ; Myocytes, Cardiac/cytology ; Random Allocation ; }, abstract = {We have recently demonstrated that repeated administrations of c-kit[POS] cardiac progenitor cells (CPCs) have cumulative beneficial effects in rats with old myocardial infarction (MI), resulting in markedly greater improvement in left ventricular (LV) function compared with a single administration. To determine whether this paradigm applies to other species and cell types, mice with a 3-week-old MI received one or three doses of cardiac mesenchymal cells (CMCs), a novel cell type that we have recently described. CMCs or vehicle were infused percutaneously into the LV cavity, 14 days apart. Compared with vehicle-treated mice, the single-dose group exhibited improved LV ejection fraction (EF) after the 1st infusion (consisting of CMCs) but not after the 2nd and 3rd (vehicle). In contrast, in the multiple-dose group, LV EF improved after each CMC infusion, so that at the end of the study, LV EF averaged 35.5 ± 0.7% vs. 32.7 ± 0.6% in the single-dose group (P < 0.05). The multiple-dose group also exhibited less collagen in the non-infarcted region vs. the single-dose group. Engraftment and differentiation of CMCs were negligible in both groups, indicating paracrine effects. These results demonstrate that, in mice with ischemic cardiomyopathy, the beneficial effects of three doses of CMCs are significantly greater than those of one dose, supporting the concept that multiple treatments are necessary to properly evaluate the full therapeutic potential of cell therapy. Thus, the repeated-treatment paradigm is not limited to c-kit [POS] CPCs or to rats, but applies to other cell types and species. The generalizability of this concept dramatically augments its significance.}, } @article {pmid28197165, year = {2017}, author = {Nonogaki, M and Nonogaki, H}, title = {Prevention of Preharvest Sprouting through Hormone Engineering and Germination Recovery by Chemical Biology.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {90}, pmid = {28197165}, issn = {1664-462X}, abstract = {Vivipary, germination of seeds on the maternal plant, is observed in nature and provides ecological advantages in certain wild species, such as mangroves. However, precocious seed germination in agricultural species, such as preharvest sprouting (PHS) in cereals, is a serious issue for food security. PHS reduces grain quality and causes economical losses to farmers. PHS can be prevented by translating the basic knowledge of hormone biology in seeds into technologies. Biosynthesis of abscisic acid (ABA), which is an essential hormone for seed dormancy, can be engineered to enhance dormancy and prevent PHS. Enhancing nine-cis-epoxycarotenoid dioxygenase (NCED), a rate-limiting enzyme of ABA biosynthesis, through a chemically induced gene expression system, has successfully been used to suppress germination of Arabidopsis seeds. The more advanced system NCED positive-feedback system, which amplifies ABA biosynthesis in a seed-specific manner without chemical induction, has also been developed. The proofs of concept established in the model species are now ready to be applied to crops. A potential problem is recovery of germination from hyperdormant crop grains. Hyperdormancy induced by the NCED systems can be reversed by inducing counteracting genes, such as NCED RNA interference or gibberellin (GA) biosynthesis genes. Alternatively, seed sensitivity to ABA can be modified to rescue germination using the knowledge of chemical biology. ABA antagonists, which were developed recently, have great potential to recover germination from the hyperdormant seeds. Combination of the dormancy-imposing and -releasing approaches will establish a comprehensive technology for PHS prevention and germination recovery.}, } @article {pmid28187649, year = {2017}, author = {Lopes, LE}, title = {Variation of plumage patterns, geographic distribution and taxonomy of the Unicolored Blackbird (Aves: Icteridae).}, journal = {Zootaxa}, volume = {4221}, number = {4}, pages = {zootaxa.4221.4.2}, doi = {10.11646/zootaxa.4221.4.2}, pmid = {28187649}, issn = {1175-5334}, mesh = {Animal Distribution ; Animals ; Brazil ; Feathers ; *Passeriformes ; Phylogeny ; }, abstract = {The Unicolored Blackbird Agelasticus cyanopus (Vieillot, 1819) is a marsh bird with four allopatric subspecies restricted to lowlands in South America east of the Andes. I conducted a taxonomic revision of the species based on analysis of external morphological characters of 288 study skins, including all types available. My revision shows that: 1) Leistes unicolor Swainson, 1838, is a senior synonym of A. c. xenicus (Parkes, 1966) and, therefore, the correct name of the taxon should be A. c. unicolor (Swainson, 1838); 2) the range of A. c. unicolor (Swainson, 1838) is much wider than previously thought, extending from the mouth of the Rio Amazonas to the state of São Paulo, in southeastern Brazil, where it intergrades with A. c. atroolivaceus (zu Wied-Neuwied, 1831); 3) A. c. atroolivaceus extends its range well beyond the coast of Rio de Janeiro, reaching the coast of São Paulo, the central part of Minas Gerais, Bahia and Espírito Santo; and 4) specimens attributed to A. c. beniensis are highly variable, so this name must be considered a subjective junior synonym of the nominotypical taxon. Under the Biological Species Concept, two broadly parapatric species should be recognized, A. cyanopus and A. atroolivaceus (including unicolor as a subspecies). Under the Phylogenetic Species Concept or the General Lineage Concept of Species, the best taxonomic treatment is to recognize three species: A. cyanopus, A. atroolivaceus, and A. unicolor.}, } @article {pmid28187619, year = {2017}, author = {Tantawi, TI and Whitworth, TL and Sinclair, BJ}, title = {Revision of the Nearctic Calliphora Robineau-Desvoidy (Diptera: Calliphoridae).}, journal = {Zootaxa}, volume = {4226}, number = {3}, pages = {zootaxa.4226.3.1}, doi = {10.11646/zootaxa.4226.3.1}, pmid = {28187619}, issn = {1175-5334}, mesh = {Animals ; *Diptera ; Female ; Male ; Montana ; North America ; Orthoptera ; }, abstract = {The Nearctic species of Calliphora Robineau-Desvoidy are revised and all species are redescribed and/or diagnosed. Diagnostic characters to permit reliable identification of both sexes of Calliphora aldrichia (Shannon) and C. montana (Shannon) and detailed distributional records for both species are provided for the first time. A lectotype is designated for Calliphora loewi Enderlein, 1903. A revised key to the 13 species of Nearctic Calliphora is also included. The key is based on examination of over 1,000 specimens from across North America and the structure of the terminalia of both sexes of each species. Complete illustrations of the terminalia of both sexes are provided for all species, including those of eight poorly known species: Calliphora alaskensis (Shannon), C. aldrichia (Shannon), C. coloradensis Hough, C. grahami Aldrich, C. latifrons Hough, C. livida Hall, C. montana (Shannon) and C. terraenovae Macquart. The female terminalia of C. alaskensis, C. aldrichia, C. coloradensis, C. livida and C. montana are illustrated for the first time. Barcode data for all 13 species of Nearctic Calliphora are provided, several for the first time. Results support current species concepts but barcodes failed to distinguish C. aldrichia and C. montana.}, } @article {pmid28187594, year = {2017}, author = {Mizsei, E and Jablonski, D and Roussos, SA and Dimaki, M and Ioannidis, Y and Nilson, G and Nagy, ZT}, title = {Nuclear markers support the mitochondrial phylogeny of Vipera ursinii-renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper.}, journal = {Zootaxa}, volume = {4227}, number = {1}, pages = {zootaxa.4227.1.4}, doi = {10.11646/zootaxa.4227.1.4}, pmid = {28187594}, issn = {1175-5334}, mesh = {Animals ; Bayes Theorem ; China ; DNA, Mitochondrial ; France ; Grassland ; Greece ; Phylogeny ; Sequence Analysis, DNA ; *Viperidae ; }, abstract = {Meadow vipers (Vipera ursinii-renardi complex) are small-bodied snakes that live in either lowland grasslands or montane subalpine-alpine meadows spanning a distribution from France to western China. This complex has previously been the focus of several taxonomic studies which were based mainly on morphological, allozyme or immunological characters and did not clearly resolve the relationships between the various taxa. Recent mitochondrial DNA analyses found unexpected relationships within the complex which had taxonomical consequences for the detected lineages. The most surprising was the basal phylogenetic position of Vipera ursinii graeca, a taxon described almost 30 years ago from the mountains of Greece. We present here new analyses of three nuclear markers (BDNF, NT3, PRLR; a first for studies of meadow and steppe vipers) as well as analyses of newly obtained mitochondrial DNA sequences (CYT B, ND4).Our Bayesian analyses of nuclear sequences are concordant with previous studies of mitochondrial DNA, in that the phylogenetic position of the graeca clade is a clearly distinguished and distinct lineage separated from all other taxa in the complex. These phylogenetic results are also supported by a distinct morphology, ecology and isolated distribution of this unique taxon. Based on several data sets and an integrative species concept we recommend to elevate this taxon to species level: Vipera graeca Nilson & Andrén, 1988 stat. nov.}, } @article {pmid28186559, year = {2017}, author = {Bobay, LM and Ochman, H}, title = {Biological species are universal across Life's domains.}, journal = {Genome biology and evolution}, volume = {9}, number = {3}, pages = {491-501}, pmid = {28186559}, issn = {1759-6653}, support = {R01 GM101209/GM/NIGMS NIH HHS/United States ; R01 GM108657/GM/NIGMS NIH HHS/United States ; R35 GM118038/GM/NIGMS NIH HHS/United States ; }, abstract = {Delineation of species is fundamental to organizing and understanding biological diversity. The most widely applied criterion for distinguishing species is the Biological Species Concept (BSC), which defines species as groups of interbreeding individuals that remain reproductively isolated from other such groups. The BSC has broad appeal; however, many organisms, most notably asexual lineages, cannot be classified according to the BSC. Despite their exclusively asexual mode of reproduction, Bacteria and Archaea can transfer and exchange genes though homologous recombination. Here we show that barriers to homologous gene exchange define biological species in prokaryotes with the same efficacy as in sexual eukaryotes. By analyzing the impact of recombination on the polymorphisms in thousands of genome sequences, we find that over half of named bacterial species undergo continuous recombination among sequenced constituents, indicative of true biological species. However, nearly a quarter of named bacterial species show sharp discontinuities and comprise multiple biological species. These interruptions of gene flow are not a simple function of genome identity, indicating that bacterial speciation does not uniformly proceed by the gradual divergence of genome sequences. The same genomic approach based on recombinant polymorphisms retrieves known species boundaries in sexually reproducing eukaryotes. Thus, a single biological species definition based on gene flow, once thought to be limited only to sexually reproducing organisms, is applicable to all cellular lifeforms.}, } @article {pmid28151701, year = {2017}, author = {Wright, AA and Magnotti, JF and Katz, JS and Leonard, K and Vernouillet, A and Kelly, DM}, title = {Corvids Outperform Pigeons and Primates in Learning a Basic Concept.}, journal = {Psychological science}, volume = {28}, number = {4}, pages = {437-444}, doi = {10.1177/0956797616685871}, pmid = {28151701}, issn = {1467-9280}, mesh = {Animals ; Behavior, Animal/*physiology ; Concept Formation/*physiology ; Female ; Male ; Passeriformes/*physiology ; Species Specificity ; }, abstract = {Corvids (birds of the family Corvidae) display intelligent behavior previously ascribed only to primates, but such feats are not directly comparable across species. To make direct species comparisons, we used a same/different task in the laboratory to assess abstract-concept learning in black-billed magpies (Pica hudsonia). Concept learning was tested with novel pictures after training. Concept learning improved with training-set size, and test accuracy eventually matched training accuracy-full concept learning-with a 128-picture set; this magpie performance was equivalent to that of Clark's nutcrackers (a species of corvid) and monkeys (rhesus, capuchin) and better than that of pigeons. Even with an initial 8-item picture set, both corvid species showed partial concept learning, outperforming both monkeys and pigeons. Similar corvid performance refutes the hypothesis that nutcrackers' prolific cache-location memory accounts for their superior concept learning, because magpies rely less on caching. That corvids with "primitive" neural architectures evolved to equal primates in full concept learning and even to outperform them on the initial 8-item picture test is a testament to the shared (convergent) survival importance of abstract-concept learning.}, } @article {pmid28134514, year = {2017}, author = {Stadie, NP and Wang, S and Kravchyk, KV and Kovalenko, MV}, title = {Zeolite-Templated Carbon as an Ordered Microporous Electrode for Aluminum Batteries.}, journal = {ACS nano}, volume = {11}, number = {2}, pages = {1911-1919}, doi = {10.1021/acsnano.6b07995}, pmid = {28134514}, issn = {1936-086X}, abstract = {High surface area porous carbon frameworks exhibit potential advantages over crystalline graphite as an electrochemical energy storage material owing to the possibility of faster ion transport and up to double the ion capacity, assuming a surface-based mechanism of storage. When detrimental surface-related effects such as irreversible capacity loss due to interphase formation (known as solid-electrolyte interphase, SEI) can be mitigated or altogether avoided, the greatest advantage can be achieved by maximizing the gravimetric and volumetric surface area and by tailoring the porosity to accommodate the relevant ion species. We investigate this concept by employing zeolite-templated carbon (ZTC) as the cathode in an aluminum battery based on a chloroaluminate ionic liquid electrolyte. Its ultrahigh surface area and dense, conductive network of homogeneous channels (12 Å in width) render ZTC suitable for the fast, dense storage of AlCl4[-] ions (6 Å in ionic diameter). With aluminum as the anode, full cells were prepared which simultaneously exhibited both high specific energy (up to 64 Wh kg[-1], 30 Wh L[-1]) and specific power (up to 290 W kg[-1], 93 W L[-1]), highly stable cycling performance, and complete reversibility within the potential range of 0.01-2.20 V.}, } @article {pmid28131362, year = {2017}, author = {Lymbery, AJ}, title = {Phylogenetic Pattern, Evolutionary Processes and Species Delimitation in the Genus Echinococcus.}, journal = {Advances in parasitology}, volume = {95}, number = {}, pages = {111-145}, doi = {10.1016/bs.apar.2016.07.002}, pmid = {28131362}, issn = {2163-6079}, mesh = {Animals ; *Biological Evolution ; Echinococcosis/*parasitology ; Echinococcus/classification/*genetics ; Genetic Speciation ; Genetics, Population ; Humans ; Phenotype ; *Phylogeny ; Phylogeography ; }, abstract = {An accurate and stable alpha taxonomy requires a clear conception of what constitutes a species and agreed criteria for delimiting different species. An evolutionary or general lineage concept defines a species as a single lineage of organisms with a common evolutionary trajectory, distinguishable from other such lineages. Delimiting evolutionary species is a two-step process. In the first step, phylogenetic reconstruction identifies putative species as groups of organisms that are monophyletic (share a common ancestor) and exclusive (more closely related to each other than to organisms outside the group). The second step is to assess whether members of the group possess genetic exchangeability (where cohesion is maintained by gene flow among populations) or ecological exchangeability (where cohesion is maintained because populations occupy the same ecological niche). Recent taxonomic reviews have recognized nine species within the genus Echinococcus. Phylogenetic reconstructions of the relationships between these putative species using mtDNA and nuclear gene sequences show that for the most part these nine species are monophyletic, although there are important incongruences that need to be resolved. Applying the criteria of genetic and ecological exchangeability suggests that seven of the currently recognized species represent evolutionarily distinct lineages. The species status of Echinococcus canadensis and Echinococcus ortleppi could not be confirmed. Coalescent-based analyses represent a promising approach to species delimitation in these closely related taxa. It seems likely, from a comparison of sister species groups, that speciation in the genus has been driven by geographic isolation, but biogeographic scenarios are largely speculative and require further testing.}, } @article {pmid28115687, year = {2017}, author = {Lafon-Placette, C and Johannessen, IM and Hornslien, KS and Ali, MF and Bjerkan, KN and Bramsiepe, J and Glöckle, BM and Rebernig, CA and Brysting, AK and Grini, PE and Köhler, C}, title = {Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {6}, pages = {E1027-E1035}, pmid = {28115687}, issn = {1091-6490}, mesh = {Arabidopsis/classification/*genetics ; Diploidy ; Endosperm/*genetics ; Europe ; *Gene Flow ; Geography ; Hybridization, Genetic/*genetics ; *Reproductive Isolation ; Seeds/genetics ; Species Specificity ; Tetraploidy ; }, abstract = {Based on the biological species concept, two species are considered distinct if reproductive barriers prevent gene flow between them. In Central Europe, the diploid species Arabidopsis lyrata and Arabidopsis arenosa are genetically isolated, thus fitting this concept as "good species." Nonetheless, interspecific gene flow involving their tetraploid forms has been described. The reasons for this ploidy-dependent reproductive isolation remain unknown. Here, we show that hybridization between diploid A. lyrata and A. arenosa causes mainly inviable seed formation, revealing a strong postzygotic reproductive barrier separating these two species. Although viability of hybrid seeds was impaired in both directions of hybridization, the cause for seed arrest differed. Hybridization of A. lyrata seed parents with A. arenosa pollen donors resulted in failure of endosperm cellularization, whereas the endosperm of reciprocal hybrids cellularized precociously. Endosperm cellularization failure in both hybridization directions is likely causal for the embryo arrest. Importantly, natural tetraploid A. lyrata was able to form viable hybrid seeds with diploid and tetraploid A. arenosa, associated with the reestablishment of normal endosperm cellularization. Conversely, the defects of hybrid seeds between tetraploid A. arenosa and diploid A. lyrata were aggravated. According to these results, we hypothesize that a tetraploidization event in A. lyrata allowed the production of viable hybrid seeds with A. arenosa, enabling gene flow between the two species.}, } @article {pmid28082757, year = {2016}, author = {Wang, XW and Houbraken, J and Groenewald, JZ and Meijer, M and Andersen, B and Nielsen, KF and Crous, PW and Samson, RA}, title = {Diversity and taxonomy of Chaetomium and chaetomium-like fungi from indoor environments.}, journal = {Studies in mycology}, volume = {84}, number = {}, pages = {145-224}, pmid = {28082757}, issn = {0166-0616}, abstract = {During a study of indoor fungi, 145 isolates belonging to Chaetomiaceae were cultured from air, swab and dust samples from 19 countries. Based on the phylogenetic analyses of DNA-directed RNA polymerase II second largest subunit (rpb2), β-tubulin (tub2), ITS and 28S large subunit (LSU) nrDNA sequences, together with morphological comparisons with related genera and species, 30 indoor taxa are recognised, of which 22 represent known species, seven are described as new, and one remains to be identified to species level. In our collection, 69 % of the indoor isolates with six species cluster with members of the Chaetomium globosum species complex, representing Chaetomium sensu stricto. The other indoor species fall into nine lineages that are separated from each other with several known chaetomiaceous genera occurring among them. No generic names are available for five of those lineages, and the following new genera are introduced here: Amesia with three indoor species, Arcopilus with one indoor species, Collariella with four indoor species, Dichotomopilus with seven indoor species and Ovatospora with two indoor species. The generic concept of Botryotrichum is expanded to include Emilmuelleria and the chaetomium-like species B. muromum (= Ch. murorum) in which two indoor species are included. The generic concept of Subramaniula is expanded to include several chaetomium-like taxa as well as one indoor species. Humicola is recognised as a distinct genus including two indoor taxa. According to this study, Ch. globosum is the most abundant Chaetomiaceae indoor species (74/145), followed by Ch. cochliodes (17/145), Ch. elatum (6/145) and B. piluliferum (5/145). The morphological diversity of indoor Chaetomiaceae as well as the morphological characteristics of the new genera are described and illustrated. This taxonomic study redefines the generic concept of Chaetomium and provides new insight into the phylogenetic relationships among different genera within Chaetomiaceae.}, } @article {pmid28073746, year = {2018}, author = {Zhang, H and Vieira Resende E Silva, B and Cui, J}, title = {miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis.}, journal = {Briefings in bioinformatics}, volume = {19}, number = {3}, pages = {415-424}, pmid = {28073746}, issn = {1477-4054}, support = {P20 GM104320/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Internet ; MicroRNAs/*analysis/*genetics ; Molecular Sequence Annotation ; Sequence Analysis, RNA/*methods ; *Software ; }, abstract = {Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes. In this article, we present microRNA Discovery (miRDis), a new small RNA sequencing data analysis pipeline for both endogenous and exogenous miRNA detection. Specifically, we developed and deployed a Web service that supports the annotation and expression profiling data of known host miRNAs and the detection of novel miRNAs, other noncoding RNAs, and the exogenous miRNAs from dietary species. As a proof-of-concept, we analyzed a set of human plasma sequencing data from a milk-feeding study where 225 human miRNAs were detected in the plasma samples and 44 show elevated expression after milk intake. By examining the bovine-specific sequences, data indicate that three bovine miRNAs (bta-miR-378, -181* and -150) are present in human plasma possibly because of the dietary uptake. Further evaluation based on different sets of public data demonstrates that miRDis outperforms other state-of-the-art tools in both detection and quantification of miRNA from either animal or plant sources. The miRDis Web server is available at: http://sbbi.unl.edu/miRDis/index.php.}, } @article {pmid28073501, year = {2016}, author = {Telesh, IV and Schubert, H and Skarlato, SO}, title = {Ecological niche partitioning of the invasive dinoflagellate Prorocentrum minimum and its native congeners in the Baltic Sea.}, journal = {Harmful algae}, volume = {59}, number = {}, pages = {100-111}, doi = {10.1016/j.hal.2016.09.006}, pmid = {28073501}, issn = {1878-1470}, mesh = {Baltic States ; Biodiversity ; Dinoflagellida/*physiology ; *Ecosystem ; Environmental Monitoring ; Hydrogen-Ion Concentration ; *Introduced Species ; Oceans and Seas ; Salinity ; Seawater/chemistry ; Temperature ; }, abstract = {This study analyses three decades of the peculiar bloom-formation history of the potentially toxic invasive planktonic dinoflagellates Prorocentrum minimum (Pavillard) Schiller in the SW Baltic Sea. We tested a research hypothesis that the unexpectedly long delay (nearly two decades) in population development of P. minimum prior to its first bloom was caused by competition with one or several closely related native dinoflagellate species due to ecological niche partitioning which hampered the spread and bloom-forming potential of the invader. We applied the ecological niche concept to a large, long-term phytoplankton database and analysed the invasion history and population dynamics of P. minimum in the SW Baltic Sea coastal waters using the data on phytoplankton composition, abundance and biomass. The ecological niche dimensions of P. minimum and its congener P. balticum were identified as the optimum environmental conditions for the species during the bloom events based on water temperature, salinity, pH, concentration of nutrients (PO4[3-]; total phosphorus, TP; total nitrogen, TN; SiO4[4-]), TN/TP-ratio and habitat type. The data on spatial distribution and ecological niche dimensions of P. minimum have contributed to the development of the "protistan species maximum concept". High microplankton diversity at critical salinities in the Baltic Sea may be considered as a possible reason for the significant niche overlap and strong competitive interactions among congeners leading to prolonged delay in population growth of P. minimum preceding its first bloom in the highly variable brackishwater environment.}, } @article {pmid28072485, year = {2017}, author = {Yang, Q and Shi, M and Zhao, H and Lin, J and An, L and Cui, L and Yang, H and Zhou, Z and Tian, Q and Yang, S}, title = {Water-Soluble Polymer Nanoparticles Constructed by Three-Component Self-Assembly: An Efficient Theranostic Agent for Phosphorescent Imaging and Photodynamic Therapy.}, journal = {Chemistry (Weinheim an der Bergstrasse, Germany)}, volume = {23}, number = {15}, pages = {3728-3734}, doi = {10.1002/chem.201605150}, pmid = {28072485}, issn = {1521-3765}, abstract = {Water-soluble polymer nanoparticles NP-1 and NP-2 were prepared by using a three-component self-assembly of an iridium complex, poly(4-vinyl pyridine-b-ethylene oxide) (P4VP-b-PEO), and methane sulfonic acid (MSA). Due to the unique metal-ligand charge-transfer transition property and the heavy-atom effect of the iridium atom, NP-1 and NP-2 showed bright phosphorescence and generated the singlet oxygen ([1] O2) species effectively under visible-light irradiation (λ>400 nm) with a power density of 300 mW cm[-2] . NP-2, an example of the polymer nanoparticles, showed minimal cytotoxic activity in the dark. Laser confocal fluorescence and flow-cytometry microscopy experiments demonstrated that NP-2 could be taken up by a model cancer-cell line of 4T1 cells, which could be used as a phosphorescent probe for cell imaging by preferentially staining the cytoplasm. After 6 hours of incubation with NP-2 (100 μg mL[-1]), the cell viability of 4T1 cells decreased to approximately 10 % upon visible-light irradiation (λ>400 nm, 300 mW cm[-2]) only for 10 minutes as a result of the generation of the [1] O2 species, thus indicating a proof of concept for effective photodynamic therapy for cancer cells.}, } @article {pmid28041840, year = {2017}, author = {Patil, VU and Girimalla, V and Sagar, V and Chauhan, RS and Chakrabarti, SK}, title = {Genome sequencing of four strains of Phylotype I, II and IV of Ralstonia solanacearum that cause potato bacterial wilt in India.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {48}, number = {2}, pages = {193-195}, pmid = {28041840}, issn = {1678-4405}, mesh = {DNA, Bacterial/*chemistry/genetics ; *Genome, Bacterial ; *Genotype ; India ; Plant Diseases/*microbiology ; Ralstonia solanacearum/classification/*genetics/isolation & purification ; *Sequence Analysis, DNA ; Solanum tuberosum/*microbiology ; }, abstract = {Ralstonia solanacearum is a heterogeneous species complex causing bacterial wilts in more than 450 plant species distributed in 54 families. The complexity of the genome and the wide diversity existing within the species has led to the concept of R. solanacearum species complex (RsSC). Here we report the genome sequence of the four strains (RS2, RS25, RS48 and RS75) belonging to three of the four phylotypes of R. solanacearum that cause potato bacterial wilt in India. The genome sequence data would be a valuable resource for the evolutionary, epidemiological studies and quarantine of this phytopathogen.}, } @article {pmid28027292, year = {2016}, author = {Roux, C and Fraïsse, C and Romiguier, J and Anciaux, Y and Galtier, N and Bierne, N}, title = {Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence.}, journal = {PLoS biology}, volume = {14}, number = {12}, pages = {e2000234}, pmid = {28027292}, issn = {1545-7885}, mesh = {Animals ; *Genetic Variation ; Genetics, Population ; Hybridization, Genetic ; Models, Biological ; }, abstract = {Speciation results from the progressive accumulation of mutations that decrease the probability of mating between parental populations or reduce the fitness of hybrids-the so-called species barriers. The speciation genomic literature, however, is mainly a collection of case studies, each with its own approach and specificities, such that a global view of the gradual process of evolution from one to two species is currently lacking. Of primary importance is the prevalence of gene flow between diverging entities, which is central in most species concepts and has been widely discussed in recent years. Here, we explore the continuum of speciation thanks to a comparative analysis of genomic data from 61 pairs of populations/species of animals with variable levels of divergence. Gene flow between diverging gene pools is assessed under an approximate Bayesian computation (ABC) framework. We show that the intermediate "grey zone" of speciation, in which taxonomy is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective of species life history traits or ecology. Thanks to appropriate modeling of among-locus variation in genetic drift and introgression rate, we clarify the status of the majority of ambiguous cases and uncover a number of cryptic species. Our analysis also reveals the high incidence in animals of semi-isolated species (when some but not all loci are affected by barriers to gene flow) and highlights the intrinsic difficulty, both statistical and conceptual, of delineating species in the grey zone of speciation.}, } @article {pmid28004868, year = {2017}, author = {Ward, JPT}, title = {Physiological redox signalling and regulation of ion channels: implications for pulmonary hypertension.}, journal = {Experimental physiology}, volume = {102}, number = {9}, pages = {1078-1082}, doi = {10.1113/EP086040}, pmid = {28004868}, issn = {1469-445X}, support = {087776/WT_/Wellcome Trust/United Kingdom ; 087776/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Hypertension, Pulmonary/*metabolism/*physiopathology ; Ion Channels/*metabolism ; Oxidation-Reduction ; Reactive Oxygen Species/metabolism ; Signal Transduction/*physiology ; }, abstract = {What is the topic of this review? The review concerns the role of reactive oxygen species as physiological second messengers in potentiating G-protein-coupled receptor-mediated vasoconstriction and its potential dysregulation by oxidant stress in pulmonary hypertension. What advances does it highlight? The review highlights the concept that physiological signalling by reactive oxygen species must normally be highly compartmentalized to prevent self-regenerating oxidant stress and promiscuous and uncontrolled signalling, which contribute to the aetiology. Pulmonary hypertension is associated with oxidant stress and increased generation of reactive oxygen species (ROS) by NADPH oxidases (NOX), mitochondria and other sources. There is considerable evidence that these contribute to the aetiology via promotion of pulmonary vascular remodelling, endothelial dysfunction and enhanced vasoreactivity. However, it is now recognized that ROS act as important signalling mediators and second messengers in normal physiological conditions. Many ion channels and protein kinases crucial to pulmonary vascular function are directly or indirectly affected by redox/ROS, including K[+] , Ca[2+] and non-selective cation channels and Rho kinase. However, the inherent difficulties in quantifying ROS, particularly in subcellular compartments, make it uncertain whether these reported effects are of relevance in physiological rather than pathological conditions. In an attempt to address such issues, we have focused on the role of physiologically generated ROS in the regulation of G-protein-coupled receptor (GPCR)-activated vasoconstrictor pathways. We have recently reported a novel mechanism whereby low concentrations of GPCR-linked vasoconstrictors greatly potentiate Ca[2+] entry via a NOX1- and ROS-mediated pathway parallel to the classical vasoconstrictor pathways of Ca[2+] mobilization and activation of Rho kinase. Our findings imply that ROS signalling is highly compartmentalized in physiological conditions, but that this may be compromised by pathological increases in oxidant production, for example in pulmonary hypertension, leading to promiscuous actions that contribute to the aetiology. This model is consistent with the proposal that targeted antioxidants could prove to be an effective therapy for pulmonary hypertension.}, } @article {pmid27994208, year = {2016}, author = {Singh, BN}, title = {The genus Drosophila is characterized by a large number of sibling species showing evolutionary significance.}, journal = {Journal of genetics}, volume = {95}, number = {4}, pages = {1053-1064}, pmid = {27994208}, issn = {0973-7731}, mesh = {Animals ; *Biological Evolution ; Drosophila/*classification/*genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; *Siblings ; Species Specificity ; }, abstract = {Mayr (1942) defined sibling species as sympatric forms which are morphologically very similar or indistinguishable, but which possess specific biological characteristics and are reproductively isolated. Another term, cryptic species has also been used for such species. However, this concept changed later. Sibling species are as similar as twins. This category does not necessarily include phylogenetic siblings as members of a superspecies. Since the term sibling species was defined by Mayr, a large number of cases of sibling species pairs/groups have been reported and thus they are widespread in the animal kingdom. However, they seem to be more common in some groups such as insects. In insects, they have been reported in diptera, lepidoptera, coleoptera, orthoptera, hymenoptera and others. Sibling species are widespread among the dipteran insects and as such are well studied because some species are important medically (mosquitoes), genetically (Drosophila) and cytologically (Sciara and Chironomus). The well-studied classical pairs of sibling species in Drosophila are: D. pseudoobscura and D. persimilis, and D. melanogaster and D. simulans. Subsequently, a number of sibling species have been added to these pairs and a large number of other sibling species pairs/groups in different species groups of the genus Drosophila have been reported in literature. The present review briefly summarizes the cases of sibling species pairs/groups in the genus Drosophila with their evolutionary significance.}, } @article {pmid27988692, year = {2016}, author = {Bocalini, F and Silveira, LF}, title = {A taxonomic revision of the Musician Wren, Cyphorhinus arada (Aves, Troglodytidae), reveals the existence of six valid species endemic to the Amazon basin.}, journal = {Zootaxa}, volume = {4193}, number = {3}, pages = {zootaxa.4193.3.5}, doi = {10.11646/zootaxa.4193.3.5}, pmid = {27988692}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Body Size ; Ecosystem ; Female ; Male ; Organ Size ; Phylogeny ; Songbirds/anatomy & histology/*classification/genetics/growth & development ; }, abstract = {Cyphorhinus arada, an Amazonian endemic, shows considerable geographic variation in plumage that has led to the recognition of eight subspecies. These include C. a. arada, C. a. salvini, C. a. modulator, C. a. transfluvialis, C. a. interpositus, C. a. griseolateralis, C. a. urbanoi and C. a. faroensis. However, a thorough taxonomic revision of the Cyphorhinus arada complex has never been undertaken, so we revise the taxonomy based on morphological and vocal characters. We analyzed a total of 515 museum specimens and 146 voice recordings representing and encompassing the distributions of all named taxa, including those currently considered not valid. Vocal analyses showed major variation within the complex, from which several trends could be identified between populations. We concluded that six species (C. arada, C. transfluvialis, C. modulator, C. salvini, C. interpositus and C. griseolateralis) should be recognized under the Phylogenetic Species Concept based on the diagnosis of stable plumage and vocal patterns of each.}, } @article {pmid27988640, year = {2016}, author = {Schuchmann, KL and Weller, AA and Jürgens, D}, title = {Biogeography and taxonomy of racket-tail hummingbirds (Aves: Trochilidae: Ocreatus): evidence for species delimitation from morphology and display behavior.}, journal = {Zootaxa}, volume = {4200}, number = {1}, pages = {zootaxa.4200.1.3}, doi = {10.11646/zootaxa.4200.1.3}, pmid = {27988640}, issn = {1175-5334}, mesh = {Animals ; Birds/anatomy & histology/*classification ; Bolivia ; Colombia ; Ecuador ; Peru ; Phylogeography ; Sexual Behavior, Animal ; Venezuela ; }, abstract = {We analyzed geographic variation, biogeography, and intrageneric relationships of racket-tail hummingbirds Ocreatus (Aves, Trochilidae). Presently, the genus is usually considered monospecific, with O. underwoodii including eight subspecies (polystictus, discifer, underwoodii, incommodus, melanantherus, peruanus, annae, addae), although up to three species have been recognized by some authors. In order to evaluate the current taxonomy we studied geographic variation in coloration, mensural characters, and behavioral data of all Ocreatus taxa. We briefly review the taxonomic history of the genus. Applying the Biological Species Concept, species delimitation was based on a qualitative-quantitative criteria analysis including an evaluation of character states. Our results indicate that the genus should be considered a superspecies with four species, the monotypic Ocreatus addae, O. annae, and O. peruanus, and the polytypic O. underwoodii (including the subspecies underwoodii, discifer, incommodus, melanantherus, polystictus). In this taxonomic treatment, O. annae becomes an endemic species to Peru and O. addae is endemic to Bolivia. We recommend additional sampling of distributional, ethological, and molecular data for an improved resolution of the evolutionary history of Ocreatus.}, } @article {pmid27924531, year = {2017}, author = {Munkvold, GP}, title = {Fusarium Species and Their Associated Mycotoxins.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1542}, number = {}, pages = {51-106}, doi = {10.1007/978-1-4939-6707-0_4}, pmid = {27924531}, issn = {1940-6029}, mesh = {Animals ; Biodiversity ; Crops, Agricultural/microbiology ; Food Contamination ; Food Safety ; Fusarium/*classification/genetics/*metabolism ; Host-Pathogen Interactions ; Humans ; Mycotoxins/chemistry/classification/*metabolism ; }, abstract = {The genus Fusarium includes numerous toxigenic species that are pathogenic to plants or humans, and are able to colonize a wide range of environments on earth. The genus comprises around 70 well-known species, identified by using a polyphasic approach, and as many as 300 putative species, according to phylogenetic species concepts; many putative species do not yet have formal names. Fusarium is one of the most economically important fungal genera because of yield loss due to plant pathogenic activity; mycotoxin contamination of food and feed products which often render them unaccep for marketing; and health impacts to humans and livestock, due to consumption of mycotoxins. Among the most important mycotoxins produced by species of Fusarium are the trichothecenes and the fumonisins. Fumonisins cause fatal livestock diseases and are considered potentially carcinogenic mycotoxins for humans, while trichothecenes are potent inhibitors of protein synthesis. This chapter summarizes the main aspects of morphology, pathology, and toxigenicity of the main Fusarium species that colonize different agricultural crops and environments worldwide, and cause mycotoxin contamination of food and feed.}, } @article {pmid27907259, year = {2016}, author = {Dahlin, KM}, title = {Spectral diversity area relationships for assessing biodiversity in a wildland-agriculture matrix.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {26}, number = {8}, pages = {2756-2766}, doi = {10.1002/eap.1390}, pmid = {27907259}, issn = {1051-0761}, mesh = {*Agriculture ; *Biodiversity ; Forests ; Michigan ; Plants ; }, abstract = {Species-area relationships have long been used to assess patterns of species diversity across scales. Here, this concept is extended to spectral diversity using hyperspectral data collected by NASA's Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) over western Michigan. This mixture of mesic forest and agricultural lands offers two end-points on the local-scale diversity continuum; one set of well-mixed forest patches and one set of highly homogeneous agricultural patches. Using the sum of the first three principal component values and the principal components' convex hull volume, spectral diversity was compared within and among these plots and to null expectations for perfectly random and perfectly patchy landscapes. Overall, the spectral diversity-area relationship confirms the patterns that would be expected for this landscape, but this application suggests that this approach could be extended to less well-understood landscapes and could reveal key insights about the relative importance of different drivers of community assembly, even in the absence of additional data about plant functional traits or species' identities.}, } @article {pmid32480530, year = {2016}, author = {Munns, R and James, RA and Gilliham, M and Flowers, TJ and Colmer, TD}, title = {Tissue tolerance: an essential but elusive trait for salt-tolerant crops.}, journal = {Functional plant biology : FPB}, volume = {43}, number = {12}, pages = {1103-1113}, doi = {10.1071/FP16187}, pmid = {32480530}, issn = {1445-4416}, abstract = {For a plant to persist in saline soil, osmotic adjustment of all plant cells is essential. The more salt-tolerant species accumulate Na+ and Cl- to concentrations in leaves and roots that are similar to the external solution, thus allowing energy-efficient osmotic adjustment. Adverse effects of Na+ and Cl- on metabolism must be avoided, resulting in a situation known as 'tissue tolerance'. The strategy of sequestering Na+ and Cl- in vacuoles and keeping concentrations low in the cytoplasm is an important contributor to tissue tolerance. Although there are clear differences between species in the ability to accommodate these ions in their leaves, it remains unknown whether there is genetic variation in this ability within a species. This viewpoint considers the concept of tissue tolerance, and how to measure it. Four conclusions are drawn: (1) osmotic adjustment is inseparable from the trait of tissue tolerance; (2) energy-efficient osmotic adjustment should involve ions and only minimal organic solutes; (3) screening methods should focus on measuring tolerance, not injury; and (4) high-throughput protocols that avoid the need for control plants and multiple Na+ or Cl- measurements should be developed. We present guidelines to identify useful genetic variation in tissue tolerance that can be harnessed for plant breeding of salt tolerance.}, } @article {pmid27880775, year = {2016}, author = {Barrowclough, GF and Cracraft, J and Klicka, J and Zink, RM}, title = {How Many Kinds of Birds Are There and Why Does It Matter?.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0166307}, pmid = {27880775}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Birds/anatomy & histology/classification/*genetics ; Genetic Variation ; Phylogeny ; }, abstract = {Estimates of global species diversity have varied widely, primarily based on variation in the numbers derived from different inventory methods of arthropods and other small invertebrates. Within vertebrates, current diversity metrics for fishes, amphibians, and reptiles are known to be poor estimators, whereas those for birds and mammals are often assumed to be relatively well established. We show that avian evolutionary diversity is significantly underestimated due to a taxonomic tradition not found in most other taxonomic groups. Using a sample of 200 species taken from a list of 9159 biological species determined primarily by morphological criteria, we applied a diagnostic, evolutionary species concept to a morphological and distributional data set that resulted in an estimate of 18,043 species of birds worldwide, with a 95% confidence interval of 15,845 to 20,470. In a second, independent analysis, we examined intraspecific genetic data from 437 traditional avian species, finding an average of 2.4 evolutionary units per species, which can be considered proxies for phylogenetic species. Comparing recent lists of species to that used in this study (based primarily on morphology) revealed that taxonomic changes in the past 25 years have led to an increase of only 9%, well below what our results predict. Therefore, our molecular and morphological results suggest that the current taxonomy of birds understimates avian species diversity by at least a factor of two. We suggest that a revised taxonomy that better captures avian species diversity will enhance the quantification and analysis of global patterns of diversity and distribution, as well as provide a more appropriate framework for understanding the evolutionary history of birds.}, } @article {pmid27871817, year = {2017}, author = {Wee, NQ and Cribb, TH and Bray, RA and Cutmore, SC}, title = {Two known and one new species of Proctoeces from Australian teleosts: Variable host-specificity for closely related species identified through multi-locus molecular data.}, journal = {Parasitology international}, volume = {66}, number = {2}, pages = {16-26}, doi = {10.1016/j.parint.2016.11.008}, pmid = {27871817}, issn = {1873-0329}, mesh = {Animals ; Australia ; Cyclooxygenase 1/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Fish Diseases/*parasitology ; Genotype ; *Host Specificity/genetics ; Perciformes/*parasitology ; Phylogeny ; Sequence Analysis, DNA ; Trematoda/anatomy & histology/*classification/*genetics/isolation & purification ; Trematode Infections/parasitology/*veterinary ; }, abstract = {Species of Proctoeces Odhner, 1911 (Trematoda: Fellodistomidae) have been reported from a wide range of marine animals globally. Members of the genus tend to lack strongly distinguishing morphological features for diagnosis, making identification difficult and the true number of species in the genus contentious. Combined morphological and molecular analyses were used to characterise three species of Proctoeces from Moreton Bay and the southern Great Barrier Reef. Data for two ribosomal regions and one mitochondrial region were generated for specimens collected from Australia. Three unique 18S-genotypes were identified which corresponded to subtle, but reliable, morphological differences. Two species of Proctoeces were identified from fishes of Moreton Bay, Proctoeces insolitus (Nicoll, 1915) Yamaguti, 1953 and P. major Yamaguti, 1934, and a third, P. choerodoni n. sp. from off Heron Island on the southern Great Barrier Reef. Phylogenetic analyses of partial 18S and partial 28S rDNA indicated that these three species differ from the four species reported outside of Australia for which sequence data are available. Phylogenetically, Proctoeces proved to be a reliable concept, with all species of Proctoeces that have been characterised genetically forming a well-supported clade in all analyses. Dramatically different patterns of host-specificity were identified for each of the three Australian species; P. insolitus apparently infects a single species of fish, P. choerodoni n. sp. infects multiple species of a single genus of fish, and P. major infects multiple species of two teleost orders.}, } @article {pmid27834208, year = {2016}, author = {von Schaewen, M and Dorner, M and Hueging, K and Foquet, L and Gerges, S and Hrebikova, G and Heller, B and Bitzegeio, J and Doerrbecker, J and Horwitz, JA and Gerold, G and Suerbaum, S and Rice, CM and Meuleman, P and Pietschmann, T and Ploss, A}, title = {Expanding the Host Range of Hepatitis C Virus through Viral Adaptation.}, journal = {mBio}, volume = {7}, number = {6}, pages = {}, pmid = {27834208}, issn = {2150-7511}, support = {281473/ERC_/European Research Council/International ; R01 AI079031/AI/NIAID NIH HHS/United States ; R01 AI107301/AI/NIAID NIH HHS/United States ; R21 AI117213/AI/NIAID NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Adaptive Immunity ; Animals ; Antibodies, Viral/immunology ; Cell Line ; Disease Models, Animal ; Hepacivirus/genetics/immunology/*physiology ; Hepatitis C/immunology/*virology ; Hepatocytes/immunology/virology ; Host Specificity ; Humans ; Mice ; Occludin/genetics ; Scavenger Receptors, Class B/genetics ; Tetraspanin 28/genetics ; Viral Tropism ; *Virus Internalization ; }, abstract = {UNLABELLED: Hepatitis C virus (HCV) species tropism is incompletely understood. We have previously shown that at the level of entry, human CD81 and occludin (OCLN) comprise the minimal set of human factors needed for viral uptake into murine cells. As an alternative approach to genetic humanization, species barriers can be overcome by adapting HCV to use the murine orthologues of these entry factors. We previously generated a murine tropic HCV (mtHCV or Jc1/mCD81) strain harboring three mutations within the viral envelope proteins that allowed productive entry into mouse cell lines. In this study, we aimed to characterize the ability of mtHCV to enter and infect mouse hepatocytes in vivo and in vitro Using a highly sensitive, Cre-activatable reporter, we demonstrate that mtHCV can enter mouse hepatocytes in vivo in the absence of any human cofactors. Viral entry still relied on expression of mouse CD81 and SCARB1 and was more efficient when mouse CD81 and OCLN were overexpressed. HCV entry could be significantly reduced in the presence of anti-HCV E2 specific antibodies, suggesting that uptake of mtHCV is dependent on viral glycoproteins. Despite mtHCV's ability to enter murine hepatocytes in vivo, we did not observe persistent infection, even in animals with severely blunted type I and III interferon signaling and impaired adaptive immune responses. Altogether, these results establish proof of concept that the barriers limiting HCV species tropism can be overcome by viral adaptation. However, additional viral adaptations will likely be needed to increase the robustness of a murine model system for hepatitis C.

IMPORTANCE: At least 150 million individuals are chronically infected with HCV and are at risk of developing serious liver disease. Despite the advent of effective antiviral therapy, the frequency of chronic carriers has only marginally decreased. A major roadblock in developing a vaccine that would prevent transmission is the scarcity of animal models that are susceptible to HCV infection. It is poorly understood why HCV infects only humans and chimpanzees. To develop an animal model for hepatitis C, previous efforts focused on modifying the host environment of mice, for example, to render them more susceptible to HCV infection. Here, we attempted a complementary approach in which a laboratory-derived HCV variant was tested for its ability to infect mice. We demonstrate that this engineered HCV strain can enter mouse liver cells but does not replicate efficiently. Thus, additional adaptations are likely needed to construct a robust animal model for HCV.}, } @article {pmid27829374, year = {2016}, author = {Henrich, T and Kalbe, M}, title = {The role of prezygotic isolation mechanisms in the divergence of two parasite species.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {245}, pmid = {27829374}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Charadriiformes/genetics ; Gene Flow ; Genetic Speciation ; Hybridization, Genetic ; Mating Preference, Animal ; Parasites/*embryology ; *Reproductive Isolation ; Sympatry/genetics ; Time Factors ; Zygote/*metabolism ; }, abstract = {BACKGROUND: The formation of reproductive barriers in diverging lineages is a prerequisite to complete speciation according to the biological species concept. In parasites with complex life cycles, speciation may be driven by adaptation to different intermediate hosts, yet diverging lineages can still share the same definitive host where reproduction takes place. In these cases, prezygotic isolation mechanisms should evolve very early and be particularly strong, preventing costly unfavourable matings. In this study, we investigated the importance of prezygotic barriers to reproduction in two cestode species that diverged 20-25mya and show an extraordinary degree of specificity to different intermediate hosts. Both species share the same definitive hosts and hybridize in the laboratory. Yet, natural hybrids have so far not been detected.

METHODS: We used a combination of different experiments to investigate the role of prezygotic barriers to reproduction in the speciation of these parasites. First, we investigated whether hybridization is possible under natural conditions by exposing lab-reared herring gulls (Larus argentatus, the definitive hosts) to both parasites of either sympatric or allopatric combinations. In a second experiment, we tested whether the parasites prefer conspecifics over parasites from a different species in dichotomous mate choice trials.

RESULTS: Our results show that the two species hybridize under natural conditions with parasites originating either from sympatric or allopatric populations producing hybrid offspring. Surprisingly, the mate choice experiment indicated that both parasite species prefer mates of the different species to conspecifics.

CONCLUSIONS: Neither fundamental constraints against hybridization in a natural host nor assortative mate choice sufficiently explain the persistent segregation of the two tapeworm species in nature. Hence, postzygotic ecological selection against hybrids is presumably the more important driving force limiting gene flow between the two parasite sister species.}, } @article {pmid27813666, year = {2017}, author = {Schutze, MK and Virgilio, M and Norrbom, A and Clarke, AR}, title = {Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes.}, journal = {Annual review of entomology}, volume = {62}, number = {}, pages = {147-164}, doi = {10.1146/annurev-ento-031616-035518}, pmid = {27813666}, issn = {1545-4487}, mesh = {Animals ; Tephritidae/*classification ; }, abstract = {Accurate species delimitation underpins good taxonomy. Formalization of integrative taxonomy in the past decade has provided a framework for using multidisciplinary data to make species delimitation hypotheses more rigorous. We address the current state of integrative taxonomy by using as a case study an international project targeted at resolving three important tephritid species complexes: Bactrocera dorsalis complex, Anastrepha fraterculus complex, and Ceratitis FAR (C. fasciventris, C. anonae, C. rosa) complex. The integrative taxonomic approach has helped deliver significant advances in resolving these complexes: It has been used to identify some taxa as belonging to the same biological species as well as to confirm hidden cryptic diversity under a single taxonomic name. Nevertheless, the general application of integrative taxonomy has not been without issue, revealing challenges that must be considered when undertaking an integrative taxonomy project. Scrutiny of this international case study provides a unique opportunity to document lessons learned for the benefit of not only tephritid taxonomists, but also the wider taxonomic community.}, } @article {pmid27811770, year = {2016}, author = {Bowie, RC and Fjeldså, J and Kiure, J and Kristensen, JB}, title = {A new member of the greater double-collared sunbird complex (Passeriformes: Nectariniidae) from the Eastern Arc Mountains of Africa.}, journal = {Zootaxa}, volume = {4175}, number = {1}, pages = {23-42}, doi = {10.11646/zootaxa.4175.1.3}, pmid = {27811770}, issn = {1175-5334}, mesh = {Animals ; DNA, Mitochondrial/analysis ; Microsatellite Repeats ; Passeriformes/*anatomy & histology/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Tanzania ; }, abstract = {We document the discovery of the first population of greater double-collared sunbird (Cinnyris afer complex) from the Eastern Arc Mountains of Tanzania. We assessed phylogenetic relationships and taxonomic rank based on mtDNA sequence data, nine microsatellite loci and morphology. This new taxon, locally distributed in the Rubeho and Udzungwa Highlands, has close affinities (< 1% uncorrected sequence divergence) with C. whytei (split here from C. ludovicensis) of the Nyika Plateau in Malawi, but differs in having longer tarsi and in subtle plumage details. Although the birds from Nyika and Udzungwa-Rubeho are reciprocally monophyletic for mitochondrial DNA, coalescent analyses of the microsatellite data and the total molecular dataset could not reject the possibility of continued gene flow between the two populations. Thus, although we favour the phylogenetic species concept, we adopt a cautious approach and formally describe the Rubeho and Udzungwa greater double-collared sunbird population as a subspecies of Cinnyris whytei. This new sunbird taxon has been recorded only above 1700 m in scrub on the forest/grassland ecotone in a very restricted area in the Rubeho and Udzungwa Highlands of Tanzania. The effects of human settlement and agriculture threaten this taxon.}, } @article {pmid27811707, year = {2016}, author = {Buainain, N and Brito, GR and Firme, DH and Figueira, DM and Raposo, MA and De Assis, CP}, title = {Taxonomic revision of Saffron-billed Sparrow Arremon flavirostris Swainson, 1838 (Aves: Passerellidae) with comments on its holotype and type locality.}, journal = {Zootaxa}, volume = {4178}, number = {4}, pages = {547-567}, doi = {10.11646/zootaxa.4178.4.6}, pmid = {27811707}, issn = {1175-5334}, mesh = {Animals ; Female ; Male ; Phylogeny ; South America ; Sparrows/*anatomy & histology/*classification/physiology ; Species Specificity ; Vocalization, Animal ; }, abstract = {The Saffron-billed Sparrow (Arremon flavirostris) complex occurs in the undergrowth of deciduous woodlands and forests from the Andes of Bolivia and northern Argentina to Paraguay and southern, mid-western and interior eastern Brazil. Currently four subspecies are recognized: A. f. flavirostris, A. f. polionotus, A. f. devillii and A. f. dorbignii. We review the taxonomy of this complex by analyzing coloration and morphometrics of a series of 234 skins, and by comparing 101 sound recordings. Our results suggest that under both the Phylogenetic and Biological Species Concept, three species should be recognized in this complex: A. flavirostris, A. polionotus and A. dorbignii. On the other hand, A. devillii should be considered a junior synonym of A. polionotus since these two have no constant differences in morphology and vocalization. These species are diagnosable by their coloration characters, but not by morphometrics. Vocalizations are useful in diagnosing A. flavirostris from A. dorbignii, but do not diagnose A. polionotus from the others. We show that part of the previous taxonomic confusion can be attributed to variation in back color of adult and immature A. polionotus. Finally, we comment on the recently located holotype of A. flavirostris, which was believed to be lost, and its type locality.}, } @article {pmid27809775, year = {2016}, author = {Stanton, A and Harris, LM and Graham, G and Merrick, CJ}, title = {Recombination events among virulence genes in malaria parasites are associated with G-quadruplex-forming DNA motifs.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {859}, pmid = {27809775}, issn = {1471-2164}, support = {MR/K000535/1/MRC_/Medical Research Council/United Kingdom ; MR/L008823/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Conserved Sequence ; DNA, Protozoan/*chemistry/*genetics ; *G-Quadruplexes ; Genome, Protozoan ; Mitosis/genetics ; *Nucleotide Motifs ; Plasmodium/*genetics/pathogenicity ; Plasmodium falciparum/genetics ; Protozoan Proteins/chemistry/genetics ; *Recombination, Genetic ; Virulence/*genetics ; }, abstract = {BACKGROUND: Malaria parasites of the genus Plasmodium possess large hyper-variable families of antigen-encoding genes. These are often variantly-expressed and are major virulence factors for immune evasion and the maintenance of chronic infections. Recombination and diversification of these gene families occurs readily, and may be promoted by G-quadruplex (G4) DNA motifs within and close to the variant genes. G4s have been shown to cause replication fork stalling, DNA breakage and recombination in model systems, but these motifs remain largely unstudied in Plasmodium.

RESULTS: We examined the nature and distribution of putative G4-forming sequences in multiple Plasmodium genomes, finding that their co-distribution with variant gene families is conserved across different Plasmodium species that have different types of variant gene families. In P. falciparum, where a large set of recombination events that occurred over time in cultured parasites has been mapped, we found a strong spatial association between these recombination events and putative G4-forming sequences. Finally, we searched Plasmodium genomes for the three classes of helicase that can unwind G4s: Plasmodium spp. have no identifiable homologue of the highly efficient G4 helicase PIF1, but they do encode two putative RecQ helicases and one homologue of the RAD3-family helicase FANCJ.

CONCLUSIONS: Our analyses, conducted at the whole-genome level in multiple species of Plasmodium, support the concept that G4s are likely to be involved in recombination and diversification of antigen-encoding gene families in this important protozoan pathogen.}, } @article {pmid27113272, year = {2016}, author = {Lind-Riehl, JF and Mayer, AL and Wellstead, AM and Gailing, O}, title = {Hybridization, agency discretion, and implementation of the U.S. Endangered Species Act.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {30}, number = {6}, pages = {1288-1296}, doi = {10.1111/cobi.12747}, pmid = {27113272}, issn = {1523-1739}, mesh = {Animals ; Animals, Wild ; Biodiversity ; *Conservation of Natural Resources ; Endangered Species/*legislation & jurisprudence ; *Hybridization, Genetic ; United States ; }, abstract = {The U.S. Endangered Species Act (ESA) requires that the "best available scientific and commercial data" be used to protect imperiled species from extinction and preserve biodiversity. However, it does not provide specific guidance on how to apply this mandate. Scientific data can be uncertain and controversial, particularly regarding species delineation and hybridization issues. The U.S. Fish and Wildlife Service (FWS) had an evolving hybrid policy to guide protection decisions for individuals of hybrid origin. Currently, this policy is in limbo because it resulted in several controversial conservation decisions in the past. Biologists from FWS must interpret and apply the best available science to their recommendations and likely use considerable discretion in making recommendations for what species to list, how to define those species, and how to recover them. We used semistructured interviews to collect data on FWS biologists' use of discretion to make recommendations for listed species with hybridization issues. These biologists had a large amount of discretion to determine the best available science and how to interpret it but generally deferred to the scientific consensus on the taxonomic status of an organism. Respondents viewed hybridization primarily as a problem in the context of the ESA, although biologists who had experience with hybridization issues were more likely to describe it in more nuanced terms. Many interviewees expressed a desire to continue the current case-by-case approach for handling hybridization issues, but some wanted more guidance on procedures (i.e., a "flexible" hybrid policy). Field-level information can provide critical insight into which policies are working (or not working) and why. The FWS biologists' we interviewed had a high level of discretion, which greatly influenced ESA implementation, particularly in the context of hybridization.}, } @article {pmid27798406, year = {2017}, author = {Freudenstein, JV and Broe, MB and Folk, RA and Sinn, BT}, title = {Biodiversity and the Species Concept-Lineages are not Enough.}, journal = {Systematic biology}, volume = {66}, number = {4}, pages = {644-656}, doi = {10.1093/sysbio/syw098}, pmid = {27798406}, issn = {1076-836X}, mesh = {*Biodiversity ; Biological Evolution ; *Classification ; Ecology ; *Phylogeny ; }, abstract = {The nature and definition of species continue to be matters of debate. Current views of species often focus on their nature as lineages-maximal reproductive communities through time. Whereas many authors point to the Evolutionary Species Concept as optimal, in its original form it stressed the ecological role of species as well as their history as lineages, but most recent authors have ignored the role aspect of the concept, making it difficult to apply unambiguously in a time-extended way. This trend has been exacerbated by the application of methods and concepts emphasizing the notion of monophyly, originally applied only at higher levels, to the level of individuals, as well as by the current emphasis on molecular data. Hence, some current authors recognize units that are no more than probable exclusive lineages as species. We argue that biodiversity is inherently a phenotypic concept and that role, as manifested in the organismal extended phenotype, is a necessary component of the species concept. Viewing species as historically connected populations with unique role brings together the temporal and phenotypic natures of species, providing a clear way to view species both in a time-limited and time-extended way. Doing so alleviates perceived issues with "paraphyletic species" and returns the focus of species to units that are most relevant for biodiversity.}, } @article {pmid27081924, year = {2016}, author = {Leung, J and Witt, JD and Norwood, W and Dixon, DG}, title = {Implications of Cu and Ni toxicity in two members of the Hyalella azteca cryptic species complex: Mortality, growth, and bioaccumulation parameters.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {11}, pages = {2817-2826}, doi = {10.1002/etc.3457}, pmid = {27081924}, issn = {1552-8618}, mesh = {Amphipoda/*drug effects/genetics/growth & development/metabolism ; Animals ; Copper/metabolism/*toxicity ; Electron Transport Complex IV/genetics ; Fresh Water ; Lethal Dose 50 ; Mitochondria/drug effects/enzymology/genetics ; Nickel/metabolism/*toxicity ; North America ; Phylogeny ; Species Specificity ; Survival Analysis ; Toxicity Tests ; Water Pollutants, Chemical/metabolism/*toxicity ; }, abstract = {Hyalella azteca, an amphipod crustacean, is frequently used in freshwater toxicity tests. Since the mid-1980s, numerous organizations have collected and established cultures of H. azteca originating from localities across North America. However, H. azteca is actually a large cryptic species complex whose members satisfy both the biological and the phylogenetic species concepts. Genetic analysis at the mitochondrial COI gene has revealed that only 2 clades are cultured in 17 North American laboratories; however, there are 85 genetically divergent lineages within this complex in the wild. In the present study, 2 members (clades 1 and 8) of the H. azteca species complex were identified using the mitochondrial COI gene. These 2 clades were exposed to Cu or Ni for 14 d. A saturation-based mortality model and the general growth model were used to determine mortality (lethal concentration, 25% and 50% [LC25 and LC50], lethal body concentration, 25% and 50% [LBC25 and LBC50]) and growth (inhibitory concentration, 25% [IC25, IBC25]) endpoints, respectively. A modified saturation-based model was used to estimate metal bioaccumulation parameters. Clade 8 was significantly more tolerant than clade 1, with differences in LC50s. However, the effects of the metals on growth were not significantly different between clades, even though clade 1 was significantly larger than then clade 8. Differences in Cu or Ni bioaccumulation were not observed between clades 1 and 8. The differences in Cu and Ni LC50s may have implications for risk assessments, and it is recommended that toxicity experiments should only be performed with properly identified members of the H. azteca complex to maintain consistency among laboratories. Environ Toxicol Chem 2016;35:2817-2826. © 2016 SETAC.}, } @article {pmid27542338, year = {2016}, author = {Duco, W and Grosso, V and Zaccari, D and Soltermann, AT}, title = {Generation of ROS mediated by mechanical waves (ultrasound) and its possible applications.}, journal = {Methods (San Diego, Calif.)}, volume = {109}, number = {}, pages = {141-148}, doi = {10.1016/j.ymeth.2016.07.015}, pmid = {27542338}, issn = {1095-9130}, mesh = {Anthracenes/chemistry ; Antineoplastic Agents/chemistry/therapeutic use ; Artemisinins/*chemistry ; Free Radicals/chemistry ; Humans ; Hydrogen Peroxide/*chemistry ; Hydroxyl Radical/*chemistry/radiation effects ; Reactive Oxygen Species/*chemistry/radiation effects ; Singlet Oxygen/chemistry ; Ultrasonic Waves ; }, abstract = {The thermal decomposition of 9,10 diphenylanthracene peroxide (DPAO2) generates DPA and a mix of triplet and singlet molecular oxygen. For DPAO2 the efficiency to produce singlet molecular oxygen is 0.35. On the other hand, it has shown that many thermal reactions can be carried out through the interaction of molecules with ultrasound. Ultrasound irradiation can create hydrodynamic stress (sonomechanical process), inertial cavitation (pyrolitic process) and long range effects mediated by radicals or ROS. Sonochemical reactions can be originated by pyrolytic like process, shock mechanical waves, thermal reactions and radical and ROS mediated reactions. Sonolysis of pure water can yield hydrogen or hydroxyl radicals and hydrogen peroxide (ROS). When DPAO2 in 1,4 dioxane solution is treated with 20 or 24kHz and different power intensity the production of molecular singlet oxygen is observed. Specific scavengers like tetracyclone (TC) are used to demonstrate it. The efficiency now is 0.85 showing that the sonochemical process is much more efficient that the thermal one. Another endoperoxide, artemisinin was also studied. Unlike the concept of photosensitizer of photodynamic therapy, in spite of large amount of reported results in literature, the term sonosensitizer and the sonosensitization process are not well defined. We define sonosensitized reaction as one in which a chemical species decompose as consequence of cavitation phenomena producing ROS or other radicals and some other target species does undergo a chemical reaction. The concept could be reach rapidly other peroxides which are now under experimental studies. For artemisinin, an important antimalarian and anticancer drug, was established that ultrasound irradiation increases the effectiveness of the treatment but without any explanation. We show that artemisinin is an endoperoxide and behaves as a sonosensitizer in the sense of our definition.}, } @article {pmid27742098, year = {2016}, author = {Tanney, JB and McMullin, DR and Green, BD and Miller, JD and Seifert, KA}, title = {Production of antifungal and antiinsectan metabolites by the Picea endophyte Diaporthe maritima sp. nov.}, journal = {Fungal biology}, volume = {120}, number = {11}, pages = {1448-1457}, doi = {10.1016/j.funbio.2016.05.007}, pmid = {27742098}, issn = {1878-6146}, mesh = {Animals ; Antifungal Agents/chemistry/*metabolism/pharmacology ; Ascomycota/*chemistry/classification/*isolation & purification/metabolism ; Endophytes/*chemistry/classification/*isolation & purification/metabolism ; Insecta/drug effects ; Insecticides/chemistry/*metabolism/pharmacology ; Molecular Structure ; Phylogeny ; Picea/*microbiology ; }, abstract = {The genus Diaporthe comprises close to 800 species, with around 2000 names attributed to it and its asexual morphs previously recognized in Phomopsis. Diaporthe species are common plant associates, including saprotrophs, pathogens, and endophytes affiliated with a diverse range of hosts worldwide. In this study, an unknown Diaporthe sp. was frequently isolated as an endophyte from healthy Picea mariana and Picea rubens needles in the Acadian forest of Eastern Canada. Morphological observations and the application of the genealogical concordance phylogenetic species recognition concept using four unlinked loci (internal transcribed spacer (ITS), DNA-lyase (Apn2), translation elongation factor 1-α (EF1-α), and beta-tubulin (TUB)) support the distinctiveness of this species, described here as Diaporthe maritima. Crude liquid culture extracts from this new species showed potent antifungal activity towards the biotrophic pathogen Microbotryum violaceum in a screening assay necessitating an investigation of its natural products. Three dihydropyrones, phomopsolides A (1), B (2), and C (3), and a stable alpha-pyrone (4), were characterized by mass spectrometry and spectroscopic techniques. All isolated metabolites individually demonstrated in vitro antifungal and antibiotic activity towards Bacillus subtilis. The Acadian forest has proven to be a rich source of biodiversity that has the potential to deliver environmentally sustainable pest management tools.}, } @article {pmid27742096, year = {2016}, author = {Crous, PW and Groenewald, JZ}, title = {They seldom occur alone.}, journal = {Fungal biology}, volume = {120}, number = {11}, pages = {1392-1415}, doi = {10.1016/j.funbio.2016.05.009}, pmid = {27742096}, issn = {1878-6146}, mesh = {Ascomycota/classification/genetics/growth & development/*isolation & purification ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Phylogeny ; Plant Diseases/*microbiology ; Plants/*microbiology ; Spores, Fungal/classification/genetics/growth & development/isolation & purification ; }, abstract = {Species of Coleophoma have been reported as plant pathogenic, saprobic or endophytic on a wide host range. The genus is characterised by having pycnidial conidiomata, phialidic conidiogenous cells intermingled among paraphyses, and cylindrical conidia. Coleophoma has had a confusing taxonomic history with numerous synonyms, and its phylogeny has remained unresolved. The aim of the present study was to use a polyphasic approach incorporating morphology, ecology, and molecular data of the partial large subunit of nrDNA (LSU), the internal transcribed spacer region with intervening 5.8S nrDNA (ITS), partial β-tubulin (tub2), and translation elongation factor 1-alpha (tef1) gene sequences to resolve its taxonomy and phylogeny. Based on these results the genus was found to be polyphyletic, with taxa tentatively identified as Coleophoma clustering in Dothideomycetes and Leotiomycetes. Species corresponding to the concept of Coleophoma s.str. (Dermateaceae, Helotiales, Leotiomycetes) were found to form a distinct clade, with five new species. Furthermore, Coleophoma was found to be linked to the newly established sexual genus, Parafabraea, which is reduced to synonymy. Isolates occurring on Ilex aquifolium in the Netherlands also clustered in Dermateaceae, representing a novel genus, Davidhawksworthia. In the Dothideomycetes, several taxa clustered in Dothiora (Dothideaceae, Dothideales), which is shown to have Dothichiza and Hormonema-like asexual morphs, with four new species. Furthermore, Pseudocamaropycnis is introduced as a new genus (Mytilinidiaceae, Mytilinidiales), along with Briansuttonomyces (Didymellaceae, Pleosporales) and Dimorphosporicola (Pleosporaceae, Pleosporales).}, } @article {pmid27738199, year = {2016}, author = {Haight, JE and Laursen, GA and Glaeser, JA and Taylor, DL}, title = {Phylogeny of Fomitopsis pinicola: a species complex.}, journal = {Mycologia}, volume = {108}, number = {5}, pages = {925-938}, doi = {10.3852/14-225R1}, pmid = {27738199}, issn = {0027-5514}, mesh = {Cluster Analysis ; Coriolaceae/*classification/*genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Europe ; North America ; Peptide Elongation Factor 1/genetics ; *Phylogeography ; RNA Polymerase II/genetics ; Sequence Analysis, DNA ; Southwestern United States ; }, abstract = {Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an abundant saprotrophic fungus found on decaying logs throughout temperate regions of the Northern Hemisphere. Phylogenetic studies have addressed the relationship of F. pinicola to other wood-rotting fungi, but pan-continental variation within F. pinicola has not been addressed using molecular data. While forms found growing on hardwood and softwood hosts exhibit variation in habit and appearance, it is unknown if these forms are genetically distinct. In this study, we generated DNA sequences of the nuc rDNA internal transcribed spacers (ITS), the TEF1 gene encoding translation elongation factor 1-α, and the RPB2 gene encoding the second largest subunit of RNA polymerase II for collections across all major geographic regions where this fungus occurs, with a primary focus on North America. We used Bayesian and maximum likelihood analyses and evaluated the gene trees within the species tree using coalescent methods to elucidate evolutionarily independent lineages. We find that F. pinicola sensu lato encompasses four well-supported, congruent clades: a European clade, southwestern US clade, and two sympatric northern North American clades. Each clade represents distinct species according to phylogenetic and population-genetic species concepts. Morphological data currently available for F. pinicola do not delimit these species, and three of the species are not specific to either hardwood or softwood trees. Originally described from Europe, F. pinicola appears to be restricted to Eurasia. Based on DNA data obtained from an isotype, one well-defined and widespread clade found only in North America represents the recently described Fomitopsis ochracea The remaining two North American clades represent previously undescribed species.}, } @article {pmid27734501, year = {2016}, author = {Darienko, T and Gustavs, L and Pröschold, T}, title = {Species concept and nomenclatural changes within the genera Elliptochloris and Pseudochlorella (Trebouxiophyceae) based on an integrative approach.}, journal = {Journal of phycology}, volume = {52}, number = {6}, pages = {1125-1145}, doi = {10.1111/jpy.12481}, pmid = {27734501}, issn = {1529-8817}, mesh = {Amino Acid Sequence ; Base Sequence ; Chlorophyta/*classification/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Algal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Phylogeny ; Sequence Alignment ; Species Specificity ; }, abstract = {The genera Elliptochloris and Pseudochlorella were erected for Chlorella-like green algae producing two types of autospores and cell packages, respectively. Both genera are widely distributed in different soil habitats, either as free living or as photobionts of lichens. The species of these genera are often difficult to identify because of the high phenotypic plasticity and occasional lack of characteristic features. The taxonomic and nomenclatural status of these species, therefore, remains unclear. In this study, 34 strains were investigated using an integrative approach. Phylogenetic analyses demonstrated that the isolates belong to two independent lineages of the Trebouxiophyceae (Elliptochloris and Prasiola clades) and confirmed that the genera are not closely related. The comparison of morphology, molecular phylogeny, and analyses of secondary structures of SSU and ITS rDNA sequences revealed that all of the strains belong to three genera: Elliptochloris, Pseudochlorella, and Edaphochlorella. As a consequence of the taxonomic revisions, we propose two new combinations (Elliptochloris antarctica and Pseudochlorella signiensis) and validate Elliptochloris reniformis, which is invalidly described according to the International Code for Nomenclature (ICN), by designating a holotype. To reflect the high phenotypic plasticity of P. signiensis, two new varieties were described: P. signiensis var. magna and P. signiensis var. communis. Chlorella mirabilis was not closely related to any of these genera and was, therefore, transferred to the new genus Edaphochlorella. All of the taxonomic changes were highly supported by all phylogenetic analyses and were confirmed by the ITS-2 Barcodes using the ITS-2/CBC approach.}, } @article {pmid27721808, year = {2016}, author = {Stegen, JC and Hurlbert, AH and Bond-Lamberty, B and Chen, X and Anderson, CG and Chu, RK and Dini-Andreote, F and Fansler, SJ and Hess, NJ and Tfaily, M}, title = {Aligning the Measurement of Microbial Diversity with Macroecological Theory.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1487}, pmid = {27721808}, issn = {1664-302X}, abstract = {The number of microbial operational taxonomic units (OTUs) within a community is akin to species richness within plant/animal ("macrobial") systems. A large literature documents OTU richness patterns, drawing comparisons to macrobial theory. There is, however, an unrecognized fundamental disconnect between OTU richness and macrobial theory: OTU richness is commonly estimated on a per-individual basis, while macrobial richness is estimated per-area. Furthermore, the range or extent of sampled environmental conditions can strongly influence a study's outcomes and conclusions, but this is not commonly addressed when studying OTU richness. Here we (i) propose a new sampling approach that estimates OTU richness per-mass of soil, which results in strong support for species energy theory, (ii) use data reduction to show how support for niche conservatism emerges when sampling across a restricted range of environmental conditions, and (iii) show how additional insights into drivers of OTU richness can be generated by combining different sampling methods while simultaneously considering patterns that emerge by restricting the range of environmental conditions. We propose that a more rigorous connection between microbial ecology and macrobial theory can be facilitated by exploring how changes in OTU richness units and environmental extent influence outcomes of data analysis. While fundamental differences between microbial and macrobial systems persist (e.g., species concepts), we suggest that closer attention to units and scale provide tangible and immediate improvements to our understanding of the processes governing OTU richness and how those processes relate to drivers of macrobial species richness.}, } @article {pmid27718041, year = {2016}, author = {Adebowale, A and Lamb, J and Nicholas, A and Naidoo, Y}, title = {ITS2 secondary structure for species circumscription: case study in southern African Strychnos L. (Loganiaceae).}, journal = {Genetica}, volume = {144}, number = {6}, pages = {639-650}, pmid = {27718041}, issn = {1573-6857}, mesh = {Base Sequence ; DNA, Intergenic/*genetics ; Evolution, Molecular ; Phylogeny ; Strychnos/*classification/*genetics ; }, abstract = {Recently developed computational tools in ITS2 sequence-structure phylogenetics are improving tree robustness by exploitation of the added information content of the secondary structure. Despite this strength, however, their adoption for species-level clarifications in angiosperms has been slow. We investigate the utility of combining ITS2 sequence and secondary structure to separate species of southern African Strychnos, and assess correlation between compensatory base changes (CBCs) and currently recognised species boundaries. Combined phylogenetic analysis of sequence and secondary structure datasets performed better, in terms of robustness and species resolution, than analysis involving primary sequences only, achieving 100 and 88.2 % taxa discriminations respectively. Further, the Strychnos madagascariensis complex is well-resolved by sequence-structure phylogenetic analysis. The 17 Strychnos species corresponded to 14 ITS2 CBC clades. Four of the five taxa in section Densiflorae belong to a single CBC clade, whose members tend to form natural hybrids. Our finding supports the application of ITS2 as a complementary barcoding marker for species identification. It also highlights the potential of comparative studies of ITS2 CBC features among prospective parental pairs in breeding experiments as a rapid proxy for cross compatibility assessment. This could save valuable time in crop improvement. Patterns of CBC evolution and species boundaries in Strychnos suggests a positive correlation. We conclude that the CBC pattern coupled with observed ITS2 sequence paraphyly in section Densiflorae points to a speciation work-in-progress.}, } @article {pmid27697556, year = {2017}, author = {Sungani, H and Ngatunga, BP and Koblmüller, S and Mäkinen, T and Skelton, PH and Genner, MJ}, title = {Multiple colonisations of the Lake Malawi catchment by the genus Opsaridium (Teleostei: Cyprinidae).}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {256-265}, doi = {10.1016/j.ympev.2016.09.027}, pmid = {27697556}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Calibration ; Cell Nucleus/genetics ; Cyprinidae/*classification/genetics ; DNA, Mitochondrial/genetics ; *Lakes ; Malawi ; Phylogeny ; Time Factors ; }, abstract = {It has been proposed that the fish faunas of African rivers assemble through multiple colonisation events, while lake faunas form additionally through intralacustine speciation. While this pattern has been established for many lineages, most notably cichlids, there are opportunities to further investigate the concept using phylogenies of congeneric endemic species within ancient lake catchments. The Lake Malawi catchment contains three river-spawning cyprinids of the genus Opsaridium, two of which are endemic. These species differ in body size, migratory behaviour and habitat use, but it has never previously been tested if these represent a monophyletic radiation, or have instead colonised the lake independently. We placed these species in a broader phylogeny of Opsaridium and the related genus Raiamas, including all known species from the river systems surrounding Lake Malawi. Our results suggest that each of the species has independently colonised the lake catchment, with all three taxa having well-defined sister taxa outside of the lake, and all sharing a common ancestor ∼14.9million years ago, before the Lake Malawi basin started to form ∼8.6million years ago. Additionally, the results strongly support previous observations that Opsaridium is not a monophyletic group, but instead contains Raiamas from the Congo drainage. Together these results are supportive of the concept that river fish faunas within African catchments are primarily assembled through a process of accumulation from independent origins, rather than within-catchment speciation and adaptive radiation. In light of these results we also suggest there is scope for a re-evaluation of systematics of both Opsaridium and Raiamas.}, } @article {pmid27648231, year = {2016}, author = {Paterson, ID and Mangan, R and Downie, DA and Coetzee, JA and Hill, MP and Burke, AM and Downey, PO and Henry, TJ and Compton, SG}, title = {Two in one: cryptic species discovered in biological control agent populations using molecular data and crossbreeding experiments.}, journal = {Ecology and evolution}, volume = {6}, number = {17}, pages = {6139-6150}, pmid = {27648231}, issn = {2045-7758}, abstract = {There are many examples of cryptic species that have been identified through DNA-barcoding or other genetic techniques. There are, however, very few confirmations of cryptic species being reproductively isolated. This study presents one of the few cases of cryptic species that has been confirmed to be reproductively isolated and therefore true species according to the biological species concept. The cryptic species are of special interest because they were discovered within biological control agent populations. Two geographically isolated populations of Eccritotarsus catarinensis (Carvalho) [Hemiptera: Miridae], a biological control agent for the invasive aquatic macrophyte, water hyacinth, Eichhornia crassipes (Mart.) Solms [Pontederiaceae], in South Africa, were sampled from the native range of the species in South America. Morphological characteristics indicated that both populations were the same species according to the current taxonomy, but subsequent DNA analysis and breeding experiments revealed that the two populations are reproductively isolated. Crossbreeding experiments resulted in very few hybrid offspring when individuals were forced to interbreed with individuals of the other population, and no hybrid offspring were recorded when a choice of mate from either population was offered. The data indicate that the two populations are cryptic species that are reproductively incompatible. Subtle but reliable diagnostic characteristics were then identified to distinguish between the two species which would have been considered intraspecific variation without the data from the genetics and interbreeding experiments. These findings suggest that all consignments of biological control agents from allopatric populations should be screened for cryptic species using genetic techniques and that the importation of multiple consignments of the same species for biological control should be conducted with caution.}, } @article {pmid27625654, year = {2016}, author = {Sattar, S and Thompson, GA}, title = {Small RNA Regulators of Plant-Hemipteran Interactions: Micromanagers with Versatile Roles.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {1241}, pmid = {27625654}, issn = {1664-462X}, abstract = {Non-coding small RNAs (sRNAs) in plants have important roles in regulating biological processes, including development, reproduction, and stress responses. Recent research indicates significant roles for sRNA-mediated gene silencing during plant-hemipteran interactions that involve all three of these biological processes. Plant responses to hemipteran feeding are determined by changes in the host transcriptome that appear to be fine-tuned by sRNAs. The role of sRNA in plant defense responses is complex. Different forms of sRNAs, with specific modes of action, regulate changes in the host transcriptome primarily through post-transcriptional gene silencing and occasionally through translational repression. Plant genetic resistance against hemipterans provides a model to explore the regulatory roles of sRNAs in plant defense. Aphid-induced sRNA expression in resistance genotypes delivers a new paradigm in understanding the regulation of R gene-mediated resistance in host plants. Unique sRNA profiles, including changes in sRNA biogenesis and expression can also provide insights into susceptibility to insect herbivores. Activation of phytohormone-mediated defense responses against insect herbivory is another hallmark of this interaction, and recent studies have shown that regulation of phytohormone signaling is under the control of sRNAs. Hemipterans feeding on resistant plants also show changes in insect sRNA profiles, possibly influencing insect development and reproduction. Changes in insect traits such as fecundity, host range, and resistance to insecticides are impacted by sRNAs and can directly contribute to the success of certain insect biotypes. In addition to causing direct damage to the host plant, hemipteran insects are often vectors of viral pathogens. Insect anti-viral RNAi machinery is activated to limit virus accumulation, suggesting a role in insect immunity. Virus-derived long sRNAs strongly resemble insect piRNAs, leading to the speculation that the piRNA pathway is induced in response to viral infection. Evidence for robust insect RNAi machinery in several hemipteran species is of immense interest and is being actively pursued as a possible tool for insect control. RNAi-induced gene silencing following uptake of exogenous dsRNA was successfully demonstrated in several hemipterans and the presence of sid-1 like genes support the concept of a systemic response in some species.}, } @article {pmid27616791, year = {2016}, author = {Lombard, L and Houbraken, J and Decock, C and Samson, RA and Meijer, M and Réblová, M and Groenewald, JZ and Crous, PW}, title = {Generic hyper-diversity in Stachybotriaceae.}, journal = {Persoonia}, volume = {36}, number = {}, pages = {156-246}, pmid = {27616791}, issn = {0031-5850}, abstract = {The family Stachybotriaceae was recently introduced to include the genera Myrothecium, Peethambara and Stachybotrys. Members of this family include important plant and human pathogens, as well as several species used in industrial and commercial applications as biodegraders and biocontrol agents. However, the generic boundaries in Stachybotriaceae are still poorly defined, as type material and sequence data are not readily available for taxonomic studies. To address this issue, we performed multi-locus phylogenetic analyses using partial gene sequences of the 28S large subunit (LSU), the internal transcribed spacer regions and intervening 5.8S nrRNA (ITS), the RNA polymerase II second largest subunit (rpb2), calmodulin (cmdA), translation elongation factor 1-alpha (tef1) and β-tubulin (tub2) for all available type and authentic strains. Supported by morphological characters these data resolved 33 genera in the Stachybotriaceae. These included the nine already established genera Albosynnema, Alfaria, Didymostilbe, Myrothecium, Parasarcopodium, Peethambara, Septomyrothecium, Stachybotrys and Xepicula. At the same time the generic names Melanopsamma, Memnoniella and Virgatospora were resurrected. Phylogenetic inference further showed that both the genera Myrothecium and Stachybotrys are polyphyletic resulting in the introduction of 13 new genera with myrothecium-like morphology and eight new genera with stachybotrys-like morphology.}, } @article {pmid27616789, year = {2016}, author = {Wang, XW and Lombard, L and Groenewald, JZ and Li, J and Videira, SI and Samson, RA and Liu, XZ and Crous, PW}, title = {Phylogenetic reassessment of the Chaetomium globosum species complex.}, journal = {Persoonia}, volume = {36}, number = {}, pages = {83-133}, pmid = {27616789}, issn = {0031-5850}, abstract = {Chaetomium globosum, the type species of the genus, is ubiquitous, occurring on a wide variety of substrates, in air and in marine environments. This species is recognised as a cellulolytic and/or endophytic fungus. It is also known as a source of secondary metabolites with various biological activities, having great potential in the agricultural, medicinal and industrial fields. On the negative side, C. globosum has been reported as an air contaminant causing adverse health effects and as causal agent of human fungal infections. However, the taxonomic status of C. globosum is still poorly understood. The contemporary species concept for this fungus includes a broadly defined morphological diversity as well as a large number of synonymies with limited phylogenetic evidence. The aim of this study is, therefore, to resolve the phylogenetic limits of C. globosum s.str. and related species. Screening of isolates in the collections of the CBS-KNAW Fungal Biodiversity Centre (The Netherlands) and the China General Microbiological Culture Collection Centre (China) resulted in recognising 80 representative isolates of the C. globosum species complex. Thirty-six species are identified based on phylogenetic inference of six loci, supported by typical morphological characters, mainly ascospore shape. Of these, 12 species are newly described here. Additionally, C. cruentum, C. mollipilium, C. rectum, C. subterraneum and two varieties of C. globosum are synonymised under C. globosum s.str., and six species are resurrected, i.e. C. angustispirale, C. coarctatum, C. cochliodes, C. olivaceum, C. spiculipilium and C. subglobosum. Chaetomium ascotrichoides is segregated from C. madrasense and the genus name Chaetomidium is rejected. Five species, including C. globosum s.str., are typified here to stabilise their taxonomic status. A further evaluation of the six loci used in this study as potential barcodes indicated that the 28S large subunit (LSU) nrDNA and the internal transcribed spacer regions and intervening 5.8S nrRNA (ITS) gene regions were unreliable to resolve species, whereas β-tubulin (tub2) and RNA polymerase II second largest subunit (rpb2) showed the greatest promise as DNA barcodes for differentiating Chaetomium species. This study provides a starting point to establish a more robust classification system for Chaetomium and for the Chaetomiaceae.}, } @article {pmid27616787, year = {2016}, author = {Yilmaz, N and Visagie, CM and Frisvad, JC and Houbraken, J and Jacobs, K and Samson, RA}, title = {Taxonomic re-evaluation of species in Talaromyces section Islandici, using a polyphasic approach.}, journal = {Persoonia}, volume = {36}, number = {}, pages = {37-56}, pmid = {27616787}, issn = {0031-5850}, abstract = {The taxonomy of Talaromyces rugulosus, T. wortmannii and closely related species, classified in Talaromyces sect. Islandici, is reviewed in this paper. The species of Talaromyces sect. Islandici have restricted growth on MEA and CYA, generally have yellow mycelia and produce rugulosin and/or skyrin. They are important in biotechnology (e.g. T. rugulosus, T. wortmannii) and in medicine (e.g. T. piceus, T. radicus). The taxonomy of sect. Islandici was resolved using a combination of morphological, extrolite and phylogenetic data, using the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) concept, with special focus on the T. rugulosus and T. wortmannii species complexes. In this paper, we synonymise T. variabilis, Penicillium concavorugulosum and T. sublevisporus with T. wortmannii, and introduce four new species as T. acaricola, T. crassus, T. infraolivaceus and T. subaurantiacus. Finally, we provide a synoptic table for the identification of the 19 species classified in the section.}, } @article {pmid27605227, year = {2016}, author = {Lin, CY and Fu, KL and Lin, CY}, title = {Optimal Subdivision for Treatment and Management of Catastrophic Landslides in a Watershed Using Topographic Factors.}, journal = {Environmental management}, volume = {58}, number = {5}, pages = {833-842}, pmid = {27605227}, issn = {1432-1009}, mesh = {Climate Change ; Conservation of Natural Resources/*methods ; *Disasters ; Environmental Monitoring/*methods ; Geological Phenomena ; *Landslides ; Models, Theoretical ; Multivariate Analysis ; *Rivers ; Taiwan ; }, abstract = {Recent extreme rainfall events led to many landslides due to climate changes in Taiwan. How to effectively promote post-disaster treatment and/or management works in a watershed/drainage basin is a crucial issue. Regarding the processes of watershed treatment and/or management works, disaster hotspot scanning and treatment priority setup should be carried out in advance. A scanning method using landslide ratio to determine the appropriate outlet of an interested watershed, and an optimal subdivision system with better homogeneity and accuracy in landslide ratio estimation were developed to help efficient executions of treatment and/or management works. Topography is a key factor affecting watershed landslide ratio. Considering the complexity and uncertainty of the natural phenomenon, multivariate analysis was applied to understand the relationship between topographic factors and landslide ratio in the interested watershed. The concept of species-area curve, which is usually adopted at on-site vegetation investigation to determinate the suitable quadrate size, was used to derive the optimal threshold in subdivisions. Results show that three main component axes including factors of scale, network and shape extracted from Digital Terrain Model coupled with areas of landslide can effectively explain the characteristics of landslide ratio in the interested watershed, and a relation curve obtained from the accuracy of landslide ratio classification and number of subdivisions could be established to derive optimal subdivision of the watershed. The subdivision method promoted in this study could be further used for priority rank and benefit assessment of landslide treatment in a watershed.}, } @article {pmid27584038, year = {2016}, author = {Matson, PG and Ladd, TM and Halewood, ER and Sangodkar, RP and Chmelka, BF and Iglesias-Rodriguez, MD}, title = {Intraspecific Differences in Biogeochemical Responses to Thermal Change in the Coccolithophore Emiliania huxleyi.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0162313}, pmid = {27584038}, issn = {1932-6203}, mesh = {Carbon/metabolism ; *Climate Change ; Eukaryota/*classification/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Species Specificity ; }, abstract = {The species concept in marine phytoplankton is defined based on genomic, morphological, and functional properties. Reports of intraspecific diversity are widespread across major phytoplankton groups but the impacts of this variation on ecological and biogeochemical processes are often overlooked. Intraspecific diversity is well known within coccolithophores, which play an important role in the marine carbon cycle via production of particulate inorganic carbon. In this study, we investigated strain-specific responses to temperature in terms of morphology, carbon production, and carbonate mineralogy using a combination of microscopy, elemental analysis, flow cytometry, and nuclear magnetic resonance. Two strains of the cosmopolitan coccolithophore E. huxleyi isolated from different regions (subtropical, CCMP371; temperate, CCMP3266) were cultured under a range of temperature conditions (10°C, 15°C, and 20°C) using batch cultures and sampled during both exponential and stationary growth. Results for both strains showed that growth rates decreased at lower temperatures while coccosphere size increased. Between 15°C and 20°C, both strains produced similar amounts of total carbon, but differed in allocation of that carbon between particulate inorganic carbon (PIC) and particulate organic carbon (POC), though temperature effects were not detected. Between 10°C and 20°C, temperature effects on daily production of PIC and POC, as well as the cellular quota of POC were detected in CCMP3266. Strain-specific differences in coccolith shedding rates were found during exponential growth. In addition, daily shedding rates were negatively related to temperature in CCMP371 but not in CCMP3266. Despite differences in rates of particulate inorganic carbon production, both strains were found to produce coccoliths composed entirely of pure calcite, as established by solid-state 13C and 43Ca NMR and X-ray diffraction measurements. These results highlight the limitations of the species concept and the need for a trait-based system to better quantify diversity within marine phytoplankton communities.}, } @article {pmid27567287, year = {2016}, author = {Dyer, MA}, title = {Lessons from Retinoblastoma: Implications for Cancer, Development, Evolution, and Regenerative Medicine.}, journal = {Trends in molecular medicine}, volume = {22}, number = {10}, pages = {863-876}, pmid = {27567287}, issn = {1471-499X}, support = {R01 EY018599/EY/NEI NIH HHS/United States ; R01 EY014867/EY/NEI NIH HHS/United States ; R01 CA168875/CA/NCI NIH HHS/United States ; P30 CA021765/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Child ; Humans ; Precision Medicine/methods ; Regenerative Medicine/methods ; Retina/growth & development/metabolism/*pathology ; Retinal Neoplasms/genetics/metabolism/*pathology/therapy ; Retinoblastoma/genetics/metabolism/*pathology/therapy ; Translational Research, Biomedical/methods ; }, abstract = {Retinoblastoma is a rare childhood cancer of the developing retina, and studies on this orphan disease have led to fundamental discoveries in cancer biology. Retinoblastoma has also emerged as a model for translational research for pediatric solid tumors, which is particularly important as personalized medicine expands in oncology. Research on retinoblastomas has been combined with the exploration of retinal development and retinal degeneration to advance a new model of cell type-specific disease susceptibility termed 'cellular pliancy'. The concept can even be extended to species-specific regeneration. This review discusses the remarkable path of retinoblastoma research and how it has shaped the most current efforts in basic, translational, and clinical research in oncology and beyond.}, } @article {pmid27563273, year = {2016}, author = {Roháček, J}, title = {Herniosina Roháček: revised concept, two new species, new key and atlas of male and female terminalia (Diptera, Sphaeroceridae).}, journal = {ZooKeys}, volume = {}, number = {609}, pages = {69-106}, pmid = {27563273}, issn = {1313-2989}, abstract = {The taxonomic concept of Herniosina Roháček, 1983 (Diptera: Sphaeroceridae) is revised on the basis of five W. Palaearctic species, thus excluding the E. Nearctic Herniosina voluminosa Marshall, 1987 whose inclusion caused the paraphyly of the genus. Two new species, Herniosina erymantha sp. n. (male only, Greece: Peloponnese) and Herniosina hamata sp. n. (both sexes, Cyprus), are described and illustrated, and the other three species, Herniosina bequaerti (Villeneuve, 1917), Herniosina horrida (Roháček, 1978) and Herniosina pollex Roháček, 1993, are diagnosed with an atlas of their male and female terminalia. The relationships of the redefined genus and of all its species are discussed, and their biology and distribution are reviewed. A new illustrated key to Herniosina species is given.}, } @article {pmid27560369, year = {2017}, author = {Yassin, A}, title = {Drosophila yakuba mayottensis, a new model for the study of incipient ecological speciation.}, journal = {Fly}, volume = {11}, number = {1}, pages = {37-45}, pmid = {27560369}, issn = {1933-6942}, mesh = {Adaptation, Biological ; Animals ; Comoros ; DNA, Mitochondrial ; Drosophila/*classification/*genetics/physiology ; Ecology ; *Genetic Speciation ; Genetic Variation ; Genome, Mitochondrial ; Reproductive Isolation ; }, abstract = {A full understanding of how ecological factors drive the fixation of genetic changes during speciation is obscured by the lack of appropriate models with clear natural history and powerful genetic toolkits. In a recent study, we described an early stage of ecological speciation in a population of the generalist species Drosophila yakuba (melanogaster subgroup) on the island of Mayotte (Indian Ocean). On this island, flies are strongly associated with the toxic fruits of noni (Morinda citrifolia) and show a partial degree of pre-zygotic reproductive isolation. Here, I mine the nuclear and mitochondrial genomes and provide a full morphological description of this population. Only 29 nuclear sites (< 4 × 10[-7] of the genome) are fixed in this population and absent from 3 mainland populations and the closest relative D. santomea, but no mitochondrial or morphological character distinguish Mayotte flies from the mainland. This result indicates that physiological and behavioral traits may evolve faster than morphology at the early stages of speciation. Based on these differences, the Mayotte population is designated as a new subspecies, Drosophila yakuba mayottensis subsp. nov., and its strong potential in understanding the genetics of speciation and plant-insect interactions is discussed.}, } @article {pmid27549617, year = {2016}, author = {Haight, JE and Laursen, GA and Glaeser, J and Taylor, L}, title = {Phylogeny of Fomitopsis pinicola: a species complex.}, journal = {Mycologia}, volume = {}, number = {}, pages = {}, doi = {10.3852/14-225}, pmid = {27549617}, issn = {0027-5514}, abstract = {Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an abundant saprotrophic fungus found on decaying logs throughout temperate regions of the Northern Hemisphere. Phylogenetic studies have addressed the relationship of F. pinicola to other wood-rotting fungi, but pan-continental variation within F. pinicola has not been addressed using molecular data. While forms found growing on hardwood and softwood hosts exhibit variation in habit and appearance, it is unknown if these forms are genetically distinct. In this study, we generated DNA sequences of the nuc rDNA internal transcribed spacers (ITS), the TEF1 gene encoding translation elongation factor 1-α, and the RPB2 gene encoding the second largest subunit of RNA polymerase II for collections across all major geographic regions where this fungus occurs, with a primary focus on North America. We used Bayesian and maximum likelihood analyses and evaluated the gene trees within the species tree using coalescent methods to elucidate evolutionarily independent lineages. We find that F. pinicola sensu lato encompasses four well-supported, congruent clades: a European clade, southwestern US clade, and two sympatric northern North American clades. Each clade represents distinct species according to phylogenetic and population-genetic species concepts. Morphological data currently available for F. pinicola do not delimit these species, and three of the species are not specific to either hardwood or softwood trees. Originally described from Europe, F. pinicola appears to be restricted to Eurasia. Based on DNA data obtained from an isotype, one well-defined and widespread clade found only in North America represents the recently described Fomitopsis ochracea The remaining two North American clades represent previously undescribed species.}, } @article {pmid27549583, year = {2016}, author = {Botasini, S and Martí, AC and Méndez, E}, title = {Thin-layer voltammetry of soluble species on screen-printed electrodes: proof of concept.}, journal = {The Analyst}, volume = {141}, number = {21}, pages = {5996-6001}, doi = {10.1039/c6an01374k}, pmid = {27549583}, issn = {1364-5528}, abstract = {Thin-layer diffusion conditions were accomplished on screen-printed electrodes by placing a controlled-weight onto the cast solution and allowing for its natural spreading. The restricted diffusive conditions were assessed by cyclic voltammetry at low voltage scan rates and electrochemical impedance spectroscopy. The relationship between the weight exerted over the drop and the thin-layer thickness achieved was determined, in such a way that the simple experimental set-up designed for this work could be developed into a commercial device with variable control of the thin-layer conditions. The experimental results obtained resemble those reported for the voltammetric features of electroactive soluble species employing electrodes modified with carbon nanotubes or graphene layers, suggesting that the attainment of the benefits reported for these nanomaterials could be done simply by forcing the solution to spread over the screen-printed electrodic system to form a thin layer solution. The advantages of thin-layer voltammetry in the kinetic characterization of quasi-reversible and irreversible processes are highlighted.}, } @article {pmid27517578, year = {2016}, author = {Caldararo, N}, title = {Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept.}, journal = {Journal of molecular evolution}, volume = {83}, number = {1-2}, pages = {78-87}, pmid = {27517578}, issn = {1432-1432}, mesh = {Animals ; Biological Evolution ; DNA/genetics ; DNA, Ancient/*analysis ; Fossils ; Hominidae/genetics ; Humans ; Neanderthals/*genetics ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; }, abstract = {A number of recent articles have appeared on the Denisova fossil remains and attempts to produce DNA sequences from them. One of these recently appeared in Science by Vernot et al. (Science 352:235-239, 2016). We would like to advance an alternative interpretation of the data presented. One concerns the problem of contamination/degradation of the determined DNA sequenced. Just as the publication of the first Neandertal sequence included an interpretation that argued that Neandertals had not contributed any genes to modern humans, the Denisovan interpretation has considerable influence on ideas regarding human evolution. The new papers, however, confuse established ideas concerning the nature of species, as well as the use of terms like premodern, Archaic Homo, and Homo heidelbergensis. Examination of these problems presents a solution by means of reinterpreting the results. Given the claims for gene transfer among a number of Mid Pleistocene hominids, it may be time to reexamine the idea of anagenesis in hominid evolution.}, } @article {pmid27504607, year = {2016}, author = {Jacquet, J and Chaumont, P and Gontard, G and Orio, M and Vezin, H and Blanchard, S and Desage-El Murr, M and Fensterbank, L}, title = {C-N Bond Formation from a Masked High-Valent Copper Complex Stabilized by Redox Non-Innocent Ligands.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {55}, number = {36}, pages = {10712-10716}, doi = {10.1002/anie.201605132}, pmid = {27504607}, issn = {1521-3773}, abstract = {The reactivity of a stable copper(II) complex bearing fully oxidized iminobenzoquinone redox ligands towards nucleophiles is described. In sharp contrast with its genuine low-valent counterpart bearing reduced ligands, this complex performs high-yielding C-N bond formations. Mechanistic studies suggest that this behavior could stem from a mechanism akin to reductive elimination occurring at the metal center but facilitated by the ligand: it is proposed that a masked high oxidation state of the metal can be stabilized as a lower copper(II) oxidation state by the redox ligands without forfeiting its ability to behave as a high-valent copper(III) center. These observations are substantiated by a combination of advanced EPR spectroscopy techniques with DFT studies. This work sheds light on the potential of redox ligands as promoters of unusual reactivities at metal centers and illustrates the concept of masked high-valent metallic species.}, } @article {pmid27501861, year = {2016}, author = {Perbal, B}, title = {A la Pêche aux Moules.}, journal = {Journal of cell communication and signaling}, volume = {10}, number = {3}, pages = {263-265}, pmid = {27501861}, issn = {1873-9601}, abstract = {In a recent manuscript, Goff and collaborators (Metzger et al. 2016) reported data arguing for the spread of contagious cancer cells among different species of shellfish. Although horizontal transmission of cancer cells has been observed in a few cases in higher organisms, it appears to be rather frequent among molluscs. Recent evidence supports the concept of inter-species horizontal infectious transmission of cancer cells both in molluscs but also in mammals, including humans.}, } @article {pmid27470779, year = {2016}, author = {Krysko, KL and Granatosky, MC and Nuñez, LP and Smith, DJ}, title = {A cryptic new species of Indigo Snake (genus Drymarchon) from the Florida Platform of the United States.}, journal = {Zootaxa}, volume = {4138}, number = {3}, pages = {549-569}, doi = {10.11646/zootaxa.4138.3.9}, pmid = {27470779}, issn = {1175-5334}, mesh = {Animals ; Colubridae/*anatomy & histology/*classification/genetics ; Female ; Florida ; Male ; Mississippi ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Indigo Snakes (genus Drymarchon) occur from northern Argentina northward into to the United States, where they inhabit southern Texas and disjunct populations in Mississippi, Florida and Georgia. Based on allopatry and morphological differences Collins (1991) hypothesized that the two United States taxa-the Western Indigo Snake, D. melanurus erebennus (Cope, 1860), and the Eastern Indigo Snake, D. couperi (Holbrook, 1842)-deserved full species recognition. Building upon this hypothesis with molecular and morphological analyses we illustrate that D. couperi is split into two distinct lineages. Based on the General Lineage Concept of Species, we describe the lineage that occurs along the Gulf coast of Florida and Mississippi as a new species, Drymarchon kolpobasileus. The new species is distinguished from D. couperi by a suite of morphological features, including a shorter and shallower head, deeper and shorter 7[th] infralabial scales, and shorter temporal scales. Overall, the presence of a deep 7[th] infralabial scale provides the best univariate identifier of D. kolpobasileus sp. nov. This study illustrates the usefulness of using both morphological and genetic data in refining accurate descriptions of geographical distributions.}, } @article {pmid27439775, year = {2016}, author = {Mende, MB and Bartel, M and Hundsdoerfer, AK}, title = {A comprehensive phylogeography of the Hyles euphorbiae complex (Lepidoptera: Sphingidae) indicates a 'glacial refuge belt'.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29527}, pmid = {27439775}, issn = {2045-2322}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Evolution, Molecular ; Gene Flow ; Mediterranean Region ; *Microsatellite Repeats ; Middle East ; Moths/*classification/genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; }, abstract = {We test the morphology based hypothesis that the Western Palaearctic spurge hawkmoths represent two species, the Eurasian H. euphorbiae and Afro-Macaronesian H. tithymali. It has been suggested that these species merged into several hybrid swarm populations, although a mitochondrial phylogeography revealed substructure with local differentiation. We analysed a three-gene mt-dataset (889 individuals) and 12 microsatellite loci (892 individuals). Microsatellite analyses revealed an overall weak differentiation and corroborated the superordinate division into two clusters. The data indicate that the populations studied belong to only one species according to the biological species concept, refuting the opening hypothesis. A future taxonomic revision appears necessary to reflect the division into two subgroups. Ancestral mitochondrial polymorphisms are retained in H. euphorbiae, indicating gene flow within a broad 'glacial refuge belt' and ongoing postglacial gene flow. Diverse patterns of extensive mito-nuclear discordance in the Mediterranean and the Middle East presumably evolved by more recent processes. This discordance indicates introgression of H. tithymali-related mitochondrial haplogroups, accompanied (to a lesser degree) by nuclear alleles, into Italian and Aegean H. euphorbiae populations as recently as the late Holocene. The complex mosaic of divergence and reintegration is assumed to have been influenced by locally differing environmental barriers to gene flow.}, } @article {pmid27433442, year = {2016}, author = {Visagie, CM and Seifert, KA and Houbraken, J and Samson, RA and Jacobs, K}, title = {A phylogenetic revision of Penicillium sect. Exilicaulis, including nine new species from fynbos in South Africa.}, journal = {IMA fungus}, volume = {7}, number = {1}, pages = {75-117}, pmid = {27433442}, issn = {2210-6340}, abstract = {A survey of the fynbos biome in South Africa resulted in the isolation of 61 Penicillium species from Protea repens infructescences, air, and soil samples. Fourteen of these belong to Penicillium sect. Exilicaulis and therefore we considered it an opportunity to re-evaluate the taxonomy of the section. Phylogenetic comparisons of the ITS, β-tubulin, calmodulin and RPB2 gene regions of the 76 section Exilicaulis species, revealed 52 distinct species, including nine new species from fynbos. Morphological comparisons confirmed the novelty for most of these, however, new species closely related to P. rubefaciens did not show significant or consistent morphological differences and we thus placed a bias on phylogenetic data applying the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) concept. In this paper we describe the nine new species and update the accepted species list and resolve synonyms in the section. Importantly, we reveal that P. citreosulfuratum is the correct name for the clade previously considered to represent P. toxicarium fide Serra et al. (2008). The nine new species are: Penicillium atrolazulinum, P. consobrinum, P. cravenianum, P. hemitrachum, P. pagulum, P. repensicola, P. momoii, P. subturcoseum, and P. xanthomelinii spp. nov.}, } @article {pmid27422802, year = {2017}, author = {Serrano-Villavicencio, JE and Vendramel, RL and Siniciato Terra Garbino, G}, title = {Species, subspecies, or color morphs? Reconsidering the taxonomy of Callicebus Thomas, 1903 in the Purus-Madeira interfluvium.}, journal = {Primates; journal of primatology}, volume = {58}, number = {1}, pages = {159-167}, pmid = {27422802}, issn = {1610-7365}, mesh = {Animals ; Brazil ; Hair ; *Phenotype ; *Pigmentation ; Pitheciidae/*classification/genetics/physiology ; }, abstract = {There have been recent disagreements as to how many taxa of titi monkeys, genus Callicebus, occur in the region between the Purus and Madeira rivers in western Brazilian Amazonia. Three parapatric taxa were proposed for the area: Callicebus caligatus, Callicebus stephennashi, and Callicebus dubius, but the latter has recently been considered a synonym of C. caligatus, even though both form monophyletic groups and are morphologically distinct. We analyzed the geographic variation in the pelage of Callicebus occurring between the Madeira and Purus rivers and concluded that the phenotypes attributed to C. caligatus and C. dubius are not individual morphs, but rather well-marked and geographically restricted varieties. For this reason, we classify Callicebus caligatus as a polytypic species with two subspecies: Callicebus caligatus caligatus and Callicebus caligatus dubius. This classification is corroborated by molecular evidence as well. The morphological and distributional data indicate that Callicebus stephennashi is a hybrid form of C. c. caligatus and C. c. dubius, due to the presence of intermediate characters. Therefore, until more precise locality records are provided and further evidence is presented, we consider Callicebus stephennashi to be a homonym of the two parental forms.}, } @article {pmid27394524, year = {2016}, author = {Imada, Y}, title = {Bryophyte-feeding of Litoleptis (Diptera: Rhagionidae) with descriptions of new species from Japan.}, journal = {Zootaxa}, volume = {4097}, number = {1}, pages = {41-58}, doi = {10.11646/zootaxa.4097.1.2}, pmid = {27394524}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Body Size ; Bryophyta/parasitology ; Diptera/*anatomy & histology/*classification/growth & development/physiology ; Ecosystem ; Feeding Behavior ; Female ; Japan ; Male ; Organ Size ; Spiders/anatomy & histology/*classification/growth & development ; }, abstract = {Here we report the larval phytophagous habit of Litoleptis for the first time, and describe six new species of Litoleptis in Japan; L. japonica n. sp., L. kiiensis n. sp., L. niyodoensis n. sp., L. himukaensis n. sp., L. izuensis n. sp., and L. asterellaphile n. sp. All the species described here are thallus-miners of liverworts belonging to Aytoniaceae and Conocephalaceae (Marchantiopsida: Marchantiophyta). Each fly species mined thalli of only one of the following genera: Conocephalum, Reboulia, and Asterella. The descriptions of the Japanese Litoleptis species here expand the concept of this genus. The female genital morphology of Litoleptis strengthened the current placement of Litoleptis as a member of Spaniinae.}, } @article {pmid27394513, year = {2016}, author = {Ellenrieder, NV and Watson, GW and Kinnee, SA and Franco, JC and Mazzeo, G}, title = {Paracoccus leucadendri Mazzeo & Franco in Mazzeo, Franco & Russo, 2009, a junior synonym of Paracoccus hakeae (Williams, 1985) comb. nov. <br />(Coccomorpha: Pseudococcidae).}, journal = {Zootaxa}, volume = {4093}, number = {4}, pages = {552-558}, doi = {10.11646/zootaxa.4093.4.6}, pmid = {27394513}, issn = {1175-5334}, mesh = {Animal Structures/anatomy & histology/growth & development ; Animals ; Australia ; Body Size ; California ; Female ; Hemiptera/anatomy & histology/*classification/genetics/growth & development ; Organ Size ; Phylogeny ; Portugal ; }, abstract = {Two mealybug species (Hemiptera: Coccomorpha: Pseudococcidae) feeding on Proteaceae in U.S.A. (California), Portugal and Australia were studied: Paracoccus leucadendri Mazzeo & Franco in Mazzeo, Franco & Russo, 2009, described from Portugal, and Phenacoccus hakeae Williams, 1985, described from Australia. A comparative morphological analysis was made of relevant paratypes and additional specimens from Australia, California and Portugal, and the variability of the morphological characters in the populations in each country was documented. Molecular analysis of the COI gene of specimens from Australia and California showed them to be identical, and comparative morphological analysis among specimens from Australia, California and Portugal revealed no differences either; therefore Paracoccus leucadendri is placed as a junior synonym of Phenacoccus hakeae. A comparison of the COI sequences with those of species of Paracoccus, Phenacoccus and other mealybug genera revealed that Phenacoccus hakeae does not belong in Phenacoccus. Even though its COI shows no close match to any other species its morphology fits within the generic concept of Paracoccus, and we transfer it to that genus under the new combination Paracoccus hakeae (Williams, 1985) as a holding option until a comprehensive phylogenetic analysis of the group is carried out.}, } @article {pmid27388271, year = {2016}, author = {Roberts, A and Austin, W and Evans, K and Bird, C and Schweizer, M and Darling, K}, title = {A New Integrated Approach to Taxonomy: The Fusion of Molecular and Morphological Systematics with Type Material in Benthic Foraminifera.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0158754}, pmid = {27388271}, issn = {1932-6203}, mesh = {Atlantic Ocean ; Biodiversity ; *Classification ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Foraminifera/*classification ; Fossils ; Geography ; Microscopy, Electron, Scanning ; Multivariate Analysis ; Paleontology/methods ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal/*analysis ; Ribosome Subunits, Small ; }, abstract = {A robust and consistent taxonomy underpins the use of fossil material in palaeoenvironmental research and long-term assessment of biodiversity. This study presents a new integrated taxonomic protocol for benthic foraminifera by unequivocally reconciling the traditional taxonomic name to a specific genetic type. To implement this protocol, a fragment of the small subunit ribosomal RNA (SSU rRNA) gene is used in combination with 16 quantitative morphometric variables to fully characterise the benthic foraminiferal species concept of Elphidium williamsoni Haynes, 1973. A combination of live contemporary topotypic specimens, original type specimens and specimens of genetic outliers were utilised in this study. Through a series of multivariate statistical tests we illustrate that genetically characterised topotype specimens are morphologically congruent with both the holotype and paratype specimens of E. williamsoni Haynes, 1973. We present the first clear link between morphologically characterised type material and the unique SSU rRNA genetic type of E. williamsoni. This example provides a standard framework for the benthic foraminifera which bridges the current discontinuity between molecular and morphological lines of evidence, allowing integration with the traditional Linnaean roots of nomenclature to offer a new prospect for taxonomic stability.}, } @article {pmid27375052, year = {2016}, author = {Wang, C and Shokuhfar, T and Klie, RF}, title = {Precise In Situ Modulation of Local Liquid Chemistry via Electron Irradiation in Nanoreactors Based on Graphene Liquid Cells.}, journal = {Advanced materials (Deerfield Beach, Fla.)}, volume = {28}, number = {35}, pages = {7716-7722}, doi = {10.1002/adma.201602273}, pmid = {27375052}, issn = {1521-4095}, abstract = {A controlled electron-water radiolysis process is used to generate predictable concentrations of radical and ionic species in graphene liquid cells, allowing the concept of a nanoscale chemical reactor. A differential scanning technique is used to generate the desired time- and space-varying electron dose rate. Precise control of the local concentration of H2 , the dominant radiolysis species, is demonstrated experimentally at the nanometer scale.}, } @article {pmid27371560, year = {2016}, author = {Pörtner, HO and Gutt, J}, title = {Impacts of Climate Variability and Change on (Marine) Animals: Physiological Underpinnings and Evolutionary Consequences.}, journal = {Integrative and comparative biology}, volume = {56}, number = {1}, pages = {31-44}, doi = {10.1093/icb/icw019}, pmid = {27371560}, issn = {1557-7023}, mesh = {*Adaptation, Biological ; Animals ; Aquatic Organisms/*physiology ; *Biological Evolution ; *Climate Change ; Invertebrates/physiology ; Oceans and Seas ; *Temperature ; Vertebrates/physiology ; }, abstract = {Understanding thermal ranges and limits of organisms becomes important in light of climate change and observed effects on ecosystems as reported by the IPCC (2014). Evolutionary adaptation to temperature is presently unable to keep animals and other organisms in place; if they can these rather follow the moving isotherms. These effects of climate change on aquatic and terrestrial ecosystems have brought into focus the mechanisms by which temperature and its oscillations shape the biogeography and survival of species. For animals, the integrative concept of oxygen and capacity limited thermal tolerance (OCLTT) has successfully characterized the sublethal limits to performance and the consequences of such limits for ecosystems. Recent models illustrate how routine energy demand defines the realized niche. Steady state temperature-dependent performance profiles thus trace the thermal window and indicate a key role for aerobic metabolism, and the resulting budget of available energy (power), in defining performance under routine conditions, from growth to exercise and reproduction. Differences in the performance and productivity of marine species across latitudes relate to changes in mitochondrial density, capacity, and other features of cellular design. Comparative studies indicate how and why such mechanisms underpinning OCLTT may have developed on evolutionary timescales in different climatic zones and contributed to shaping the functional characteristics and species richness of the respective fauna. A cause-and-effect understanding emerges from considering the relationships between fluctuations in body temperature, cellular design, and performance. Such principles may also have been involved in shaping the functional characteristics of survivors in mass extinction events during earth's history; furthermore, they may provide access to understanding the evolution of endothermy in mammals and birds. Accordingly, an understanding is emerging how climate changes and variability throughout earth's history have influenced animal evolution and co-defined their success or failure from a bio-energetic point of view. Deepening such understanding may further reduce uncertainty about projected impacts of anthropogenic climate variability and change on the distribution, productivity and last not least, survival of aquatic and terrestrial species.}, } @article {pmid27364231, year = {2016}, author = {Longin, CFH and Würschum, T}, title = {Back to the Future - Tapping into Ancient Grains for Food Diversity.}, journal = {Trends in plant science}, volume = {21}, number = {9}, pages = {731-737}, doi = {10.1016/j.tplants.2016.05.005}, pmid = {27364231}, issn = {1878-4372}, mesh = {Breeding ; *Food ; Genetic Variation/genetics/*physiology ; Genotype ; Triticum/genetics/physiology ; }, abstract = {Einkorn, emmer, and spelt are old wheat species that have fed the world for centuries before they have nearly completely been replaced by modern bread wheat. Nowadays, the diversity of these old species lies frozen in gene banks and rare attempts aim to exploit them as a source for genetic diversity in modern wheat breeding. Here, we want to raise a debate on a more holistic exploitation of ancient species via their direct introduction to the consumer market as high quality products. Although exemplified only for ancient wheat species, this innovative self-financing strategy can be directly extended to other species. A central requirement for this concept is intensive communication, coordination, and interdisciplinary research along the entire production chain from farm to fork.}, } @article {pmid27351595, year = {2016}, author = {Walker, LM and Stephenson, SL}, title = {The Species Problem in Myxomycetes Revisited.}, journal = {Protist}, volume = {167}, number = {4}, pages = {319-338}, doi = {10.1016/j.protis.2016.05.003}, pmid = {27351595}, issn = {1618-0941}, mesh = {*Biodiversity ; *Classification ; Myxomycetes/*classification/cytology/genetics/physiology ; }, abstract = {Species identification in the myxomycetes (plasmodial slime molds or myxogastrids) poses particular challenges to researchers as a result of their morphological plasticity and frequent alteration between sexual and asexual life strategies. Traditionally, myxomycete morphology has been used as the primary method of species delimitation. However, with the increasing availability of genetic information, traditional myxomycete taxonomy is being increasingly challenged, and new hypotheses continue to emerge. Due to conflicts that sometimes occur between traditional and more modern species concepts that are based largely on molecular data, there is a pressing need to revisit the discussion surrounding the species concept used for myxomycetes. Biological diversity is being increasingly studied with molecular methods and data accumulates at ever-faster rates, making resolution of this matter urgent. In this review, currently used and potentially useful species concepts (biological, morphological, phylogenetic and ecological) are reviewed, and an integrated approach to resolve the myxomycete species problem is discussed.}, } @article {pmid27343033, year = {2016}, author = {Bartoszek, K}, title = {Phylogenetic effective sample size.}, journal = {Journal of theoretical biology}, volume = {407}, number = {}, pages = {371-386}, doi = {10.1016/j.jtbi.2016.06.026}, pmid = {27343033}, issn = {1095-8541}, mesh = {Animals ; Biodiversity ; Computer Simulation ; Conserved Sequence ; Phenotype ; *Phylogeny ; *Sample Size ; }, abstract = {In this paper I address the question-how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein-Uhlenbeck processes-the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.}, } @article {pmid27328691, year = {2017}, author = {Du, Y and Deng, W and Wang, Z and Ning, M and Zhang, W and Zhou, Y and Lo, EH and Xing, C}, title = {Differential subnetwork of chemokines/cytokines in human, mouse, and rat brain cells after oxygen-glucose deprivation.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {37}, number = {4}, pages = {1425-1434}, pmid = {27328691}, issn = {1559-7016}, support = {R01 NS067139/NS/NINDS NIH HHS/United States ; R01 NS093415/NS/NINDS NIH HHS/United States ; R01 NS094392/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Astrocytes/immunology/metabolism ; Brain/cytology/*immunology/metabolism ; Cell Culture Techniques ; Cells, Cultured ; Chemokines/genetics/*metabolism ; Down-Regulation ; Gene Expression ; Glucose/*metabolism ; Humans ; Interleukins/genetics/*metabolism ; Mice, Inbred C57BL ; Microglia/immunology/metabolism ; Neurons/immunology/metabolism ; Oxygen/*metabolism ; Rats, Sprague-Dawley ; Species Specificity ; Tumor Necrosis Factor-alpha/genetics/*metabolism ; Up-Regulation ; }, abstract = {Mice and rats are the most commonly used animals for preclinical stroke studies, but it is unclear whether targets and mechanisms are always the same across different species. Here, we mapped the baseline expression of a chemokine/cytokine subnetwork and compared responses after oxygen-glucose deprivation in primary neurons, astrocytes, and microglia from mouse, rat, and human. Baseline profiles of chemokines (CX3CL1, CXCL12, CCL2, CCL3, and CXCL10) and cytokines (IL-1α, IL-1β, IL-6, IL-10, and TNFα) showed significant differences between human and rodents. The response of chemokines/cytokines to oxygen-glucose deprivation was also significantly different between species. After 4 h oxygen-glucose deprivation and 4 h reoxygenation, human and rat neurons showed similar changes with a downregulation in many chemokines, whereas mouse neurons showed a mixed response with up- and down-regulated genes. For astrocytes, subnetwork response patterns were more similar in rats and mice compared to humans. For microglia, rat cells showed an upregulation in all chemokines/cytokines, mouse cells had many down-regulated genes, and human cells showed a mixed response with up- and down-regulated genes. This study provides proof-of-concept that species differences exist in chemokine/cytokine subnetworks in brain cells that may be relevant to stroke pathophysiology. Further investigation of differential gene pathways across species is warranted.}, } @article {pmid27302887, year = {2016}, author = {Kaplinsky, J and Arnaout, R}, title = {Robust estimates of overall immune-repertoire diversity from high-throughput measurements on samples.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {11881}, pmid = {27302887}, issn = {2041-1723}, support = {K08 AI114958/AI/NIAID NIH HHS/United States ; R01 AI148747/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; B-Lymphocytes/*immunology ; Computer Simulation ; Genetic Variation ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Reference Standards ; Reproducibility of Results ; T-Lymphocytes/*immunology ; }, abstract = {The diversity of an organism's B- and T-cell repertoires is both clinically important and a key measure of immunological complexity. However, diversity is hard to estimate by current methods, because of inherent uncertainty in the number of B- and T-cell clones that will be missing from a blood or tissue sample by chance (the missing-species problem), inevitable sampling bias, and experimental noise. To solve this problem, we developed Recon, a modified maximum-likelihood method that outputs the overall diversity of a repertoire from measurements on a sample. Recon outputs accurate, robust estimates by any of a vast set of complementary diversity measures, including species richness and entropy, at fractional repertoire coverage. It also outputs error bars and power tables, allowing robust comparisons of diversity between individuals and over time. We apply Recon to in silico and experimental immune-repertoire sequencing data sets as proof of principle for measuring diversity in large, complex systems.}, } @article {pmid27288478, year = {2016}, author = {Mutanen, M and Kivelä, SM and Vos, RA and Doorenweerd, C and Ratnasingham, S and Hausmann, A and Huemer, P and Dincă, V and van Nieukerken, EJ and Lopez-Vaamonde, C and Vila, R and Aarvik, L and Decaëns, T and Efetov, KA and Hebert, PD and Johnsen, A and Karsholt, O and Pentinsaari, M and Rougerie, R and Segerer, A and Tarmann, G and Zahiri, R and Godfray, HC}, title = {Species-Level Para- and Polyphyly in DNA Barcode Gene Trees: Strong Operational Bias in European Lepidoptera.}, journal = {Systematic biology}, volume = {65}, number = {6}, pages = {1024-1040}, pmid = {27288478}, issn = {1076-836X}, mesh = {Animals ; Bias ; Classification/*methods ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Genes, Mitochondrial ; Lepidoptera/*classification/*genetics ; *Phylogeny ; }, abstract = {The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service "Monophylizer" to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric-conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.}, } @article {pmid27265649, year = {2016}, author = {Groves, C}, title = {Systematics of the Artiodactyla of China in the 21(st) century.}, journal = {Dong wu xue yan jiu = Zoological research}, volume = {37}, number = {3}, pages = {119-125}, pmid = {27265649}, issn = {2095-8137}, mesh = {Animals ; Artiodactyla/*classification ; China ; Classification/*methods ; Evolution, Molecular ; }, abstract = {In this paper, I have introduced the concept of the Evolutionary Species, and shown how it affects the taxonomy of the Artiodactyla of China. The "traditional" taxonomy of the Artiodactyla, which has remained almost unchanged for 100 years, relies on ill-formulated notions of species and subspecies, only slightly modified by the population-thinking of the 1930s. Species are populations (or metapopulations) differentiated by the possession of fixed heritable differences from other such populations (or metapopulations). In the Artiodactyla, there are many more species than "traditionally" recognised; this is by no means a drawback, as it enables the units of biodiversity to be identified in a testable fashion, and brings the taxonomy of large mammals into line with that long practised for small mammals. Species are likely to differentiate where there are natural gaps in the distribution of a genus, such as mountain blocks (for example in the genus Budorcas) or otherwise dissected habitat (for example in the genus Cervus). Natural hybridisation between distinct species is not an uncommon phenomenon, again illustrated well in the genus Cervus, where hybridisation between the elaphus and nippon groups occurs today and evidently occurred in the past, as shown by the distribution of mtDNA.}, } @article {pmid27209799, year = {2016}, author = {Bichet, O and Dupuch, A and Hébert, C and Le Borgne, HL and Fortin, D}, title = {Maintaining animal assemblages through single-species management: the case of threatened caribou in boreal forest.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {26}, number = {2}, pages = {612-623}, doi = {10.1890/15-0525}, pmid = {27209799}, issn = {1051-0761}, mesh = {Animals ; Biodiversity ; Birds/classification ; *Endangered Species ; *Forests ; Insecta/classification ; Models, Biological ; Quebec ; Reindeer/*physiology ; Time Factors ; }, abstract = {With the intensification of human activities, preserving animal populations is a contemporary challenge of critical importance. In this context, the umbrella species concept is appealing because preserving a single species should result in the protection of multiple co-occurring species. Practitioners, though, face the task of having to find suitable umbrellas to develop single-species management guidelines. In North America, boreal forests must be managed to facilitate the recovery of the threatened boreal caribou (Rangifer tarandus). Yet, the effect of caribou conservation on co-occurring animal species remains poorly documented. We tested if boreal caribou can constitute an effective umbrella for boreal fauna. Birds, small mammals, and insects were sampled along gradients of post-harvest and post-fire forest succession. Predictive models of occupancy were developed from the responses of 95 species to characteristics of forest stands and their surroundings. We then assessed the similarity of species occupancy expected between simulated harvested landscapes and a 90 000-km2 uncut landscape. Managed landscapes were simulated based on three levels of disturbance, two timber-harvest rotation cycles, and dispersed or aggregated cut-blocks. We found that management guidelines that were more likely to maintain caribou populations should also better preserve animal assemblages. Relative to fragmentation or harvest cycle, we detected a stronger effect of habitat loss on species assemblages. Disturbing 22%, 35%, and 45% of the landscape should result, respectively, in 80%, 60%, and 40% probability for caribou populations to be sustainable; in turn, this should result in regional species assemblages with Jaccard similarity indices of 0.86, 0.79, and 0.74, respectively, relative to the uncut landscape. Our study thus demonstrates the value of single-species management for animal conservation. Our quantitative approach allows for the evaluation of management guidelines prior to implementation, thereby providing a tool for establishing suitable compromises between economic and environmental sustainability of human activities.}, } @article {pmid30159448, year = {2016}, author = {Volis, S}, title = {How to conserve threatened Chinese plant species with extremely small populations?.}, journal = {Plant diversity}, volume = {38}, number = {1}, pages = {45-52}, pmid = {30159448}, issn = {2468-2659}, abstract = {The Chinese flora occupies a unique position in global plant diversity, but is severely threatened. Although biodiversity conservation in China has made significant progress over the past decades, many wild plant species have extremely small population sizes and therefore are in extreme danger of extinction. The concept of plant species with extremely small populations (PSESPs), recently adopted and widely accepted in China, lacks a detailed description of the methodology appropriate for conserving PSESPs. Strategies for seed sampling, reintroduction, protecting PSESP locations, managing interactions with the local human population, and other conservation aspects can substantially differ from those commonly applied to non-PSESPs. The present review is an attempt to provide a detailed conservation methodology with realistic and easy-to-follow guidelines for PSESPs in China.}, } @article {pmid27165412, year = {2016}, author = {Amanfo, SA and Mduluza, T and Midzi, N and Cavanagh, DR and Mutapi, F}, title = {Seroepidemiology of Plasmodium species infections in Zimbabwean population.}, journal = {Malaria journal}, volume = {15}, number = {1}, pages = {267}, pmid = {27165412}, issn = {1475-2875}, support = {//Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Adolescent ; Antibodies, Protozoan/*blood ; Child ; Child, Preschool ; Cohort Studies ; Enzyme-Linked Immunosorbent Assay ; Female ; Humans ; Immunoglobulin G/blood ; Malaria/*epidemiology/*parasitology ; Male ; Merozoite Surface Protein 1/immunology ; Plasmodium/*classification/*immunology ; Seroepidemiologic Studies ; Zimbabwe/epidemiology ; }, abstract = {BACKGROUND: Individuals living in malaria-endemic regions may be exposed to more than one Plasmodium species; there is paucity of data on the distribution of the different species of Plasmodium in affected populations, in part due to the diagnostic method of microscopy, which cannot easily differentiate between the species. Sero-epidemiological data can overcome some of the shortcomings of microscopy.

METHODS: The specificity of IgG antibodies to recombinant merozoite surface protein 1 (MSP-119) derived from four human Plasmodium species (Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae, Plasmodium ovale) was investigated using competition enzyme-linked immunosorbent assay. Subsequently, these antigens were used to determine the exposure prevalence to the different Plasmodium species in serum samples of participants. One-hundred individuals, aged five-18 years, from each of the three Plasmodium meso-endemic Zimbabwean villages (Burma Valley, Mutoko, Chiredzi) were recruited in the study.

RESULTS: The study demonstrated that the host serum reactivity to MSP-119 antigens was species-specific and that no cross-reactivity occurred. The overall prevalence of antibody response to MSP-119 antigens was 61 % in Burma Valley, 31 % in Mutoko and 32 % in Chiredzi. Single species IgG responses to MSP-119 were most frequent against P. falciparum, followed by P. malariae and P. ovale, with responses to P. vivax being the least prevalent. Interestingly, 78-87 and 50 % of sera with IgG responses to P. malariae and P. ovale MSP-119, respectively, also had IgG specific response for P. falciparum MSP-119 antigens, indicating that exposure to these species is a common occurrence in these populations. Single species IgG responses to the non-falciparum species were at a very low frequency, ranging between 0 and 13 % for P. malariae.

CONCLUSIONS: There is evidence of a higher exposure to the non-falciparum parasite species than previously reported in Zimbabwe. The recombinant MSP-119 antigens could be used as additional diagnostic tools in antibody assays for the detection of exposure to the different Plasmodium species. The results also introduce an interesting concept of the co-infection of non-falciparum Plasmodium almost always with P. falciparum, which requires further validation and mechanistic studies.}, } @article {pmid27150030, year = {2016}, author = {Radchenko, V and Bouziotis, P and Tsotakos, T and Paravatou-Petsotas, M and la Fuente, Ad and Loudos, G and Harris, AL and Xanthopoulos, S and Filosofov, D and Hauser, H and Eisenhut, M and Ponsard, B and Roesch, F}, title = {Labeling and preliminary in vivo assessment of niobium-labeled radioactive species: A proof-of-concept study.}, journal = {Nuclear medicine and biology}, volume = {43}, number = {5}, pages = {280-287}, doi = {10.1016/j.nucmedbio.2016.02.003}, pmid = {27150030}, issn = {1872-9614}, mesh = {Animals ; Bevacizumab/chemistry ; Chlorides/chemistry ; Deferoxamine/chemistry ; Drug Stability ; Female ; Half-Life ; Isotope Labeling/*methods ; Mice ; Niobium/*chemistry/pharmacokinetics ; Oxalates/chemistry ; Positron-Emission Tomography ; *Radioisotopes ; Tissue Distribution ; }, abstract = {The application of radionuclide-labeled biomolecules such as monoclonal antibodies or antibody fragments for imaging purposes is called immunoscintigraphy. More specifically, when the nuclides used are positron emitters, such as zirconium-89, the technique is referred to as immuno-PET. Currently, there is an urgent need for radionuclides with a half-life which correlates well with the biological kinetics of the biomolecules under question and which can be attached to the proteins by robust labeling chemistry. (90)Nb is a promising candidate for in vivo immuno-PET, due its half-life of 14.6h and low β(+) energy of Emean=0.35MeV per decay. (95)Nb on the other hand, is a convenient alternative for longer-term ex vivo biodistribution studies, due to its longer half-life of (t½=35days) and its convenient, lower-cost production (reactor-based production). In this proof-of-principle work, the monoclonal antibody bevacizumab (Avastin(®)) was labeled with (95/90)Nb and in vitro and in vivo stability was evaluated in normal Swiss mice and in tumor-bearing SCID mice. Initial ex vivo experiments with (95)Nb-bevacizumab showed adequate tumor uptake, however at the same time high uptake in the liver, spleen and kidneys was observed. In order to investigate whether this behavior is due to instability of (⁎)Nb-bevacizumab or to the creation of other (⁎)Nb species in vivo, we performed biodistribution studies of (95)Nb-oxalate, (95)Nb-chloride and (95)Nb-Df. These potential metabolite species did not show any specific uptake, apart from bone accumulation for (95)Nb-oxalate and (95)Nb-chloride, which, interestingly, may serve as an "indicator" for the release of (90)Nb from labeled biomolecules. Concerning the initial uptake of (95)Nb-bevacizumab in non-tumor tissue, biodistribution of a higher specific activity radiolabeled antibody sample did show only negligible uptake in the liver, spleen, kidneys or bones. In-vivo imaging of a tumor-bearing SCID mouse after injection with (90)Nb-bevacizumab was acquired on an experimental small-animal PET camera, and indeed showed localization of the radiotracer in the tumor area. It is the first time that such results are described in the literature, and indicates promise of application of (90)Nb-labeled antibodies for the purposes of immuno-PET.}, } @article {pmid27142661, year = {2016}, author = {Jankowski, R and Rumeau, C and de Saint Hilaire, T and Tonnelet, R and Nguyen, DT and Gallet, P and Perez, M}, title = {The olfactory fascia: an evo-devo concept of the fibrocartilaginous nose.}, journal = {Surgical and radiologic anatomy : SRA}, volume = {38}, number = {10}, pages = {1161-1168}, pmid = {27142661}, issn = {1279-8517}, mesh = {Adult ; Biological Evolution ; Cadaver ; Developmental Biology ; Dissection ; Ethmoid Bone/anatomy & histology ; Fascia/*anatomy & histology/embryology ; Humans ; Nasal Cartilages/*anatomy & histology/embryology ; Olfactory Mucosa/*anatomy & histology/embryology ; Rhinoplasty/*methods ; }, abstract = {PURPOSE: Evo-devo is the science that studies the link between evolution of species and embryological development. This concept helps to understand the complex anatomy of the human nose. The evo-devo theory suggests the persistence in the adult of an anatomical entity, the olfactory fascia, that unites the cartilages of the nose to the olfactory mucosa.

METHODS: We dissected two fresh specimens. After resecting the superficial tissues of the nose, dissection was focused on the disarticulation of the fibrocartilaginous noses from the facial and skull base skeleton.

RESULTS: Dissection shows two fibrocartilaginous sacs that were invaginated side-by-side in the midface and attached to the anterior skull base. These membranous sacs were separated in the midline by the perpendicular plate of the ethmoid. Their walls contained the alar cartilages and the lateral expansions of the septolateral cartilage, which we had to separate from the septal cartilage. The olfactory mucosa was located inside their cranial ends.

CONCLUSION: The olfactory fascia is a continuous membrane uniting the nasal cartilages to the olfactory mucosa. Its origin can be found in the invagination and differentiation processes of the olfactory placodes. The fibrous portions of the olfactory fascia may be described as ligaments that unit the different components of the olfactory fascia one to the other and the fibrocartilaginous nose to the facial and skull base skeleton. The basicranial ligaments, fixing the fibrocartilaginous nose to the skull base, represent key elements in the concept of septorhinoplasty by disarticulation.}, } @article {pmid27095213, year = {2016}, author = {Arteel, GE}, title = {Leveraging oxidative stress questions in vivo: Implications and limitations.}, journal = {Archives of biochemistry and biophysics}, volume = {595}, number = {}, pages = {40-45}, pmid = {27095213}, issn = {1096-0384}, support = {R01 AA021978/AA/NIAAA NIH HHS/United States ; }, mesh = {Animals ; Humans ; Kinetics ; *Oxidative Stress ; Reactive Nitrogen Species/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {The elegance of Helmut Sies' original definition of oxidative stress belies the complexity of the reactions that are potentially involved. This is by no means a criticism of the author, but rather how the words have been used to oversimplify the concept by some. Reactive oxygen and nitrogen species (ROS and RNS, respectively) can be products of a myriad of events within the living body. Indeed, it is now understood that ROS/RNS are critical for normal cellular metabolism and have beneficial effects (e.g., cytotoxicity against invading bacteria). A general problem of studying prooxidants in vivo is that, due to their inherent reactivity, they generally cannot be measured directly. This indirect detection of 'footprints' leaves a very large black box that we are to this day only beginning to understand. This manuscript will summarize some considerations that are of utmost importance when translating oxidative stress into in vivo research. Helmut has been a key thought leader, researcher and mentor whose contributions to this field are immeasurable.}, } @article {pmid27091389, year = {2016}, author = {Chen, J and Cui, B and He, S and Cooper, JA and Barrett, MD and Chen, J and Song, J and Dai, Y}, title = {Molecular phylogeny and global diversity of the remarkable genus Bondarzewia (Basidiomycota, Russulales).}, journal = {Mycologia}, volume = {108}, number = {4}, pages = {697-708}, doi = {10.3852/14-216}, pmid = {27091389}, issn = {0027-5514}, mesh = {Basidiomycota/*classification/genetics/*isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Phylogeography ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; }, abstract = {Bondarzewia is a remarkable polypore genus due to its relatively large poroid basidiocarps and belongs to order Russulales according to recent phylogenetic analyses. Two species, B. berkeleyi and B. mesenterica, are commonly reported in North America and Europe but the genus is poorly known elsewhere. We explored the phylogeny and species diversity of Bondarzewia based on a larger number of samples covering a wider geographic range, including eastern Asia, Europe, North America, Oceania and South America. Sequences were generated from the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) and nuc 28S rDNA D1-D2 domains (28S), and the final dataset included 28 samples of which 21 ITS and 28S sequences were newly generated. As a result of phylogenetic analyses and comparison of morphological features we propose a new classification of the genus recognizing 10 species. Most of the novel taxonomic concepts are geographically restricted in contrast to the past broad species concepts, especially of B. berkeleyi In addition, a degree of host specificity is observed with B. mesenterica, B. occidentalis, B. podocarpi, B. propria and B. submesenterica apparently restricted to gymnosperms and all others on angiosperm hosts where known. Three new species, B. kirkii, B. occidentalis and B. submesenterica, are described and illustrated. Three new combinations (B. dickinsii, B. propria, B. retipora) are revived from synonymy under B. berkeleyi A key to known species of Bondarzewia is provided.}, } @article {pmid27087822, year = {2016}, author = {Li, S and Tan, HY and Wang, N and Hong, M and Li, L and Cheung, F and Feng, Y}, title = {Substitutes for Bear Bile for the Treatment of Liver Diseases: Research Progress and Future Perspective.}, journal = {Evidence-based complementary and alternative medicine : eCAM}, volume = {2016}, number = {}, pages = {4305074}, pmid = {27087822}, issn = {1741-427X}, abstract = {Bear bile has been a well-known Chinese medicine for thousands of years. Because of the endangered species protection, the concept on substitutes for bear bile was proposed decades ago. Based on their chemical composition and pharmacologic actions, artificial bear bile, bile from other animals, synthetic compounds, and medicinal plants may be the promising candidates to replace bear bile for the similar therapeutic purpose. Accumulating research evidence has indicated that these potential substitutes for bear bile have displayed the same therapeutic effects as bear bile. However, stopping the use of bear bile is a challenging task. In this review, we extensively searched PubMed and CNKI for literatures, focusing on comparative studies between bear bile and its substitutes for the treatment of liver diseases. Recent research progress in potential substitutes for bear bile in the last decade is summarized, and a strategy for the use of substitutes for bear bile is discussed carefully.}, } @article {pmid27074931, year = {2016}, author = {Lee, C and Hong, S and Kwon, BO and Lee, JH and Ryu, J and Park, YG and Kang, SG and Khim, JS}, title = {Lethal and sub-lethal effects of elevated CO2 concentrations on marine benthic invertebrates and fish.}, journal = {Environmental science and pollution research international}, volume = {23}, number = {15}, pages = {14945-14956}, pmid = {27074931}, issn = {1614-7499}, mesh = {Animals ; Aquatic Organisms/*drug effects/growth & development ; Bivalvia/drug effects/growth & development ; Carbon Dioxide/analysis/*toxicity ; Copper/analysis/toxicity ; Fishes/*growth & development ; Hydrogen-Ion Concentration ; Metals/chemistry ; Seawater/chemistry ; Starfish/drug effects/growth & development ; Water Pollutants, Chemical/analysis/*toxicity ; }, abstract = {Concern about leakage of carbon dioxide (CO2) from deep-sea storage in geological reservoirs is increasing because of its possible adverse effects on marine organisms locally or at nearby coastal areas both in sediment and water column. In the present study, we examined how elevated CO2 affects various intertidal epibenthic (benthic copepod), intertidal endobenthic (Manila clam and Venus clam), sub-tidal benthic (brittle starfish), and free-living (marine medaka) organisms in areas expected to be impacted by leakage. Acute lethal and sub-lethal effects were detected in the adult stage of all test organisms exposed to varying concentrations of CO2, due to the associated decline in pH (8.3 to 5.2) during 96-h exposure. However, intertidal organisms (such as benthic copepods and clams) showed remarkable resistance to elevated CO2, with the Venus clam being the most tolerant (LpH50 = 5.45). Sub-tidal species (such as brittle starfish [LpH50 = 6.16] and marine medaka [LpH50 = 5.91]) were more sensitive to elevated CO2 compared to intertidal species, possibly because they have fewer defensive capabilities. Of note, the exposure duration might regulate the degree of acute sub-lethal effects, as evidenced by the Venus clam, which showed a time-dependent effect to elevated CO2. Finally, copper was chosen as a model toxic element to find out the synergistic or antagonistic effects between ocean acidification and metal pollution. Combination of CO2 and Cu exposure enhances the adverse effects to organisms, generally supporting a synergistic effect scenario. Overall, the significant variation in the degree to which CO2 adversely affected organisms (viz., working range and strength) was clearly observed, supporting the general concept of species-dependent effects of elevated CO2.}, } @article {pmid27057123, year = {2016}, author = {Nair, AB and Jacob, S}, title = {A simple practice guide for dose conversion between animals and human.}, journal = {Journal of basic and clinical pharmacy}, volume = {7}, number = {2}, pages = {27-31}, pmid = {27057123}, issn = {0976-0105}, abstract = {Understanding the concept of extrapolation of dose between species is important for pharmaceutical researchers when initiating new animal or human experiments. Interspecies allometric scaling for dose conversion from animal to human studies is one of the most controversial areas in clinical pharmacology. Allometric approach considers the differences in body surface area, which is associated with animal weight while extrapolating the doses of therapeutic agents among the species. This review provides basic information about translation of doses between species and estimation of starting dose for clinical trials using allometric scaling. The method of calculation of injection volume for parenteral formulation based on human equivalent dose is also briefed.}, } @article {pmid27054895, year = {2016}, author = {Sepúlveda, D and Lorenzen, N}, title = {Can VHS Virus Bypass the Protective Immunity Induced by DNA Vaccination in Rainbow Trout?.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153306}, pmid = {27054895}, issn = {1932-6203}, mesh = {Animals ; Antibodies, Viral/*immunology ; Fish Diseases/*immunology ; Novirhabdovirus/*immunology ; Oncorhynchus mykiss/*immunology ; Rhabdoviridae Infections/*immunology/prevention & control/virology ; Vaccination ; Vaccines, DNA/*administration & dosage ; Viral Vaccines/*administration & dosage ; }, abstract = {DNA vaccines encoding viral glycoproteins have been very successful for induction of protective immunity against diseases caused by rhabdoviruses in cultured fish species. However, the vaccine concept is based on a single viral gene and since RNA viruses are known to possess high variability and adaptation capacity, this work aimed at evaluating whether viral haemorrhagic septicaemia virus (VHSV), an RNA virus and member of Rhabdoviridae family, was able to evade the protective immune response induced by the DNA vaccination of rainbow trout. The experiments comprised repeated passages of a highly pathogenic VHSV isolate in a fish cell line in the presence of neutralizing fish serum (in vitro approach), and in rainbow trout immunized with the VHS DNA vaccine (in vivo approach). For the in vitro approach, the virus collected from the last passage (passaged virus) was as sensitive as the parental virus to serum neutralization, suggesting that the passaging did not promote the selection of virus populations able to bypass the neutralization by serum antibodies. Also, in the in vivo approach, where virus was passaged several times in vaccinated fish, no increased virulence nor increased persistence in vaccinated fish was observed in comparison with the parental virus. However, some of the vaccinated fish did get infected and could transmit the infection to naïve cohabitant fish. The results demonstrated that the DNA vaccine induced a robust protection, but also that the immunity was non-sterile. It is consequently important not to consider vaccinated fish as virus free in veterinary terms.}, } @article {pmid27033204, year = {2016}, author = {Han, JG and Hyun, MW and Kim, CS and Jo, JW and Cho, JH and Lee, KH and Kong, WS and Han, SK and Oh, J and Sung, GH}, title = {Species identity of Phellinus linteus (sanghuang) extensively used as a medicinal mushroom in Korea.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {54}, number = {4}, pages = {290-295}, pmid = {27033204}, issn = {1976-3794}, mesh = {Basidiomycota/*classification/genetics ; DNA, Fungal/genetics ; DNA, Intergenic/genetics ; Medicine, Korean Traditional ; Phylogeny ; Republic of Korea ; }, abstract = {Sanghuang is a medicinal mushroom that has gained particular attention in Korea. It has been extensively studied for the past few decades as a natural immune booster and cancer suppressor. Although the scientific name, Phellinus linteus, has been commonly used to refer to the sanghuang mushroom, the species identity of sanghuang has been called into question due to the ambiguity of its circumscription and the inadequacy of morphological distinctions within allied species. Because the species concept of sanghuang has been elucidated by recent molecular phylogenetic studies, it has become necessary to clarify the taxonomic positions of sanghuang strains extensively utilized in Korea. We conducted a phylogenetic analysis of 74 strains belonging to the P. linteus-baumii complex based on ITS nrDNA sequences. Parental stains of sanghuang varieties formally registered in the Korea Seed & Variety Service, including ASI 26046 (Corea sanghuang), 26114 (Boolro), and 26115 (HK 1-ho) were grouped with Sanghuangporus sanghuang instead of P. linteus in the inferred phylogeny.}, } @article {pmid27028195, year = {2016}, author = {Malavasi, V and Škaloud, P and Rindi, F and Tempesta, S and Paoletti, M and Pasqualetti, M}, title = {DNA-Based Taxonomy in Ecologically Versatile Microalgae: A Re-Evaluation of the Species Concept within the Coccoid Green Algal Genus Coccomyxa (Trebouxiophyceae, Chlorophyta).}, journal = {PloS one}, volume = {11}, number = {3}, pages = {e0151137}, pmid = {27028195}, issn = {1932-6203}, mesh = {Chlorophyta/classification/*genetics/ultrastructure ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Evolution, Molecular ; Microalgae/classification/*genetics/ultrastructure ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Coccomyxa is a genus of unicellular green algae of the class Trebouxiophyceae, well known for its cosmopolitan distribution and great ecological amplitude. The taxonomy of this genus has long been problematic, due to reliance on badly-defined and environmentally variable morphological characters. In this study, based on the discovery of a new species from an extreme habitat, we reassess species circumscription in Coccomyxa, a unicellular genus of the class Trebouxiophyceae, using a combination of ecological and DNA sequence data (analyzed with three different methods of algorithmic species delineation). Our results are compared with those of a recent integrative study of Darienko and colleagues that reassessed the taxonomy of Coccomyxa, recognizing 7 species in the genus. Expanding the dataset from 43 to 61 sequences (SSU + ITS rDNA) resulted in a different delimitation, supporting the recognition of a higher number of species (24 to 27 depending on the analysis used, with the 27-species scenario receiving the strongest support). Among these, C. melkonianii sp. nov. is described from material isolated from a river highly polluted by heavy metals (Rio Irvi, Sardinia, Italy). Analyses performed on ecological characters detected a significant phylogenetic signal in six different characters. We conclude that the 27-species scenario is presently the most realistic for Coccomyxa and we suggest that well-supported lineages distinguishable by ecological preferences should be recognized as different species in this genus. We also recommend that for microbial lineages in which the overall diversity is unknown and taxon sampling is sparse, as is often the case for green microalgae, the results of analyses for algorithmic DNA-based species delimitation should be interpreted with extreme caution.}, } @article {pmid26994861, year = {2016}, author = {Franco-Trecu, V and Abud, C and Feijoo, M and Kloetzer, G and Casacuberta, M and Costa-Urrutia, P}, title = {Sex beyond species: the first genetically analyzed case of intergeneric fertile hybridization in pinnipeds.}, journal = {Evolution & development}, volume = {18}, number = {2}, pages = {127-136}, doi = {10.1111/ede.12183}, pmid = {26994861}, issn = {1525-142X}, mesh = {Animals ; Feeding Behavior ; Female ; Fur Seals/*genetics/physiology ; *Hybridization, Genetic ; Male ; Phylogeny ; Sea Lions/*genetics/physiology ; }, abstract = {A species, according to the biological concept, is a natural group of potentially interbreeding individuals isolated by diverse mechanisms. Hybridization is considered the production of offspring resulting from the interbreeding of two genetically distinct taxa. It has been documented in over 10% of wild animals, and at least in 34 cases for Artic marine mammals. In Otariids, intergeneric hybridization has been reported though neither confirming it through genetic analyses nor presenting evidence of fertile offspring. In this study, we report the finding of a hybrid adult female between a South American fur seal (Arctocephalus australis) and a South American sea lion (Otaria byronia), and its offspring, a male pup, in Uruguay. Further based on morphological constraints and breeding seasons, sex-biased hybridization between the two species is hypothesized. Morphological and genetic (nuclear and mitochondrial) results confirm de hybrid nature of the female-pup pair. Here we discuss a genetic dilution effect, considering other hybridization events must be occurring, and how isolation mechanisms could be circumvented. Moreover, the results obtained from stable isotope analysis suggest feeding habits may be a trait transmitted maternally, leading to consider broader issues regarding hybridization as an evolutionary innovation phenomenon.}, } @article {pmid26987087, year = {2016}, author = {Spalding, HL and Conklin, KY and Smith, CM and O'Kelly, CJ and Sherwood, AR}, title = {New Ulvaceae (Ulvophyceae, Chlorophyta) from mesophotic ecosystems across the Hawaiian Archipelago.}, journal = {Journal of phycology}, volume = {52}, number = {1}, pages = {40-53}, doi = {10.1111/jpy.12375}, pmid = {26987087}, issn = {1529-8817}, mesh = {Chlorophyta/classification ; Ecosystem ; Hawaii ; Marine Biology/instrumentation/methods ; *Phylogeny ; Seaweed/classification/genetics ; Ulva/*classification/genetics/physiology ; }, abstract = {Ulvalean algae (Chlorophyta) are most commonly described from intertidal and shallow subtidal marine environments worldwide, but are less well known from mesophotic environments. Their morphological simplicity and phenotypic plasticity make accurate species determinations difficult, even at the generic level. Here, we describe the mesophotic Ulvales species composition from 13 locations across 2,300 km of the Hawaiian Archipelago. Twenty-eight representative Ulvales specimens from 64 to 125 m depths were collected using technical diving, submersibles, and remotely operated vehicles. Morphological and molecular characters suggest that mesophotic Ulvales in Hawaiian waters form unique communities comprising four species within the genera Ulva and Umbraulva, each with discrete geographic and/or depth-related distributional patterns. Three genetically distinct taxa are supported by both plastid (rbcL and tufA) and nuclear (ITS1) markers, and are presented here as new species: Umbraulva kaloakulau, Ulva ohiohilulu, and Ulva iliohaha. We also propose a new Umbraulva species (Umbraulva kuaweuweu), which is closely related to subtidal records from New Zealand and Australia, but not formally described. To our knowledge, these are the first marine species descriptions from Hawai'i resulting from the collaboration of traditional Hawaiian nomenclature specialists, cultural practitioners and scientists. The difficulty of finding reliable diagnostic morphological characters for these species reflects a common problem worldwide of achieving accurate identification of ulvalean taxa using solely morphological criteria. Mesophotic Ulvales appear to be distinct from shallow-water populations in Hawai'i, but their degree of similarity to mesophotic floras in other locations in the Pacific remains unknown.}, } @article {pmid26986533, year = {2015}, author = {Darienko, T and Pröschold, T}, title = {Genetic variability and taxonomic revision of the genus Auxenochlorella (Shihira et Krauss) Kalina et Puncocharova (Trebouxiophyceae, Chlorophyta).}, journal = {Journal of phycology}, volume = {51}, number = {2}, pages = {394-400}, doi = {10.1111/jpy.12279}, pmid = {26986533}, issn = {1529-8817}, abstract = {The monotypic genus Auxenochlorella with its type species A. protothecoides is so far only known from specific habitats such as the sap of several tree species. Several varieties were described according to physiological performances in culture on different organic substrates. However, two strains designated as Auxenochlorella were isolated from other habitats (an endosymbiont of Hydra viridis and an aquatic strain from an acidic volcano stream). We studied those isolates and compared them with six strains of Auxenochlorella belonging to different varieties. The integrative approach used in this study revealed that all strains showed similar morphology but differed in their SSU and ITS rDNA sequences. The Hydra endosymbiont formed a sister taxon to A. protothecoides, which included the varieties protothecoides, galactophila, and communis. The variety acidicola is not closely related to Auxenochlorella and represented its own lineage within the Trebouxiophyceae. In view of these results, we propose a new species of Auxenochlorella, A. symbiontica, for the Hydra symbiont, and a new genus Pumiliosphaera, with its type species, P. acidophila, for acidophilic strain. These results are supported by several compensatory base changes in the conserved region of ITS-2 and ITS-2 DNA barcodes.}, } @article {pmid26955194, year = {2015}, author = {Lombard, L and Chen, SF and Mou, X and Zhou, XD and Crous, PW and Wingfield, MJ}, title = {New species, hyper-diversity and potential importance of Calonectria spp. from Eucalyptus in South China.}, journal = {Studies in mycology}, volume = {80}, number = {}, pages = {151-188}, pmid = {26955194}, issn = {0166-0616}, abstract = {Plantation forestry is expanding rapidly in China to meet an increasing demand for wood and pulp products globally. Fungal pathogens including species of Calonectria represent a serious threat to the growth and sustainability of this industry. Surveys were conducted in the Guangdong, Guangxi and Hainan Provinces of South China, where Eucalyptus trees in plantations or cuttings in nurseries displayed symptoms of leaf blight. Isolations from symptomatic leaves and soils collected close to infected trees resulted in a large collection of Calonectria isolates. These isolates were identified using the Consolidated Species Concept, employing morphological characters and DNA sequence comparisons for the β-tubulin, calmodulin, histone H3 and translation elongation factor 1-alpha gene regions. Twenty-one Calonectria species were identified of which 18 represented novel taxa. Of these, 12 novel taxa belonged to Sphaero-Naviculate Group and the remaining six to the Prolate Group. Southeast Asia appears to represent a centre of biodiversity for the Sphaero-Naviculate Group and this fact could be one of the important constraints to Eucalyptus forestry in China. The remarkable diversity of Calonectria species in a relatively small area of China and associated with a single tree species is surprising.}, } @article {pmid26912890, year = {2016}, author = {Öpik, M and Davison, J and Moora, M and Pärtel, M and Zobel, M}, title = {Response to Comment on "Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism".}, journal = {Science (New York, N.Y.)}, volume = {351}, number = {6275}, pages = {826}, doi = {10.1126/science.aad5495}, pmid = {26912890}, issn = {1095-9203}, mesh = {Animals ; *Ecosystem ; Humans ; *Mycorrhizae ; Plant Roots/*microbiology ; *Symbiosis ; }, abstract = {Bruns and Taylor argue that our finding of widespread distribution among Glomeromycota "virtual taxa" is undermined by the species definition applied. Although identifying appropriate species concepts and accessing taxonomically informative traits are challenges for microorganism biogeography, the virtual taxa represent a pragmatic classification that corresponds approximately to the species rank of classical Glomeromycota taxonomy, yet is applicable to environmental DNA.}, } @article {pmid26899167, year = {2016}, author = {Zou, S and Li, Q}, title = {Pay Attention to the Overlooked Cryptic Diversity in Existing Barcoding Data: the Case of Mollusca with Character-Based DNA Barcoding.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {18}, number = {3}, pages = {327-335}, pmid = {26899167}, issn = {1436-2236}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources ; DNA/genetics ; DNA Barcoding, Taxonomic/*statistics & numerical data ; Electron Transport Complex IV ; *Genetic Speciation ; Genetic Variation ; Mollusca/*classification/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {With the global biodiversity crisis, DNA barcoding aims for fast species identification and cryptic species diversity revelation. For more than 10 years, large amounts of DNA barcode data have been accumulating in publicly available databases, most of which were conducted by distance or tree-building methods that have often been argued, especially for cryptic species revelation. In this context, overlooked cryptic diversity may exist in the available barcoding data. The character-based DNA barcoding, however, has a good chance for detecting the overlooked cryptic diversity. In this study, marine mollusk was as the ideal case for detecting the overlooked potential cryptic species from existing cytochrome c oxidase I (COI) sequences with character-based DNA barcode. A total of 1081 COI sequences of mollusks, belonging to 176 species of 25 families of Gastropoda, Cephalopoda, and Lamellibranchia, were conducted by character analysis. As a whole, the character-based barcoding results were consistent with previous distance and tree-building analysis for species discrimination. More importantly, quite a number of species analyzed were divided into distinct clades with unique diagnostical characters. Based on the concept of cryptic species revelation of character-based barcoding, these species divided into separate taxonomic groups might be potential cryptic species. The detection of the overlooked potential cryptic diversity proves that the character-based barcoding mode possesses more advantages of revealing cryptic biodiversity. With the development of DNA barcoding, making the best use of barcoding data is worthy of our attention for species conservation.}, } @article {pmid26893959, year = {2016}, author = {Barrett, PZ}, title = {Taxonomic and systematic revisions to the North American Nimravidae (Mammalia, Carnivora).}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e1658}, pmid = {26893959}, issn = {2167-8359}, abstract = {The Nimravidae is a family of extinct carnivores commonly referred to as "false saber-tooth cats." Since their initial discovery, they have prompted difficulty in taxonomic assignments and number of valid species. Past revisions have only examined a handful of genera, while recent advances in cladistic and morphometric analyses have granted us additional avenues to answering questions regarding our understanding of valid nimravid taxa and their phylogenetic relationships. To resolve issues of specific validity, the phylogenetic species concept (PSC) was utilized to maintain consistency in diagnosing valid species, while simultaneously employing character and linear morphometric analyses for confirming the validity of taxa. Determined valid species and taxonomically informative characters were then employed in two differential cladistic analyses to create competing hypotheses of interspecific relationships. The results suggest the validity of twelve species and six monophyletic genera. The first in depth reviews of Pogonodon and Dinictis returned two valid species (P. platycopis, P. davisi) for the former, while only one for the latter (D. felina). The taxonomic validity of Nanosmilus is upheld. Two main clades with substantial support were returned for all cladistic analyses, the Hoplophoneini and Nimravini, with ambiguous positions relative to these main clades for the European taxa: Eofelis, Dinailurictis bonali, and Quercylurus major; and the North American taxa Dinictis and Pogonodon. Eusmilus is determined to represent a non-valid genus for North American taxa, suggesting non-validity for Old World nimravid species as well. Finally, Hoplophoneus mentalis is found to be a junior synonym of Hoplophoneus primaevus, while the validity of Hoplophoneus oharrai is reinstated.}, } @article {pmid26886443, year = {2016}, author = {Rezaei-Matehkolaei, A and Rafiei, A and Makimura, K and Gräser, Y and Gharghani, M and Sadeghi-Nejad, B}, title = {Epidemiological Aspects of Dermatophytosis in Khuzestan, southwestern Iran, an Update.}, journal = {Mycopathologia}, volume = {181}, number = {7-8}, pages = {547-553}, pmid = {26886443}, issn = {1573-0832}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Arthrodermataceae/*classification/genetics/*isolation & purification ; Child ; Child, Preschool ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Female ; Humans ; Infant ; Iran/epidemiology ; Male ; Microbiological Techniques ; Microscopy ; Middle Aged ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Prospective Studies ; Sequence Analysis, DNA ; Tinea/*epidemiology/*microbiology ; Young Adult ; }, abstract = {Dermatophytosis is among the most common superficial mycoses in Iran. The purpose of this report was to update the clinical and mycological features of human dermatophytosis in the Khuzestan, southwestern Iran. In the framework of a one-year survey, a total of 4120 skin, hair and nail samples obtained from the outpatients with symptoms suggestive of tinea were analyzed by using direct microscopy, culture and molecular identification methods. Strains isolated from cultures were subjected to amplification of the nuclear rDNA ITS regions in a PCR assay followed by an early established RFLP analysis. For confirmation of species identification, 100 isolates as representatives of all presumable species were subjected to ITS sequencing. Infection was confirmed in 1123 individuals (27.25 %) in the age range of 1-89 years by direct microscopy and/or culture including 603 males versus 520 females. Frequencies of infections were the highest and the lowest in age groups of 21-30 and 11-20 years, respectively. Tinea corporis was the most prevalent clinical manifestation followed by tinea cruris, tinea capitis, tinea manuum, tinea pedis, tinea unguium, tinea faciei and tinea barbae. Trichophyton interdigitale (58.7 %) was the most dominant isolate followed by Epidermophyton floccosum (35.4 %), Microsporum canis (3 %), T. rubrum (1.5 %), T. species of Arthroderma benhamiae (0.5 %), T. tonsurans (0.3 %) and T. violaceum (0.3 %). Other species included M. gypseum, M. fulvum and T. verrucosum (each one 0.1 %). Such a high occurrence of infection with T. interdigitale, which has not been reported from Iran, is due to the use of accurate molecular methods based on new species concept in dermatophytes. The prevalence of dermatophytoses caused by zoophilic species remarkably increased and Trichophyton species of A. benhamiae has emerged as a new agent of dermatophytosis in southwestern Iran, while infections due to anthropophilic species, except E. floccosum, took a decreasing trend.}, } @article {pmid26884102, year = {2016}, author = {Jarvis, ED}, title = {Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class.}, journal = {Annual review of animal biosciences}, volume = {4}, number = {}, pages = {45-59}, doi = {10.1146/annurev-animal-021815-111216}, pmid = {26884102}, issn = {2165-8110}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Algorithms ; Animals ; Birds/classification/*genetics ; Evolution, Molecular ; Genome/*genetics ; Genome-Wide Association Study ; *Genomics/trends ; Molecular Sequence Annotation ; Phylogeny ; Vertebrates/classification/genetics ; }, abstract = {The rapid pace of advances in genome technology, with concomitant reductions in cost, makes it feasible that one day in our lifetime we will have available extant genomes of entire classes of species, including vertebrates. I recently helped cocoordinate the large-scale Avian Phylogenomics Project, which collected and sequenced genomes of 48 bird species representing most currently classified orders to address a range of questions in phylogenomics and comparative genomics. The consortium was able to answer questions not previously possible with just a few genomes. This success spurred on the creation of a project to sequence the genomes of at least one individual of all extant ∼10,500 bird species. The initiation of this project has led us to consider what questions now impossible to answer could be answered with all genomes, and could drive new questions now unimaginable. These include the generation of a highly resolved family tree of extant species, genome-wide association studies across species to identify genetic substrates of many complex traits, redefinition of species and the species concept, reconstruction of the genomes of common ancestors, and generation of new computational tools to address these questions. Here I present visions for the future by posing and answering questions regarding what scientists could potentially do with available genomes of an entire vertebrate class.}, } @article {pmid26868901, year = {2016}, author = {Ahmadi, B and Mirhendi, H and Makimura, K and de Hoog, GS and Shidfar, MR and Nouripour-Sisakht, S and Jalalizand, N}, title = {Phylogenetic analysis of dermatophyte species using DNA sequence polymorphism in calmodulin gene.}, journal = {Medical mycology}, volume = {54}, number = {5}, pages = {500-514}, doi = {10.1093/mmy/myw004}, pmid = {26868901}, issn = {1460-2709}, mesh = {Arthrodermataceae/*classification/*genetics ; Calmodulin/*genetics ; Cluster Analysis ; DNA, Ribosomal Spacer/genetics ; Humans ; Mycology/*methods ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; Tubulin/genetics ; }, abstract = {Use of phylogenetic species concepts based on rDNA internal transcribe spacer (ITS) regions have improved the taxonomy of dermatophyte species; however, confirmation and refinement using other genes are needed. Since the calmodulin gene has not been systematically used in dermatophyte taxonomy, we evaluated its intra- and interspecies sequence variation as well as its application in identification, phylogenetic analysis, and taxonomy of 202 strains of 29 dermatophyte species. A set of primers was designed and optimized to amplify the target followed by bilateral sequencing. Using pairwise nucleotide comparisons, a mean similarity of 81% was observed among 29 dermatophyte species, with inter-species diversity ranging from 0 to 200 nucleotides (nt). Intraspecies nt differences were found within strains of Trichophyton interdigitale, Arthroderma simii, T. rubrum and A. vanbreuseghemii, while T. tonsurans, T. violaceum, Epidermophyton floccosum, Microsporum canis, M. audouinii, M. cookei, M. racemosum, M. gypseum, T. mentagrophytes, T schoenleinii, and A. benhamiae were conserved. Strains of E. floccosum/M. racemosum/M. cookei, A. obtosum/A. gertleri, T. tonsurans/T. equinum and a genotype of T. interdigitale had identical calmodulin sequences. For the majority of the species, tree topology obtained for calmodulin gene showed a congruence with coding and non-coding regions including ITS, BT2, and Tef-1α. Compared with the phylogenetic tree derived from ITS, BT2, and Tef-1α genes, some species such as E. floccosum and A. gertleri took relatively remote positions. Here, characterization and obtained dendrogram of calmodulin gene on a broad range of dermatophyte species provide a basis for further discovery of relationships between species. Studies of other loci are necessary to confirm the results.}, } @article {pmid26860271, year = {2016}, author = {Jiang, W and He, H and Li, Y and Ren, M and Ma, Y and Zheng, L and Zhu, J and Yu, W}, title = {Taxonomic status and molecular phylogeography of two sibling species of Polytremis (Lepidoptera: Hesperiidae).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {20820}, pmid = {26860271}, issn = {2045-2322}, mesh = {Animals ; China ; Evolution, Molecular ; Female ; Lepidoptera/*classification/*genetics ; Male ; *Phylogeography ; Sequence Analysis, DNA ; }, abstract = {The skipper Polytremis theca species complex is widely distributed in the south of the Qinling Mountains in China. A recent study of the Polytremis genus suggested that this species might encompass two differentiated lineages. We tested this hypothesis, by carrying out a phylogenetic study of this agricultural pest based on nationwide sampling and the evaluation of mitochondrial and nuclear DNA markers. We show that this species is actually an amalgamation of two sibling taxa (P. t. theca and P. t. fukia), which displayed levels of genetic divergence as great as those generally found between sister species in the Polytremis genus, suggesting that they actually correspond to two distinct species. The Divergence time estimates suggest that an active period of speciation within Polytremis occurred within the Pleistocene eras. Based on its distinct phylogenetic placement and geographical isolation, we suggest that the subspecies should be elevated to full species status under the phylogenetic species concept, which has significant management implications.}, } @article {pmid26856386, year = {2016}, author = {Liu, B and He, J and Zeng, F and Lei, J and Arndt, SK}, title = {Life span and structure of ephemeral root modules of different functional groups from a desert system.}, journal = {The New phytologist}, volume = {211}, number = {1}, pages = {103-112}, doi = {10.1111/nph.13880}, pmid = {26856386}, issn = {1469-8137}, mesh = {China ; Desert Climate ; Ecosystem ; Magnoliopsida/anatomy & histology/physiology ; Morus/anatomy & histology/physiology ; Nitrogen/metabolism ; Plant Roots/*anatomy & histology/*physiology ; Plants/*anatomy & histology ; Populus/anatomy & histology/physiology ; Time Factors ; Trees ; }, abstract = {The terminal branch orders of plant root systems have been proposed as short-lived 'ephemeral' modules specialized for resource absorption. The occurrence of ephemeral root modules has so far only been reported for a temperate tree species and it is unclear if the concept also applies to other woody (shrub, tree) and herb species. Fine roots of 12 perennial dicotyledonous herb, shrub and tree species were monitored for two growing seasons using a branch-order classification, sequential sampling and rhizotrons in the Taklamakan desert. Two root modules existed in all three plant functional groups. Among the first five branch orders, the first two (perennial herbs, shrubs) or three (trees) root orders were ephemeral and had a primary anatomical structure, high nitrogen (N) concentrations, high respiration rates and very short life spans of 1-4 months, whereas the last two branch orders in all functional groups were perennial, with thicker diameters, no or collapsed cortex, distinct secondary growth, low N concentrations, low respiration rates, but much longer life spans. Ephemeral, short-lived root modules and long-lived, persistent root modules seem to be a general feature across many plant functional groups and could represent a basic root system design.}, } @article {pmid26834710, year = {2015}, author = {Melendrez, MC and Becraft, ED and Wood, JM and Olsen, MT and Bryant, DA and Heidelberg, JF and Rusch, DB and Cohan, FM and Ward, DM}, title = {Recombination Does Not Hinder Formation or Detection of Ecological Species of Synechococcus Inhabiting a Hot Spring Cyanobacterial Mat.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1540}, pmid = {26834710}, issn = {1664-302X}, abstract = {Recent studies of bacterial speciation have claimed to support the biological species concept-that reduced recombination is required for bacterial populations to diverge into species. This conclusion has been reached from the discovery that ecologically distinct clades show lower rates of recombination than that which occurs among closest relatives. However, these previous studies did not attempt to determine whether the more-rapidly recombining close relatives within the clades studied may also have diversified ecologically, without benefit of sexual isolation. Here we have measured the impact of recombination on ecological diversification within and between two ecologically distinct clades (A and B') of Synechococcus in a hot spring microbial mat in Yellowstone National Park, using a cultivation-free, multi-locus approach. Bacterial artificial chromosome (BAC) libraries were constructed from mat samples collected at 60°C and 65°C. Analysis of multiple linked loci near Synechococcus 16S rRNA genes showed little evidence of recombination between the A and B' lineages, but a record of recombination was apparent within each lineage. Recombination and mutation rates within each lineage were of similar magnitude, but recombination had a somewhat greater impact on sequence diversity than mutation, as also seen in many other bacteria and archaea. Despite recombination within the A and B' lineages, there was evidence of ecological diversification within each lineage. The algorithm Ecotype Simulation identified sequence clusters consistent with ecologically distinct populations (ecotypes), and several hypothesized ecotypes were distinct in their habitat associations and in their adaptations to different microenvironments. We conclude that sexual isolation is more likely to follow ecological divergence than to precede it. Thus, an ecology-based model of speciation appears more appropriate than the biological species concept for bacterial and archaeal diversification.}, } @article {pmid26827928, year = {2016}, author = {Machado Pagani, D and Brandão, LR and Santos, ARO and Felix, CR and Pais Ramos, J and Broetto, L and Scorzetti, G and Fell, JW and Augusto Rosa, C and Valente, P and Fontes Landell, M}, title = {Papiliotrema leoncinii sp. nov. and Papiliotrema miconiae sp. nov., two tremellaceous yeast species from Brazil.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {66}, number = {4}, pages = {1799-1806}, doi = {10.1099/ijsem.0.000945}, pmid = {26827928}, issn = {1466-5034}, mesh = {Basidiomycota/*classification/genetics/isolation & purification ; Brazil ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Flowers/microbiology ; Genes, rRNA ; Melastomataceae/*microbiology ; Molecular Sequence Data ; Mycological Typing Techniques ; *Phylogeny ; Plant Leaves/microbiology ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {Two yeast species, Papiliotrema leoncinii sp. nov. and Papiliotrema miconiae sp. nov., in the family Rhynchogastremataceae of the Tremellales are proposed. The two species are related to six species of the genus Papiliotrema: Papiliotrema aureus, P. flavescens, P. terrestris, P. baii, P. ruineniae and P. wisconsinensis. The novel species are proposed on the basis of the sequence-based phylogenetic species concept with analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region. A total of 16 strains of Papiliotrema leoncinii sp. nov. were obtained from freshwater and bromeliad leaves collected in Brazil. Papiliotrema leoncinii sp. nov. differs by 11, 12, 16, 14, 11 and 13 substitutions in the D1/D2 domain from the related species P. aureus, P. flavescens, P. terrestris, P. baii, P. ruineniae and P. wisconsinensis, respectively. Differences of 11 substitutions and 21 or more substitutions in ITS regions were found when the sequences of Papiliotrema leoncinii sp. nov. were compared with P. wisconsinensis and its closest relatives. The type strain of Papiliotrema leoncinii sp. nov. is UFMG-CM-Y374T (=CBS 13918T). Papiliotrema miconiae sp. nov. is represented by two strains isolated from a flower of Miconia sp. and a water sample in Brazil. Papiliotrema miconiae sp. nov. differs from the related species P. aureus and P. ruineniae by eight substitutions, from P. flavescens and P. terrestris by 11 substitutions, from P. baii by 10 substitutions and from P. wisconsinensis by 6 substitutions in the D1/D2 domain, and by 7 substitutions from P. wisconsinensis and more than 19 substitutions in the ITS region from its closest relatives. The type strain of Papiliotrema miconiae sp. nov. is CBS 8358T (ML 3666T=DBVPG-4492T). The MycoBank numbers for Papiliotrema leoncinii sp. nov. and Papiliotrema miconiae sp. nov. are MB 813594 and MB 814882, respectively.}, } @article {pmid30121071, year = {2016}, author = {Jiang, Y and Zhang, Y and Guo, YH}, title = {[Research Progress of DNA Barcoding Technique in Mollusca Taxonomy].}, journal = {Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology & parasitic diseases}, volume = {34}, number = {1}, pages = {80-83}, pmid = {30121071}, issn = {1000-7423}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV ; *Mollusca ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {DNA barcoding technique is a fast and accurate method for species identification. Currently, the barcoding using cytochrome oxidase Ⅰ(COI) gene has been successfully applied for identification of mollusca species. This paper introduces the concept, advantages and limitations of DNA barcoding, and gives an overview on its recent applications in mollusca taxonomy, particularly in classification of mollusca of medical importance. Research on COI gene sequence is also updated.}, } @article {pmid26823631, year = {2015}, author = {Eberhardt, U and Beker, HJ and Vesterholt, J}, title = {Decrypting the Hebeloma crustuliniforme complex: European species of Hebeloma section Denudata subsection Denudata (Agaricales).}, journal = {Persoonia}, volume = {35}, number = {}, pages = {101-147}, pmid = {26823631}, issn = {0031-5850}, abstract = {Hebeloma subsection Denudata includes the type of H. section Denudata, Hebeloma crustuliniforme, as well as the majority of the taxa commonly included in the Hebeloma crustuliniforme complex. Complementing the work of D.K. Aanen and co-workers, and using refined morphological and molecular methods we were able to recognize further individual taxa within the section. Fifteen species occurring in Europe are assigned to H. subsect. Denudata. Of these, we describe eight species as new, namely H. aanenii, H. aurantioumbrinum, H. geminatum, H. louiseae, H. luteicystidiatum, H. pallidolabiatum, H. perexiguum and H. salicicola. Naucoria bellotiana, a species very similar to H. alpinum is recombined into Hebeloma. A key to Hebeloma subsect. Denudata is provided. We demonstrate that within this subsection there is good overall consistency between morphological, phylogenetic and biological species concepts. In contrast to current opinion, in this group there is little species overlap, particularly when also considering species frequencies, between arctic and alpine floras on one hand and temperate on the other.}, } @article {pmid26779191, year = {2015}, author = {Vannier, N and Mony, C and Bittebière, AK and Vandenkoornhuyse, P}, title = {Epigenetic Mechanisms and Microbiota as a Toolbox for Plant Phenotypic Adjustment to Environment.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {1159}, pmid = {26779191}, issn = {1664-462X}, abstract = {The classic understanding of organisms focuses on genes as the main source of species evolution and diversification. The recent concept of genetic accommodation questions this gene centric view by emphasizing the importance of phenotypic plasticity on evolutionary trajectories. Recent discoveries on epigenetics and symbiotic microbiota demonstrated their deep impact on plant survival, adaptation and evolution thus suggesting a novel comprehension of the plant phenotype. In addition, interplays between these two phenomena controlling plant plasticity can be suggested. Because epigenetic and plant-associated (micro-) organisms are both key sources of phenotypic variation allowing environmental adjustments, we argue that they must be considered in terms of evolution. This 'non-conventional' set of mediators of phenotypic variation can be seen as a toolbox for plant adaptation to environment over short, medium and long time-scales.}, } @article {pmid26748267, year = {2016}, author = {Koch, EL and Neiber, MT and Walther, F and Hausdorf, B}, title = {Presumable incipient hybrid speciation of door snails in previously glaciated areas in the Caucasus.}, journal = {Molecular phylogenetics and evolution}, volume = {97}, number = {}, pages = {120-128}, doi = {10.1016/j.ympev.2015.12.016}, pmid = {26748267}, issn = {1095-9513}, mesh = {Acclimatization/genetics ; *Altitude ; Amplified Fragment Length Polymorphism Analysis ; Animals ; DNA, Mitochondrial/genetics ; *Ecosystem ; *Genetic Speciation ; Haplotypes ; *Hybridization, Genetic ; *Ice Cover ; Snails/*classification/*genetics ; }, abstract = {Homoploid hybrid speciation, speciation by hybridization without a change in chromosome number, may be the result of an encounter of closely related species in a habitat that is different from that usually occupied by these species. In the northwestern Caucasus the land snail species Micropontica caucasica and M. circassica form two distinct entities with little admixture at low and intermediate altitudes. However, at higher altitudes in the Lagonaki plateau, which were repeatedly glaciated, Micropontica populations with intermediate characters occur. Admixture analyses based on AFLP data demonstrated that the populations from the Lagonaki plateau are homoploid hybrids that now form a cluster separate from the parental species. The Lagonaki populations are characterized by a mtDNA haplotype clade that has been found in the parental species only once. The fixation of this haplotype clade in most hybrid populations suggests that these haplotypes are better adapted to the cooler conditions in high altitude habitats and have replaced the haplotypes of the parental species in a selective sweep. The fixation of a presumably adaptive mitochondrial haplotype clade in the Lagonaki populations is an important step towards speciation under the differential fitness species concept.}, } @article {pmid26748095, year = {2016}, author = {Simoneau, A and Ricard, É and Weber, S and Hammond-Martel, I and Wong, LH and Sellam, A and Giaever, G and Nislow, C and Raymond, M and Wurtele, H}, title = {Chromosome-wide histone deacetylation by sirtuins prevents hyperactivation of DNA damage-induced signaling upon replicative stress.}, journal = {Nucleic acids research}, volume = {44}, number = {6}, pages = {2706-2726}, pmid = {26748095}, issn = {1362-4962}, support = {MOP 123438//Canadian Institutes of Health Research/Canada ; }, mesh = {Acetylation/drug effects ; Cell Cycle Proteins/genetics/metabolism ; Checkpoint Kinase 2/genetics/metabolism ; Chromatin/chemistry/drug effects/*enzymology ; DNA Damage ; Endodeoxyribonucleases/genetics/metabolism ; *Gene Expression Regulation, Fungal ; *Genome, Fungal ; Histone Deacetylase Inhibitors/pharmacology ; Histone Deacetylases/genetics/metabolism ; Histones/*genetics/metabolism ; Niacinamide/pharmacology ; Phosphoprotein Phosphatases/genetics/metabolism ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/drug effects/enzymology/*genetics ; Saccharomyces cerevisiae Proteins/antagonists & inhibitors/genetics/metabolism ; Signal Transduction ; Silent Information Regulator Proteins, Saccharomyces cerevisiae/*genetics/metabolism ; Sirtuin 2/*genetics/metabolism ; Stress, Physiological ; }, abstract = {The Saccharomyces cerevisiae genome encodes five sirtuins (Sir2 and Hst1-4), which constitute a conserved family of NAD-dependent histone deacetylases. Cells lacking any individual sirtuin display mild growth and gene silencing defects. However, hst3Δ hst4Δ double mutants are exquisitely sensitive to genotoxins, and hst3Δ hst4Δ sir2Δmutants are inviable. Our published data also indicate that pharmacological inhibition of sirtuins prevents growth of several fungal pathogens, although the biological basis is unclear. Here, we present genome-wide fitness assays conducted with nicotinamide (NAM), a pan-sirtuin inhibitor. Our data indicate that NAM treatment causes yeast to solicit specific DNA damage response pathways for survival, and that NAM-induced growth defects are mainly attributable to inhibition of Hst3 and Hst4 and consequent elevation of histone H3 lysine 56 acetylation (H3K56ac). Our results further reveal that in the presence of constitutive H3K56ac, the Slx4 scaffolding protein and PP4 phosphatase complex play essential roles in preventing hyperactivation of the DNA damage-response kinase Rad53 in response to spontaneous DNA damage caused by reactive oxygen species. Overall, our data support the concept that chromosome-wide histone deacetylation by sirtuins is critical to mitigate growth defects caused by endogenous genotoxins.}, } @article {pmid26742614, year = {2016}, author = {Rossouw, D and Bauer, FF}, title = {Exploring the phenotypic space of non-Saccharomyces wine yeast biodiversity.}, journal = {Food microbiology}, volume = {55}, number = {}, pages = {32-46}, doi = {10.1016/j.fm.2015.11.017}, pmid = {26742614}, issn = {1095-9998}, mesh = {*Biodiversity ; Ethanol/metabolism ; Fermentation ; Flavoring Agents/metabolism ; Phenotype ; Vitis/*microbiology ; Wine/*microbiology ; Yeasts/classification/isolation & purification/*metabolism ; }, abstract = {Tremendous microbial diversity exists in vineyards, and the potential to harness this diversity for novel mixed or pure starter cultures for wine fermentation has received significant attention in recent years. However, most studies are limited to a small subset of strains and species. Here we present data from a systematic screen of 91 yeast isolates from South African grape must and vineyard samples for oenologically relevant traits. One focus area was finding non-Saccharomyces isolates showing both reduced ethanol yields, as well as improved aromatic characteristics. Of the 91 isolates evaluated initially, 21 showed lower ethanol yields when compared to commercial wine yeast strain controls. Collectively, the metabolic data (primary fermentation and secondary aroma compounds) highlight the enormity of the 'phenotypic space' of yeast communities in South African vineyards. The data also emphasise intraspecies variability, challenging our concept of species typicity. Of particular oenological interest was the ability of several isolates to produce high levels of terpenoid compounds. A few strains were ultimately found which showed a substantial reduction (>1.5%) in the final ethanol content of sequential fermentations, as well as unique aroma compound production profiles. Four of these strains were selected for comprehensive wine trials in both red and white grape musts, complete with microbial, chemical and sensory analyses of the red wines. This presents, for the first time, a full bench-to-bottle characterisation of non-Saccharomyces strains showing the most potential for commercial application. The findings of this study enlarge the potential range of oenological applications for non-Saccharomyces yeast, while also suggesting the potential usefulness of several yeast species that have previously not been considered for winemaking applications.}, } @article {pmid26740545, year = {2016}, author = {Tanney, JB and Douglas, B and Seifert, KA}, title = {Sexual and asexual states of some endophytic Phialocephala species of Picea.}, journal = {Mycologia}, volume = {108}, number = {2}, pages = {255-280}, doi = {10.3852/15-136}, pmid = {26740545}, issn = {0027-5514}, mesh = {Animals ; Ascomycota/classification/genetics/*physiology/ultrastructure ; Endophytes/*physiology ; Phylogeny ; Picea/*microbiology ; Reproduction ; Species Specificity ; }, abstract = {Unidentified DNA sequences in isolation-based or culture-free studies of conifer endophytes are a persistent problem that requires a field approach to resolve. An investigation of foliar endophytes of Picea glauca, P. mariana, P. rubens and Pinus strobus in eastern Canada, using a combined field, morphological, cultural and DNA sequencing approach, resulted in the frequent isolation of Phialocephala spp. and the first verified discovery of their mollisia-like sexual states in the field. Phialocephala scopiformis and Ph. piceae were the most frequent species isolated as endophytes from healthy conifer needles. Corresponding Mollisia or mollisioid sexual states for Ph. scopiformis, Ph. piceae and several undescribed species in a clade containing Ph. dimorphospora were collected in the sampling area and characterized by analysis of the nuc internal transcribed spacer rDNA (ITS) and gene for the largest subunit of RNA polymerase II (RPB1) loci. Four novel species and one new combination in a clade containing Ph. dimorphospora, the type of Phialocephala, are presented, accompanied by descriptions of apothecia and previously undocumented synanamorphs. An epitype culture and corresponding reference sequences for Phialocephala dimorphospora are proposed. The resulting ITS barcodes linked with robust taxonomic species concepts are an important resource for future research on forest ecosystems and endophytes.}, } @article {pmid26709836, year = {2016}, author = {Mallet, J and Besansky, N and Hahn, MW}, title = {How reticulated are species?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {2}, pages = {140-149}, pmid = {26709836}, issn = {1521-1878}, support = {BB/G006903/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01 AI076584/AI/NIAID NIH HHS/United States ; R01 AI76584/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; *Genetic Speciation ; Genomics/methods ; Organisms, Genetically Modified/genetics ; *Phylogeny ; Plants/genetics ; }, abstract = {Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.}, } @article {pmid26693681, year = {2016}, author = {Van de Putte, K and Nuytinck, J and De Crop, E and Verbeken, A}, title = {Lactifluus volemus in Europe: Three species in one--Revealed by a multilocus genealogical approach, Bayesian species delimitation and morphology.}, journal = {Fungal biology}, volume = {120}, number = {1}, pages = {1-25}, doi = {10.1016/j.funbio.2015.08.015}, pmid = {26693681}, issn = {1878-6146}, mesh = {Agaricales/classification/*genetics/growth & development/isolation & purification ; Bayes Theorem ; DNA, Fungal/genetics ; Europe ; Molecular Sequence Data ; Multilocus Sequence Typing/*methods ; Mycological Typing Techniques/*methods ; Phylogeny ; }, abstract = {This study provides morphological and molecular evidence (from nuclear ITS, LSU, and rpb2 DNA sequences) for three previously unrecognized species within the morphospecies Lactifluus volemus from Europe. Phylogenetic species are supported by both a multi-locus tree-based method and Bayesian species delimitation. Lactifluus volemus and Lactifluus oedematopus are provided with a new description, and a third species, Lactifluus subvolemus, is described as new to science. Lactifluus oedematopus can be easily recognized by its short pileipellis hairs. Both L. volemus and L. subvolemus have longer pileipellis hairs and can only be distinguished from each other based on cap colour. Intermediary colour forms, however, occur as well, and cannot be identified as either L. volemus or L. subvolemus without molecular data. Revealing that L. volemus--already considered extinct in the Netherlands and the Belgian Flemish region, and declining in other European countries--is actually a complex of three species that are even more vulnerable to extinction, this study emphasizes the fundamental role of taxonomy in species conservation.}, } @article {pmid26672013, year = {2015}, author = {Cornejo, C and Scheidegger, C}, title = {Multi-gene phylogeny of the genus Lobaria: Evidence of species-pair and allopatric cryptic speciation in East Asia.}, journal = {American journal of botany}, volume = {102}, number = {12}, pages = {2058-2073}, doi = {10.3732/ajb.1500207}, pmid = {26672013}, issn = {1537-2197}, mesh = {Ascomycota/*classification/*genetics ; *Evolution, Molecular ; Far East ; Fungal Proteins/*genetics ; *Genetic Speciation ; Lichens/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {PREMISE OF THE STUDY: Accurate species delimitation has critical implications for ecological and conservation studies. The lichen genus Lobaria is widely distributed in old-growth forests. Particularly in East Asia, this genus includes many rare and poorly known taxa that are circumscribed as morpho- or chemospecies, as well as species-pairs.

METHODS: To critically examine the relationships between species identified via morphological and chemical criteria, phylogenetic species recognition (PSR) was applied to the genus Lobaria. Morphological and chemical patterns of 87 individuals were examined and three independent nuclear loci were sequenced. The East Asian L. meridionalis-group was additionally studied using split decomposition and haplotype network analysis.

KEY RESULTS: The genus Lobaria and most of its species were strongly supported statistically. Split decomposition and haplotype networks suggest complex evolutionary histories of species within the East Asian L. meridionalis-group.

CONCLUSIONS: Phylogenetic analyses confirmed the monophyly of the genus Lobaria, including L. anomala. Within Lobaria, three major clades were found. These clades associate with different photobionts and comprise 18 known species and 5 undescribed species. Several chemical compounds were found to be neither stable nor invariant characters. Some taxa of the L. meridionalis-group appear to be monophyletic but remain as allopatric cryptic species. In three clades, this study found evidence for diversification processes between isidiate and nonisidiate specimens (species-pair). These findings are discussed in the context of evolutionary hypotheses for speciation processes.}, } @article {pmid26649784, year = {2016}, author = {Thines, M and Choi, YJ}, title = {Evolution, Diversity, and Taxonomy of the Peronosporaceae, with Focus on the Genus Peronospora.}, journal = {Phytopathology}, volume = {106}, number = {1}, pages = {6-18}, doi = {10.1094/PHYTO-05-15-0127-RVW}, pmid = {26649784}, issn = {0031-949X}, mesh = {Biological Evolution ; Classification ; *Genetic Variation ; Peronospora/*genetics ; }, abstract = {Downy mildews are a notorious group of oomycete plant pathogens, causing high economic losses in various crops and ornamentals. The most species-rich genus of oomycetes is the genus Peronospora. This review provides a wide overview of these pathogens, ranging from macro- and micro-evolutionary patterns, their biodiversity and ecology to short overviews for the currently economically most important pathogens and potential emerging diseases. In this overview, the taxonomy of economically relevant species is also discussed, as the application of the correct names and species concepts is a prerequisite for effective quarantine regulations and phytosanitary measures.}, } @article {pmid26643889, year = {2015}, author = {Burgess, MB and Cushman, KR and Doucette, ET and Frye, CT and Campbell, CS}, title = {Understanding diploid diversity: A first step in unraveling polyploid, apomictic complexity in Amelanchier.}, journal = {American journal of botany}, volume = {102}, number = {12}, pages = {2041-2057}, doi = {10.3732/ajb.1500330}, pmid = {26643889}, issn = {1537-2197}, mesh = {*Apomixis ; *Biological Evolution ; Chloroplast Proteins/genetics ; DNA, Intergenic/genetics ; *Diploidy ; *Genetic Variation ; Introns ; Phylogeny ; Plant Proteins/genetics ; Rosaceae/genetics/*physiology ; }, abstract = {PREMISE OF THE STUDY: Delimitation of Amelanchier species is difficult because of polyploidy and gametophytic apomixis. A first step in unraveling this species problem is understanding the diversity of the diploids that contributed genomes to polyploid apomicts. This research helps clarify challenging species-delimitation problems attending polyploid, apomictic complexity.

METHODS: We sampled 431 diploid accessions from 13 species, of which 10 are North American and three are Old World. Quantitative morphological analyses tested the null hypothesis of no discrete groups. Using three to nine diploid accessions per species, we constructed phylogenies with DNA sequences from ETS, ITS, the second intron of LEAFY, and chloroplast regions rpoB-trnC, rpl16, trnD-trnT, and ycf6-psbM.

KEY RESULTS: Most Amelanchier diploid taxa are morphologically and ecogeographically distinct and genetically exclusive lineages. They rarely hybridize with one another. Nuclear and chloroplast DNA sequences almost completely resolve the Amelanchier phylogeny. The backbone is the mostly western North American clade A, eastern North American clade B, and Old World clade O. DNA sequences and morphology support clades A and O as sister taxa. Despite extensive paralogy, our LEAFY data are phylogenetically informative and identify a clade (T) of three arborescent taxa within clade B.

CONCLUSIONS: Amelanchier diploids differ strikingly from polyploid apomicts, in that hybridization among them is rare, and they form taxa that would qualify as species by most species concepts. Knowledge of diploid morphology, phylogeny, and ecogeography provides a foundation for understanding the evolutionary history of polyploid apomicts, their patterns of diversification, and their species status.}, } @article {pmid26625345, year = {2016}, author = {Lafon-Placette, C and Vallejo-Marín, M and Parisod, C and Abbott, RJ and Köhler, C}, title = {Current plant speciation research: unravelling the processes and mechanisms behind the evolution of reproductive isolation barriers.}, journal = {The New phytologist}, volume = {209}, number = {1}, pages = {29-33}, doi = {10.1111/nph.13756}, pmid = {26625345}, issn = {1469-8137}, mesh = {Alleles ; Breeding ; Epigenesis, Genetic ; *Genetic Speciation ; Plants/*genetics ; Polyploidy ; Reproduction ; *Reproductive Isolation ; }, } @article {pmid26624343, year = {2015}, author = {Boano, G and Vinals, N and Durante, A and Pavia, M}, title = {Apparent sympatry of Stiphrornis pyrrholaemus Schmidt & Angehr, 2008 and S. xanthogaster Sharpe, 1903 (Passeriformes: Muscicapidae) in Gabon, and taxonomic implications.}, journal = {Zootaxa}, volume = {4032}, number = {1}, pages = {127-133}, doi = {10.11646/zootaxa.4032.1.7}, pmid = {26624343}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Body Size ; Ecosystem ; Female ; Gabon ; Male ; Organ Size ; Passeriformes/anatomy & histology/*classification/genetics/growth & development ; *Sympatry ; }, abstract = {We report the occurrence of the recently-described Stiphrornis pyrrholaemus in the Makokou area, northeastern Gabon, more than 600 kilometers NE from its type locality, in areas covered by dense primary to secondary forest. The previous records of Stiphrornis from the same area were referred to S. xanthogaster. We confirm this attribution on the basis of museum specimens. Although several recent sources treat all Stiphrornis as a single species, our findings strongly suggest the sympatric coexistence of two Stiphrornis species and thus that they should be treated as separate species under the Biological Species Concept.}, } @article {pmid26624104, year = {2015}, author = {Davis, DR and Watters, JL and Köhler, G and Whitsett, C and Huron, NA and Brown, RM and Diesmos, AC and Siler, CD}, title = {Redescription of the rare Philippine false gecko Pseudogekko brevipes (Reptilia: Squamata: Gekkonidae) and description of a new species.}, journal = {Zootaxa}, volume = {4020}, number = {2}, pages = {357-374}, doi = {10.11646/zootaxa.4020.2.7}, pmid = {26624104}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures ; Animals ; Body Size ; Ecosystem ; Female ; Lizards/anatomy & histology/*classification/genetics/growth & development ; Male ; Organ Size ; Philippines ; Phylogeny ; }, abstract = {Recent investigations into the species diversity of false geckos (genus Pseudogekko Taylor) have revealed several cryptic species, highlighting the need for a more thorough understanding of diversity within this enigmatic genus of endemic Philippine geckos. Newly available genetic data reveal that two of the four currently recognized species are complexes of multiple deeply divergent evolutionary lineages. In this paper we evaluate species diversity in one of these complexes, P. brevipes Boettger, and describe one additional new species. For nearly a century, P. brevipes has been recognized as a single, "widespread" species with a geographic range spanning two major faunal regions and several island groups. Poor understanding of this species has persisted due to both limited sampling and its apparent rarity. We evaluate both morphological and genetic data to define species limits in P. brevipes, and find character-based evidence to justify the recognition of two unique evolutionary lineages, one of which we describe as a new species (P. atiorum sp. nov.). The species included in this study have allopatric distributions and differ from congeners by numerous diagnostic characters of external morphology, and therefore should be recognized as full species in accordance with lineage-based species concepts. This newly described species increases the total number of species of Pseudogekko to seven.}, } @article {pmid26590450, year = {2015}, author = {Kutcherov, D}, title = {Temperature-dependent development in Chrysomela vigintipunctata (Coleoptera: Chrysomelidae), a stenothermal early-season breeder.}, journal = {Journal of thermal biology}, volume = {53}, number = {}, pages = {9-14}, doi = {10.1016/j.jtherbio.2015.08.001}, pmid = {26590450}, issn = {0306-4565}, mesh = {Adaptation, Physiological ; Animals ; Body Weight ; Coleoptera/genetics/growth & development/*physiology ; Genetic Speciation ; *Hot Temperature ; *Oviposition ; Selection, Genetic ; }, abstract = {Chrysomela vigintipunctata (Scopoli) is a univoltine leaf beetle commonly encountered on willows across the Palearctic forest zone. The preimaginal development in this species takes place during a short time period, from May to June, because larvae are unable to consume mature leaves of the host plant. Therefore, the diet quality imposes a time constraint, and it was expected that the temperature dependence of development in C. vigintipunctata should be adaptively adjusted to the shortness and cool conditions of the favorable season. It was experimentally determined that this leaf beetle was stenothermal at the larval stage, required 275.5 degree-days above the threshold of 9.0°C for total development from oviposition to adult emergence, and attained greater body mass at lower temperatures. However, in all of these aspects, the thermal ecology of C. vigintipunctata was similar to that of two related multivoltine species, C. populi and C. scripta. The interspecific similarity of thermal reaction norms for development rate and body size suggests that these reaction norms in C. vigintipunctata were unlikely to have been shaped by selection favoring faster development or growth early in the season. The results are discussed in terms of the "ecological fitting" concept, which states that a species may be successful in exploiting novel environments while retaining ecophysiological traits evolved elsewhere.}, } @article {pmid26581393, year = {2015}, author = {Roux, B and Bolot, S and Guy, E and Denancé, N and Lautier, M and Jardinaud, MF and Fischer-Le Saux, M and Portier, P and Jacques, MA and Gagnevin, L and Pruvost, O and Lauber, E and Arlat, M and Carrère, S and Koebnik, R and Noël, LD}, title = {Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {975}, pmid = {26581393}, issn = {1471-2164}, mesh = {Bacterial Proteins/genetics/metabolism ; *Gene Expression Profiling ; *Genomics ; Molecular Sequence Annotation ; Open Reading Frames ; Regulon/genetics ; Xanthomonas campestris/*genetics/immunology ; }, abstract = {BACKGROUND: The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani).

RESULTS: In this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins.

CONCLUSIONS: This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.}, } @article {pmid26568458, year = {2016}, author = {Gratton, P and Trucchi, E and Trasatti, A and Riccarducci, G and Marta, S and Allegrucci, G and Cesaroni, D and Sbordoni, V}, title = {Testing Classical Species Properties with Contemporary Data: How "Bad Species" in the Brassy Ringlets (Erebia tyndarus complex, Lepidoptera) Turned Good.}, journal = {Systematic biology}, volume = {65}, number = {2}, pages = {292-303}, doi = {10.1093/sysbio/syv087}, pmid = {26568458}, issn = {1076-836X}, mesh = {Algorithms ; Animals ; Butterflies/*classification/genetics ; Classification/*methods ; Genetic Speciation ; Genotype ; Geography ; *Phylogeny ; }, abstract = {All species concepts are rooted in reproductive, and ultimately genealogical, relations. Genetic data are thus the most important source of information for species delimitation. Current ease of access to genomic data and recent computational advances are blooming a plethora of coalescent-based species delimitation methods. Despite their utility as objective approaches to identify species boundaries, coalescent-based methods (1) rely on simplified demographic models that may fail to capture some attributes of biological species, (2) do not make explicit use of the geographic information contained in the data, and (3) are often computationally intensive. In this article, we present a case of species delimitation in the Erebia tyndarus species complex, a taxon regarded as a classic example of problematic taxonomic resolution. Our approach to species delimitation used genomic data to test predictions rooted in the biological species concept and in the criterion of coexistence in sympatry. We (1) obtained restriction-site associated DNA (RAD) sequencing data from a carefully designed sample, (2) applied two genotype clustering algorithms to identify genetic clusters, and (3) performed within-clusters and between-clusters analyses of isolation by distance as a test for intrinsic reproductive barriers. Comparison of our results with those from a Bayes factor delimitation coalescent-based analysis, showed that coalescent-based approaches may lead to overconfident splitting of allopatric populations, and indicated that incorrect species delimitation is likely to be inferred when an incomplete geographic sample is analyzed. While we acknowledge the theoretical justification and practical usefulness of coalescent-based species delimitation methods, our results stress that, even in the phylogenomic era, the toolkit for species delimitation should not dismiss more traditional, biologically grounded, approaches coupling genomic data with geographic information.}, } @article {pmid26554940, year = {2015}, author = {Ojima-Kato, T and Yamamoto, N and Iijima, Y and Tamura, H}, title = {Assessing the performance of novel software Strain Solution on automated discrimination of Escherichia coli serotypes and their mixtures using matrix-assisted laser desorption ionization-time of flight mass spectrometry.}, journal = {Journal of microbiological methods}, volume = {119}, number = {}, pages = {233-238}, doi = {10.1016/j.mimet.2015.11.005}, pmid = {26554940}, issn = {1872-8359}, mesh = {Automation/instrumentation/*methods ; Bacterial Typing Techniques/instrumentation/*methods ; Enterohemorrhagic Escherichia coli/chemistry/genetics/*isolation & purification ; Escherichia coli Infections/*microbiology ; Escherichia coli Proteins/chemistry/genetics ; Humans ; Software ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation/*methods ; }, abstract = {O157, O26, and O111 are the most important O serogroups of enterohemorrhagic Escherichia coli worldwide. Recently we reported a strategy for discriminating these serotypes from the others using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) based on the S10-spc-alpha operon gene-encoded ribosomal protein mass spectrum (S10-GERMS) method. To realize the fully automated identification of microorganisms at species- or serotype-level with the concept of S10-GERMS method, novel software named Strain Solution for MALDI-TOF MS was developed. In this study, the Strain Solution was evaluated with a total of 45 E. coli isolates including O26, O91, O103, O111, O115, O121, O128, O145, O157, O159, and untyped serotypes. The Strain Solution could accurately discriminate 92% (11/12) of O157 strains, 100% (13/13) of O26 and O111 strains from the others with three biomarkers in an automated manner. In addition, this software could identify 2 different E. coli strains (K-12 as a non-O157 representative and O157) in mixed samples. The results suggest that Strain Solution will be useful for species- or serotype-level classification of microorganisms in the fields of food safety and diagnostics.}, } @article {pmid26545322, year = {2016}, author = {Padhi, BK and Singh, M and Huang, N and Pelletier, G}, title = {A PCR-based approach to assess genomic DNA contamination in RNA: Application to rat RNA samples.}, journal = {Analytical biochemistry}, volume = {494}, number = {}, pages = {49-51}, doi = {10.1016/j.ab.2015.10.012}, pmid = {26545322}, issn = {1096-0309}, mesh = {Animals ; Cerebellum/metabolism ; DNA/metabolism ; DNA Contamination ; Deoxyribonucleases/metabolism ; Electron Transport Complex II/genetics ; Gene Expression ; *Genetic Techniques ; Male ; RNA/*analysis/isolation & purification ; Rats ; *Real-Time Polymerase Chain Reaction ; }, abstract = {Genomic DNA (gDNA) contamination of RNA samples can lead to inaccurate measurement of gene expression by reverse transcription quantitative real-time PCR (RT-qPCR). We describe an easily adoptable PCR-based method where gDNA contamination in RNA samples is assessed by comparing the amplification of intronic and exonic sequences from a housekeeping gene. Although this alternative assay was developed for rat RNA samples, it could be easily adapted to other species. As a proof of concept, we assessed the effects of detectable gDNA contamination levels on the expression of a few genes that illustrate the importance of RNA quality in acquiring reliable data.}, } @article {pmid26519917, year = {2016}, author = {Kaya, S and Kaya, C and Obot, IB and Islam, N}, title = {A novel method for the calculation of bond stretching force constants of diatomic molecules.}, journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy}, volume = {154}, number = {}, pages = {103-107}, doi = {10.1016/j.saa.2015.10.030}, pmid = {26519917}, issn = {1873-3557}, abstract = {Chemical hardness is one of the chemical reactivity descriptors of chemical species and this concept has widely benefited from the development of Density Functional Theory (DFT). In the present report, chemical hardness values for approximately fifty diatomic molecules have been calculated using a new molecular hardness (η(M)) equation derived by us in recent times. Then, correlation between force constant (k) and chemical hardness for the above mentioned diatomic molecules that situate hydrides, halides, oxides and sulfides among them has been investigated. Consequently, a relation that can be presented by a simple equation between chemical hardness with bond stretching force constants has been found.}, } @article {pmid26516030, year = {2016}, author = {Catalá, S and Del Campo, EM and Barreno, E and García-Breijo, FJ and Reig-Armiñana, J and Casano, LM}, title = {Coordinated ultrastructural and phylogenomic analyses shed light on the hidden phycobiont diversity of Trebouxia microalgae in Ramalina fraxinea.}, journal = {Molecular phylogenetics and evolution}, volume = {94}, number = {Pt B}, pages = {765-777}, doi = {10.1016/j.ympev.2015.10.021}, pmid = {26516030}, issn = {1095-9513}, mesh = {Ascomycota/*classification/genetics/ultrastructure ; Biological Evolution ; Chlorophyta/*classification/genetics/ultrastructure ; Genetic Variation ; Lichens/*classification/genetics/ultrastructure ; Microalgae/classification/genetics ; Phylogeny ; Symbiosis ; }, abstract = {The precise boundary delineations between taxa in symbiotic associations are very important for evolutionary and ecophysiological studies. Growing evidence indicates that in many cases, the use of either morphological characters or molecular markers results in diversity underestimation. In lichen symbioses, Trebouxia is the most common genus of lichen phycobionts, however, the diversity within this genus has been poorly studied and as such there is no clear species concept. This study constitutes a multifaceted approach incorporating aspects of ultrastructural characterization by TEM and phylogenomics to evaluate the morphological and genetic diversity of phycobionts within the sexually reproducing lichen Ramalina fraxinea in the context of Mediterranean and temperate populations. Results reveal an association with at least seven different Trebouxia lineages belonging to at least two species, T. decolorans and T. jamesii, and diverse combinations of such lineages coexisting within the same thallus depending on the analyzed sample. Some of these lineages are shared by several other non-related lichen taxa. Our findings indicate the existence of a highly diverse assemblage of Trebouxia algae associating with R. fraxinea and suggest a possible incipient speciation within T. decolorans rendering a number of lineages or even actual species. This study stresses the importance of coordinated ultrastructural and molecular analyses to improve estimates of diversity and reveal the coexistence of more than one Trebouxia species within the same thallus. It is also necessary to have clearer species delimitation criteria within the genus Trebouxia and microalgae in general.}, } @article {pmid26487148, year = {2015}, author = {Gomes, GL and da Nóbrega, MM}, title = {Anxiety in children following hospitalization: a proposal for a nursing diagnosis.}, journal = {Revista latino-americana de enfermagem}, volume = {23}, number = {5}, pages = {963-970}, pmid = {26487148}, issn = {1518-8345}, mesh = {Anxiety/*diagnosis/*epidemiology ; Child ; Female ; *Hospitalization ; Humans ; Male ; *Nursing Diagnosis ; *Pediatric Nursing ; }, abstract = {OBJECTIVE: to describe the process of developing a nursing diagnosis regarding child anxiety following hospitalization, which is to be submitted to the international classification for nursing practice, in accordance with the guidelines set out by the International Council of Nurses and the ISO standard 18104:2014.

METHOD: this methodological study includes a conceptual analysis that bases itself on analyzing the phenomena of anxiety and hospitalization, while identifying the critical attributes of the concept and developing an operational definition.

RESULTS: all the criteria for including a new nursing concept were followed and there was no violation of the framework of the International Classification for Nursing Practice with the proposed inclusion, since the concept of anxiety already exists in this classification system and the concept of anxiety from hospitalization would be considered a species or subclass of this concept.

CONCLUSION: this analysis of the concept of hospitalization anxiety in children allowed its meaning to be clarified and, consequently, understanding to be constructed regarding its practical applicability. This achievement contributed in terms of providing incentive to develop new proposals for nursing diagnoses to be included in the International Classification for Nursing Practice.}, } @article {pmid26484802, year = {2015}, author = {Granger, DN and Kvietys, PR}, title = {Reperfusion injury and reactive oxygen species: The evolution of a concept.}, journal = {Redox biology}, volume = {6}, number = {}, pages = {524-551}, pmid = {26484802}, issn = {2213-2317}, support = {R01 HL026441/HL/NHLBI NIH HHS/United States ; HL26441-32/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Cell Hypoxia ; Humans ; Oxidation-Reduction ; Oxidative Stress ; Reactive Oxygen Species/*metabolism ; Reperfusion Injury/*metabolism ; }, abstract = {Reperfusion injury, the paradoxical tissue response that is manifested by blood flow-deprived and oxygen-starved organs following the restoration of blood flow and tissue oxygenation, has been a focus of basic and clinical research for over 4-decades. While a variety of molecular mechanisms have been proposed to explain this phenomenon, excess production of reactive oxygen species (ROS) continues to receive much attention as a critical factor in the genesis of reperfusion injury. As a consequence, considerable effort has been devoted to identifying the dominant cellular and enzymatic sources of excess ROS production following ischemia-reperfusion (I/R). Of the potential ROS sources described to date, xanthine oxidase, NADPH oxidase (Nox), mitochondria, and uncoupled nitric oxide synthase have gained a status as the most likely contributors to reperfusion-induced oxidative stress and represent priority targets for therapeutic intervention against reperfusion-induced organ dysfunction and tissue damage. Although all four enzymatic sources are present in most tissues and are likely to play some role in reperfusion injury, priority and emphasis has been given to specific ROS sources that are enriched in certain tissues, such as xanthine oxidase in the gastrointestinal tract and mitochondria in the metabolically active heart and brain. The possibility that multiple ROS sources contribute to reperfusion injury in most tissues is supported by evidence demonstrating that redox-signaling enables ROS produced by one enzymatic source (e.g., Nox) to activate and enhance ROS production by a second source (e.g., mitochondria). This review provides a synopsis of the evidence implicating ROS in reperfusion injury, the clinical implications of this phenomenon, and summarizes current understanding of the four most frequently invoked enzymatic sources of ROS production in post-ischemic tissue.}, } @article {pmid26479135, year = {2015}, author = {Nekaris, KA and Arnell, AP and Svensson, MS}, title = {Selecting a Conservation Surrogate Species for Small Fragmented Habitats Using Ecological Niche Modelling.}, journal = {Animals : an open access journal from MDPI}, volume = {5}, number = {1}, pages = {27-40}, pmid = {26479135}, issn = {2076-2615}, abstract = {Flagship species are traditionally large, charismatic animals used to rally conservation efforts. Accepted flagship definitions suggest they need only fulfil a strategic role, unlike umbrella species that are used to shelter cohabitant taxa. The criteria used to select both flagship and umbrella species may not stand up in the face of dramatic forest loss, where remaining fragments may only contain species that do not suit either set of criteria. The Cinderella species concept covers aesthetically pleasing and overlooked species that fulfil the criteria of flagships or umbrellas. Such species are also more likely to occur in fragmented habitats. We tested Cinderella criteria on mammals in the fragmented forests of the Sri Lankan Wet Zone. We selected taxa that fulfilled both strategic and ecological roles. We created a shortlist of ten species, and from a survey of local perceptions highlighted two finalists. We tested these for umbrella characteristics against the original shortlist, utilizing Maximum Entropy (MaxEnt) modelling, and analysed distribution overlap using ArcGIS. The criteria highlighted Loris tardigradus tardigradus and Prionailurus viverrinus as finalists, with the former having highest flagship potential. We suggest Cinderella species can be effective conservation surrogates especially in habitats where traditional flagship species have been extirpated.}, } @article {pmid26472550, year = {2016}, author = {Caldwell, HK and Albers, HE}, title = {Oxytocin, Vasopressin, and the Motivational Forces that Drive Social Behaviors.}, journal = {Current topics in behavioral neurosciences}, volume = {27}, number = {}, pages = {51-103}, doi = {10.1007/7854_2015_390}, pmid = {26472550}, issn = {1866-3370}, mesh = {Aggression/physiology ; Animals ; Autism Spectrum Disorder/physiopathology/psychology ; Behavior, Animal/*physiology ; Brain/*physiology ; Competitive Behavior/physiology ; Cooperative Behavior ; Dopamine/physiology ; Female ; Humans ; Mental Disorders/physiopathology/*psychology ; Motivation/*physiology ; Oxytocin/*physiology ; Pair Bond ; Personality Disorders/physiopathology/psychology ; Schizophrenia/physiopathology ; Schizophrenic Psychology ; *Social Behavior ; Stress Disorders, Post-Traumatic/physiopathology/psychology ; Vasopressins/*physiology ; }, abstract = {The motivation to engage in social behaviors is influenced by past experience and internal state, but also depends on the behavior of other animals. Across species, the oxytocin (Oxt) and vasopressin (Avp) systems have consistently been linked to the modulation of motivated social behaviors. However, how they interact with other systems, such as the mesolimbic dopamine system, remains understudied. Further, while the neurobiological mechanisms that regulate prosocial/cooperative behaviors have been extensively examined, far less is understood about competitive behaviors, particularly in females. In this chapter, we highlight the specific contributions of Oxt and Avp to several cooperative and competitive behaviors and discuss their relevance to the concept of social motivation across species, including humans. Further, we discuss the implications for neuropsychiatric diseases and suggest future areas of investigation.}, } @article {pmid26466872, year = {2015}, author = {Mbenoun, M and Wingfield, MJ and Letsoalo, T and Bihon, W and Wingfield, BD and Roux, J}, title = {Independent origins and incipient speciation among host-associated populations of Thielaviopsis ethacetica in Cameroon.}, journal = {Fungal biology}, volume = {119}, number = {11}, pages = {957-972}, doi = {10.1016/j.funbio.2015.05.009}, pmid = {26466872}, issn = {1878-6146}, mesh = {Ananas/microbiology ; Arecaceae/microbiology ; Ascomycota/*classification/*genetics/isolation & purification ; Cacao/microbiology ; Cameroon ; *Genetic Variation ; *Genotype ; Microsatellite Repeats ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Thielaviopsis ethacetica was recently reinstated as a distinct taxon using DNA phylogenies. It is widespread affecting several crop plants of global economic importance. In this study, microsatellite markers were developed and used in conjunction with sequence data to investigate the genetic diversity and structure of Th. ethacetica in Cameroon. A collection of 71 isolates from cacao, oil palm, and pineapple, supplemented with nine isolates from other countries were analysed. Four genetic groups were identified. Two of these were associated with oil palm in Cameroon and showed high genetic diversity, suggesting that they might represent an indigenous population of the pathogen. In contrast, the remaining two groups, associated with cacao and pineapple, had low genetic diversity and, most likely, represent introduced populations. There was no evidence of gene flow between these groups. Phylogenetic analyses based on sequences of the tef1-α as well as the combined flanking regions of six microsatellite loci were consistent with population genetic analyses and suggested that Th. ethacetica is comprised of two divergent genetic lineages.}, } @article {pmid26426290, year = {2016}, author = {Prosser, SW and deWaard, JR and Miller, SE and Hebert, PD}, title = {DNA barcodes from century-old type specimens using next-generation sequencing.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {487-497}, doi = {10.1111/1755-0998.12474}, pmid = {26426290}, issn = {1755-0998}, support = {5UO1TW006671/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Lepidoptera/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {Type specimens have high scientific importance because they provide the only certain connection between the application of a Linnean name and a physical specimen. Many other individuals may have been identified as a particular species, but their linkage to the taxon concept is inferential. Because type specimens are often more than a century old and have experienced conditions unfavourable for DNA preservation, success in sequence recovery has been uncertain. This study addresses this challenge by employing next-generation sequencing (NGS) to recover sequences for the barcode region of the cytochrome c oxidase 1 gene from small amounts of template DNA. DNA quality was first screened in more than 1800 century-old type specimens of Lepidoptera by attempting to recover 164-bp and 94-bp reads via Sanger sequencing. This analysis permitted the assignment of each specimen to one of three DNA quality categories--high (164-bp sequence), medium (94-bp sequence) or low (no sequence). Ten specimens from each category were subsequently analysed via a PCR-based NGS protocol requiring very little template DNA. It recovered sequence information from all specimens with average read lengths ranging from 458 bp to 610 bp for the three DNA categories. By sequencing ten specimens in each NGS run, costs were similar to Sanger analysis. Future increases in the number of specimens processed in each run promise substantial reductions in cost, making it possible to anticipate a future where barcode sequences are available from most type specimens.}, } @article {pmid26418652, year = {2015}, author = {Airi, M and Kaur, S}, title = {Confirmation of Culex (Culex) tritaeniorhynchus summorosus (Diptera: Culicidae) as a separate species.}, journal = {Journal of vector borne diseases}, volume = {52}, number = {3}, pages = {219-223}, pmid = {26418652}, issn = {0972-9062}, mesh = {Animals ; Culex/anatomy & histology/*classification ; Eggs ; Female ; India ; Insect Vectors/anatomy & histology/*classification/physiology ; Larva/anatomy & histology ; Male ; Microscopy ; Sexual Behavior, Animal ; }, abstract = {BACKGROUND & OBJECTIVES: Culex tritaeniorhynchus, a member of Cx. vishnui subgroup, is an important vector of Japanese encephalitis (JE) virus. Cx. tritaeniorhynchus summorosus considered as a variety or subspecies of Cx. tritaeniorhynchus, has been studied in detail to settle its taxonomic status. Surveys for the collection of Cx. tritaeniorhynchus from Chandigarh and adjoining areas have established the availability of Cx. summorosus from this area.

METHODS: For the present investigation, collections have been made from Chandigarh and its adjoining areas (up to 60 km) for procuring the material. The detailed morphology including scanning electron microscopy of immatures (eggs and larvae) and adults of Cx. tritaeniorhynchus and Cx. summorosus has been studied and compared. Further, the interbreeding experiments of the two species were also conducted and efforts had been made to allow cross- breeding among the members of these two species.

RESULTS: Comparison of egg, larval and adult morphology of Cx. summorosus with the parental species Cx. tritaeniorhynchus under the light and electron microscope, revealed significant differences. Moreover, these two species have also been found to be reproductively isolated as indicated by laboratory experiments. This settles the controversy on the status of Cx. summorosus and confirms its status as a distinct species.

The study establishes that the two species show considerable number of differences which are sufficient to consider them as separate species rather than subspecies or variant of Cx. tritaeniorhynchus. Furthermore, the absence of interbreeding between these two again confirms their separate specific status according to biological species concept. But, it is yet to ascertain whether Cx. summorosus is a vector of Japanese encephalitis like Cx. tritaeniorhynchus or not.}, } @article {pmid26412210, year = {2015}, author = {Liu, C and Zhao, Y and He, W and Wang, W and Chen, Y and Zhang, S and Ma, Y and Gohda, J and Ishida, T and Walter, TS and Owens, RJ and Stuart, DI and Ren, J and Gao, B}, title = {A RANKL mutant used as an inter-species vaccine for efficient immunotherapy of osteoporosis.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14150}, pmid = {26412210}, issn = {2045-2322}, support = {MR/N00065X/1/MRC_/Medical Research Council/United Kingdom ; MR/K018779/1/MRC_/Medical Research Council/United Kingdom ; G1100525/MRC_/Medical Research Council/United Kingdom ; 090532//Wellcome Trust/United Kingdom ; G1000099/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Antibodies/immunology ; Autoantigens/immunology/pharmacology ; Bone Resorption/genetics/metabolism ; Cell Differentiation/drug effects ; Disease Models, Animal ; Humans ; Immunization ; *Immunotherapy ; Mice ; Models, Molecular ; Osteoclasts/cytology/immunology/metabolism ; Osteoporosis/diagnosis/*genetics/*immunology/therapy ; Ovariectomy ; Protein Binding ; Protein Conformation ; RANK Ligand/chemistry/*genetics/*immunology/metabolism ; Rats ; Receptor Activator of Nuclear Factor-kappa B/chemistry/metabolism ; *Vaccines ; X-Ray Microtomography ; }, abstract = {Anti-cytokine therapeutic antibodies have been demonstrated to be effective in the treatment of several auto-immune disorders. However, The problems in antibody manufacture and the immunogenicity caused by multiple doses of antibodies inspire people to use auto-cytokine as immunogen to induce anti-cytokine antibodies. Nevertheless, the tolerance for inducing immune response against self-antigen has hindered the wide application of the strategy. To overcome the tolerance, here we proposed a strategy using the inter-species cytokine as immunogen for active immunization (TISCAI) to induce anti-cytokine antibody. As a proof of concept, an inter-species cytokine RANKL was successfully used as immunogen to induce anti-RANKL immune response. Furthermore, to prevent undesirable side-effects, the human RANKL was mutated based on the crystal structure of the complex of human RANKL and its rodent counterpart receptor RANK. We found, the antibodies produced blocked the osteoclast development in vitro and osteoporosis in OVX rat models. The results demonstrated this strategy adopted is very useful for general anti-cytokine immunotherapy for different diseases settings.}, } @article {pmid26407618, year = {2016}, author = {Ashraf, BH and Byrne, S and Fé, D and Czaban, A and Asp, T and Pedersen, MG and Lenk, I and Roulund, N and Didion, T and Jensen, CS and Jensen, J and Janss, LL}, title = {Estimating genomic heritabilities at the level of family-pool samples of perennial ryegrass using genotyping-by-sequencing.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {129}, number = {1}, pages = {45-52}, pmid = {26407618}, issn = {1432-2242}, mesh = {Disease Resistance/genetics ; Gene Frequency ; Gene Library ; *Gene Pool ; *Genome, Plant ; Genomics/*methods ; Genotyping Techniques/methods ; Lolium/*genetics ; Models, Genetic ; Phenotype ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Sequence Analysis, DNA/methods ; }, abstract = {By using the genotyping-by-sequencing method, it is feasible to characterize genomic relationships directly at the level of family pools and to estimate genomic heritabilities from phenotypes scored on family-pools in outbreeding species. Genotyping-by-sequencing (GBS) has recently become a promising approach for characterizing plant genetic diversity on a genome-wide scale. We use GBS to extend the concept of heritability beyond individuals by genotyping family-pool samples by GBS and computing genomic relationship matrices (GRMs) and genomic heritabilities directly at the level of family-pools from pool-frequencies obtained by sequencing. The concept is of interest for species where breeding and phenotyping is not done at the individual level but operates uniquely at the level of (multi-parent) families. As an example we demonstrate the approach using a set of 990 two-parent F2 families of perennial ryegrass (Lolium Perenne). The families were phenotyped as a family-unit in field plots for heading date and crown rust resistance. A total of 728 K single nucleotide polymorphism (SNP) variants were available and were divided in groups of different sequencing depths. GRMs based on GBS data showed diagonal values biased upwards at low sequencing depth, while off-diagonals were little affected by the sequencing depth. Using variants with high sequencing depth, genomic heritability for crown rust resistance was 0.33, and for heading date 0.22, and these genomic heritabilities were biased downwards when using variants with lower sequencing depth. Broad sense heritabilities were 0.61 and 0.66, respectively. Underestimation of genomic heritability at lower sequencing depth was confirmed with simulated data. We conclude that it is feasible to use GBS to describe relationships between family-pools and to estimate genomic heritability directly at the level of F2 family-pool samples, but estimates are biased at low sequencing depth.}, } @article {pmid26390223, year = {2015}, author = {Zitouni-Haouar, Fel-H and Alvarado, P and Sbissi, I and Boudabous, A and Fortas, Z and Moreno, G and Manjón, JL and Gtari, M}, title = {Contrasted Genetic Diversity, Relevance of Climate and Host Plants, and Comments on the Taxonomic Problems of the Genus Picoa (Pyronemataceae, Pezizales).}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0138513}, pmid = {26390223}, issn = {1932-6203}, mesh = {Ascomycota/classification/*genetics/ultrastructure ; Climate ; *Genetic Variation ; Magnoliopsida/*microbiology ; Mediterranean Region ; Phylogeny ; }, abstract = {The species concept within the genus Picoa Vittad. is here revisited in light of new molecular and ecological data obtained from samples collected throughout the Mediterranean basin. Two highly diverse widespread clades and four additional minor lineages were significantly supported by three genes dataset (ITS, 28s LSU and RPB2) inferences for 70 specimens. The two widespread clades occur in very different geographical and ecological areas associated with exclusive host plants in the genus Helianthemum. SEM study of spore surface morphology in these lineages revealed the existence of smooth ascospores in the majority of these clades. However the most frequent lineage in Europe and coastal North Africa displayed either smooth or verrucose spores. Hence this morphological criterion cannot be reliably used to discriminate between the different clades. In addition, SEM observations made on ascospores from several original collections of P. juniperi and P. lefebvrei supported the hypothesis that ornamentation depends on the degree of maturity in some of these lineages. Geographical and ecological, rather than morphological data are here suggested as the most useful characters to separate the different lineages in Picoa. Further studies focusing on these features are needed before the names P. juniperi and P. lefebvrei can be unambiguously linked with the genetic lineages observed.}, } @article {pmid26390221, year = {2015}, author = {Dobosz, P and Morais, S and Bonet, E and Puchades, R and Maquieira, Á}, title = {Massive immuno multiresidue screening of water pollutants.}, journal = {Analytical chemistry}, volume = {87}, number = {19}, pages = {9817-9824}, doi = {10.1021/acs.analchem.5b02354}, pmid = {26390221}, issn = {1520-6882}, mesh = {Antibodies, Immobilized/*chemistry ; Environmental Monitoring/*methods ; Immunoassay/*methods ; Nanoparticles/*chemistry ; Rivers/*chemistry ; Water Pollutants/*analysis ; }, abstract = {An immuno multiresidue screening assay in microarray format for the determination of complex chemical mixtures at the microgram per liter level, using antibody-functionalized gold nanoparticles, is presented. The analytical method relies on the use of a cocktail of nanogold-labeled specific antibodies, acting as recognition and detection species. The concept of multireside screening is proved by developing a multiplex assay on a compact disk support for the determination of 2-(2,4,5-trichlorophenoxy)propionic acid, 3-phenoxybenozic acid, 4-nitrophenol, alachlor, atrazine, azoxystrobin, chlorpyrifos, diazinon, diuron, endosulfan, fenthion, forchlorfenuron, imidacloprid, malathion, pentachlorophenol, pyraclostrobin, sulfasalazine, and triclosan, achieving detection limits of 0.07, 0.24, 10.9, 0.21, 0.14, 0.11, 0.11, 102, 0.36, 1.8, 1.7, 0.06, 0.08, 5.8, 1.0, 0.39, 0.003, and 12 μg/L, respectively. Due to the selectivity of the antibody-functionalized nanoparticles, the developed screening methodology allows the simultaneous determination of mixtures of water pollutants in a 10-plex configuration. The analytical performances were compared with those of reference chromatographic methods by the analysis of spiked water samples, the sensitivity and recovery results being in good agreement. The presented screening approach directly quantifies the concentration of complex chemical mixtures without sample treatment or preconcentration steps in a total time of 35 min.}, } @article {pmid26357267, year = {2015}, author = {Mehmood, T and Bohlin, J and Snipen, L}, title = {A Partial Least Squares Based Procedure for Upstream Sequence Classification in Prokaryotes.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {12}, number = {3}, pages = {560-567}, doi = {10.1109/TCBB.2014.2366146}, pmid = {26357267}, issn = {1557-9964}, mesh = {Algorithms ; DNA, Bacterial/analysis/genetics ; Genome, Bacterial/*genetics ; Genomics/*methods ; Least-Squares Analysis ; Regulatory Sequences, Nucleic Acid/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The upstream region of coding genes is important for several reasons, for instance locating transcription factor, binding sites, and start site initiation in genomic DNA. Motivated by a recently conducted study, where multivariate approach was successfully applied to coding sequence modeling, we have introduced a partial least squares (PLS) based procedure for the classification of true upstream prokaryotic sequence from background upstream sequence. The upstream sequences of conserved coding genes over genomes were considered in analysis, where conserved coding genes were found by using pan-genomics concept for each considered prokaryotic species. PLS uses position specific scoring matrix (PSSM) to study the characteristics of upstream region. Results obtained by PLS based method were compared with Gini importance of random forest (RF) and support vector machine (SVM), which is much used method for sequence classification. The upstream sequence classification performance was evaluated by using cross validation, and suggested approach identifies prokaryotic upstream region significantly better to RF (p-value < 0.01) and SVM (p-value < 0.01). Further, the proposed method also produced results that concurred with known biological characteristics of the upstream region.}, } @article {pmid26356773, year = {2015}, author = {Akhtar, S}, title = {Some psychoanalytic reflections on the concept of dignity.}, journal = {American journal of psychoanalysis}, volume = {75}, number = {3}, pages = {244-266}, doi = {10.1057/ajp.2015.37}, pmid = {26356773}, issn = {1573-6741}, mesh = {Existentialism ; Humans ; Metaphysics ; Morals ; Personality ; *Personhood ; *Psychoanalytic Interpretation ; }, abstract = {After reviewing the pertinent philosophical and psychoanalytic writings on the concept of dignity, this paper proposes three categories of dignity. Conceptualized as phenomenological clusters, heuristic viewpoints, and levels of abstraction, these include (i) metaphysical dignity which extends the concept of dignity beyond the human species to all that exists in this world, (ii) existential dignity which applies to human beings alone and rests upon their inherent capacity for moral transcendence, and (iii) characterological dignity which applies more to some human beings than others since they possess a certain set of personality traits that are developmentally derived. The paper discusses the pros and cons of each category and acknowledges the limitations of such classification. It also discusses the multiple ways in which these concepts impact upon clinical work and concludes with some remarks on the relationship of dignity to choice, narcissism, and suicide.}, } @article {pmid26354700, year = {2015}, author = {Lee, JW and Won, EJ and Raisuddin, S and Lee, JS}, title = {Significance of adverse outcome pathways in biomarker-based environmental risk assessment in aquatic organisms.}, journal = {Journal of environmental sciences (China)}, volume = {35}, number = {}, pages = {115-127}, doi = {10.1016/j.jes.2015.05.002}, pmid = {26354700}, issn = {1001-0742}, mesh = {Animals ; Aquatic Organisms/drug effects ; Benzo(a)pyrene/toxicity ; Biomarkers/metabolism ; *Environmental Exposure ; Environmental Monitoring ; Fishes/*embryology/*metabolism ; Metal Nanoparticles/toxicity ; Neoplasms/chemically induced/veterinary ; Risk Assessment ; Selenium/toxicity ; Silver/toxicity ; Teratogens/*toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {In environmental risk assessments (ERA), biomarkers have been widely used as an early warning signal of environmental contamination. However, biomarker responses have limitation due to its low relevance to adverse outcomes (e.g., fluctuations in community structure, decreases in population size, and other similar ecobiologically relevant indicators of community structure and function). To mitigate these limitations, the concept of adverse outcome pathways (AOPs) was developed. An AOP is an analytical, sequentially progressive pathway that links a molecular initiating event (MIE) to an adverse outcome. Recently, AOPs have been recognized as a potential informational tool by which the implications of molecular biomarkers in ERA can be better understood. To demonstrate the utility of AOPs in biomarker-based ERA, here we discuss a series of three different biological repercussions caused by exposure to benzo(a)pyrene (BaP), silver nanoparticles (AgNPs), and selenium (Se). Using mainly aquatic invertebrates and selected vertebrates as model species, we focus on the development of the AOP concept. Aquatic organisms are suitable bioindicator species whose entire lifespans can be observed over a short period; moreover, these species can be studied on the molecular and population levels. Also, interspecific differences between aquatic organisms are important to consider in an AOP framework, since these differences are an integral part of the natural environment. The development of an environmental pollutant-mediated AOP may enable a better understanding of the effects of environmental pollutants in different scenarios in the diverse community of an ecosystem.}, } @article {pmid26353399, year = {2015}, author = {Baskevich, MI and Potapov, SG and Mironova, TA}, title = {[Caucasian cryptic species of rodents as models for studying the problem of species and speciation].}, journal = {Zhurnal obshchei biologii}, volume = {76}, number = {4}, pages = {319-335}, pmid = {26353399}, issn = {0044-4596}, mesh = {Animals ; *Genetic Speciation ; *Karyotype ; Mice ; *Phylogeny ; Rodentia/*classification/genetics ; Species Specificity ; }, abstract = {The problem of species and speciation is considered using as a model the cryptic species of rodents inhabiting the Caucasus, the mountain chain with prominent altitude environmental gradient and insular pattern of mountain habitats. These circumstances open additional possibilities for the choice of species conception (biological or phylogenetic), exploration of ancestry pathways (sympatric or allopatric speciation) of model cryptic species groups, and testing the 'refuge' hypothesis. As model species, sibling-species Sicista from the group 'caucasica' (a group of unstriped birch mice) and representatives of the vole subspecies Terricola (Microtus, Arvicolinae) were used. Based on the new data on karyology, nucleotide sequences of mitochondrial gene cytb, multivariate statistical analysis of odontologic traits, and biogeography of sibling-species Sicista from the group 'caucasica' and voles from subspecies Terricola (Microtus, Arvicolinae), their evolutionary history is reconstructed and applicable species concepts are examined. For the present sibling-species Sicista from the group 'caucasica' the allopatric dispersion is typical, which agrees with the hypothesis of speciation in refuges. The sympatry of Terricola sibling-species in the Caucasus is considered as being secondary, and their phenotypic likeness--as an adaptation to similar environmental conditions. Affirmed coexistence of sibling-species Microtus (Terricola) majori and Microtus (Terricola) daghestanicus in the Caucasus (without their hybridization) supports the biological conception of species. The existence of Sicista allospecies from the group of Caucasian unstriped birch mice is best conformed to the phylogenetic conception. However, the high level of chromosomal differences between sibling-species and, in particular, between extreme variants of common evolutionary line (Sicista kazbegica, Sicista kluchorica) does not contradict the biological conception of species.}, } @article {pmid26346701, year = {2015}, author = {de Lafontaine, G and Prunier, J and Gérardi, S and Bousquet, J}, title = {Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana × P. rubens).}, journal = {Molecular ecology}, volume = {24}, number = {20}, pages = {5229-5247}, doi = {10.1111/mec.13377}, pmid = {26346701}, issn = {1365-294X}, mesh = {DNA, Plant/genetics ; Gene Flow ; Genes, Plant ; *Genetic Speciation ; Genetics, Population ; Genotype ; *Hybridization, Genetic ; Picea/classification/*genetics ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {The genic species concept implies that while most of the genome can be exchanged somewhat freely between species through introgression, some genomic regions remain impermeable to interspecific gene flow. Hence, interspecific differences can be maintained despite ongoing gene exchange within contact zones. This study assessed the heterogeneous patterns of introgression at gene loci across the hybrid zone of an incipient progenitor-derivative species pair, Picea mariana (black spruce) and Picea rubens (red spruce). The spruce taxa likely diverged in geographic isolation during the Pleistocene and came into secondary contact during late Holocene. A total of 300 SNPs distributed across the 12 linkage groups (LG) of black spruce were genotyped for 385 individual trees from 33 populations distributed across the allopatric zone of each species and within the zone of sympatry. An integrative framework combining three population genomic approaches was used to scan the genomes, revealing heterogeneous patterns of introgression. A total of 23 SNPs scattered over 10 LG were considered impermeable to introgression and putatively under diverging selection. These loci revealed the existence of impermeable genomic regions forming the species boundary and are thus indicative of ongoing speciation between these two genetic lineages. Another 238 SNPs reflected selectively neutral diffusion across the porous species barrier. Finally, 39 highly permeable SNPs suggested ancestral polymorphism along with balancing selection. The heterogeneous patterns of introgression across the genome indicated that the speciation process between black spruce and red spruce is young and incomplete, albeit some interspecific differences are maintained, allowing ongoing species divergence even in sympatry. The approach developed in this study can be used to track the progression of ongoing speciation processes.}, } @article {pmid26345798, year = {2015}, author = {Du, SH and Wang, ZS and Li, YX and Wang, DS and Zhang, JG}, title = {Consistency between molecular phylogeny and morphological classification of the Salix matsudana Koidz. complex (Salicaceae).}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {3}, pages = {8663-8671}, doi = {10.4238/2015.July.31.15}, pmid = {26345798}, issn = {1676-5680}, mesh = {Genes, Plant ; Genetic Association Studies ; Genetic Loci ; Molecular Typing ; Phylogeny ; Plant Proteins/genetics ; Salix/anatomy & histology/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {The morphological species concept is based on morpho-logical traits, which are often subject to subjectivity or artifact. Molecular evidence is needed to test the reliability of morphological classification of taxa that are controversial and to provide appropriate taxonomic de-limitation. In this study, we used 15 single-copy nuclear loci and 2 chloroplast fragments to verify the morphological classification of the Salix matsudana Koidz. complex using phylogenetic approaches. Complete sequence alignment showed slight diversification in nuclear sequences and no variety in chloroplast DNA fragments. Phylogenetic trees revealed a monophyletic group consisting of all individuals of S. matsudana and 2 clades within this group, with a 100% bootstrap support value and 1.00 posterior probability. The topology of the phylogenetic trees was highly consistent with the morphological classification of the S. matsudana complex. Verifying the genetic background of these classification units based on remarkable morphological differences will provide a foundation for future studies of Salix and the breeding of new horticultural varieties.}, } @article {pmid26316424, year = {2015}, author = {Krause, DJ and Whitaker, RJ}, title = {Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes.}, journal = {Systematic biology}, volume = {64}, number = {6}, pages = {926-935}, pmid = {26316424}, issn = {1076-836X}, mesh = {Bacteria/*classification ; *Genetic Speciation ; *Genetic Variation ; Genome, Bacterial/genetics ; Genomics ; Models, Genetic ; }, abstract = {Microbial species concepts have long been the focus of contentious debate, fueled by technological limitations to the genetic resolution of species, by the daunting task of investigating phenotypic variation among individual microscopic organisms, and by a lack of understanding of gene flow in reproductively asexual organisms that are prone to promiscuous horizontal gene transfer. Population genomics, the emerging approach of analyzing the complete genomes of a multitude of closely related organisms, is poised to overcome these limitations by providing a window into patterns of genome variation revealing the evolutionary processes through which species diverge. This new approach is more than just an extension of previous multilocus sequencing technologies, in that it provides a comprehensive view of interacting evolutionary processes. Here we argue that the application of population genomic tools in a rigorous population genetic framework will help to identify the processes of microbial speciation and ultimately lead to a general species concept based on the unique biology and ecology of microorganisms.}, } @article {pmid26316330, year = {2016}, author = {Rosenlöcher, J and Sandig, G and Kannicht, C and Blanchard, V and Reinke, SO and Hinderlich, S}, title = {Recombinant glycoproteins: The impact of cell lines and culture conditions on the generation of protein species.}, journal = {Journal of proteomics}, volume = {134}, number = {}, pages = {85-92}, doi = {10.1016/j.jprot.2015.08.011}, pmid = {26316330}, issn = {1876-7737}, mesh = {Cell Culture Techniques/*methods ; Glycosylation ; HEK293 Cells ; Humans ; Recombinant Proteins/biosynthesis/genetics ; alpha 1-Antitrypsin/*biosynthesis/genetics ; }, abstract = {UNLABELLED: Glycosylation is the most complex post-translational modification. Thus, it contributes to versatile chemical compositions of proteins, leading to high amounts of protein species. The structural heterogeneity of glycoproteins was also described by the definition of glycoforms. We therefore introduced a new term called "glycoprotein species" to join the two concepts from different fields of biology. In this study, we further determined the theoretical numbers of glycoprotein species of two recombinant glycoproteins - a therapeutical antibody and the human protease inhibitor alpha-1-antitrypsin (A1AT) - based on structural analysis of their N-glycans. Moreover, we showed that variations in the used cell lines and their cultivation conditions strongly influence the number of glycoprotein species in case of recombinant A1AT production.

BIOLOGICAL SIGNIFICANCE: Protein glycosylation is a major source for the huge amount of protein species. This study extends the sight of protein species by the following contributions: 1) The new term "glycoprotein species" was defined to introduce the concept of glycoforms into the field. 2) An estimation of the number of potential glycoprotein species of two particular glycoproteins was given. 3) The influence of production conditions for recombinant glycoproteins on glycoprotein species generation was displayed.}, } @article {pmid26313925, year = {2015}, author = {Al-Saari, N and Gao, F and Rohul, AA and Sato, K and Sato, K and Mino, S and Suda, W and Oshima, K and Hattori, M and Ohkuma, M and Meirelles, PM and Thompson, FL and Thompson, C and Filho, GM and Gomez-Gil, B and Sawabe, T and Sawabe, T}, title = {Advanced Microbial Taxonomy Combined with Genome-Based-Approaches Reveals that Vibrio astriarenae sp. nov., an Agarolytic Marine Bacterium, Forms a New Clade in Vibrionaceae.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0136279}, pmid = {26313925}, issn = {1932-6203}, mesh = {*Aquatic Organisms/classification/genetics ; Bacterial Proteins/*genetics ; *Genome, Bacterial ; *Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Vibrio/classification/genetics ; }, abstract = {Advances in genomic microbial taxonomy have opened the way to create a more universal and transparent concept of species but is still in a transitional stage towards becoming a defining robust criteria for describing new microbial species with minimum features obtained using both genome and classical polyphasic taxonomies. Here we performed advanced microbial taxonomies combined with both genome-based and classical approaches for new agarolytic vibrio isolates to describe not only a novel Vibrio species but also a member of a new Vibrio clade. Two novel vibrio strains (Vibrio astriarenae sp. nov. C7T and C20) showing agarolytic, halophilic and fermentative metabolic activity were isolated from a seawater sample collected in a coral reef in Okinawa. Intraspecific similarities of the isolates were identical in both sequences on the 16S rRNA and pyrH genes, but the closest relatives on the molecular phylogenetic trees on the basis of 16S rRNA and pyrH gene sequences were V. hangzhouensis JCM 15146T (97.8% similarity) and V. agarivorans CECT 5085T (97.3% similarity), respectively. Further multilocus sequence analysis (MLSA) on the basis of 8 protein coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) obtained by the genome sequences clearly showed the V. astriarenae strain C7T and C20 formed a distinct new clade protruded next to V. agarivorans CECT 5085T. The singleton V. agarivorans has never been included in previous MLSA of Vibrionaceae due to the lack of some gene sequences. Now the gene sequences are completed and analysis of 100 taxa in total provided a clear picture describing the association of V. agarivorans into pre-existing concatenated network tree and concluded its relationship to our vibrio strains. Experimental DNA-DNA hybridization (DDH) data showed that the strains C7T and C20 were conspecific but were separated from all of the other Vibrio species related on the basis of both 16S rRNA and pyrH gene phylogenies (e.g., V. agarivorans CECT 5085T, V. hangzhouensis JCM 15146T V. maritimus LMG 25439T, and V. variabilis LMG 25438T). In silico DDH data also supported the genomic relationship. The strains C7T also had less than 95% average amino acid identity (AAI) and average nucleotide identity (ANI) towards V. maritimus C210, V. variabilis C206, and V. mediterranei AK1T, V. brasiliensis LMG 20546T, V. orientalis ATCC 33934T, and V. sinaloensis DSM 21326. The name Vibrio astriarenae sp. nov. is proposed with C7 as the type strains. Both V. agarivorans CECT 5058T and V. astriarenae C7T are members of the newest clade of Vibrionaceae named Agarivorans.}, } @article {pmid26249381, year = {2015}, author = {Khaironizam, MZ and Akaria-Ismail, M and Armbruster, JW}, title = {Cyprinid fishes of the genus Neolissochilus in Peninsular Malaysia.}, journal = {Zootaxa}, volume = {3962}, number = {}, pages = {139-157}, doi = {10.11646/zootaxa.3962.1.7}, pmid = {26249381}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Body Size ; Cyprinidae/anatomy & histology/*classification/growth & development ; Ecosystem ; Female ; Malaysia ; Male ; Organ Size ; }, abstract = {Meristic, morphometric and distributional patterns of cyprinid fishes of the genus Neolissochilus found in Peninsular Malaysia are presented. Based on the current concept of Neolissochilus, only two species are present: N. soroides and N. hendersoni. Neolissochilus hendersoni differs from N. soroides by having lower scale and gill raker counts. Neolissochilus soroides has three mouth types (normal with a rounded snout, snout with a truncate edge, and lobe with a comparatively thick lower lip). A PCA of log-transformed measurements did not reveal significant differences between N. hendersoni and N. soroides, or between any of the morphotypes of N. soroides; however, a CVA of log-transformed measurements successfully classified 87.1% of all specimens. Removing body size by running a CVA on all of the principal components except PC1 (which was correlated with length) only slightly decreased the successful classification rate to 86.1%. Differences in morphometrics were as great between the three morphotypes of N. soroides as between any of the morphotypes and N. hendersoni suggesting that the morphotypes should be examined in greater detail with genetic tools. The PCA of morphometrics revealed separate clouds for N. hendersoni and N. soroides, but no differences between the N. soroides morphotypes. This study revealed that N. hendersoni is recorded for the first time in the mainland area of Peninsular Malaysia. Other nominal species of Neolissochilus reported to occur in the river systems of Peninsular Malaysia are discussed. Lissochilus tweediei Herre in Herre & Myers 1937 and Tor soro Bishop 1973 are synonyms of Neolissochilus soroides.}, } @article {pmid26249081, year = {2015}, author = {Griswold, T and Herndon, JD and Gonzalez, VH}, title = {First record of the orchid bee genus Eufriesea Cockerell (Hymenoptera: Apidae: Euglossini) in the United States.}, journal = {Zootaxa}, volume = {3957}, number = {3}, pages = {342-346}, doi = {10.11646/zootaxa.3957.3.7}, pmid = {26249081}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Bees/anatomy & histology/*classification/growth & development ; Body Size ; Male ; Mexico ; Organ Size ; Seasons ; Texas ; }, abstract = {The orchid bee genus Eufriesea Cockerell is documented for the first time from the southwestern United States, extending its apparent range north well beyond its previous tropical/subtropical boundaries. Eufriesea coerulescens (Lepeletier de Saint Fargeau 1841) is recorded from the Guadalupe Mountains of western Texas and southeastern New Mexico, USA. Whether E. coerulescens is resident in the USA, or merely a vagrant from Mexico, remains unclear. Distinctive morphological traits shared with the holotype are enumerated and illustrated. In addition, observations that question the current species concept and distribution of E. coerulescens are provided.}, } @article {pmid26243504, year = {2015}, author = {Gardner, CJ and Jasper, LD}, title = {Discovery of an island population of dwarf lemurs (Cheirogaleidae: Cheirogaleus) on Nosy Hara, far northern Madagascar.}, journal = {Primates; journal of primatology}, volume = {56}, number = {4}, pages = {307-310}, pmid = {26243504}, issn = {1610-7365}, mesh = {Animals ; Biological Evolution ; Cheirogaleidae/*anatomy & histology/classification/*physiology ; Islands ; Madagascar ; }, abstract = {The species-level diversity of Madagascar's lemurs has increased hugely over the last two decades, growing from 32 species in 1994 to 102 species in 2014. This growth is primarily due to the application of molecular phylogenetic analyses and the phylogenetic species concept to known populations, and few previously unknown lemur populations have been discovered during this time. We report on a new population of dwarf lemurs (Cheirogaleus sp.) from Nosy Hara, a 312-ha island in far northern Madagascar, which constitutes the northernmost distribution record for the genus. The dwarf lemurs appeared to show two characteristics of island populations-insular dwarfism and predator naïveté-that suggest a long isolation, and may thus represent an undescribed taxon. If this is the case, the dwarf lemurs of Nosy Hara are probably one of the rarest primate taxa on Earth.}, } @article {pmid26240446, year = {2015}, author = {Bakhshi, M and Arzanlou, M and Babai-Ahari, A and Groenewald, JZ and Braun, U and Crous, PW}, title = {Application of the consolidated species concept to Cercospora spp. from Iran.}, journal = {Persoonia}, volume = {34}, number = {}, pages = {65-86}, pmid = {26240446}, issn = {0031-5850}, abstract = {The genus Cercospora includes many important plant pathogenic fungi associated with leaf spot diseases on a wide range of hosts. The mainland of Iran covers various climatic regions with a great biodiversity of vascular plants, and a correspondingly high diversity of cercosporoid fungi. However, most of the cercosporoid species found to date have been identified on the basis of morphological characteristics and there are no cultures that support these identifications. In this study the Consolidated Species Concept was applied to differentiate Cercospora species collected from Iran. A total of 161 Cercospora isolates recovered from 74 host species in northern Iran were studied by molecular phylogenetic analysis. Our results revealed a rich diversity of Cercospora species in northern Iran. Twenty species were identified based on sequence data of five genomic loci (ITS, TEF1-α, actin, calmodulin and histone H3), host, cultural and morphological data. Six novel species, viz. C. convolvulicola, C. conyzae-canadensis, C. cylindracea, C. iranica, C. pseudochenopodii and C. sorghicola, are introduced. The most common taxon was Cercospora cf. flagellaris, which remains an unresolved species complex with a wide host range. New hosts were recorded for previously known Cercospora species, including C. apii, C. armoraciae, C. beticola, C. cf. richardiicola, C. rumicis, Cercospora sp. G and C. zebrina.}, } @article {pmid26240442, year = {2015}, author = {Giraldo, A and Gené, J and Sutton, DA and Madrid, H and de Hoog, GS and Cano, J and Decock, C and Crous, PW and Guarro, J}, title = {Phylogeny of Sarocladium (Hypocreales).}, journal = {Persoonia}, volume = {34}, number = {}, pages = {10-24}, pmid = {26240442}, issn = {0031-5850}, abstract = {The circumscription of the genus Acremonium (Hypocreales) was recently reviewed on the basis of a DNA phylogenetic study. Several species were subsequently transferred to Sarocladium, but the relationships between both genera remained unresolved. Based on multilocus phylogenetic inferences combined with phenotypic data, we have revised the species concepts within Sarocladium and some genetically related species of Acremonium. As a result of these studies, six species are described as new, viz. S. bifurcatum, S. gamsii, S. hominis, S. pseudostrictum, S. subulatum and S. summerbellii. In addition, the new combinations S. implicatum and S. terricola are proposed for A. implicatum and A. terricola, respectively. Sarocladium attenuatum is confirmed as synonym of the type species of the genus, S. oryzae. An epitype and neotype are also introduced for S. oryzae and S. implicatum, respectively. Although Sarocladium species have traditionally been considered as important phytopathogens, the genus also contains opportunistic human pathogens. This study extends the spectrum of clinical species that could be diagnosed as causal agents of human infections.}, } @article {pmid26222615, year = {2015}, author = {Schwen, LO and Schenk, A and Kreutz, C and Timmer, J and Bartolomé Rodríguez, MM and Kuepfer, L and Preusser, T}, title = {Representative Sinusoids for Hepatic Four-Scale Pharmacokinetics Simulations.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0133653}, pmid = {26222615}, issn = {1932-6203}, mesh = {Adult ; Animals ; Blood Circulation ; Caffeine/pharmacokinetics ; Fatty Liver/metabolism ; Humans ; Insulin/pharmacokinetics ; Liver/blood supply/cytology/*metabolism/physiology ; Male ; Mice ; *Models, Biological ; *Pharmacokinetics ; Regeneration ; }, abstract = {The mammalian liver plays a key role for metabolism and detoxification of xenobiotics in the body. The corresponding biochemical processes are typically subject to spatial variations at different length scales. Zonal enzyme expression along sinusoids leads to zonated metabolization already in the healthy state. Pathological states of the liver may involve liver cells affected in a zonated manner or heterogeneously across the whole organ. This spatial heterogeneity, however, cannot be described by most computational models which usually consider the liver as a homogeneous, well-stirred organ. The goal of this article is to present a methodology to extend whole-body pharmacokinetics models by a detailed liver model, combining different modeling approaches from the literature. This approach results in an integrated four-scale model, from single cells via sinusoids and the organ to the whole organism, capable of mechanistically representing metabolization inhomogeneity in livers at different spatial scales. Moreover, the model shows circulatory mixing effects due to a delayed recirculation through the surrounding organism. To show that this approach is generally applicable for different physiological processes, we show three applications as proofs of concept, covering a range of species, compounds, and diseased states: clearance of midazolam in steatotic human livers, clearance of caffeine in mouse livers regenerating from necrosis, and a parameter study on the impact of different cell entities on insulin uptake in mouse livers. The examples illustrate how variations only discernible at the local scale influence substance distribution in the plasma at the whole-body level. In particular, our results show that simultaneously considering variations at all relevant spatial scales may be necessary to understand their impact on observations at the organism scale.}, } @article {pmid26207159, year = {2015}, author = {Heath, MD and Collis, J and Batten, T and Hutchings, JW and Swan, N and Skinner, MA}, title = {Molecular, proteomic and immunological parameters of allergens provide inclusion criteria for new candidates within established grass and tree homologous groups.}, journal = {The World Allergy Organization journal}, volume = {8}, number = {1}, pages = {21}, pmid = {26207159}, issn = {1939-4551}, abstract = {BACKGROUND: Our knowledge of allergen structure and function continues to rise and new scientific data on the homology and cross-reactivity of allergen sources should be considered to extend the work of Lorenz et al., 2009 (Int Arch Allergy Immunol. 148(1):1-1, 2009) and the concept of homologous groups. In addition to this, sophisticated techniques such as mass spectrometry (MS) are increasingly utilised to better characterise the complex mix and nature of allergen extracts.

METHODS: Homology models were used of Fag s 1 (Beech) and Cyn d 1 (Bermuda grass) and compared with template crystal structures of Bet v 1 and Phl p 1 from the 'exemplar' species of Birch and Timothy grass, respectively. ELISA experiments were performed to assess cross-reactivity of Beech (tree) and Bermuda (grass) extracts to rabbit sera raised to either "3-Tree" (Birch, Alder and Hazel) extract or "Grass" (12-grass mix extract), respectively. The comparability of biochemical stability of different allergen sources was assessed through statistical methods for a range of tree and grass species.

RESULTS: Allergen cross-reactivity and/or structural homology have been described providing justification for inclusion of Beech within the Birch homologous tree group. Data from Bermuda grass (Cyn d 1) provides further justification for the inclusion of this species into the homologous group of the sweet grasses. However, further characterisation of relevant allergens from Bermuda grass and, in particular, comparison of cross-reactive patterns between subjects specifically in areas with high abundance of both Pooideae and Chloridoideae is sought.

CONCLUSION: MS allows the possibility to identify individual proteins or allergens from complex mixes by mass and/or sequence, and this has been extensively applied to the allergen field. New data on the homology, cross-reactivity and biological parameters of allergen sources have been considered to extend the work of Lorenz et al., 2009 in the context of tree and grass species. The concept of homologous groups is certainly dynamic allowing the flexibility and potential in streamlining quality parameters, such as stability profiles, due to extrapolation of exemplar data to a wider range of allergens.}, } @article {pmid26193914, year = {2015}, author = {Seo, SM and Jeon, JW and Kim, TY and Paek, SH}, title = {An innate immune system-mimicking, real-time biosensing of infectious bacteria.}, journal = {The Analyst}, volume = {140}, number = {17}, pages = {6061-6070}, doi = {10.1039/c5an00912j}, pmid = {26193914}, issn = {1364-5528}, mesh = {Animals ; Antibodies/immunology ; Bacteriological Techniques/*methods ; *Biosensing Techniques ; Cell Line ; Listeria monocytogenes/*physiology ; Macrophages/cytology/metabolism/microbiology ; Mice ; Milk/microbiology ; Paracrine Communication ; Shigella sonnei/*physiology ; Staphylococcus aureus/*physiology ; Tumor Necrosis Factor-alpha/*analysis/immunology ; }, abstract = {An animal cell-based biosensor was investigated to monitor bacterial contamination in an unattended manner by mimicking the innate immune response. The cells (RAW 264.7 cell line) were first attached onto the solid surfaces of a 96-well microtiter plate and co-incubated in the culture medium with a sample that might contain bacterial contaminants. As Toll-like receptors were present on the cell membrane surfaces, they acted as a sentinel by binding to pathogen-associated molecular patterns (PAMPs) of any contaminant. Such biological recognition initiates signal transmission along various pathways to produce different proinflammatory mediators, one of which, tumor necrosis factor-α (TNF-α) was measured using an immunosensor. To demonstrate automated bacterium monitoring, a capture antibody specific for TNF-α was immobilized on an optical fiber sensor tip and then used to measure complex formation in a label-free sensor system (e.g., Octet Red). The sensor response time depended significantly on the degree of agitation of the culture medium, controlling the biological recognition and further autocrine/paracrine signaling by cytokines. The response, particularly under non-agitated conditions, was also influenced by the medium volume, revealing a local gradient change of the cytokine concentration and also acidity, caused by bacterial growth near the bottom surfaces. A biosensor system retaining 50 μL medium and not employing agitation could be used for the early detection of bacterial contamination. This novel biosensing model was applied to the real-time monitoring of different bacteria, Shigella sonnei, Staphylococcus aureus, and Listeria monocytogenes. They (<100 CFU mL(-1)) could be detected automatically within the working time. Such analysis was carried out without any manual handling regardless of the bacterial species, suggesting the concept of non-targeted bacterial real-time monitoring. This technique was further applied to real sample testing (e.g., with milk) to exemplify, for example, the food quality control process without using any additional sample pretreatment such as magnetic concentration.}, } @article {pmid26172261, year = {2015}, author = {Bruffaerts, N and Pedersen, LE and Vandermeulen, G and Préat, V and Stockhofe-Zurwieden, N and Huygen, K and Romano, M}, title = {Increased B and T Cell Responses in M. bovis Bacille Calmette-Guérin Vaccinated Pigs Co-Immunized with Plasmid DNA Encoding a Prototype Tuberculosis Antigen.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132288}, pmid = {26172261}, issn = {1932-6203}, mesh = {Alleles ; Animals ; Antibodies, Bacterial/immunology ; Antigens, Bacterial/genetics/*immunology ; B-Lymphocytes/*immunology ; BCG Vaccine/genetics/*immunology ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Epitopes, T-Lymphocyte/immunology ; Immunity, Cellular ; Immunity, Humoral ; Interferon-gamma/biosynthesis/metabolism ; Mycobacterium bovis/*immunology ; Plasmids/genetics ; Species Specificity ; Swine ; T-Lymphocytes/*immunology/metabolism ; Time Factors ; *Vaccination ; Vaccines, DNA/genetics/*immunology ; }, abstract = {The only tuberculosis vaccine currently available, bacille Calmette-Guérin (BCG) is a poor inducer of CD8(+) T cells, which are particularly important for the control of latent tuberculosis and protection against reactivation. As the induction of strong CD8(+) T cell responses is a hallmark of DNA vaccines, a combination of BCG with plasmid DNA encoding a prototype TB antigen (Ag85A) was tested. As an alternative animal model, pigs were primed with BCG mixed with empty vector or codon-optimized pAg85A by the intradermal route and boosted with plasmid delivered by intramuscular electroporation. Control pigs received unformulated BCG. The BCG-pAg85A combination stimulated robust and sustained Ag85A specific antibody, lymphoproliferative, IL-6, IL-10 and IFN-γ responses. IgG1/IgG2 antibody isotype ratio reflected the Th1 helper type biased response. T lymphocyte responses against purified protein derivative of tuberculin (PPD) were induced in all (BCG) vaccinated animals, but responses were much stronger in BCG-pAg85A vaccinated pigs. Finally, Ag85A-specific IFN-γ producing CD8(+) T cells were detected by intracellular cytokine staining and a synthetic peptide, spanning Ag85A131-150 and encompassing two regions with strong predicted SLA-1*0401/SLA-1*0801 binding affinity, was promiscuously recognized by 6/6 animals vaccinated with the BCG-pAg85A combination. Our study provides a proof of concept in a large mammalian species, for a new Th1 and CD8(+) targeting tuberculosis vaccine, based on BCG-plasmid DNA co-administration.}, } @article {pmid26170472, year = {2015}, author = {Kanzaki, N and Woodruff, GC and Akiba, M and Maehara, N}, title = {Diplogasteroides asiaticus n. sp. is Associated with Monochamus alternatus in Japan.}, journal = {Journal of nematology}, volume = {47}, number = {2}, pages = {105-115}, pmid = {26170472}, issn = {0022-300X}, abstract = {Diplogasteroides asiaticus n. sp. is described and illustrated, and its molecular profile and phylogenetic status within the family Diplogastridae are inferred. Morphologically, the new species is characterized by its stomatal structure, a tube-like stoma with three small, rod-like dorsal teeth and two subventral ridges; a spicule clearly ventrally bent at 1/3 from the anterior end; a gubernaculum with a rounded anterior end and sharply pointed distal end in lateral view; nine pairs of genital papillae with an arrangement of ; a short tail spike in males; and a well-developed receptaculum seminis, i.e., the antiparallel blind sacs of the uteri beyond the vulva region and elongated conical tail in females. This new species is morphologically similar to D. haslacheri, but it can be distinguished by the morphology of the somewhat shorter tail in females. D. asiaticus n. sp. shares high sequence conservation with D. andrassyi as there is only one base pair difference in the nearly full-length 18S rDNA and seven base pair differences in the D2-D3 expansion segments of the 28S rDNA. Despite this sequence conservation, the species status of D. asiaticus n. sp. was confirmed using the biological species concept, as D. asiaticus n. sp. and D. andrassyi failed to generate viable F2 progeny in hybridization tests.}, } @article {pmid26150657, year = {2015}, author = {Laydon, DJ and Bangham, CR and Asquith, B}, title = {Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1675}, pages = {}, pmid = {26150657}, issn = {1471-2970}, support = {103865/WT_/Wellcome Trust/United Kingdom ; 100291/WT_/Wellcome Trust/United Kingdom ; MR/K019090/1/MRC_/Medical Research Council/United Kingdom ; K019090/MRC_/Medical Research Council/United Kingdom ; G0601072/MRC_/Medical Research Council/United Kingdom ; MR/J007439/1/MRC_/Medical Research Council/United Kingdom ; J007439/MRC_/Medical Research Council/United Kingdom ; G1001052/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Gene Rearrangement, T-Lymphocyte ; Genetic Variation ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Lymphocyte Count ; Models, Genetic ; Models, Immunological ; Receptors, Antigen, T-Cell/chemistry/*genetics/*immunology ; Statistics, Nonparametric ; T-Lymphocytes/immunology ; }, abstract = {A highly diverse T-cell receptor (TCR) repertoire is a fundamental property of an effective immune system, and is associated with efficient control of viral infections and other pathogens. However, direct measurement of total TCR diversity is impossible. The diversity is high and the frequency distribution of individual TCRs is heavily skewed; the diversity therefore cannot be captured in a blood sample. Consequently, estimators of the total number of TCR clonotypes that are present in the individual, in addition to those observed, are essential. This is analogous to the 'unseen species problem' in ecology. We review the diversity (species richness) estimators that have been applied to T-cell repertoires and the methods used to validate these estimators. We show that existing approaches have significant shortcomings, and frequently underestimate true TCR diversity. We highlight our recently developed estimator, DivE, which can accurately estimate diversity across a range of immunological and biological systems.}, } @article {pmid26149864, year = {2015}, author = {Shaw, J and Pratlong, F and Floeter-Winter, L and Ishikawa, E and El Baidouri, F and Ravel, C and Dedet, JP}, title = {Characterization of Leishmania (Leishmania) waltoni n.sp. (Kinetoplastida: Trypanosomatidae), the Parasite Responsible for Diffuse Cutaneous Leishmaniasis in the Dominican Republic.}, journal = {The American journal of tropical medicine and hygiene}, volume = {93}, number = {3}, pages = {552-558}, pmid = {26149864}, issn = {1476-1645}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Antibodies, Protozoan/immunology ; Base Sequence ; Dominican Republic/epidemiology ; Fluorescent Antibody Technique, Indirect ; Humans ; Isoenzymes/genetics ; *Leishmania/enzymology/genetics/isolation & purification/physiology ; Leishmaniasis, Diffuse Cutaneous/epidemiology/*parasitology ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; }, abstract = {Leishmania parasites isolated, between 1979 and 1988 by the late Bryce Walton, from Dominican Republic (DR) patients with diffuse cutaneous leishmaniasis, were characterized using a panel of 12 isoenzymes, 23 monoclonal antibodies, small subunit ribosomal DNA (SSu rDNA), and multilocus sequence analysis (MLSA). The isoenzyme and monoclonal antibody profiles and the MLSA results showed that the Dominican Republic parasites were distinct from other described Leishmania species. This new species belongs to the mexicana complex, which is distributed in central and parts of northern South America. It is suggested that the parasites uniqueness from other members of the mexicana complex is related to it being isolated on an island for millions of years. If Leishmania (Leishmania) waltoni fails to adapt to some imported mammal, such as the house rat, it will be the only Leishmania to be classified as an endangered species. The excessive destruction of habitats on Hispaniola threatens the survival of its vectors and presumed natural reservoirs, such as the rodent hutias and the small insectivorous mammal solenodon. The concept of Leishmania species is discussed in the light of recent evaluations on criteria for defining bacterial species.}, } @article {pmid26149758, year = {2015}, author = {Lang, AS and Bocksberger, G and Stech, M}, title = {Phylogeny and species delimitations in European Dicranum (Dicranaceae, Bryophyta) inferred from nuclear and plastid DNA.}, journal = {Molecular phylogenetics and evolution}, volume = {92}, number = {}, pages = {217-225}, doi = {10.1016/j.ympev.2015.06.019}, pmid = {26149758}, issn = {1095-9513}, mesh = {Base Sequence ; Bayes Theorem ; Bryophyta/*classification/*genetics ; Cell Nucleus/*genetics ; DNA, Chloroplast/*genetics ; Likelihood Functions ; *Phylogeny ; Species Specificity ; }, abstract = {DNA sequences have been widely used for taxonomy, inferring phylogenetic relationships and identifying species boundaries. Several specific methods to define species delimitations based on molecular phylogenies have appeared recently, with the generalized mixed Yule coalescent (GMYC) method being most popular. However, only few studies on land plants have been published so far and GMYC analyses of bryophytes are missing. Dicranum is a large genus of mosses whose (morpho-)species are partly ill-defined and frequently confused. To infer molecular species delimitations, we reconstructed phylogenetic trees based on five chloroplast markers and nuclear ribosomal ITS sequences from 27 out of 30 species occurring in Europe. We applied the species delimitation methods GMYC and Poisson tree processes (PTP) in order to compare their discriminatory power with species boundaries inferred from the molecular phylogenetic reconstructions and with the morphological species concept. Phylogenetic circumscriptions were congruent with the morphological concept for 19 species, while eight species were molecularly not well delimited, mostly forming closely related species pairs. The automated species delimitation methods achieved similar results but tended to overestimate the number of potential species and exposed several incongruences between the morphological concept and inference from molecular phylogenetic reconstructions. It is concluded that GMYC and PTP methods potentially provide a useful and objective way of delimiting bryophyte species, but studies on further bryophyte data sets are necessary to infer whether incongruences might ensue from evolutionary processes and to test the suitability of these approaches.}, } @article {pmid26123765, year = {2015}, author = {Lefebvre, A and Laporte, S and Faure, S and Tiv, M and Chavanet, P and Belpois-Duchamp, C and Astruc, K and Aho-Glélé, LS}, title = {Information concerning multidrug-resistant bacterial colonization or infection in the medical transfer letter.}, journal = {Medecine et maladies infectieuses}, volume = {45}, number = {7}, pages = {286-292}, doi = {10.1016/j.medmal.2015.05.008}, pmid = {26123765}, issn = {1769-6690}, mesh = {*Drug Resistance, Multiple, Bacterial ; *Enterobacteriaceae/isolation & purification ; *Enterobacteriaceae Infections ; Humans ; *Infection Control ; *Medical Records ; *Methicillin-Resistant Staphylococcus aureus/isolation & purification ; Patient Discharge ; *Patient Transfer ; *Pseudomonas Infections ; *Pseudomonas aeruginosa/isolation & purification ; Retrospective Studies ; *Staphylococcal Infections ; }, abstract = {OBJECTIVES: The aim of this study was to evaluate the proportion of transfer letters that contained information relative to infection or colonization by multidrug-resistant (MDR) bacteria and factors associated with the presence of that information.

PATIENTS AND METHODS: Patients for whom at least one of these selected MDR bacteria (methicillin-resistant Staphylococcus aureus, extended-spectrum β-lactamase-producing Enterobacteriaceae, or MDR Pseudomonas aeruginosa) was isolated during their hospitalization and who were transferred to another health care facility between 2009 and 2012 were included. Information of the MDR bacterium and the mention of isolation precautions were evaluated in the electronic medical record.

RESULTS: Information (mention of MDR bacterium or isolation precaution) was present in 57% [52; 65] of records. Full information (genus and species, concept of MDR bacterium and mention of isolation precaution) was found in 20% [16; 25]. The presence of a dedicated item in the standard medical discharge letter was associated with more frequent information. Less information was retrieved with P. aeruginosa cases than with the other 2 MDR bacteria.

CONCLUSION: The presence of the information has improved, but it is still insufficiently reported. Measures to improve information are needed. Indeed, information on MDR bacterial colonization or infection is the first step for isolation precautions. An item could be added to all standard medical discharge letters. An item could also be added to the indicators used to assess quality and safety in healthcare facilities.}, } @article {pmid26123545, year = {2015}, author = {Rosser, N and Kozak, KM and Phillimore, AB and Mallet, J}, title = {Extensive range overlap between heliconiine sister species: evidence for sympatric speciation in butterflies?.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {125}, pmid = {26123545}, issn = {1471-2148}, support = {BB/G006903/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biodiversity ; Butterflies/anatomy & histology/*classification/*genetics ; Climate ; Computer Simulation ; Databases, Factual ; Ecology ; Genetic Speciation ; Phylogeny ; Sympatry ; Wings, Animal/anatomy & histology ; }, abstract = {BACKGROUND: Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry.

RESULTS: Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32%-95% of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved.

CONCLUSIONS: Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on "strict and " "relaxed" biological species concepts (BSC), as well as on a surrogate for the widely-used "diagnostic" version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two groups. To establish whether heliconiines are exceptional will require biogeographic comparative studies for a wider range of animal taxa including many more invertebrates.}, } @article {pmid26117705, year = {2015}, author = {Stenz, NW and Larget, B and Baum, DA and Ané, C}, title = {Exploring Tree-Like and Non-Tree-Like Patterns Using Genome Sequences: An Example Using the Inbreeding Plant Species Arabidopsis thaliana (L.) Heynh.}, journal = {Systematic biology}, volume = {64}, number = {5}, pages = {809-823}, doi = {10.1093/sysbio/syv039}, pmid = {26117705}, issn = {1076-836X}, mesh = {Arabidopsis/*classification/*genetics ; Classification/*methods ; Genome, Plant ; Inbreeding ; *Phylogeny ; }, abstract = {Genome sequence data contain abundant information about genealogical history, but methods for extracting and interpreting this information are not yet fully developed. We analyzed genome sequences for multiple accessions of the selfing plant, Arabidopsis thaliana, with the goal of better understanding its genealogical history. As expected from accessions of the same species, we found much discordance between nuclear gene trees. Nonetheless, we inferred the optimal population tree under the assumption that all discordance is due to incomplete lineage sorting. To cope with the size of the data (many genes and many taxa), our pipeline is based on parallel computing and divides the problem into four-taxon trees. However, just because a population tree can be estimated does not mean that the assumptions of the multispecies coalescent model hold. Therefore, we implemented a new, nonparametric test to evaluate whether a population tree adequately explains the observed quartet frequencies (the frequencies of gene trees with each resolution of each four-taxon set). This test also considers other models: panmixia and a partially resolved population tree, that is, a tree in which some nodes are collapsed into local panmixia. We found that a partially resolved population tree provides the best fit to the data, providing evidence for tree-like structure within A. thaliana, qualitatively similar to what might be expected between different, closely related species. Further, we show that the pattern of deviation from expectations can be used to identify instances of introgression and detect one clear case of reticulation among ecotypes that have come into contact in the United Kingdom. Our study illustrates how we can use genome sequence data to evaluate whether phylogenetic relationships are strictly tree-like or reticulating.}, } @article {pmid26090501, year = {2015}, author = {Těšický, M and Vinkler, M}, title = {Trans-Species Polymorphism in Immune Genes: General Pattern or MHC-Restricted Phenomenon?.}, journal = {Journal of immunology research}, volume = {2015}, number = {}, pages = {838035}, pmid = {26090501}, issn = {2314-7156}, mesh = {Alleles ; Animals ; Evolution, Molecular ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Immunity, Innate/*genetics/immunology ; Major Histocompatibility Complex/*genetics/immunology ; Polymorphism, Genetic/*genetics/immunology ; }, abstract = {Immunity exhibits extraordinarily high levels of variation. Evolution of the immune system in response to host-pathogen interactions in particular ecological contexts appears to be frequently associated with diversifying selection increasing the genetic variability. Many studies have documented that immunologically relevant polymorphism observed today may be tens of millions years old and may predate the emergence of present species. This pattern can be explained by the concept of trans-species polymorphism (TSP) predicting the maintenance and sharing of favourable functionally important alleles of immune-related genes between species due to ongoing balancing selection. Despite the generality of this concept explaining the long-lasting adaptive variation inherited from ancestors, current research in TSP has vastly focused only on major histocompatibility complex (MHC). In this review we summarise the evidence available on TSP in human and animal immune genes to reveal that TSP is not a MHC-specific evolutionary pattern. Further research should clearly pay more attention to the investigation of TSP in innate immune genes and especially pattern recognition receptors which are promising candidates for this type of evolution. More effort should also be made to distinguish TSP from convergent evolution and adaptive introgression. Identification of balanced TSP variants may represent an accurate approach in evolutionary medicine to recognise disease-resistance alleles.}, } @article {pmid26046925, year = {2015}, author = {Rovira, L and Trobajo, R and Sato, S and Ibáñez, C and Mann, DG}, title = {Genetic and Physiological Diversity in the Diatom Nitzschia inconspicua.}, journal = {The Journal of eukaryotic microbiology}, volume = {62}, number = {6}, pages = {815-832}, doi = {10.1111/jeu.12240}, pmid = {26046925}, issn = {1550-7408}, mesh = {Biodiversity ; Diatoms/classification/cytology/genetics/*physiology ; Ecology ; Genetic Variation ; Phylogeny ; Plankton/genetics/physiology ; Reproduction ; Rivers ; Sequence Analysis, DNA ; Spain ; Species Specificity ; }, abstract = {Nitzschia inconspicua is an ecologically important diatom species, which is believed to have a widespread distribution and to be tolerant to salinity and to organic or nutrient pollution. However, its identification is not straightforward and there is no information on genetic and ecophysiological diversity within the species. We used morphological, molecular (rbcL and LSU D1-D3), ecophysiological and reproductive data to investigate whether N. inconspicua constitutes a single species with a broad ecological tolerance or two or more cryptic species with shared or different ecological preferences. Molecular genetic data for clones from upstream and deltaic sites in the Ebro River basin (Catalonia, Spain) revealed seven N. inconspicua rbcL + LSU genotypes grouped into three major clades. Two of the clades were related to other Nitzschia and Denticula species, making N. inconspicua paraphyletic and suggesting the need for taxonomic revision. Most clones were observed to be automictic, exhibiting paedogamy, and so the biological species concept cannot be used to establish species boundaries. Although there were morphological differences among clones, we found no consistent differences among genotypes belonging to different clades, which are definable only through sequence data. Nevertheless, separating the genotypes could be important for ecological purposes because two different ecophysiological responses were encountered among them.}, } @article {pmid26037697, year = {2015}, author = {Bendif, el M and Probert, I and Young, JR and von Dassow, P}, title = {Morphological and Phylogenetic Characterization of New Gephyrocapsa Isolates Suggests Introgressive Hybridization in the Emiliania/Gephyrocapsa Complex (Haptophyta).}, journal = {Protist}, volume = {166}, number = {3}, pages = {323-336}, doi = {10.1016/j.protis.2015.05.003}, pmid = {26037697}, issn = {1618-0941}, mesh = {Biodiversity ; Chile ; Genes, Protozoan/genetics ; Haptophyta/*classification/genetics/isolation & purification/*ultrastructure ; Pacific Ocean ; *Phylogeny ; Species Specificity ; }, abstract = {The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the Noëlaerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.}, } @article {pmid26024223, year = {2015}, author = {, }, title = {Correction: Application of the Phylogenetic Species Concept to Wallemia sebi from House Dust and Indoor Air Revealed by Multi-Locus Genealogical Concordance.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0129752}, pmid = {26024223}, issn = {1932-6203}, } @article {pmid26013644, year = {2015}, author = {Nash, R}, title = {William Keith Brooks and the naturalist's defense of Darwinism in the late-nineteenth century.}, journal = {History and philosophy of the life sciences}, volume = {37}, number = {2}, pages = {158-179}, doi = {10.1007/s40656-015-0060-3}, pmid = {26013644}, issn = {0391-9714}, mesh = {*Biological Evolution ; *Heredity ; History, 19th Century ; Natural History/*history ; *Selection, Genetic ; }, abstract = {William Keith Brooks was an American zoologist at Johns Hopkins University from 1876 until his death in 1908. Over the course of his career, Brooks staunchly defended Darwinism, arguing for the centrality of natural selection in evolutionary theory at a time when alternative theories, such as neo-Lamarckism, grew prominent in American biology. In his book The Law of Heredity (1883), Brooks addressed problems raised by Darwin's theory of pangenesis. In modifying and developing Darwin's pangenesis, Brooks proposed a new theory of heredity that sought to avoid the pitfalls of Darwin's hypothesis. In so doing he strengthened Darwin's theory of natural selection by undermining arguments for the inheritance of acquired characteristics. In later attacks on neo-Lamarckism, Brooks consistently defended Darwin's theory of natural selection on logical grounds, continued to challenge the idea of the inheritance of acquired characteristics, and argued that natural selection best explained a wide range of adaptations. Finally, he critiqued Galton's statistical view of heredity and argued that Galton had resurrected an outmoded typological concept of species, one which Darwin and other naturalists had shown to be incorrect. Brooks's ideas resemble the "biological species concept" of the twentieth century, as developed by evolutionary biologist Ernst Mayr and others. The late-nineteenth century was not a period of total "eclipse" of Darwinism, as biologists and historians have hitherto seen it. Although the "Modern Synthesis" refers to the reconciliation of post-Mendelian genetics with evolution by natural selection, we might adjust our understanding of how the synthesis developed by seeing it as the culmination of a longer discussion that extends back to the late-nineteenth century.}, } @article {pmid26010442, year = {2015}, author = {Bourjade, M and Thierry, B and Hausberger, M and Petit, O}, title = {Is leadership a reliable concept in animals? An empirical study in the horse.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0126344}, pmid = {26010442}, issn = {1932-6203}, mesh = {Animals ; *Behavior, Animal ; Empirical Research ; Female ; Horses/*physiology ; *Leadership ; Male ; Movement ; }, abstract = {Leadership is commonly invoked when accounting for the coordination of group movements in animals, yet it remains loosely defined. In parallel, there is increased evidence of the sharing of group decisions by animals on the move. How leadership integrates within this recent framework on collective decision-making is unclear. Here, we question the occurrence of leadership in horses, a species in which this concept is of prevalent use. The relevance of the three main definitions of leadership--departing first, walking in front travel position, and eliciting the joining of mates--was tested on the collective movements of two semi-free ranging groups of Przewalski horses (Equus ferus przewalskii). We did not find any leader capable of driving most group movements or recruiting mates more quickly than others. Several group members often displayed pre-departure behaviours at the same time, and the simultaneous departure of several individuals was common. We conclude that the decision-making process was shared by several group members a group movement (i.e., partially shared consensus) and that the leadership concept did not help to depict individual departure and leading behaviour across movements in both study groups. Rather, the different proxies of leadership produced conflicting information about individual contributions to group coordination. This study discusses the implications of these findings for the field of coordination and decision-making research.}, } @article {pmid25985485, year = {2015}, author = {Vinarski, MV}, title = {[The fate of subspecies category in zoological systematics. 2. The present].}, journal = {Zhurnal obshchei biologii}, volume = {76}, number = {2}, pages = {99-110}, pmid = {25985485}, issn = {0044-4596}, mesh = {Animals ; *Classification ; *Genetic Speciation ; Lymnaea/*classification ; *Phylogeography ; Sequence Analysis, DNA ; Zoology/classification ; }, abstract = {The present approach to the use of subspecies category in zoological systematics is an integrative one. It counts as obligatory to confirm the validity of subspecies, defined by morphological data, with genetic criteria. This allows marking out those subspecies that really exist as separate monophyletic population groups. As a result, the system would be cleared of many 'phantom' taxa established in course of non-critical use of the subspecies concept. However, detailed analyses of intra-species variability by methods of molecular taxonomy in many cases reveal a quite complicated divergence pattern which cannot be adequately described in terms of the classic scheme of 'species and its subspecies'. Keeping in mind the irregularity of intra-species divergence rate when dealing with molecular and morphological traits, it is proposed to use an extended system of subspecies taxa when describing 'extra complicated' situations. In addition to a 'subspecies' such categories as 'allospecies', 'morphotype', 'morphospecies' may be used for which operational definitions are suggested. As an example, the micro-systematics of the great pond snails (the complex Lymnaea stagnalis s. lato) from Palaearctic region is examined. The provisional system of this group, developed by the author, is based on morphological and phylogeographical data. Applying the series of subspecies categories of different level allows reflecting with maximal completeness the intra-species variability of great pond snails and, to some extent, the process of their genetic divergence and geographic range forming. The second part of the article deals with modern approaches to subspecies category usage in zoological systematics as well as the problems of so called micro-systematics, i.e., systematics operating at the lowest level of categories such as ones of subspecies and infra-subspecies rank (Mayr, 1982).}, } @article {pmid25984507, year = {2015}, author = {MacGillivary, ML and Kaczmarska, I}, title = {Paralia (Bacillariophyta) stowaways in ship ballast: implications for biogeography and diversity of the genus.}, journal = {Journal of biological research (Thessalonike, Greece)}, volume = {22}, number = {1}, pages = {2}, pmid = {25984507}, issn = {1790-045X}, abstract = {BACKGROUND: The genus Paralia Heiberg is one of the most recognizable, widely distributed and commonly reported diatoms from contemporary coastal marine environments and ship ballast. Species discovery has historically been made in diatoms through the recognition of morphological discontinuities between specimens, first using light and later electron microscopy. However, recently, morphologically semi-cryptic species of Paralia were delineated using genetic analyses, among mostly tropical and subtropical sites.

RESULTS: Ten morphological characters of the frustules and sequence fragments from the nuclear genome (conserved 18S regions of ribosomal RNA and the variable internal transcribed spacer [ITS]), and from the RuBisCo large subunit (rbcL) gene of the chloroplast genome were examined. Frustule morphology did not segregate species, however, comparisons of sequence fragments and ITS2 secondary structures yielded a new species from North American waters, P. guyana (with four genodemes), and another widely-distributed species, P. marina. The latter was lecto- and epitypified here because it is most similar to specimens in the type preparation BM1021 representing Smith's concept of the species. Paralia marina and certain genodemes of P. guyana were morphologically cryptic. Only those genodemes of P. guyana that possess prickly separation valves could be morphologically distinguished from P. marina with relative confidence in SEM preparations. All clones established from chains isolated from the ballast sediment of the ships sailing along the Atlantic coast of North America belonged to P. guyana. All DNA sequences of preserved Paralia chains recovered from the three trans-Atlantic voyages (TAVs) samples arriving to eastern Canada from Europe shared 100% identity with P. marina.

CONCLUSION: First, if the [Formula: see text] = 130592 P. marina cells per ballast tank at the end of the TAVs represents their abundance in ballast tanks of similar crossings and following mid-ocean ballast water exchange, then this diatom, if de-ballasted, exerts a strong and continued propagule pressure on Eastern Canadian coasts. Despite this, as of 2009, P. marina was found only in Cheticamp, Nova Scotia, Canada. Second, genetic analysis readily segregated cryptic and semi-cryptic taxa of Paralia, highlighting the usefulness of the molecular approach to species recognition, e.g., in programs monitoring alien introductions.}, } @article {pmid25982328, year = {2015}, author = {Spagnul, C and Turner, LC and Boyle, RW}, title = {Immobilized photosensitizers for antimicrobial applications.}, journal = {Journal of photochemistry and photobiology. B, Biology}, volume = {150}, number = {}, pages = {11-30}, doi = {10.1016/j.jphotobiol.2015.04.021}, pmid = {25982328}, issn = {1873-2682}, mesh = {Animals ; Anti-Infective Agents/*therapeutic use ; Humans ; Indoles/therapeutic use ; Light ; Phenothiazines/therapeutic use ; *Photochemotherapy ; Photosensitizing Agents/*therapeutic use ; Porphyrins/therapeutic use ; Rose Bengal/therapeutic use ; Ruthenium/therapeutic use ; }, abstract = {Photodynamic antimicrobial chemotherapy (PACT) is a very promising alternative to conventional antibiotics for the efficient inactivation of pathogenic microorganisms; this is due to the fact that it is virtually impossible for resistant strains to develop due to the mode of action employed. PACT employs a photosensitizer, which preferentially associates with the microorganism, and is then activated with non-thermal visible light of appropriate wavelength(s) to generate high localized concentrations of reactive oxygen species (ROS), inactivating the microorganism. The concept of using photosensitizers immobilized on a surface for this purpose is intended to address a range of economic, ecological and public health issues. Photosensitising molecules that have been immobilized on solid support for PACT applications are described herein. Different supports have been analyzed as well as the target microorganism and the effectiveness of particular combinations of support and photosensitizer.}, } @article {pmid25979677, year = {2015}, author = {Cui, Y and Béthoux, O and Klass, KD and Ren, D}, title = {The Jurassic Bajanzhargalanidae (Insecta: Grylloblattida?): New genera and species, and data on postabdominal morphology.}, journal = {Arthropod structure & development}, volume = {44}, number = {6 Pt B}, pages = {688-716}, doi = {10.1016/j.asd.2015.04.008}, pmid = {25979677}, issn = {1873-5495}, mesh = {Animals ; China ; Female ; Fossils/*anatomy & histology ; Insecta/*anatomy & histology/physiology ; Male ; Phylogeny ; Sex Characteristics ; Wings, Animal/anatomy & histology ; }, abstract = {The presumed phylogenetic link between extant ice-crawlers (Grylloblattidae = 'crown-Grylloblattida') and fossil species of the taxon concept Grylloblattida sensu Storozhenko (2002) is essentially based on postabdominal morphology. However, the fossil data are limited, and the interpretation is open to debate. Here we investigate a sample of a poorly known fossil 'grylloblattidan' family, the Bajanzhargalanidae, collected from the Daohugou locality (Middle Jurassic, China). We describe Sinonele fangi gen. nov., sp. nov., Sinonele hei gen. nov., sp. nov., Sinonele phasmoides gen. nov., sp. nov., and Sinonele mini gen. nov., sp. nov. Thanks to the abundance and exceptional preservation of the material, we could document wing venation intra-specific variability, provide cues to identify male and female individuals, describe and tentatively interpret various body structures of both sexes, and discuss them with a broad pterygotan phylogenetic perspective. The Bajanzhargalanidae exhibit a puzzling combination of postabdominal characters leaving us inconclusive on their affinities, or lack thereof, with crown-Grylloblattida. Our contribution suggests that a substantial effort will be needed to further investigate postabdominal structures from comparatively ancient fossil insects preserved as rock imprints, because of their broad morphological disparity.}, } @article {pmid25973975, year = {2015}, author = {Warwick, AR and Travis, J and Lemmon, EM}, title = {Geographic variation in the Pine Barrens Treefrog (Hyla andersonii): concordance of genetic, morphometric and acoustic signal data.}, journal = {Molecular ecology}, volume = {24}, number = {13}, pages = {3281-3298}, doi = {10.1111/mec.13242}, pmid = {25973975}, issn = {1365-294X}, mesh = {Acoustics ; Animals ; Anura/*genetics/physiology ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Endangered Species ; Forests ; *Genetic Variation ; *Genetics, Population ; Genotype ; Geography ; Male ; Microsatellite Repeats ; Molecular Sequence Data ; Phylogeny ; Pinus ; Sequence Analysis, DNA ; United States ; Vocalization, Animal ; }, abstract = {Delimiting species is important to every subfield in biology. Templeton's cohesion species concept uses genetic and ecological exchangeability to identify sets of populations that ought to be considered as the same species, and the lack of exchangeability helps determine which populations can be grouped as evolutionarily significant units (ESU) in conservation science. However, previous work assessing genetic and ecological interchangeability among populations has been limited in scope. Here, we provide a method for assessing exchangeability that incorporates multiple, independent lines of multivariate evidence in genetic, behavioural and morphological data. We use this approach to assess exchangeability across three disjunct groups of populations of the Pine Barrens Treefrog (Hyla andersonii) from the eastern United States. This species is considered threatened by each state in which it occurs and conservation management of this taxon requires a clearer understanding of how populations in these three regions may differ from one another. We find a strikingly concordant pattern in which the first axis of variation for each of the three types of data distinguishes populations along a latitudinal gradient and the second axis distinguishes the set of populations occurring in the Carolinas from those occurring in the New Jersey and Florida/Alabama regions. We know of no comparable data set that displays such concordance among different types of data across so large a geographic range. The overlap in trait values (i.e. exchangeability) between neighbouring regions, however, is substantial in all three types of data, which supports continued consideration of this taxon as a single species.}, } @article {pmid25972399, year = {2015}, author = {Magnotti, JF and Katz, JS and Wright, AA and Kelly, DM}, title = {Superior abstract-concept learning by Clark's nutcrackers (Nucifraga columbiana).}, journal = {Biology letters}, volume = {11}, number = {5}, pages = {20150148}, pmid = {25972399}, issn = {1744-957X}, mesh = {Animals ; *Concept Formation ; *Discrimination Learning ; Songbirds/*physiology ; }, abstract = {The ability to learn abstract relational concepts is fundamental to higher level cognition. In contrast to item-specific concepts (e.g. pictures containing trees versus pictures containing cars), abstract relational concepts are not bound to particular stimulus features, but instead involve the relationship between stimuli and therefore may be extrapolated to novel stimuli. Previous research investigating the same/different abstract concept has suggested that primates might be specially adapted to extract relations among items and would require fewer exemplars of a rule to learn an abstract concept than non-primate species. We assessed abstract-concept learning in an avian species, Clark's nutcracker (Nucifraga columbiana), using a small number of exemplars (eight pairs of the same rule, and 56 pairs of the different rule) identical to that previously used to compare rhesus monkeys, capuchin monkeys and pigeons. Nutcrackers as a group (N = 9) showed more novel stimulus transfer than any previous species tested with this small number of exemplars. Two nutcrackers showed full concept learning and four more showed transfer considerably above chance performance, indicating partial concept learning. These results show that the Clark's nutcracker, a corvid species well known for its amazing feats of spatial memory, learns the same/different abstract concept better than any non-human species (including non-human primates) yet tested on this same task.}, } @article {pmid25948612, year = {2015}, author = {Drake, JM}, title = {Range bagging: a new method for ecological niche modelling from presence-only data.}, journal = {Journal of the Royal Society, Interface}, volume = {12}, number = {107}, pages = {}, pmid = {25948612}, issn = {1742-5662}, mesh = {*Ecosystem ; *Models, Biological ; }, abstract = {The ecological niche is the set of environments in which a population of a species can persist without introduction of individuals from other locations. A good mathematical or computational representation of the niche is a prerequisite to addressing many questions in ecology, biogeography, evolutionary biology and conservation. A particularly challenging question for ecological niche modelling is the problem of presence-only modelling. That is, can an ecological niche be identified from records drawn only from the set of niche environments without records from non-niche environments for comparison? Here, I introduce a new method for ecological niche modelling from presence-only data called range bagging. Range bagging draws on the concept of a species' environmental range, but was inspired by the empirical performance of ensemble learning algorithms in other areas of ecological research. This paper extends the concept of environmental range to multiple dimensions and shows that range bagging is computationally feasible even when the number of environmental dimensions is large. The target of the range bagging base learner is an environmental tolerance of the species in a projection of its niche and is therefore an ecologically interpretable property of a species' biological requirements. The computational complexity of range bagging is linear in the number of examples, which compares favourably with the main alternative, Qhull. In conclusion, range bagging appears to be a reasonable choice for niche modelling in applications in which a presence-only method is desired and may provide a solution to problems in other disciplines where one-class classification is required, such as outlier detection and concept learning.}, } @article {pmid25948569, year = {2015}, author = {Sefbom, J and Sassenhagen, I and Rengefors, K and Godhe, A}, title = {Priority effects in a planktonic bloom-forming marine diatom.}, journal = {Biology letters}, volume = {11}, number = {5}, pages = {20150184}, pmid = {25948569}, issn = {1744-957X}, mesh = {Diatoms/genetics/*physiology ; *Genotype ; Phytoplankton/genetics/*physiology ; Population Dynamics ; }, abstract = {Priority effects occur when a species or genotype with earlier arrival has an advantage such that its relative abundance in the community or population is increased compared with later-arriving species. Few studies have dealt with this concept in the context of within-species competition. Skeletonema marinoi is a marine diatom that shows a high degree of genetic differentiation between populations over small geographical distances. To test whether historical events such as priority effects may have been important in inducing these patterns of population differentiation, we performed microcosm experiments with successive inoculation of different S. marinoi strains. Our results show that even in the absence of a numerical advantage, significant priority effects were evident. We propose that priority effects may be an important mechanism in initiating population genetic differentiation.}, } @article {pmid25947832, year = {2015}, author = {Rognes, K}, title = {Revision of the frog fly genus Caiusa Surcouf, 1920 (Diptera, Calliphoridae), with a note on the identity of Plinthomyia emimelania Rondani, 1875.}, journal = {Zootaxa}, volume = {3952}, number = {}, pages = {1-80}, doi = {10.11646/zootaxa.3952.1.1}, pmid = {25947832}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Asia ; Body Size ; Diptera/anatomy & histology/*classification/genetics/growth & development ; Female ; Male ; Organ Size ; Phylogeny ; }, abstract = {The Oriental, Australasian and Oceanian genus Caiusa Surcouf, 1920 is revised, species concepts being based on male and female genitalia. A key to males for all known species, and a key to females for all except one are given. All relevant types still in existence have been studied, complete synonymies given and the geographical distribution reconsidered. The eight species included in the genus are: Caiusa borneoensis sp. nov. (Malaysia, Thailand, Vietnam); Caiusa coomani Séguy, 1948 (China, Malaysia, Singapore, Thailand, Vietnam); Caiusa indica Surcouf, 1920 (Australia, Cambodia, India, Indonesia, Malaysia, Papua New Guinea, Philippines, Singapore, Solomon Islands, Sri Lanka, Thailand, Vietnam); Caiusa karrakerae sp. nov. (Malaysia, Thailand); Caiusa kurahashii sp. nov. (Indonesia, Japan, Philippines); Caiusa pooae sp. nov. (Thailand); Caiusa testacea Senior-White, 1923 (India, Nepal, Sri Lanka) and Caiusa violacea Séguy, 1925, stat. rev. (Cambodia, China, Laos, Malaysia, Taiwan, Thailand, Vietnam). A lectotype is designated for Caiusa indica to fix the interpretation of the name. Caiusa nigronitens Senior-White, 1923, syn. nov. and Caiusa surcoufi Bezzi, 1927, syn. nov. are established as junior synonyms of Caiusa indica. Caiusa violacea is correctly diagnosed and errors in the original description of the female holotype are pointed out. Caiusa dubiosa Villeneuve, 1927 is established as a junior synonym of C. violacea, syn. nov. Seven Caiusa species have been reared from the egg mass of various species of frogs. The reproductive mode of the eighth species, i.e., C. indica, is unknown. Five species, i.e., C. borneoensis, C. coomani, C. karrakerae, C. kurahashii and C. violacea have been reared from one or more of the foam nesting frog species Chiromantis nongkhorensis (Cochran, 1927), Polypedates leucomystax (Gravenhorst, 1927), Polypedates megacephalus Hallowell, 1861, Rhacophorus annamensis Smith, 1924, Rhacophorus dulitensis Boulenger, 1892, Rhacophorus kio Ohler & Delorme, 2005 and Rhacophorus owstoni (Stejneger, 1907) all belonging in the family Rhacophoridae in Anura. These five Caiusa species all have a specialised ovipositor tip, with small spine-like setae on the ST8 and the hypoproct, probably enabling the flies to oviposit on a foam nest with a hardened outer surface. They form a monophyletic group on account of these features of the ovipositor, unique in the Oestroidea. The sixth species, C. testacea, has been reared from a frog egg mass, the frog species being unknown. Its ovipositor structure is also unknown. The seventh species, C. pooae, has been reared once from the jelly-like egg mass of Feihyla hansenae (Cochran, 1927), also in Rhacophoridae. Caiusa pooae females do not have spine-like setae on the ovipositor, a fact correlated with the soft outer surface of the jelly-like egg mass on which a C. pooae female had oviposited. The extreme rarity of C. pooae oviposition on Feihyla hansenae egg masses may indicate that this fly perhaps has another, unknown, regular oviposition substrate. Caiusa pooae and C. indica make up a second monophyletic group within Caiusa. Caiusa indica, the most common and most widespread species of the genus, has an ovipositor structure similar to C. pooae. Its breeding substrate is unknown and it occurs both within and outside the distributional area of Rhacophoridae. Possibly both C. indica and C. pooae share a regular oviposition substrate that has still to be discovered. The holotype female of Plinthomyia emimelania Rondani, 1875 from Sarawak is established as a member of the genus Bengalia Robineau-Desvoidy, 1830, thus Plinthomyia Rondani, 1875 becomes a junior synonym of Bengalia Robineau-Desvoidy, 1830, syn. nov. It is removed from the synonymy of Phumosia Robineau-Desvoidy, 1830.}, } @article {pmid25932996, year = {2015}, author = {Singh, G and Dal Grande, F and Divakar, PK and Otte, J and Leavitt, SD and Szczepanska, K and Crespo, A and Rico, VJ and Aptroot, A and Cáceres, ME and Lumbsch, HT and Schmitt, I}, title = {Coalescent-based species delimitation approach uncovers high cryptic diversity in the cosmopolitan lichen-forming fungal genus Protoparmelia (Lecanorales, Ascomycota).}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0124625}, pmid = {25932996}, issn = {1932-6203}, mesh = {Ascomycota/*physiology ; Base Sequence ; Bayes Theorem ; *Biodiversity ; Cell Nucleus/genetics ; Genetic Loci ; Lichens/*microbiology ; Likelihood Functions ; Models, Genetic ; Phylogeny ; Reproducibility of Results ; Species Specificity ; }, abstract = {Species recognition in lichen-forming fungi has been a challenge because of unsettled species concepts, few taxonomically relevant traits, and limitations of traditionally used morphological and chemical characters for identifying closely related species. Here we analyze species diversity in the cosmopolitan genus Protoparmelia s.l. The ~25 described species in this group occur across diverse habitats from the boreal-arctic/alpine to the tropics, but their relationship to each other remains unexplored. In this study, we inferred the phylogeny of 18 species currently assigned to this genus based on 160 specimens and six markers: mtSSU, nuLSU, ITS, RPB1, MCM7, and TSR1. We assessed the circumscription of species-level lineages in Protoparmelia s. str. using two coalescent-based species delimitation methods--BP&P and spedeSTEM. Our results suggest the presence of a tropical and an extra-tropical lineage, and eleven previously unrecognized distinct species-level lineages in Protoparmelia s. str. Several cryptic lineages were discovered as compared to phenotype-based species delimitation. Many of the putative species are supported by geographic evidence.}, } @article {pmid25931974, year = {2015}, author = {Robinson, H and Keeley, SC}, title = {A refined concept of the Critoniopsisbogotana species group in Colombia with two new species (Vernonieae, Asteraceae).}, journal = {PhytoKeys}, volume = {}, number = {48}, pages = {85-95}, pmid = {25931974}, issn = {1314-2011}, abstract = {Critoniopsisbogotana is more precisely delimited, and two related Colombian species are described as new. The form of trichomes on the abaxial surfaces of the leaves is found to be of major importance. A short key to the Critoniopsisbogotana group is provided.}, } @article {pmid25925738, year = {2015}, author = {Civetta, A and Gaudreau, C}, title = {Hybrid male sterility between Drosophila willistoni species is caused by male failure to transfer sperm during copulation.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {75}, pmid = {25925738}, issn = {1471-2148}, mesh = {Animals ; Copulation ; Drosophila/*classification/genetics/*physiology ; Female ; Fertility ; Genetic Speciation ; *Hybridization, Genetic ; Male ; Reproduction ; Reproductive Isolation ; Spermatozoa ; }, abstract = {BACKGROUND: The biological concept of species stresses the importance of understanding what mechanisms maintain species reproductively isolated from each other. Often such mechanisms are divided into premating and postmating, with the latest being the result of either prezygotic or postzygotic isolation barriers. Drosophila willistoni quechua and Drosophila willistoni willistoni are two subspecies that experience reproductive isolation. When a D. w. quechua female is crossed with a D. w. willistoni male, the hybrid males (F1QW) are unable to father progeny; however, the reciprocal cross produces fertile hybrids. Thus, the mechanism of isolation is unidirectional hybrid male sterility. However, the sterile F1QW males contain large amounts of motile sperm. Here we explore whether pre-copulatory or post-copulatory pre-zygotic mechanisms serve as major deterrents in the ability of F1QW males to father progeny.

RESULTS: Comparisons of parental and hybrid males copulation durations showed no significant reduction in copulation duration of F1QW males. Interrupted copulations of the parental species confirmed that sperm transfer occurs before the minimum copulation duration registered for F1QW males. However, we found that when females mate with F1QW males, sperm is not present inside the female storage organs and that the lack of sperm in storage is due to failure to transfer sperm rather than spillage or active sperm dumping by females.

CONCLUSIONS: Sterility of F1QW hybrid males is primarily driven by their inability to transfer sperm during copulation.}, } @article {pmid25903381, year = {2015}, author = {de García, V and Coelho, MA and Maia, TM and Rosa, LH and Vaz, AM and Rosa, CA and Sampaio, JP and Gonçalves, P and van Broock, M and Libkind, D}, title = {Sex in the cold: taxonomic reorganization of psychrotolerant yeasts in the order Leucosporidiales.}, journal = {FEMS yeast research}, volume = {15}, number = {4}, pages = {fov019}, doi = {10.1093/femsyr/fov019}, pmid = {25903381}, issn = {1567-1364}, mesh = {Basidiomycota/*classification/genetics/physiology ; Cluster Analysis ; *Cold Temperature ; *Crosses, Genetic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; RNA, Fungal/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {Species of Leucosporidiales are a group of psychrotolerant yeasts with biotechnological potential. In the present work, we studied the phenotypic, genetic and sexual characteristics of three species of this genus (Leucosporidium scottii, Leucosporidiella creatinivora and Le. yakutica) to clarify the evolutionary relationship among these closely related taxa. From the results obtained, it becomes clear that these yeasts can interbreed. Although genetic delimitation is possible for the three species, the extent of nucleotide substitutions and phenotypic differences observed between them are lower than that expected for species that have ended the speciation process. Our taxonomic conclusion is to maintain the three taxa until further genomic data are gathered. However, the concept of L. scottii species complex is proposed for this group of species. Finally, we transfer all Leucosporidiella and Mastigobasidium species to Leucosporidium (Leucosporidiales), and, in order to end the polyphyly condition of these taxa, we propose the new genus Pseudoleucosporidium gen. nov. and the new combination Peudoleucosporidium fasciculatum comb. nov.}, } @article {pmid25898535, year = {2015}, author = {Vinarskiĭ, MV}, title = {[The fate of subspecies category in zoological systematics. 1. The history].}, journal = {Zhurnal obshchei biologii}, volume = {76}, number = {1}, pages = {3-14}, pmid = {25898535}, issn = {0044-4596}, mesh = {Animals ; *Biological Evolution ; *Classification ; DNA, Mitochondrial/genetics ; Genetic Speciation ; Invertebrates/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; *Zoology ; }, abstract = {Subspecies is the only taxonomical category inferior to species which application is governed by the International Code of Zoological Nomenclature. Although the first attempts to use it are dated by the end of XVIII century, it becomes regularly applied only by the middle of XIX century, along with trinomial nomenclature. At that, the current sense of the term, i.e. subspecies as a morphologically and spatially separated population group or as a synonym for "geographical race", has become established even later, by the end of XIX century. The concept of polytypic species, which has already taken shape in 1900s (in the works by ornithologist E. Hartert and entomologist K. Jordan), has been incorporated later into the modern evolutionary synthesis. The peak of the concept popularity fell on 1940-50s, then the evident crisis of subspecies systematics began to show, and is still showing nowadays, especially in systematics of invertebrates. The reasons behind the drop of subspecies category popularity are discussed, among them the emergence of novel species concepts where the rank of subspecies is not used (the phylogenetic species concept), impossibility to verify the validity of previously described subspecies by means of statistics or molecular systematics, etc. Nevertheless, in systematics of vertebrates, the category of subspecies still remains called-for.}, } @article {pmid25857524, year = {2015}, author = {Ferrer, RP and Lunsford, ET and Candido, CM and Strawn, ML and Pierce, KM}, title = {Saxitoxin and the Ochre Sea Star: Molecule of Keystone Significance and a Classic Keystone Species.}, journal = {Integrative and comparative biology}, volume = {55}, number = {3}, pages = {533-542}, doi = {10.1093/icb/icv010}, pmid = {25857524}, issn = {1557-7023}, mesh = {Animal Distribution/drug effects ; Animals ; Chromatography, High Pressure Liquid ; Feeding Behavior/drug effects ; Reproduction/drug effects ; Saxitoxin/*toxicity ; Starfish/*drug effects/*physiology ; Tissue Distribution ; Washington ; }, abstract = {Saxitoxins (STXs) are paralytic alkaloids produced by marine dinoflagellates in response to biotic and abiotic stressors yielding harmful algal blooms. Because STX impacts coastal, near-shore communities to a greater extent than would be predicted by its relative abundance, it has been referred to as a "molecule of keystone significance" in reference to Robert Paine's Keystone Species Concept. Pisaster ochraceus, the predator upon which Paine's concept was founded, inhabits waters regularly plagued by harmful algal blooms, but the effects of STX on Pisaster have not yet been investigated. Here, we used laboratory and field experiments to examine the potential consequences of exposure to STX on sea stars' feeding, attachment to the substrate, and success in fertilization. Pisaster exhibited similar feeding behaviors when offered non-toxic prey, STX-containing prey, or a combination of the two. Although feeding behavior is unaffected, consumption of STX poses a physiological tradeoff. Sea stars in the laboratory and field had significantly lower thresholds of the force needed to detach them from their substrates after either being exposed to, or consuming, STX. High pressure (or high performance) liquid chromatography analysis indicated an accumulation of STX (and structural analogues) in sea stars' viscera, likely due to trophic transfer from toxic prey. Incidence of fertilization tended to decrease when gametes were exposed to high, yet ecologically relevant, STX concentrations of STX. These findings suggest that the molecule of keystone significance, STX, produced during harmful algal blooms extends its impacts to rocky intertidal communities by way of the keystone predator P. ochraceus.}, } @article {pmid25853412, year = {2015}, author = {Dumas, P and Barbut, J and Le Ru, B and Silvain, JF and Clamens, AL and d'Alençon, E and Kergoat, GJ}, title = {Phylogenetic molecular species delimitations unravel potential new species in the pest genus Spodoptera Guenée, 1852 (Lepidoptera, Noctuidae).}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0122407}, pmid = {25853412}, issn = {1932-6203}, mesh = {Animals ; Evolution, Molecular ; *Genetic Speciation ; Molecular Sequence Data ; *Phylogeny ; Spodoptera/*genetics ; }, abstract = {Nowadays molecular species delimitation methods promote the identification of species boundaries within complex taxonomic groups by adopting innovative species concepts and theories (e.g. branching patterns, coalescence). As some of them can efficiently deal with large single-locus datasets, they could speed up the process of species discovery compared to more time consuming molecular methods, and benefit from the existence of large public datasets; these methods can also particularly favour scientific research and actions dealing with threatened or economically important taxa. In this study we aim to investigate and clarify the status of economically important moths species belonging to the genus Spodoptera (Lepidoptera, Noctuidae), a complex group in which previous phylogenetic analyses and integrative approaches already suggested the possible occurrence of cryptic species and taxonomic ambiguities. In this work, the effectiveness of innovative (and faster) species delimitation approaches to infer putative species boundaries has been successfully tested in Spodoptera, by processing the most comprehensive dataset (in terms of number of species and specimens) ever achieved; results are congruent and reliable, irrespective of the set of parameters and phylogenetic models applied. Our analyses confirm the existence of three potential new species clusters (for S. exigua (Hübner, 1808), S. frugiperda (J.E. Smith, 1797) and S. mauritia (Boisduval, 1833)) and support the synonymy of S. marima (Schaus, 1904) with S. ornithogalli (Guenée, 1852). They also highlight the ambiguity of the status of S. cosmiodes (Walker, 1858) and S. descoinsi Lalanne-Cassou & Silvain, 1994. This case study highlights the interest of molecular species delimitation methods as valuable tools for species discovery and to emphasize taxonomic ambiguities.}, } @article {pmid25847185, year = {2015}, author = {Burgain, A and Bensoussan, M and Dantigny, P}, title = {Validation of a predictive model for the growth of chalk yeasts on bread.}, journal = {International journal of food microbiology}, volume = {204}, number = {}, pages = {47-54}, doi = {10.1016/j.ijfoodmicro.2015.03.026}, pmid = {25847185}, issn = {1879-3460}, mesh = {Bread/*microbiology ; Culture Media ; Food Contamination ; *Food Microbiology ; Hydrogen-Ion Concentration ; Models, Theoretical ; Saccharomycetales/*growth & development ; Temperature ; Water ; Yeasts/*growth & development ; }, abstract = {The present study focused on the effects of temperature, T, and water activity, aw, on the growth of Hyphopichia burtonii, Pichia anomala, and Saccharomycopsis fibuligera on Sabouraud Agar Medium. Cardinal values were estimated by means of cardinal models with inflection. All the yeasts were xerophilic, and they exhibited growth at 0.85 aw. The combined effects of T, aw, and pH on the growth of these species were described by the gamma-concept and validated on bread in the range of 15-25 °C, 0.91-0.97 aw, and pH 4.6-6.8. The optimum growth rates on bread were 2.88, 0.259, and 1.06 mm/day for H. burtonii, P. anomala, and S. fibuligera, respectively. The optimal growth rate of S. fibuligera on bread was about 2 fold that obtained on Sabouraud. Due to reproduction by budding, P. anomala exhibited low growth on Sabouraud and bread. However, this species is of major concern in the baker's industry because of the production of ethyl acetate in bread.}, } @article {pmid25837892, year = {2015}, author = {McHugh, MJ and Broadhurst, MK and Sterling, DJ and Millar, RB}, title = {A 'simple anterior fish excluder' (SAFE) for mitigating penaeid-trawl bycatch.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0123124}, doi = {10.1371/journal.pone.0123124}, pmid = {25837892}, issn = {1932-6203}, mesh = {Animals ; Equipment Design ; Fisheries/*instrumentation ; *Fishes/anatomy & histology ; *Penaeidae/anatomy & histology ; Perciformes/anatomy & histology ; Plastics/chemistry ; Smegmamorpha/anatomy & histology ; Species Specificity ; }, abstract = {Various plastic strips and sheets (termed 'simple anterior fish excluders'-SAFEs) were positioned across the openings of penaeid trawls in attempts at reducing the unwanted bycatches of small teleosts. Initially, three SAFEs (a single wire without, and with small and large plastic panels) were compared against a control (no SAFE) on paired beam trawls. All SAFEs maintained targeted Metapenaeus macleayi catches, while the largest plastic SAFE significantly reduced total bycatch by 51% and the numbers of Pomatomus saltatrix, Mugil cephalus and Herklotsichthys castelnaui by up to 58%. A redesigned SAFE ('continuous plastic') was subsequently tested (against a control) on paired otter trawls, significantly reducing total bycatch by 28% and P. saltatrix and H. castelnaui by up to 42%. The continuous-plastic SAFE also significantly reduced M. macleayi catches by ~7%, but this was explained by ~5% less wing-end spread, and could be simply negated through otter-board refinement. Further work is required to refine the tested SAFEs, and to quantify species-specific escape mechanisms. Nevertheless, the SAFE concept might represent an effective approach for improving penaeid-trawl selectivity.}, } @article {pmid25831518, year = {2015}, author = {Seike, T and Nakamura, T and Shimoda, C}, title = {Molecular coevolution of a sex pheromone and its receptor triggers reproductive isolation in Schizosaccharomyces pombe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {14}, pages = {4405-4410}, pmid = {25831518}, issn = {1091-6490}, mesh = {Cell Membrane/metabolism ; DNA Replication ; *Evolution, Molecular ; Gene Expression Regulation, Fungal ; *Genes, Mating Type, Fungal ; Mutagenesis, Site-Directed ; Mutation ; Open Reading Frames ; Peptides/genetics/physiology ; Pheromones/*genetics/physiology ; Protein Conformation ; *Reproductive Isolation ; Schizosaccharomyces/*genetics/physiology ; Schizosaccharomyces pombe Proteins/metabolism ; }, abstract = {The diversification of sex pheromones is regarded as one of the causes of prezygotic isolation that results in speciation. In the fission yeast Schizosaccharomyces pombe, the molecular recognition of a peptide pheromone by its receptor plays an essential role in sexual reproduction. We considered that molecular coevolution of a peptide-mating pheromone, M factor, and its receptor, Map3, might be realized by experimentally diversifying these proteins. Here, we report the successful creation of novel mating-type pairs by searching for map3 suppressor mutations that rescued the sterility of M-factor mutants that were previously isolated. Several strong suppressors were found to also recognize WT M factor. The substituted residues of these Map3 suppressors were mapped to F204, F214, and E249, which are likely to be critical residues for M-factor recognition. These critical residues were systematically substituted with each of the other amino acids by in vitro mutagenesis. Ultimately, we successfully obtained three novel mating-type pairs constituting reproductive groups. These novel mating-type pairs could not conjugate with WT maters. Furthermore, no flow of chromosomally integrated drug-resistance genes occurred between the novel and the WT mating pairs, showing that each experimentally created reproductive group [e.g., M factor(V5H) and Map3(F214H)] was isolated from the WT group. In conclusion, we have succeeded in creating an artificial reproductive group that is isolated from the WT group. In keeping with the biological concept of species, the artificial reproductive group is a new species.}, } @article {pmid25829840, year = {2015}, author = {Wayland, MT and Vainio, JK and Gibson, DI and Herniou, EA and Littlewood, DT and Väinölä, R}, title = {The systematics of Echinorhynchus Zoega in Müller, 1776 (Acanthocephala, Echinorhynchidae) elucidated by nuclear and mitochondrial sequence data from eight European taxa.}, journal = {ZooKeys}, volume = {}, number = {484}, pages = {25-52}, pmid = {25829840}, issn = {1313-2989}, abstract = {The acanthocephalan genus Echinorhynchus Zoega in Müller, 1776 (sensuYamaguti 1963) is a large and widespread group of parasites of teleost fish and malacostracan crustaceans, distributed from the Arctic to the Antarctic in habitats ranging from freshwaters to the deep-sea. A total of 52 species are currently recognised based on the conventional morphological species concept; however, the true diversity in the genus is masked by cryptic speciation. The considerable diversity within Echinorhynchus is an argument for subdividing the genus if monophyletic groups with supporting morphological characters can be identified. With this objective in mind, partial sequences of two genes with different rates of evolution and patterns of inheritance (nuclear 28S rRNA and mitochondrial cytochrome c oxidase subunit I) were used to infer the phylogenetic relationships among eight taxa of Echinorhynchus. These included representatives of each of three genus group taxa proposed in a controversial revision of the genus based on cement gland pattern, namely Echinorhynchus (sensu stricto), Metechinorhynchus Petrochenko, 1956 and Pseudoechinorhynchus Petrochenko, 1956. These groupings have previously been rejected by some authorities, because the diagnostic character is poorly defined; this study shows that Echinorhynchus (sensu stricto) and Metechinorhynchus are not natural, monophyletic groups. A revision of Echinorhynchus will require tandem molecular phylogenetic and morphological analyses of a larger sample of taxa, but this study has identified two morhological characters that might potentially be used to define new genera. The estimated phylogeny also provides insight into the zoogeographical history of Echinorhynchus spp. We postulate that the ancestral Echinorhynchus had a freshwater origin and the genus subsequently invaded the sea, probably several times. The freshwater taxa of the Echinorhynchusbothniensis Zdzitowiecki & Valtonen, 1987 clade may represent a reinvasion of freshwater by one or more ancestral marine species.}, } @article {pmid25822187, year = {2015}, author = {Oliveira, LS and Harrington, TC and Ferreira, MA and Damacena, MB and Al-Sadi, AM and Al-Mahmooli, IH and Alfenas, AC}, title = {Species or Genotypes? Reassessment of Four Recently Described Species of the Ceratocystis Wilt Pathogen, Ceratocystis fimbriata, on Mangifera indica.}, journal = {Phytopathology}, volume = {105}, number = {9}, pages = {1229-1244}, doi = {10.1094/PHYTO-03-15-0065-R}, pmid = {25822187}, issn = {0031-949X}, mesh = {Ascomycota/*classification/genetics/isolation & purification ; Brazil ; DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/genetics ; Fungal Proteins/genetics ; Genetic Variation ; Genotype ; Ipomoea batatas/*microbiology ; Mangifera/*microbiology ; Microsatellite Repeats/genetics ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Ceratocystis wilt is among the most important diseases on mango (Mangifera indica) in Brazil, Oman, and Pakistan. The causal agent was originally identified in Brazil as Ceratocystis fimbriata, which is considered by some as a complex of many cryptic species, and four new species on mango trees were distinguished from C. fimbriata based on variation in internal transcribed spacer sequences. In the present study, phylogenetic analyses using DNA sequences of mating type genes, TEF-1α, and β-tubulin failed to identify lineages corresponding to the four new species names. Further, mating experiments found that the mango isolates representing the new species were interfertile with each other and a tester strain from sweet potato (Ipomoea batatas), on which the name C. fimbriata is based, and there was little morphological variation among the mango isolates. Microsatellite markers found substantial differentiation among mango isolates at the regional and population levels, but certain microsatellite genotypes were commonly found in multiple populations, suggesting that these genotypes had been disseminated in infected nursery stock. The most common microsatellite genotypes corresponded to the four recently named species (C. manginecans, C. acaciivora, C. mangicola, and C. mangivora), which are considered synonyms of C. fimbriata. This study points to the potential problems of naming new species based on introduced genotypes of a pathogen, the value of an understanding of natural variation within and among populations, and the importance of phenotype in delimiting species.}, } @article {pmid25799362, year = {2015}, author = {Nguyen, HD and Jančič, S and Meijer, M and Tanney, JB and Zalar, P and Gunde-Cimerman, N and Seifert, KA}, title = {Application of the phylogenetic species concept to Wallemia sebi from house dust and indoor air revealed by multi-locus genealogical concordance.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0120894}, pmid = {25799362}, issn = {1932-6203}, mesh = {*Air Microbiology ; *Air Pollution, Indoor ; Basidiomycota/*classification/*genetics ; *Dust ; Genes, Fungal ; Genetic Loci ; Genetic Markers ; Genetic Variation ; Geography ; Multilocus Sequence Typing ; Phylogeny ; Phylogeography ; }, abstract = {A worldwide survey of Wallemia occurring in house dust and indoor air was conducted. The isolated strains were identified as W. sebi and W. muriae. Previous studies suggested that the W. sebi phylogenetic clade contained cryptic species but conclusive evidence was lacking because only the internal transcribed spacer (ITS) marker was analyzed. The ITS and four protein-coding genes (MCM7, RPB1, RPB2, and TSR1) were sequenced for 85 isolates. Based on an initial neighbor joining analysis of the concatenated genes, W. muriae remained monophyletic but four clades were found in W. sebi, which we designated as W. sebi clades 1, 2, 3, and 4. We hypothesized that these clades represent distinct phylogenetic species within the Wallemia sebi species complex (WSSC). We then conducted multiple phylogenetic analyses and demonstrated genealogical concordance, which supports the existence of four phylogenetic species within the WSSC. Geographically, W. muriae was only found in Europe, W. sebi clade 3 was only found in Canada, W. sebi clade 4 was found in subtropical regions, while W. sebi clade 1 and 2 were found worldwide. Haplotype analysis showed that W. sebi clades 1 and 2 had multiple haplotypes while W. sebi clades 3 and 4 had one haplotype and may have been under sampled. We describe W. sebi clades 2, 3, and 4 as new species in a companion study.}, } @article {pmid25791576, year = {2015}, author = {Honenberger, P}, title = {Grene and Hull on types and typological thinking in biology.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {50}, number = {}, pages = {13-25}, doi = {10.1016/j.shpsc.2015.01.015}, pmid = {25791576}, issn = {1879-2499}, mesh = {Biological Evolution ; Biology/*history ; Classification ; History, 20th Century ; History, 21st Century ; Paleontology/history ; Philosophy/*history ; }, abstract = {Marjorie Grene (1910-2009) and David Hull (1935-2010) were among the most influential voices in late twentieth-century philosophy of biology. But, as Grene and Hull pointed out in published discussions of one another's work over the course of nearly forty years, they disagreed strongly on fundamental issues. Among these contested issues is the role of what is sometimes called "typology" and "typological thinking" in biology. In regard to taxonomy and the species problem, Hull joined Ernst Mayr's construal of typological thinking as a backward relic of pre-Darwinian science that should be overcome. Grene, however, treated the suspicion of typological thinking that characterized Hull's views, as well as those of other architects of the New Evolutionary Synthesis, as itself suspicious and even unsustainable. In this paper I review three debates between Grene and Hull bearing on the question of the validity of so-called typological thinking in biology: (1) a debate about the dispensability of concepts of "type" within evolutionary theory, paleontology, and taxonomy; (2) a debate about whether species can be adequately understood as individuals, and thereby independently of those forms of thinking Hull and Mayr had construed as "typological"; and (3) a debate about the prospects of a biologically informed theory of human nature.}, } @article {pmid25791040, year = {2014}, author = {Mourthé, Í and Barnett, AA}, title = {Crying tapir: the functionality of errors and accuracy in predator recognition in two neotropical high-canopy primates.}, journal = {Folia primatologica; international journal of primatology}, volume = {85}, number = {6}, pages = {379-398}, doi = {10.1159/000371634}, pmid = {25791040}, issn = {1421-9980}, mesh = {Animals ; Atelinae/*physiology ; Birds ; Body Size ; Brazil ; Female ; Food Chain ; Male ; Mammals ; Pitheciidae/*physiology ; Recognition, Psychology ; *Visual Perception ; *Vocalization, Animal ; }, abstract = {Predation is often considered to be a prime driver in primate evolution, but, as predation is rarely observed in nature, little is known of primate antipredator responses. Time-limited primates should be highly discerning when responding to predators, since time spent in vigilance and avoidance behaviour may supplant other activities. We present data from two independent studies describing and quantifying the frequency, nature and duration of predator-linked behaviours in 2 high-canopy primates, Ateles belzebuth and Cacajao ouakary. We introduce the concept of 'pseudopredators' (harmless species whose appearance is sufficiently similar to that of predators to elicit antipredator responses) and predict that changes in behaviour should increase with risk posed by a perceived predator. We studied primate group encounters with non-primate vertebrates across 14 (Ateles) and 19 (Cacajao) months in 2 undisturbed Amazonian forests. Although preliminary, data on both primates revealed that they distinguished the potential predation capacities of other species, as predicted. They appeared to differentiate predators from non-predators and distinguished when potential predators were not an immediate threat, although they reacted erroneously to pseudopredators, on average in about 20% of the responses given toward other vertebrates. Reacting to pseudopredators would be interesting since, in predation, one error can be fatal to the prey.}, } @article {pmid25788732, year = {2015}, author = {Xia, XJ and Zhou, YH and Shi, K and Zhou, J and Foyer, CH and Yu, JQ}, title = {Interplay between reactive oxygen species and hormones in the control of plant development and stress tolerance.}, journal = {Journal of experimental botany}, volume = {66}, number = {10}, pages = {2839-2856}, doi = {10.1093/jxb/erv089}, pmid = {25788732}, issn = {1460-2431}, mesh = {*Gene Expression Regulation, Plant ; *Plant Development ; Plant Growth Regulators/*genetics/metabolism ; Plants/*genetics/metabolism ; Reactive Oxygen Species/*metabolism ; Signal Transduction ; Stress, Physiological ; }, abstract = {As a consequence of a sessile lifestyle, plants are continuously exposed to changing environmental conditions and often life-threatening stresses caused by exposure to excessive light, extremes of temperature, limiting nutrient or water availability, and pathogen/insect attack. The flexible coordination of plant growth and development is necessary to optimize vigour and fitness in a changing environment through rapid and appropriate responses to such stresses. The concept that reactive oxygen species (ROS) are versatile signalling molecules in plants that contribute to stress acclimation is well established. This review provides an overview of our current knowledge of how ROS production and signalling are integrated with the action of auxin, brassinosteroids, gibberellins, abscisic acid, ethylene, strigolactones, salicylic acid, and jasmonic acid in the coordinate regulation of plant growth and stress tolerance. We consider the local and systemic crosstalk between ROS and hormonal signalling pathways and identify multiple points of reciprocal control, as well as providing insights into the integration nodes that involve Ca(2+)-dependent processes and mitogen-activated protein kinase phosphorylation cascades.}, } @article {pmid25784922, year = {2015}, author = {Harrington, CA and Gould, PJ}, title = {Tradeoffs between chilling and forcing in satisfying dormancy requirements for Pacific Northwest tree species.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {120}, pmid = {25784922}, issn = {1664-462X}, abstract = {Many temperate and boreal tree species have a chilling requirement, that is, they need to experience cold temperatures during fall and winter to burst bud normally in the spring. Results from trials with 11 Pacific Northwest tree species are consistent with the concept that plants can accumulate both chilling and forcing units simultaneously during the dormant season and they exhibit a tradeoff between amount of forcing and chilling. That is, the parallel model of chilling and forcing was effective in predicting budburst and well chilled plants require less forcing for bud burst than plants which have received less chilling. Genotypes differed in the shape of the possibility line which describes the quantitative tradeoff between chilling and forcing units. Plants which have an obligate chilling requirement (Douglas-fir, western hemlock, western larch, pines, and true firs) and received no or very low levels of chilling did not burst bud normally even with long photoperiods. Pacific madrone and western redcedar benefited from chilling in terms of requiring less forcing to promote bud burst but many plants burst bud normally without chilling. Equations predicting budburst were developed for each species in our trials for a portion of western North America under current climatic conditions and for 2080. Mean winter temperature was predicted to increase 3.2-5.5°C and this change resulted in earlier predicted budburst for Douglas-fir throughout much of our study area (up to 74 days earlier) but later budburst in some southern portions of its current range (up to 48 days later) as insufficient chilling is predicted to occur. Other species all had earlier predicted dates of budburst by 2080 than currently. Recent warming trends have resulted in earlier budburst for some woody plant species; however, the substantial winter warming predicted by some climate models will reduce future chilling in some locations such that budburst will not consistently occur earlier.}, } @article {pmid25781238, year = {2015}, author = {Tan, MK and Liu, C and Artchawakom, T}, title = {Taxonomic review of Tapiena (Orthoptera: Phaneropteridae: Phaneropterinae), with key to species and new species from Thailand.}, journal = {Zootaxa}, volume = {3920}, number = {1}, pages = {40-50}, doi = {10.11646/zootaxa.3920.1.2}, pmid = {25781238}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Body Size ; Female ; Gryllidae/anatomy & histology/*classification/growth & development ; Male ; Organ Size ; Thailand ; }, abstract = {The genus Tapiena (Orthoptera: Phaneropteridae: Phaneropterinae), consisting of species from around Asia and Africa, is reviewed. Henningian species concept was applied and morphology was used to estimate species boundaries. From Sakaerat Environmental Research Station, Thailand, two new species are described: Tapiena sakaerat Tan, Liu, Artchawakom sp. n. and Tapiena denticulata Tan, Liu, Artchawakom sp. n. This represents the first record of the genus Tapiena in Thailand. A key to the species of Tapiena (for males only) is also provided.}, } @article {pmid25772799, year = {2015}, author = {Choi, YJ and Klosterman, SJ and Kummer, V and Voglmayr, H and Shin, HD and Thines, M}, title = {Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach.}, journal = {Molecular phylogenetics and evolution}, volume = {86}, number = {}, pages = {24-34}, pmid = {25772799}, issn = {1095-9513}, support = {P 22739/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Bayes Theorem ; Beta vulgaris/microbiology ; DNA, Fungal/genetics ; *Genetic Speciation ; Likelihood Functions ; Models, Genetic ; Peronospora/*classification ; *Phylogeny ; Plant Diseases/microbiology ; Sequence Analysis, DNA ; Spinacia oleracea/microbiology ; }, abstract = {Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants.}, } @article {pmid25747618, year = {2015}, author = {Rosselló-Móra, R and Amann, R}, title = {Past and future species definitions for Bacteria and Archaea.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {4}, pages = {209-216}, doi = {10.1016/j.syapm.2015.02.001}, pmid = {25747618}, issn = {1618-0984}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; *Genomics ; *Sequence Analysis, DNA ; }, abstract = {Species is the basic unit of biological diversity. However, among the different microbiological disciplines there is an important degree of disagreement as to what this unit may be. In this minireview, we argue that the main point of disagreement is the definition (i.e. the way species are circumscribed by means of observable characters) rather than the concept (i.e. the idea of what a species may be as a unit of biodiversity, the meaning of the patterns of recurrence observed in nature, and the why of their existence). Taxonomists have defined species by means of genetic and expressed characters that ensure the members of the unit are monophyletic, and exhibit a large degree of genomic and phenotypic coherence. The new technologies allowing high-throughput data acquisition are expected to improve future classifications significantly and will lead to database-based taxonomy centered on portable and interactive data. Future species descriptions of Bacteria and Archaea should include a high quality genome sequence of at least the type strain as an obligatory requirement, just as today an almost full-length 16S rRNA gene sequence must be provided. Serious efforts are needed in order to re-evaluate the major guidelines for standard descriptions.}, } @article {pmid25737591, year = {2014}, author = {Quaedvlieg, W and Binder, M and Groenewald, JZ and Summerell, BA and Carnegie, AJ and Burgess, TI and Crous, PW}, title = {Introducing the Consolidated Species Concept to resolve species in the Teratosphaeriaceae.}, journal = {Persoonia}, volume = {33}, number = {}, pages = {1-40}, pmid = {25737591}, issn = {0031-5850}, abstract = {The Teratosphaeriaceae represents a recently established family that includes numerous saprobic, extremophilic, human opportunistic, and plant pathogenic fungi. Partial DNA sequence data of the 28S rRNA and RPB2 genes strongly support a separation of the Mycosphaerellaceae from the Teratosphaeriaceae, and also provide support for the Extremaceae and Neodevriesiaceae, two novel families including many extremophilic fungi that occur on a diversity of substrates. In addition, a multi-locus DNA sequence dataset was generated (ITS, LSU, Btub, Act, RPB2, EF-1α and Cal) to distinguish taxa in Mycosphaerella and Teratosphaeria associated with leaf disease of Eucalyptus, leading to the introduction of 23 novel genera, five species and 48 new combinations. Species are distinguished based on a polyphasic approach, combining morphological, ecological and phylogenetic species concepts, named here as the Consolidated Species Concept (CSC). From the DNA sequence data generated, we show that each one of the five coding genes tested, reliably identify most of the species present in this dataset (except species of Pseudocercospora). The ITS gene serves as a primary barcode locus as it is easily generated and has the most extensive dataset available, while either Btub, EF-1α or RPB2 provide a useful secondary barcode locus.}, } @article {pmid25730100, year = {2015}, author = {Stolar, M and Borau-Garcia, J and Toonen, M and Baumgartner, T}, title = {Synthesis and tunability of highly electron-accepting, N-benzylated "phosphaviologens".}, journal = {Journal of the American Chemical Society}, volume = {137}, number = {9}, pages = {3366-3371}, doi = {10.1021/ja513258j}, pmid = {25730100}, issn = {1520-5126}, abstract = {We report a structure-property study on phosphoryl-bridged viologen analogues with a remarkably low reduction threshold. Utilizing different benzyl groups for N-quaternization, we were able to confirm the p-benzyl substituent effect on the electronic tunability of the system while maintaining the characteristic chromic response of viologens with two fully reversible one-electron reductions. Due to the considerably increased electron-acceptor properties of the phosphoryl-bridged bipyridine precursor, N-benzylation was found to be very challenging and required the development of new synthetic strategies toward the target viologen species. This study also introduces a new and convenient way for the anion exchange of viologen systems by utilizing methyl triflate. Finally, the practical utility of the new species was verified in simplified proof-of-concept electrochromic devices.}, } @article {pmid25726808, year = {2016}, author = {Stepanović, S and Kosovac, A and Krstić, O and Jović, J and Toševski, I}, title = {Morphology versus DNA barcoding: two sides of the same coin. A case study of Ceutorhynchus erysimi and C. contractus identification.}, journal = {Insect science}, volume = {23}, number = {4}, pages = {638-648}, doi = {10.1111/1744-7917.12212}, pmid = {25726808}, issn = {1744-7917}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genotype ; Montenegro ; Peptide Elongation Factor 1/genetics ; Phenotype ; Sequence Analysis, DNA ; Serbia ; Species Specificity ; Weevils/anatomy & histology/*classification/*genetics ; }, abstract = {Genotyping of 2 well-known weevil species from the genus Ceutorhynchus (Coleoptera: Curculionidae) distributed in west Palearctic, C. erysimi and C. contractus, revealed phenotype versus genotype inconsistencies in a set of 56 specimens (25 C. erysimi and 31 C. contractus) collected from 25 locations in Serbia and Montenegro. An analysis of the mitochondrial cytochrome oxidase subunit I gene (COI), widely used as a barcoding region, and a nuclear gene, elongation factor-1α (EF-1α), revealed stable genetic divergence among these species. The average uncorrected pairwise distances for the COI and EF-1α genes were 3.8%, and 1.3%, respectively, indicating 2 genetically well-segregated species. However, the genetic data were not congruent with the phenotypic characteristics of the studied specimens. In the first place, C. erysimi genotypes were attached to specimens with phenotypic characteristics of C. contractus. Species-specific PCR-RFLP assays for the barcoding gene COI were applied for the molecular identification of 101 additional specimens of both morphospecies (33 C. erysimi and 68 C. contractus) and were found to confirm this incongruity. The discrepancy between the genetic and morphological data raises the question of the accuracy of using a barcoding approach, as it may result in misleading conclusions about the taxonomic position of the studied organism. Additionally, the typological species concept shows considerable weakness when genetic data are not supported with phenotypic characteristics as in case of asymmetric introgression, which may cause certain problems, especially in applied studies such as biological control programs in which the biological properties of the studied organisms are the main focus.}, } @article {pmid25689277, year = {2015}, author = {Neumann, K and Klukas, C and Friedel, S and Rischbeck, P and Chen, D and Entzian, A and Stein, N and Graner, A and Kilian, B}, title = {Dissecting spatiotemporal biomass accumulation in barley under different water regimes using high-throughput image analysis.}, journal = {Plant, cell & environment}, volume = {38}, number = {10}, pages = {1980-1996}, doi = {10.1111/pce.12516}, pmid = {25689277}, issn = {1365-3040}, mesh = {Biomass ; Droughts ; Gene-Environment Interaction ; Hordeum/anatomy & histology/genetics/*growth & development/physiology ; Image Processing, Computer-Assisted/*methods ; Models, Biological ; Phenotype ; Stress, Physiological ; Water/physiology ; }, abstract = {Phenotyping large numbers of genotypes still represents the rate-limiting step in many plant genetic experiments and in breeding. To address this issue, novel automated phenotyping technologies have been developed. We investigated for a core set of barley cultivars if high-throughput image analysis can help to dissect vegetative biomass accumulation in response to two different watering regimes under semi-controlled greenhouse conditions. We found that experiments, treatments, genotypes and genotype by environment interaction (G × E) can be characterized at any time point by certain digital traits. Biomass accumulation under control and stress conditions was highly heritable. Growth model-derived maximum vegetative biomass (K max), inflection point (I) and regrowth rate (k) were identified as promising candidate traits for genome-wide association studies. Drought stress symptoms can be visualized, dissected and modelled. Especially the highly heritable regrowth rate, which had the biggest influence on biomass accumulation in stress treatment, seems promising for future studies to improve drought tolerance in different crop species. A proof of concept study revealed potential correlations between digital traits obtained from pot experiments under greenhouse conditions and agronomic traits from field experiments. Overall, non-invasive, imaging-based phenotyping platforms under greenhouse conditions offer excellent possibilities for trait discovery, trait development and industrial applications.}, } @article {pmid25685016, year = {2015}, author = {Seifert, B and Csösz, S}, title = {Temnothoraxcrasecundus sp. n. - a cryptic Eurocaucasian ant species (Hymenoptera, Formicidae) discovered by Nest Centroid Clustering.}, journal = {ZooKeys}, volume = {}, number = {479}, pages = {37-64}, pmid = {25685016}, issn = {1313-2989}, abstract = {The paper integrates two independent studies of numeric morphology-based alpha-taxonomy of the cryptic ant species Temnothoraxcrassispinus (Karavajev, 1926) and Temnothoraxcrasecundus sp. n. conducted by different investigators, using different equipment, considering different character combinations and evaluating different samples. Samples investigated included 603 individual workers from 203 nests - thereof 104 nest samples measured by Seifert and 99 by Csösz. The material originated from Europe, Asia Minor and Caucasia. There was a very strong interspecific overlap in any of the 29 shape characters recorded and subjective expert determination failed in many cases. Primary classification hypotheses were formed by the exploratory data analysis Nest Centroid (NC) clustering and corrected to final species hypotheses by an iterative linear discriminant analysis algorithm. The evaluation of Seifert's and Csösz's data sets arrived at fully congruent conclusions. NC-Ward and NC-K-means clustering disagreed from the final species hypothesis in only 1.9 and 1.9% of the samples in Seifert's data set and by 1.1 and 2.1% in Csösz's data set which is a strong argument for heterospecificity. The type series of Temnothoraxcrassispinus and Temnothoraxcrasecundus sp. n. were allocated to different clusters with p = 0.9851 and p = 0.9912 respectively. The type series of the junior synonym Temnothoraxslavonicus (Seifert, 1995) was allocated to the Temnothoraxcrassispinus cluster with p = 0.9927. Temnothoraxcrasecundus sp. n. and Temnothoraxcrassispinus are parapatric species with a long contact zone stretching from the Peloponnisos peninsula across Bulgaria northeast to the southern Ukraine. There is no indication for occurrence of interspecifically mixed nests or intraspecific polymorphism. However, a significant reduction of interspecific morphological distance at sites with syntopic occurrence of both species indicates local hybridization. The results are discussed within the context of the Pragmatic Species Concept of Seifert (2014). The taxonomic description and a differential diagnosis of Temnothoraxcrasecundus sp. n. are given.}, } @article {pmid25681255, year = {2015}, author = {Konstantinidis, KT and Rosselló-Móra, R}, title = {Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal.}, journal = {Systematic and applied microbiology}, volume = {38}, number = {4}, pages = {223-230}, doi = {10.1016/j.syapm.2015.01.001}, pmid = {25681255}, issn = {1618-0984}, mesh = {*Bacteria/classification/genetics ; *Bacteriological Techniques ; *Computational Biology ; *Metagenomics ; *Single-Cell Analysis ; }, abstract = {Microbial taxonomists have generally been reluctant to accept the valid publication of names of uncultured taxa given that only pure cultures allow for a thorough description of the genealogy, genetics and phenotype of the putative taxa to be classified. The classification of conspicuous uncultured organisms has been considered into the Candidatus provisional status, but this is only possible with organisms for which it is possible to retrieve basic data on phylogeny, morphology, ecology and some metabolic traits that unequivocally identify them. The current developments on modern sequencing techniques, and especially metagenomics, allow the recognition of discrete populations of DNA sequences in environmental samples, which can be considered to belong to individual closely related populations that may be identified as members of yet-to-be described species. The recognition of such populations of (meta)genomes allow the retrieval of valuable taxonomic information, i.e. genealogy, genome, phenotypic coherence with other populations, and ecological relevant traits. Such traits may be included in the Candidatus proposals of environmentally occurring, yet uncultured species not exhibiting exceptional morphologies, phenotypes or ecological relevancies.}, } @article {pmid25674364, year = {2015}, author = {Forsman, Z and Wellington, GM and Fox, GE and Toonen, RJ}, title = {Clues to unraveling the coral species problem: distinguishing species from geographic variation in Porites across the Pacific with molecular markers and microskeletal traits.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e751}, pmid = {25674364}, issn = {2167-8359}, abstract = {Morphological variation in the geographically widespread coral Porites lobata can make it difficult to distinguish from other massive congeneric species. This morphological variation could be attributed to geographic variability, phenotypic plasticity, or a combination of such factors. We examined genetic and microscopic morphological variability in P. lobata samples from the Galápagos, Easter Island, Tahiti, Fiji, Rarotonga, and Australia. Panamanian P. evermanni specimens were used as a previously established distinct outgroup against which to test genetic and morphological methods of discrimination. We employed a molecular analysis of variance (AMOVA) based on ribosomal internal transcribed spacer region (ITS) sequence, principal component analysis (PCA) of skeletal landmarks, and Mantel tests to compare genetic and morphological variation. Both genetic and morphometric methods clearly distinguished P. lobata and P. evermanni, while significant genetic and morphological variance was attributed to differences among geographic regions for P. lobata. Mantel tests indicate a correlation between genetic and morphological variation for P. lobata across the Pacific. Here we highlight landmark morphometric measures that correlate well with genetic differences, showing promise for resolving species of Porites, one of the most ubiquitous yet challenging to identify architects of coral reefs.}, } @article {pmid25671634, year = {2015}, author = {Bocherens, H and Hofman-Kamińska, E and Drucker, DG and Schmölcke, U and Kowalczyk, R}, title = {European bison as a refugee species? Evidence from isotopic data on Early Holocene bison and other large herbivores in northern Europe.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0115090}, pmid = {25671634}, issn = {1932-6203}, mesh = {Animals ; *Bison ; *Ecosystem ; Europe ; Fossils ; Geography ; *Herbivory ; Isotopes/analysis ; }, abstract = {According to the refugee species concept, increasing replacement of open steppe by forest cover after the last glacial period and human pressure had together forced European bison (Bison bonasus)--the largest extant terrestrial mammal of Europe--into forests as a refuge habitat. The consequent decreased fitness and population density led to the gradual extinction of the species. Understanding the pre-refugee ecology of the species may help its conservation management and ensure its long time survival. In view of this, we investigated the abundance of stable isotopes (δ13C and δ15N) in radiocarbon dated skeletal remains of European bison and other large herbivores--aurochs (Bos primigenius), moose (Alces alces), and reindeer (Rangifer tarandus)--from the Early Holocene of northern Europe to reconstruct their dietary habits and pattern of habitat use in conditions of low human influence. Carbon and nitrogen isotopic compositions in collagen of the ungulate species in northern central Europe during the Early Holocene showed significant differences in the habitat use and the diet of these herbivores. The values of the δ13C and δ15N isotopes reflected the use of open habitats by bison, with their diet intermediate between that of aurochs (grazer) and of moose (browser). Our results show that, despite the partial overlap in carbon and nitrogen isotopic values of some species, Early Holocene large ungulates avoided competition by selection of different habitats or different food sources within similar environments. Although Early Holocene bison and Late Pleistocene steppe bison utilized open habitats, their diets were significantly different, as reflected by their δ15N values. Additional isotopic analyses show that modern populations of European bison utilize much more forested habitats than Early Holocene bison, which supports the refugee status of the species.}, } @article {pmid25661720, year = {2015}, author = {Chaverri, P and Branco-Rocha, F and Jaklitsch, W and Gazis, R and Degenkolb, T and Samuels, GJ}, title = {Systematics of the Trichoderma harzianum species complex and the re-identification of commercial biocontrol strains.}, journal = {Mycologia}, volume = {107}, number = {3}, pages = {558-590}, pmid = {25661720}, issn = {0027-5514}, support = {P 22081/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Agricultural Inoculants/*classification/genetics/growth & development/isolation & purification ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Fungal Proteins/genetics ; Molecular Sequence Data ; Peptide Elongation Factor 1/genetics ; Pest Control, Biological/economics ; Phylogeny ; Soil Microbiology ; Spores, Fungal/classification/genetics/growth & development/isolation & purification ; Trichoderma/*classification/genetics/growth & development/isolation & purification ; }, abstract = {Trichoderma harzianum is known as a cosmopolitan, ubiquitous species associated with a wide variety of substrates. It is possibly the most commonly used name in agricultural applications involving Trichoderma, including biological control of plant diseases. While various studies have suggested that T. harzianum is a species complex, only a few cryptic species are named. In the present study the taxonomy of the T. harzianum species complex is revised to include at least 14 species. Previously named species included in the complex are T. guizhouense, T. harzianum, and T. inhamatum. Two new combinations are proposed, T. lentiforme and T. lixii. Nine species are described as new, T. afarasin, T. afroharzianum, T. atrobrunneum, T. camerunense, T. endophyticum, T. neotropicale, T. pyramidale, T. rifaii and T. simmonsii. We isolated Trichoderma cultures from four commercial biocontrol products reported to contain T. harzianum. None of the biocontrol strains were identified as T. harzianum s. str. In addition, the widely applied culture 'T. harzianum T22' was determined to be T. afroharzianum. Some species in the T. harzianum complex appear to be exclusively endophytic, while others were only isolated from soil. Sexual states are rare. Descriptions and illustrations are provided. A secondary barcode, nuc translation elongation factor 1-α (TEF1) is needed to identify species in this complex.}, } @article {pmid25647587, year = {2015}, author = {Smyser, TJ and Redding, JV and Bevis, CM and Page, LK and Swihart, RK}, title = {Development of an automated dispenser for the delivery of medicinal or vaccine-laden baits to raccoons (Procyon lotor).}, journal = {Journal of wildlife diseases}, volume = {51}, number = {2}, pages = {513-518}, doi = {10.7589/2014-08-211}, pmid = {25647587}, issn = {1943-3700}, mesh = {Administration, Oral ; Animals ; Automation ; Mice ; Opossums ; Rabies/prevention & control/*veterinary ; Rabies Vaccines/*administration & dosage ; *Raccoons ; Species Specificity ; Vaccination/methods/*veterinary ; }, abstract = {Medicinal baits are distributed to manage zoonotic diseases, including raccoon (Procyon lotor) rabies, but efficient distribution strategies are needed for suburban environments. We developed an automated dispenser that transfers fishmeal polymer baits at user-specified intervals from a magazine to a receptacle fitted with a filter that exploits raccoon dexterity to limit consumption by nontarget species. We introduce the concept of automated dispensers and describe bait removal success rates for raccoons versus nontarget species. We monitored visitation with remote cameras after deploying a dispenser, programmed to present two baits per night, in three disjunct forest patches in northwest Indiana. Raccoons removed 72% of baits; nontarget, white-footed mice (Peromyscus leucopus) removed 11%; Virginia opossums (Didelphis virginiana) removed 9%. Bait removal success varied significantly between raccoons (76%) and opossums (21%), improving bait delivery specificity relative to hand baiting. Accumulation of baits in receptacles resulted in excess (more than one) bait consumption (39% of baits consumed by raccoons were excess), suggesting design improvements are needed to present additional baits only after previous baits have been consumed. Automated dispensers successfully sustained bait availability throughout the operational period. Subsequent research is needed to determine whether a sustained availability of baits achieved with automated dispensers is more effective for the treatment of raccoons in suburban environments than traditional distribution methods.}, } @article {pmid25601149, year = {2015}, author = {Travadon, R and Lawrence, DP and Rooney-Latham, S and Gubler, WD and Wilcox, WF and Rolshausen, PE and Baumgartner, K}, title = {Cadophora species associated with wood-decay of grapevine in North America.}, journal = {Fungal biology}, volume = {119}, number = {1}, pages = {53-66}, doi = {10.1016/j.funbio.2014.11.002}, pmid = {25601149}, issn = {1878-6146}, mesh = {Ascomycota/*classification/cytology/genetics/*isolation & purification ; Canada ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Microbiological Techniques ; Molecular Sequence Data ; Peptide Elongation Factor 1/genetics ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, DNA ; Tubulin/genetics ; United States ; Vitis/*microbiology ; }, abstract = {Cadophora species are reported from grapevine (Vitis vinifera L.) in California, South Africa, Spain, Uruguay, and Canada. Frequent isolation from vines co-infected with the Esca pathogens (Togninia minima and Phaeomoniella chlamydospora), and confirmation of its ability to cause wood lesions/discoloration in pathogenicity tests, suggest that C. luteo-olivacea is part of the trunk pathogen complex. In North America, little is known regarding the diversity, geographic distribution, and roles of Cadophora species as trunk pathogens. Accordingly, we characterized 37 Cadophora isolates from ten US states and two Canadian provinces, based on molecular and morphological comparisons, and pathogenicity. Phylogenetic analysis of three loci (ITS, translation elongation factor 1-alpha (TEF1-α) and beta-tubulin (BT)) distinguished two known species (C. luteo-olivacea and Cadophora melinii) and three newly-described species (Cadophora orientoamericana, Cadophora novi-eboraci, and Cadophora spadicis). C. orientoamericana, C. novi-eboraci, and C. spadicis were restricted to the northeastern US, whereas C. luteo-olivacea was only recovered from California. C. melinii was present in California and Ontario, Canada. Morphological characterization was less informative, due to significant overlap in dimensions of conidia, hyphae, conidiophores, and conidiogenous cells. Pathogenicity tests confirmed the presence of wood lesions after 24 m, suggesting that Cadophora species may have a role as grapevine trunk pathogens.}, } @article {pmid25580533, year = {2015}, author = {Haemmerle, M and Gutschner, T}, title = {Long non-coding RNAs in cancer and development: where do we go from here?.}, journal = {International journal of molecular sciences}, volume = {16}, number = {1}, pages = {1395-1405}, pmid = {25580533}, issn = {1422-0067}, mesh = {Animals ; Biomarkers, Tumor/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Humans ; Neoplasms/genetics/*pathology ; Neurodegenerative Diseases/genetics/pathology ; Oligonucleotides, Antisense/metabolism ; RNA, Long Noncoding/antagonists & inhibitors/*metabolism ; }, abstract = {Recent genome-wide expression profiling studies have uncovered a huge amount of novel, long non-protein-coding RNA transcripts (lncRNA). In general, these transcripts possess a low, but tissue-specific expression, and their nucleotide sequences are often poorly conserved. However, several studies showed that lncRNAs can have important roles for normal tissue development and regulate cellular pluripotency as well as differentiation. Moreover, lncRNAs are implicated in the control of multiple molecular pathways leading to gene expression changes and thus, ultimately modulate cell proliferation, migration and apoptosis. Consequently, deregulation of lncRNA expression contributes to carcinogenesis and is associated with human diseases, e.g., neurodegenerative disorders like Alzheimer's Disease. Here, we will focus on some major challenges of lncRNA research, especially loss-of-function studies. We will delineate strategies for lncRNA gene targeting in vivo, and we will briefly discuss important consideration and pitfalls when investigating lncRNA functions in knockout animal models. Finally, we will highlight future opportunities for lncRNAs research by applying the concept of cross-species comparison, which might contribute to novel disease biomarker discovery and might identify lncRNAs as potential therapeutic targets.}, } @article {pmid25580487, year = {2015}, author = {Niinemets, U}, title = {Is there a species spectrum within the world-wide leaf economics spectrum? Major variations in leaf functional traits in the Mediterranean sclerophyll Quercus ilex.}, journal = {The New phytologist}, volume = {205}, number = {1}, pages = {79-96}, doi = {10.1111/nph.13001}, pmid = {25580487}, issn = {1469-8137}, mesh = {Climate ; Geography ; Linear Models ; Mediterranean Region ; Photosynthesis/physiology ; Plant Leaves/*physiology ; *Quantitative Trait, Heritable ; Quercus/*genetics/*physiology ; Species Specificity ; }, abstract = {The leaf economics spectrum is a general concept describing coordinated variation in foliage structural, chemical and physiological traits across resource gradients. Yet, within this concept,the role of within-species variation, including ecotypic and plastic variation components, has been largely neglected. This study hypothesized that there is a within-species economics spectrum within the general spectrum in the evergreen sclerophyll Quercus ilex which dominates low resource ecosystems over an exceptionally wide range. An extensive database of foliage traits covering the full species range was constructed, and improved filtering algorithms were developed. Standardized data filtering was deemed absolutely essential as additional variation sources can result in trait variation of 10–300%,blurring the broad relationships. Strong trait variation, c. two-fold for most traits to up to almost an order of magnitude, was uncovered.Although the Q. ilex spectrum is part of the general spectrum, within-species trait and climatic relationships in this species partly differed from the overall spectrum. Contrary to world-wide trends, Q. ilex does not necessarily have a low nitrogen content per mass and can increase photosynthetic capacity with increasing foliage robustness. This study argues that the within-species economics spectrum needs to be considered in regional- to biome-level analyses.}, } @article {pmid25575224, year = {2015}, author = {Zehr, EP}, title = {The potential transformation of our species by neural enhancement.}, journal = {Journal of motor behavior}, volume = {47}, number = {1}, pages = {73-78}, pmid = {25575224}, issn = {1940-1027}, mesh = {Biomedical Enhancement/*ethics/methods ; Humans ; *Neuronal Plasticity ; }, abstract = {Neural enhancement represents recovery of function that has been lost due to injury or disease pathology. Restoration of functional ability is the objective. For example, a neuroprosthetic to replace a forearm and hand lost to the ravages of war or industrial accident. However, the same basic constructs used for neural enhancement after injury could amplify abilities that are already in the natural normal range. That is, neural enhancement technologies to restore function and improve daily abilities for independent living could be used to improve so-called normal function to ultimate function. Approaching that functional level by use and integration of technology takes us toward the concept of a new species. This new subspecies--homo sapiens technologicus--is one that uses technology not just to assist but to change its own inherent biological function. The author uses examples from prosthetics and neuroprosthetics to address the issue of the limitations of constructs on the accepted range of human performance ability and aims to provide a cautionary view toward reflection on where our science may take the entire species.}, } @article {pmid25562633, year = {2015}, author = {Miyajima, T and Ohta, E and Kawada, H and Maekawa, T and Obata, F}, title = {The mouse/human cross-species heterodimer of leucine-rich repeat kinase 2: possible significance in the transgenic model mouse of Parkinson's disease.}, journal = {Neuroscience letters}, volume = {588}, number = {}, pages = {142-146}, doi = {10.1016/j.neulet.2015.01.003}, pmid = {25562633}, issn = {1872-7972}, mesh = {Animals ; Disease Models, Animal ; HEK293 Cells ; Humans ; Leucine-Rich Repeat Serine-Threonine Protein Kinase-2 ; Mice ; Mice, Transgenic ; Mutation ; Parkinson Disease/genetics/*metabolism ; Protein Multimerization ; Protein Serine-Threonine Kinases/genetics/*metabolism ; }, abstract = {Leucine-rich repeat kinase (LRRK2) is the causal molecule of autosomal dominant Parkinson's disease (PD). We previously reported that intracellular degradation of wild-type (WT) LRRK2 is promoted by formation of heterodimers with the I2020T mutant LRRK2. In the present study, we investigated whether this is also the case for mouse/human cross-species heterodimers, which could be formed in transgenic mice. First, by co-transfection and immunoprecipitation, we identified the cross-species heterodimer of mouse LRRK2 and human LRRK2. Next, we found that the protein level of mouse LRRK2 decreased when co-transfected with human I2020T LRRK2, but not with human WT LRRK2. These results suggested that degradation of mouse LRRK2 was promoted by formation of a cross-species heterodimer with the mutant LRRK2. In I2020T LRRK2-transgenic mice, the lower protein level of brain LRRK2 in comparison with control mice, together with higher expression of the mRNA, suggested that endogenous LRRK2 was degraded by formation of cross-species heterodimers. Our results suggest a new concept of cross-species dimer/oligomer formation in transgenic disease-model mice.}, } @article {pmid26975144, year = {2015}, author = {Rautian, M and Przyboś, E and Beliavskaia, A}, title = {New Stands of Species of the Paramecium aurelia Complex in Yakutia, Russia.}, journal = {Folia biologica}, volume = {63}, number = {4}, pages = {289-293}, doi = {10.3409/fb63_4.289}, pmid = {26975144}, issn = {0015-5497}, mesh = {Paramecium aurelia/*classification ; Phylogeography ; Russia ; Species Specificity ; }, abstract = {Paramecium is one of the most studied genera among ciliates. In particular, it is a model organism for investigation of the sibling species problem (also known as the cryptic species problem), spatial distribution, and its role in speciation. The global distribution of Paramecium species and of sibling species belonging to the P. aurelia species complex (Ciliophora, Protista) still need study, e.g. sampling in some territories has been quite limited, while Europe has been investigated for years with the majority of the P. aurelia species isolated from here. The large territory of Yakutia (republic Sakha in the Russian Federation), known for its climate extremes and continuous permafrost that extended over several glacial and interglacial cycles of the Pleistocene, has not been studied before. In the present study we collected paramecia in the central part of Yakutia. Newly established strains were identified to species according to morphology and, in case of the P. aurelia complex, by crossing with the test strains (the reference strains for the particular species). New stands of P. primaurelia, P. biaurelia and P. novaurelia were described from the territory of Yakutia.}, } @article {pmid25550245, year = {2015}, author = {Shayesteh, TH and Radmehr, M and Khajavi, F and Mahjub, R}, title = {Application of chemometrics in determination of the acid dissociation constants (pKa) of several benzodiazepine derivatives as poorly soluble drugs in the presence of ionic surfactants.}, journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences}, volume = {69}, number = {}, pages = {44-50}, doi = {10.1016/j.ejps.2014.12.013}, pmid = {25550245}, issn = {1879-0720}, mesh = {Benzodiazepines/*chemistry ; Cetrimonium ; Cetrimonium Compounds/*chemistry ; Hydrogen-Ion Concentration ; Sodium Dodecyl Sulfate/*chemistry ; Solubility ; Spectrophotometry, Ultraviolet ; Static Electricity ; Surface-Active Agents/*chemistry ; }, abstract = {In this study, the acid dissociation constants (pKa) of some benzodiazepine derivatives including chlordiazepoxide, clonazepam, lorazepam, and oxazepam in aqueous micellar solution were determined spectrophotometrically at an ionic strength of 0.1M at 25°C. The effect of cetyl trimethylammonium bromide (CTAB) as a cationic and sodium n-dodecyl sulfate(SDS) as an anionic surfactant on the absorption spectra of benzodiazepine drugs at different pH values were studied. The acidity constants of all related species are estimated by considering the surfactant concept and the application of chemometric methods using the whole spectral fitting of the collected data to an established factor analysis model. DATAN® software (Ver. 5.0, Multid Analyses AB, and Goteborg, Sweden) was applied to determine the acidity constants. In this study, a simple and fast method to determine the ionization constant (pKa) of poorly soluble drugs was developed using surfactants. The acidity constant (i.e. pKa) for chlordiazepoxide, clonazepam, lorazepam, and oxazepam were reported as 4.62, pKa1 value of 1.52 and pKa2 value of 10.51, pKa1 value of 1.53 and pKa2 value of 10.92 and pKa1 value 1.63 and pKa2 value of 11.21 respectively. The results showed that the peak values in the spectrophotometric absorption spectra of drugs are influenced by the presence of anionic and cationic surfactants. According to the results, by changing the SDS concentration from 0 to 0.05M, the pKa of chlordiazepoxide was increased to 5.9, the pKa1 of lorazepam was decreased to 0.1 while the pKa2 was increased to 11.5. Increase in SDS concentration has not shown significant alteration in pKa of clonazepam and oxazepam. Results indicate that by Changing the CTAB concentration from 0 to 0.05M, the pKa of chlordiazepoxide was reduced to 4.4, the pKa1 of clonazepam was decreased to 0.1 and the pKa2 was decreased to 9.1, the pKa1 of lorazepam was decreased to 0.4 and the pKa2 was decreased to 9.4, the pKa1 of oxazepam was decreased to 0.3 and the pKa2 was decreased to 9.7. Based on the results obtained from the study, charge of anionic and cationic surfactants leads to an electrostatic interaction between surfactant and the protonated form of the drug molecule. The electrostatic interactions can be attractive or repulsive forces and influence of separation of protons and consequently increase or decrease the acidity constants.}, } @article {pmid25548049, year = {2015}, author = {Puri, AW and Owen, S and Chu, F and Chavkin, T and Beck, DA and Kalyuzhnaya, MG and Lidstrom, ME}, title = {Genetic tools for the industrially promising methanotroph Methylomicrobium buryatense.}, journal = {Applied and environmental microbiology}, volume = {81}, number = {5}, pages = {1775-1781}, pmid = {25548049}, issn = {1098-5336}, mesh = {Conjugation, Genetic ; Gene Deletion ; Gene Transfer, Horizontal ; Genetic Vectors ; Genetics, Microbial/*methods ; Metabolic Engineering ; Metabolic Networks and Pathways/genetics ; Methane/metabolism ; Methylococcaceae/*genetics/growth & development ; Molecular Biology/*methods ; Oxidation-Reduction ; Plasmids ; }, abstract = {Aerobic methanotrophs oxidize methane at ambient temperatures and pressures and are therefore attractive systems for methane-based bioconversions. In this work, we developed and validated genetic tools for Methylomicrobium buryatense, a haloalkaliphilic gammaproteobacterial (type I) methanotroph. M. buryatense was isolated directly on natural gas and grows robustly in pure culture with a 3-h doubling time, enabling rapid genetic manipulation compared to many other methanotrophic species. As a proof of concept, we used a sucrose counterselection system to eliminate glycogen production in M. buryatense by constructing unmarked deletions in two redundant glycogen synthase genes. We also selected for a more genetically tractable variant strain that can be conjugated with small incompatibility group P (IncP)-based broad-host-range vectors and determined that this capability is due to loss of the native plasmid. These tools make M. buryatense a promising model system for studying aerobic methanotroph physiology and enable metabolic engineering in this bacterium for industrial biocatalysis of methane.}, } @article {pmid25545789, year = {2015}, author = {Sobel, JM and Streisfeld, MA}, title = {Strong premating reproductive isolation drives incipient speciation in Mimulus aurantiacus.}, journal = {Evolution; international journal of organic evolution}, volume = {69}, number = {2}, pages = {447-461}, doi = {10.1111/evo.12589}, pmid = {25545789}, issn = {1558-5646}, mesh = {California ; *Ecotype ; Flowers/genetics ; Gene Flow ; Genetic Markers ; *Genetic Speciation ; Hybridization, Genetic ; Mimulus/*genetics/physiology ; Pigmentation/genetics ; Pollination ; *Reproductive Isolation ; }, abstract = {Determining which forms of reproductive isolation have the biggest impact on the process of divergence is a major goal of speciation research. These barriers are often divided into those that affect the potential for hybridization (premating isolation), and those that occur after mating (postmating isolation), and much debate has surrounded the relative importance of these categories. Within the species Mimulus aurantiacus, red- and yellow-flowered ecotypes occur in the southwest corner of California, and a hybrid zone occurs where their ranges overlap. We show that premating barriers are exclusively responsible for isolation in this system, with both ecogeographic and pollinator isolation contributing significantly to total isolation. Postmating forms of reproductive isolation have little or no impact on gene flow, indicating that hybrids likely contribute to introgression at neutral loci. Analysis of molecular variation across thousands of restriction-site associated DNA sequencing (RAD-seq) markers reveals that the genomes of these taxa are largely undifferentiated. However, structure analysis shows that these taxa are distinguishable genetically, likely due to the impact of loci underlying differentiated adaptive phenotypes. These data exhibit the power of divergent natural selection to maintain highly differentiated phenotypes in the face of gene flow during the early stages of speciation.}, } @article {pmid25545748, year = {2015}, author = {Luo, Z and Duan, T and Yuan, S and Chen, S and Bai, X and Zhang, D}, title = {Reproductive isolation between sympatric sister species, Mussaenda kwangtungensis and M. pubescens var. alba.}, journal = {Journal of integrative plant biology}, volume = {57}, number = {10}, pages = {859-870}, doi = {10.1111/jipb.12325}, pmid = {25545748}, issn = {1744-7909}, mesh = {Microsatellite Repeats/genetics ; Phylogeny ; Pollination/genetics/*physiology ; *Reproductive Isolation ; Rubiaceae/genetics/*physiology ; }, abstract = {Reproductive isolation defines the biological species concept and plays a key role in the formation and maintenance of species. The relative contributions of different isolating stages has been suggested to be closely associated with phylogenetic relatedness. Few studies have focused on the relative contributions of pre- versus post-zygotic mechanisms, and even fewer have been conducted under strict phylogenetic frameworks. Pre- and post-zygotic reproductive isolation stages have been investigated in the sister species Mussaenda kwangtungensis and M. pubescens var. alba. The two species have partly overlapping distribution ranges and flowering times, while the principal pollinators differed strikingly for them, demonstrating strong pre-zygotic isolations. Natural hybrids were detected by simple sequence repeat markers and their maternal parents were identified based on chloroplast gene sequences. Five out of 81 individuals were suggested to be hybrids that fall into the categories F2, BC1, and BC2 by the NewHybrids analysis. Interspecific crossings resulted in significantly reduced fruit set and seed germination rates. Phylogenetic analysis revealed short Kimura-2-parameter distance between M. kwangtungensis and M. pubescens var. alba. These findings strongly supported the hypothesis that for species with a closer phylogenetic relationship, pre-zygotic isolation plays an important part in limiting gene exchange in sympatric areas.}, } @article {pmid25543558, year = {2014}, author = {Tan, MK}, title = {New species of small scaly crickets of genus Micrornebius (Orthoptera: Mogoplistidae; Mogoplistinae) from Singapore.}, journal = {Zootaxa}, volume = {3895}, number = {1}, pages = {117-126}, doi = {10.11646/zootaxa.3895.1.7}, pmid = {25543558}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Body Size ; Female ; Gryllidae/anatomy & histology/*classification/growth & development ; Male ; Organ Size ; Singapore ; }, abstract = {The small and cryptic scaly crickets of the genus Micrornebius from Singapore are reviewed. The Henningian species concept was applied and morphology was used to estimate species boundaries. Three new species are described: Micrornebius distinctus sp. n., Micrornebius eclipsus sp. n. and Micrornebius mandai sp. n. This increases the number of species Micrornebius from Singapore to five. A tentative key to the species of Micrornebius from Singapore is provided.}, } @article {pmid25533848, year = {2015}, author = {Thompson, CC and Amaral, GR and Campeão, M and Edwards, RA and Polz, MF and Dutilh, BE and Ussery, DW and Sawabe, T and Swings, J and Thompson, FL}, title = {Microbial taxonomy in the post-genomic era: rebuilding from scratch?.}, journal = {Archives of microbiology}, volume = {197}, number = {3}, pages = {359-370}, doi = {10.1007/s00203-014-1071-2}, pmid = {25533848}, issn = {1432-072X}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Classification/*methods ; Computer Simulation ; *Genomics ; Microbiology/*trends ; }, abstract = {Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.}, } @article {pmid25530109, year = {2015}, author = {van der Lee, T and Zhang, H and van Diepeningen, A and Waalwijk, C}, title = {Biogeography of Fusarium graminearum species complex and chemotypes: a review.}, journal = {Food additives & contaminants. Part A, Chemistry, analysis, control, exposure & risk assessment}, volume = {32}, number = {4}, pages = {453-460}, pmid = {25530109}, issn = {1944-0057}, mesh = {Australia ; Canada ; China ; Europe ; Food Contamination/analysis ; Food Microbiology ; Fusarium/*chemistry/*classification/isolation & purification ; Genotype ; Hordeum/microbiology ; Iran ; Mycotoxins/*analysis ; New Zealand ; Phylogeny ; Phylogeography ; Republic of Korea ; Trichothecenes/analysis ; Triticum/microbiology ; United States ; Uruguay ; }, abstract = {Differences in the geographic distribution of distinct trichothecene mycotoxins in wheat and barley were first recorded two decades ago. The different toxicological properties of deoxynivalenol (DON), nivalenol (NIV) and their acetylated derivatives require careful monitoring of the dynamics of these mycotoxins and their producers. The phylogenetic species concept has become a valuable tool to study the global occurrence of mycotoxin-producing Fusarium species. This has revolutionised our views on the terrestrial distribution of trichothecene-producing Fusaria in the context of agronomics, climatic conditions, and human interference by the global trade and exchange of agricultural commodities. This paper presents an overview of the dynamics of the different trichothecene-producing Fusarium species as well as their chemotypes and genotypes across different continents. Clearly not one global population exists, but separate ones can be distinguished, sometimes even sympatric in combination with different hosts. A population with more pathogenic strains and chemotypes can replace another. Several displacement events appear to find their origin in the inadvertent introduction of new genotypes into new regions: 3-acetyl-DON-producing F. graminearum in Canada; 3-acetyl-DON-producing F. asiaticum in Eastern China; 15-acetyl-DON F. graminearum in Uruguay; and NIV-producing F asiaticum in the southern United States.}, } @article {pmid25516188, year = {2015}, author = {Vodstrcil, LA and Walker, SM and Hocking, JS and Law, M and Forcey, DS and Fehler, G and Bilardi, JE and Chen, MY and Fethers, KA and Fairley, CK and Bradshaw, CS}, title = {Incident bacterial vaginosis (BV) in women who have sex with women is associated with behaviors that suggest sexual transmission of BV.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {60}, number = {7}, pages = {1042-1053}, doi = {10.1093/cid/ciu1130}, pmid = {25516188}, issn = {1537-6591}, mesh = {Adult ; Cohort Studies ; Cross-Sectional Studies ; Female ; *Homosexuality, Female ; Humans ; Incidence ; Risk Factors ; Self-Examination ; Specimen Handling/methods ; Surveys and Questionnaires ; Vagina/microbiology ; Vaginosis, Bacterial/*epidemiology/*transmission ; Young Adult ; }, abstract = {BACKGROUND: Female same-sex partnerships provide a unique opportunity to study the pathogenesis and transmissibility of bacterial vaginosis (BV) because it can be diagnosed in both members of the partnership. We conducted a nationwide community-enrolled cohort study of women who have sex with women, including women coenrolled with their regular female sexual partner (FSP), to investigate the BV incidence rate and factors associated with incident BV.

METHODS: Women who have sex with women, without prevalent BV in a cross-sectional study, were enrolled in a 24-month cohort study involving 3-monthly questionnaires and self-collected vaginal swabs that were scored by the Nugent method. We assessed the BV incidence rate per 100 woman-years (WY) and used univariate and multivariable Cox regression analysis to establish factors associated with BV acquisition.

RESULTS: Two hundred ninety-eight participants were enrolled in the cohort; 122 were coenrolled with their regular FSP. There were 51 incident cases of BV (rate, 9.75/100 WY; 95% confidence interval [CI], 7.41-12.83). Incident BV was associated with exposure to a new sexual partner (adjusted hazard ratio [AHR], 2.51; 95% CI, 1.30-4.82), a partner with BV symptoms (AHR, 3.99; 95% CI, 1.39-11.45), receptive oral sex (AHR, 3.52; 95% CI, 1.41-8.79), and onset of BV symptoms (AHR, 2.80; 95% CI, 1.39-5.61). Women coenrolled with their BV-negative partner had a greatly reduced risk of incident BV (AHR, 0.26; 95% CI, .11-.61), and high concordance of Nugent category (74%), which was predominantly normal vaginal flora throughout follow-up.

CONCLUSIONS: These data highlight the strong influence of sexual relationships and behaviors on BV acquisition and the vaginal microbiota. They provide epidemiological evidence to support exchange of vaginal bacterial species between women and the concept that BV is sexually transmitted.}, } @article {pmid25515028, year = {2015}, author = {Alexander, SA and de Bruin, A and Kornet, DJ}, title = {An alternative construction of internodons: the emergence of a multi-level tree of life.}, journal = {Bulletin of mathematical biology}, volume = {77}, number = {1}, pages = {23-45}, doi = {10.1007/s11538-014-0048-2}, pmid = {25515028}, issn = {1522-9602}, mesh = {Algorithms ; Animals ; Female ; *Genetic Speciation ; Male ; Mathematical Concepts ; Models, Genetic ; *Phylogeny ; }, abstract = {Internodons are a formalization of Hennig's concept of species. We present an alternative construction of internodons imposing a tree structure on the genealogical network. We prove that the segments (trivial unary trees) from this tree structure are precisely the internodons. We obtain the following spin-offs. First, the generated tree turns out to be an organismal tree of life. Second, this organismal tree is homeomorphic to the phylogenetic Hennigian species tree of life, implying the discovery of a multi-level tree of life: this phylogenetic tree can be obtained by zooming out from the organismal tree, or conversely, the organismal tree of life can be generated by expanding the phylogenetic nodes into unary trees. Finally, the definition of the organismal tree allows an efficient algorithmic transformation of a given genealogical network into its corresponding phylogenetic species tree of life. The latter will be presented in a separate paper.}, } @article {pmid25492987, year = {2014}, author = {Klaubauf, S and Tharreau, D and Fournier, E and Groenewald, JZ and Crous, PW and de Vries, RP and Lebrun, MH}, title = {Resolving the polyphyletic nature of Pyricularia (Pyriculariaceae).}, journal = {Studies in mycology}, volume = {79}, number = {}, pages = {85-120}, pmid = {25492987}, issn = {0166-0616}, abstract = {Species of Pyricularia (magnaporthe-like sexual morphs) are responsible for major diseases on grasses. Pyricularia oryzae (sexual morph Magnaporthe oryzae) is responsible for the major disease of rice called rice blast disease, and foliar diseases of wheat and millet, while Pyricularia grisea (sexual morph Magnaporthe grisea) is responsible for foliar diseases of Digitaria. Magnaporthe salvinii, M. poae and M. rhizophila produce asexual spores that differ from those of Pyricularia sensu stricto that has pyriform, 2-septate conidia produced on conidiophores with sympodial proliferation. Magnaporthe salvinii was recently allocated to Nakataea, while M. poae and M. rhizophila were placed in Magnaporthiopsis. To clarify the taxonomic relationships among species that are magnaporthe- or pyricularia-like in morphology, we analysed phylogenetic relationships among isolates representing a wide range of host plants by using partial DNA sequences of multiple genes such as LSU, ITS, RPB1, actin and calmodulin. Species of Pyricularia s. str. belong to a monophyletic clade that includes all P. oryzae/P. grisea isolates tested, defining the Pyriculariaceae, which is sister to the Ophioceraceae, representing two novel families. These clades are clearly distinct from species belonging to the Gaeumannomyces pro parte/Magnaporthiopsis/Nakataea generic complex that are monophyletic and define the Magnaporthaceae. A few magnaporthe- and pyricularia-like species are unrelated to Magnaporthaceae and Pyriculariaceae. Pyricularia oryzae/P. grisea isolates cluster into two related clades. Host plants such as Eleusine, Oryza, Setaria or Triticum were exclusively infected by isolates from P. oryzae, while some host plant such as Cenchrus, Echinochloa, Lolium, Pennisetum or Zingiber were infected by different Pyricularia species. This demonstrates that host range cannot be used as taxonomic criterion without extensive pathotyping. Our results also show that the typical pyriform, 2-septate conidium morphology of P. grisea/P. oryzae is restricted to Pyricularia and Neopyricularia, while most other genera have obclavate to more ellipsoid 2-septate conidia. Some related genera (Deightoniella, Macgarvieomyces) have evolved 1-septate conidia. Therefore, conidium morphology cannot be used as taxonomic criterion at generic level without phylogenetic data. We also identified 10 novel genera, and seven novel species. A re-evaluation of generic and species concepts within Pyriculariaceae is presented, and novelties are proposed based on morphological and phylogenetic data.}, } @article {pmid25492986, year = {2014}, author = {Damm, U and O'Connell, RJ and Groenewald, JZ and Crous, PW}, title = {The Colletotrichum destructivum species complex - hemibiotrophic pathogens of forage and field crops.}, journal = {Studies in mycology}, volume = {79}, number = {}, pages = {49-84}, pmid = {25492986}, issn = {0166-0616}, abstract = {Colletotrichum destructivum is an important plant pathogen, mainly of forage and grain legumes including clover, alfalfa, cowpea and lentil, but has also been reported as an anthracnose pathogen of many other plants worldwide. Several Colletotrichum isolates, previously reported as closely related to C. destructivum, are known to establish hemibiotrophic infections in different hosts. The inconsistent application of names to those isolates based on outdated species concepts has caused much taxonomic confusion, particularly in the plant pathology literature. A multilocus DNA sequence analysis (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 83 isolates of C. destructivum and related species revealed 16 clades that are recognised as separate species in the C. destructivum complex, which includes C. destructivum, C. fuscum, C. higginsianum, C. lini and C. tabacum. Each of these species is lecto-, epi- or neotypified in this study. Additionally, eight species, namely C. americae-borealis, C. antirrhinicola, C. bryoniicola, C. lentis, C. ocimi, C. pisicola, C. utrechtense and C. vignae are newly described.}, } @article {pmid25492983, year = {2014}, author = {Yilmaz, N and Visagie, CM and Houbraken, J and Frisvad, JC and Samson, RA}, title = {Polyphasic taxonomy of the genus Talaromyces.}, journal = {Studies in mycology}, volume = {78}, number = {}, pages = {175-341}, pmid = {25492983}, issn = {0166-0616}, abstract = {The genus Talaromyces was described by Benjamin in 1955 as a sexual state of Penicillium that produces soft walled ascomata covered with interwoven hyphae. Phylogenetic information revealed that Penicillium subgenus Biverticillium and Talaromyces form a monophyletic clade distinct from the other Penicillium subgenera. Subsequently, in combination with the recent adoption of the one fungus one name concept, Penicillium subgenus Biverticillium was transferred to Talaromyces. At the time, the new combinations were made based only on phylogenetic information. As such, the aim of this study was to provide a monograph on Talaromyces applying a polyphasic species concept, including morphological, molecular and physiological characters. Based on an ITS, BenA and RPB2 multigene phylogeny, we propose a new sectional classification for the genus, placing the 88 accepted species into seven sections, named sections Bacillispori, Helici, Islandici, Purpurei, Subinflati, Talaromyces and Trachyspermi. We provide morphological descriptions for each of these species, as well as notes on their identification using morphology and DNA sequences. For molecular identification, BenA is proposed as a secondary molecular marker to the accepted ITS barcode for fungi.}, } @article {pmid25476286, year = {2015}, author = {Yoo, SM and Kim, DK and Lee, SY}, title = {Aptamer-functionalized localized surface plasmon resonance sensor for the multiplexed detection of different bacterial species.}, journal = {Talanta}, volume = {132}, number = {}, pages = {112-117}, doi = {10.1016/j.talanta.2014.09.003}, pmid = {25476286}, issn = {1873-3573}, mesh = {Aptamers, Nucleotide/chemical synthesis/*chemistry ; Biosensing Techniques/*instrumentation/methods ; Colony Count, Microbial ; Lab-On-A-Chip Devices ; Lactobacillus acidophilus/*isolation & purification ; Limit of Detection ; Pseudomonas aeruginosa/*isolation & purification ; Salmonella typhimurium/*isolation & purification ; Surface Plasmon Resonance/*instrumentation ; }, abstract = {A localized surface plasmon resonance (LSPR)-based sensor with an immobilized aptamer ligand was developed and used for the label-free and accurate detection of bacteria through observing the changes in the peak extinction intensity. The ability of this biosensor to recognize pathogenic bacteria was analyzed and conditions were optimized with different probe concentrations, incubation time for aptamer immobilization, and incubation time for cell binding. A single LSPR-based sensor was used to successfully detect and identify three different bacterial species as proof-of-concept experiments; in all cases, the sensor showed a detection limit of 30 cfu per assay. Furthermore, the sensor system could clearly identify various target bacterial species in a multiplexed mode with high specificities on a single chip. The label-free bacteria sensor developed by combining LSPR and aptamers will be useful for diagnosing various infectious diseases through a single convenient assay.}, } @article {pmid25475367, year = {2015}, author = {Nagai, T and Taya, K}, title = {Estimation of herbicide species sensitivity distribution using single-species algal toxicity data and information on the mode of action.}, journal = {Environmental toxicology and chemistry}, volume = {34}, number = {3}, pages = {677-684}, doi = {10.1002/etc.2828}, pmid = {25475367}, issn = {1552-8618}, mesh = {Chlorophyta/*drug effects ; Herbicides/*toxicity ; Reproducibility of Results ; Species Specificity ; *Toxicity Tests ; United States ; United States Environmental Protection Agency ; }, abstract = {Although species sensitivity distribution (SSD) is a key concept for quantitative ecological risk assessment, its application is limited owing to a lack of sufficient data for the analysis, especially on the toxicity of herbicides for primary producers. The authors developed a method of herbicide SSD estimation using single-species toxicity data and information on the herbicide mode of action. The authors' method was based on 2 assumptions: the slopes of the SSD of the same MOA herbicides are the same and the relative sensitivities of standard algae in the SSD of the same MOA herbicides are the same. The 2 parameters of log-normal SSD, mean sensitivity, and variation in sensitivity, for 92 herbicides were determined to establish the estimation model. Mean sensitivities were linearly correlated with logarithmic 50% effect concentrations (EC50) for standard algae. The average of variations in sensitivity significantly differed among MOA, and variations in sensitivity were constant independently of EC50 values for standard algae for the same MOA herbicides. These results were all consistent with the assumptions of the SSD estimation method. The outcome was validated by comparing the estimated SSDs using the proposed method with the generated SSDs using toxicity data which were independent of method development. These SSDs were consistent, and considering MOA information improved the accuracy of estimating SSD markedly.}, } @article {pmid25467127, year = {2015}, author = {Hrček, J and Godfray, HC}, title = {What do molecular methods bring to host-parasitoid food webs?.}, journal = {Trends in parasitology}, volume = {31}, number = {1}, pages = {30-35}, doi = {10.1016/j.pt.2014.10.008}, pmid = {25467127}, issn = {1471-5007}, mesh = {*Food Chain ; *Host-Parasite Interactions ; Molecular Biology/*trends ; Parasitology/*trends ; Phylogeny ; Species Specificity ; }, abstract = {Quantitative food webs are valuable tools to detect patterns in community structure and generate hypotheses for experimentation. Quantitative webs of whole communities are usually not feasible to build, and most attention focuses on assemblages of species that interact in similar ways. Hosts and parasitoids are a popular guild for study, and quantitative webs have traditionally been constructed by collecting, rearing, and identifying large samples of individuals from the field. In the past decade molecular methods have begun to be used extensively in studies of host-parasitoid webs to clarify species concepts. We review how this rapidly developing field is using molecular information to detect cryptic interactions between species and to increase our understanding of the phylogenetic and mechanistic processes which structure food webs.}, } @article {pmid25454211, year = {2014}, author = {Grandcolas, P and Nattier, R and Trewick, S}, title = {Relict species: a relict concept?.}, journal = {Trends in ecology & evolution}, volume = {29}, number = {12}, pages = {655-663}, doi = {10.1016/j.tree.2014.10.002}, pmid = {25454211}, issn = {1872-8383}, mesh = {Animals ; *Biodiversity ; *Biological Evolution ; *Extinction, Biological ; *Fossils ; Magnoliopsida/*genetics ; *Phylogeny ; Phylogeography ; Reptiles/*genetics ; }, abstract = {Relict species have always beguiled evolutionary biologists and biogeographers, who often view them as fascinating 'living fossils' or remnants of old times. Consequently, they are believed to provide interesting and important information on a vanished past and are used to understand the evolution of clades and biotas. The information that relicts provide can, however, be misleading and overemphasised when it is not remembered that they belong to groups or biotas that are mostly extinct. For example, relict species imply regional extinctions and, for this reason, they cannot simultaneously provide evidence of local biota permanence. Here we consider carefully misconceptions about relict species and highlight more clearly their evolutionary and biogeographical significance.}, } @article {pmid25453263, year = {2015}, author = {Andersson, KE}, title = {Potential of stem cell treatment in detrusor dysfunction.}, journal = {Advanced drug delivery reviews}, volume = {82-83}, number = {}, pages = {117-122}, doi = {10.1016/j.addr.2014.10.017}, pmid = {25453263}, issn = {1872-8294}, mesh = {Animals ; Humans ; Stem Cell Transplantation/*methods ; Tissue Engineering/methods ; Urinary Bladder/*surgery ; Urinary Bladder Neck Obstruction/*surgery ; Urinary Bladder, Overactive/*surgery ; }, abstract = {The current treatments of bladder dysfunctions, such as bladder overactivity and impaired ability to empty, have limitations, and new treatment alternatives are needed. Stem cell transplantation and tissue engineering have shown promising results in preclinical studies. Stem cells were originally thought to act by differentiating into various cell types, thereby replacing damaged cells and restoring functional deficits. Even if such a mechanism cannot be excluded, the current belief is that a main action is exerted by the stem cells secreting bioactive factors that direct other stem cells to the target organ. In addition, stem cells may exert a number of other effects that can improve bladder dysfunction, since they may have antiapoptotic, antifibrotic, and immunomodulatory properties, and can induce neovascularization. Tissue engineering for bladder replacement, which has had varying success in different animal species, has reached the proof-of-concept state in humans, but recent research suggests that the present approaches may not be optimal. Further studies on new approaches, using animal models with translational predictability, seem necessary for further progress.}, } @article {pmid25451802, year = {2015}, author = {Mercês, MP and Lynch Alfaro, JW and Ferreira, WA and Harada, ML and Silva Júnior, JS}, title = {Morphology and mitochondrial phylogenetics reveal that the Amazon River separates two eastern squirrel monkey species: Saimiri sciureus and S. collinsi.}, journal = {Molecular phylogenetics and evolution}, volume = {82 Pt B}, number = {}, pages = {426-435}, doi = {10.1016/j.ympev.2014.09.020}, pmid = {25451802}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Brazil ; DNA, Mitochondrial/*genetics ; Female ; Male ; *Phylogeny ; Rivers ; Saimiri/anatomy & histology/*classification/genetics ; Sequence Analysis, DNA ; Skull/anatomy & histology ; }, abstract = {Saimiri has a complicated taxonomic history, and there is continuing disagreement about the number of valid taxa. Despite these controversies, one point of consensus among morphologists has been that the eastern Amazonian populations of squirrel monkeys form a single terminal taxon, Saimiri sciureus sciureus (Linnaeus, 1758). This group is distributed to both the north and south of the middle to lower Amazon River and in the Marajó Archipelago. However, a recent molecular study by Lavergne and colleagues suggested that the Saimiri sciureus complex (comprised of S. s. sciureus sensu lato, S. s. albigena, S. s. macrodon, and S. s. cassiquiarensis) was paraphyletic. The discordance between morphological and molecular studies prompted us to conduct a new multidisciplinary analysis, employing a combination of morphological, morphometric, and molecular markers. Our results suggest the currently recognized taxon S. s. sciureus contains two distinct species, recognized by the Phylogenetic Species Concept: Saimiri sciureus (Linnaeus, 1758) and Saimiri collinsi Osgood, 1916. East Amazonian squirrel monkeys north of the Amazon have a gray crown (S. sciureus), and south of the Amazon, the crown is yellow (S. collinsi). Morphometric measurements also clearly distinguish between the two species, with the most important contributing factors including width across upper canines for both sexes. For males, the mean zygomatic breadth was significantly wider in S. sciureus compared to S. collinsi, and for females, the width across the upper molars was wider in S. sciureus compared to S. collinsi. Mitochondrial phylogenetic analyses support this separation of the eastern Amazonian squirrel monkeys into two distinct taxa, recovering one clade (S. sciureus) distributed to the north of the Amazon River, from the Negro River and Branco River to the Guiana coast and the Brazilian state of Amapá, and another clade (S. collinsi) south of the Amazon River, from the region of the Tapajós River to the state of Maranhão, as well as within the Marajó Archipelago. The revalidation of the species S. collinsi was corroborated by all of the methods in the study, as the clades recovered in our molecular study are congruent with the pattern of morphological variation. We confirm both the paraphyly of the Saimiri sciureus complex and the paraphyly of the subspecies S. s. sciureus as defined in the current literature.}, } @article {pmid25449950, year = {2015}, author = {Palinauskas, V and Žiegytė, R and Ilgūnas, M and Iezhova, TA and Bernotienė, R and Bolshakov, C and Valkiūnas, G}, title = {Description of the first cryptic avian malaria parasite, Plasmodium homocircumflexum n. sp., with experimental data on its virulence and development in avian hosts and mosquitoes.}, journal = {International journal for parasitology}, volume = {45}, number = {1}, pages = {51-62}, doi = {10.1016/j.ijpara.2014.08.012}, pmid = {25449950}, issn = {1879-0135}, mesh = {Aedes ; Animal Structures/pathology ; Animals ; Birds ; Cluster Analysis ; Culex ; Culicidae/*parasitology ; Cytochromes b/genetics ; Cytological Techniques ; DNA, Protozoan/chemistry/genetics ; Malaria, Avian/*parasitology/pathology ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeography ; Plasmodium/*classification/genetics/*isolation & purification/physiology ; Protozoan Proteins/genetics ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {For over 100 years studies on avian haemosporidian parasite species have relied on similarities in their morphology to establish a species concept. Some exceptional cases have also included information about the life cycle and sporogonic development. More than 50 avian Plasmodium spp. have now been described. However, PCR-based studies show a much broader diversity of haemosporidian parasites, indicating the possible existence of a diverse group of cryptic species. In the present study, using both similarity and phylogenetic species definition concepts, we believe that we report the first characterised cryptic speciation case of an avian Plasmodium parasite. We used sequence information on the mitochondrial cytochrome b gene and constructed phylogenies of identified Plasmodium spp. to define their position in the phylogenetic tree. After analysis of blood stages, the morphology of the parasite was shown to be identical to Plasmodium circumflexum. However, the geographic distribution of the new parasite, the phylogenetic information, as well as patterns of development of infection, indicate that this parasite differs from P. circumflexum. Plasmodium homocircumflexum n. sp. was described based on information about genetic differences from described lineages, phylogenetic position and biological characters. This parasite develops parasitemia in experimentally infected birds - the domestic canary Serinus canaria domestica, siskin Carduelis spinus and crossbill Loxia curvirostra. Anaemia caused by high parasitemia, as well as cerebral paralysis caused by exoerythrocytic stages in the brain, are the main reasons for mortality. Exoerythrocytic stages also form in other organs (heart, kidneys, liver, lungs, spleen, intestines and pectoral muscles). DNA amplification was unsuccessful from faecal samples of heavily infected birds. The sporogonic development initiates, but is abortive, at the oocyst stage in two common European mosquito species, Culex pipiens pipiens (forms pipiens and molestus) and Aedes vexans. Vectors of this Plasmodium sp. remain unknown.}, } @article {pmid25446938, year = {2015}, author = {Clauss, M and Steuer, P and Erlinghagen-Lückerath, K and Kaandorp, J and Fritz, J and Südekum, KH and Hummel, J}, title = {Faecal particle size: digestive physiology meets herbivore diversity.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {179}, number = {}, pages = {182-191}, doi = {10.1016/j.cbpa.2014.10.006}, pmid = {25446938}, issn = {1531-4332}, mesh = {Animals ; Animals, Domestic/physiology ; Body Weight ; *Digestive System Physiological Phenomena ; Feces/*chemistry ; Herbivory/*physiology ; Linear Models ; *Particle Size ; Regression Analysis ; }, abstract = {In herbivore ecophysiology, comparative chewing efficiency has only recently received increased attention. This measure is best assessed on un-processed forage-only diets; corresponding comparative datasets are missing. We measured a faecal mean particle size (MPS [mm]) in 14 large herbivore species (body mass (M) range 60–4000 kg; 8 ruminants and 6 hindgut fermenters) fed a consistent grass hay diet, in which intake, digesta mean retention times (MRT [h]) and digestive efficiency (as digestibility of faecal fibre measured by 96 h cumulative in vitro gas production GP96h [ml per 200 mg faecal fibre], and metabolic faecal nitrogen MFN [% organic faecal matter]) had been quantified simultaneously. MPS was generally lower in ruminants than in hindgut fermenters and increased with M in the total dataset, but was nearly constant among closely related taxa (e.g. within ruminants, within equids) irrespective of M. MPS (but not MRT) was significantly correlated to GP96h, whereas MRT (but not MPS) was significantly correlated to MFN, suggesting different effects of these factors on different aspects of digestibility. Combinations of measures including MPS mostly explained digestibility better than other combinations. The phylogenetic signal λ, which was mostly 1 when linking any single measure to digestibility, was estimated 0 in models that linked digestive efficiency to combinations of measures. These results support the intuitive concept that species diversification in large herbivores is tightly related to digestive physiology, and that chewing efficiency as measured by faecal particle size is an integral aspect of this scenario.}, } @article {pmid25440521, year = {2015}, author = {Lymbery, AJ and Jenkins, EJ and Schurer, JM and Thompson, RC}, title = {Echinococcus canadensis, E. borealis, and E. intermedius. What's in a name?.}, journal = {Trends in parasitology}, volume = {31}, number = {1}, pages = {23-29}, doi = {10.1016/j.pt.2014.11.003}, pmid = {25440521}, issn = {1471-5007}, mesh = {Animals ; *Classification ; Echinococcus/*classification/genetics ; *Genetic Variation ; Genotype ; Species Specificity ; *Terminology as Topic ; }, abstract = {The phylogenetic relationships of the G6, G7, G8, and G10 genotypes of Echinococcus granulosus are well defined, but their taxonomic status is currently unresolved. We apply an evolutionary species concept to infer that the G6 and G7 genotypes represent a single species that is different to both the G8 and G10 genotypes, and that the G8 and G10 genotypes are also on different evolutionary trajectories and, therefore, should be regarded as separate species. The names Echinococcus intermedius, Echinococcus canadensis, and Echinococcus borealis have been previously proposed for these three taxa (G6/7, G10 and G8, respectively) and we argue that it may be appropriate to resurrect these names. The correct delimitation and formal recognition of species of Echinococcus may have important veterinary and public health consequences.}, } @article {pmid25437612, year = {2014}, author = {Peggion, C and Sorgato, MC and Bertoli, A}, title = {Prions and prion-like pathogens in neurodegenerative disorders.}, journal = {Pathogens (Basel, Switzerland)}, volume = {3}, number = {1}, pages = {149-163}, pmid = {25437612}, issn = {2076-0817}, abstract = {Prions are unique elements in biology, being able to transmit biological information from one organism to another in the absence of nucleic acids. They have been identified as self-replicating proteinaceous agents responsible for the onset of rare and fatal neurodegenerative disorders-known as transmissible spongiform encephalopathies, or prion diseases-which affect humans and other animal species. More recently, it has been proposed that other proteins associated with common neurodegenerative disorders, such as Alzheimer's and Parkinson's disease, can self-replicate like prions, thus sustaining the spread of neurotoxic entities throughout the nervous system. Here, we review findings that have contributed to expand the prion concept, and discuss if the involved toxic species can be considered bona fide prions, including the capacity to infect other organisms, or whether these pathogenic aggregates share with prions only the capability to self-replicate.}, } @article {pmid28510922, year = {2014}, author = {Purvis, OW}, title = {Adaptation and interaction of saxicolous crustose lichens with metals.}, journal = {Botanical studies}, volume = {55}, number = {1}, pages = {23}, pmid = {28510922}, issn = {1817-406X}, abstract = {One of the most successful mechanisms enabling fungi to survive in extreme subaerial environments is by formation of mutualistic symbioses with algae and/or cyanobacteria as lichens. Collections, field and mineral weathering studies and developments in modern instrumental and analytical techniques have considerably advanced knowledge in understanding tolerance mechanisms to stress, environmental adaptation, species concepts and evolutionary processes in lichens colonising metalliferous habitats. This review focuses on the predominantly saxicolous, crustose, taxonomically notoriously challenging Acarospora sens. lat. Pioneering studies investigating element and substance localization in Acarospora sens. lat. in different geological terrains led to the discovery of novel fixation mechanisms, new minerals and substances associated with lichens, and new taxa and evolutionary lineages. Acarospora sens. lat. are generally under-represented in collections. Systematic sampling of Acarospora sens. lat. and other saxicolous lichens, in different mineralogical environments is now required, a priority being those occurring in extreme habitats at risk from climatic and other environmental changes. The potential for the discovery of new lichen and mineral species associated with Acarospora and other saxicolous crustose lichens, is high. These may represent special mechanisms to tolerate metal toxicity and other forms of environmental stress, including photoprotection.}, } @article {pmid25420573, year = {2015}, author = {Schwarzmüller, F and Eisenhauer, N and Brose, U}, title = {'Trophic whales' as biotic buffers: weak interactions stabilize ecosystems against nutrient enrichment.}, journal = {The Journal of animal ecology}, volume = {84}, number = {3}, pages = {680-691}, doi = {10.1111/1365-2656.12324}, pmid = {25420573}, issn = {1365-2656}, mesh = {Animals ; Arthropods/metabolism ; *Biodiversity ; Biomass ; Competitive Behavior ; *Ecosystem ; Eutrophication ; *Food Chain ; Oligochaeta/metabolism ; Predatory Behavior ; Soil Microbiology ; }, abstract = {Human activities may compromise biodiversity if external stressors such as nutrient enrichment endanger overall network stability by inducing unstable dynamics. However, some ecosystems maintain relatively high diversity levels despite experiencing continuing disturbances. This indicates that some intrinsic properties prevent unstable dynamics and resulting extinctions. Identifying these 'ecosystem buffers' is crucial for our understanding of the stability of ecosystems and an important tool for environmental and conservation biologists. In this vein, weak interactions have been suggested as stabilizing elements of complex systems, but their relevance has rarely been tested experimentally. Here, using network and allometric theory, we present a novel concept for a priori identification of species that buffer against externally induced instability of increased population oscillations via weak interactions. We tested our model in a microcosm experiment using a soil food-web motif. Our results show that large-bodied species feeding at the food web's base, so called 'trophic whales', can buffer ecosystems against unstable dynamics induced by nutrient enrichment. Similar to the functionality of chemical or mechanical buffers, they serve as 'biotic buffers' that take up stressor effects and thus protect fragile systems from instability. We discuss trophic whales as common functional building blocks across ecosystems. Considering increasing stressor effects under anthropogenic global change, conservation of these network-intrinsic biotic buffers may help maintain the stability and diversity of natural ecosystems.}, } @article {pmid25402812, year = {2015}, author = {Azevedo, MA}, title = {Health as a clinic-epidemiological concept.}, journal = {Journal of evaluation in clinical practice}, volume = {21}, number = {3}, pages = {365-373}, doi = {10.1111/jep.12279}, pmid = {25402812}, issn = {1365-2753}, mesh = {Disease ; *Health ; Humans ; Models, Theoretical ; *Philosophy, Medical ; Physiology ; }, abstract = {I propose a clinic-epidemiological concept of health as the best description of what physicians actually think about health within medical practice. Its aim is to be an alternative to the best approach in the philosophy of medicine about health, Christopher Boorse's biostatistical theory. Contrary to Boorse's 'theoretical' approach, I propose to take health as a practical clinical concept. In the first two parts of the paper, I will present my complaints against Boorse's view that health is a theoretical concept, a 'species normal functional ability'. I will claim that Boorse's view is actually a view on normal physiology. My claim is that health is best described as the state of absence of chronic diseases or disabilities (clinic-epidemiologically associated with a morbimortality index higher than the risk of death, disease and disabilities for individuals of the same population group or reference class free of that chronic clinical conditions). Health, therefore, is not the mere absence of disease. Diseases that do not increase patients' morbimortality and disability indexes are not incompatible with health; after all, clinical health is compatible with appropriate health care and medical treatments.}, } @article {pmid25398876, year = {2015}, author = {Vivet-Boudou, V and Isel, C and El Safadi, Y and Smyth, RP and Laumond, G and Moog, C and Paillart, JC and Marquet, R}, title = {Evaluation of anti-HIV-1 mutagenic nucleoside analogues.}, journal = {The Journal of biological chemistry}, volume = {290}, number = {1}, pages = {371-383}, pmid = {25398876}, issn = {1083-351X}, mesh = {Anti-HIV Agents/*chemistry/metabolism/pharmacology ; Base Pair Mismatch ; Base Pairing ; Base Sequence ; Deoxycytidine/analogs & derivatives/chemistry/metabolism/pharmacology ; Drug Design ; HIV Reverse Transcriptase/antagonists & inhibitors/chemistry/*genetics ; HIV-1/drug effects/enzymology/*genetics ; High-Throughput Screening Assays/*economics ; Molecular Sequence Data ; Mutagenesis ; Mutagens/*chemistry/metabolism/pharmacology ; Nucleic Acid Denaturation ; Predictive Value of Tests ; Reverse Transcriptase Inhibitors/*chemistry/metabolism/pharmacology ; Reverse Transcription ; Thermodynamics ; Thymidine/analogs & derivatives/chemistry/metabolism/pharmacology ; Time Factors ; }, abstract = {Because of their high mutation rates, RNA viruses and retroviruses replicate close to the threshold of viability. Their existence as quasi-species has pioneered the concept of "lethal mutagenesis" that prompted us to synthesize pyrimidine nucleoside analogues with antiviral activity in cell culture consistent with an accumulation of deleterious mutations in the HIV-1 genome. However, testing all potentially mutagenic compounds in cell-based assays is tedious and costly. Here, we describe two simple in vitro biophysical/biochemical assays that allow prediction of the mutagenic potential of deoxyribonucleoside analogues. The first assay compares the thermal stabilities of matched and mismatched base pairs in DNA duplexes containing or not the nucleoside analogues as follows. A promising candidate should display a small destabilization of the matched base pair compared with the natural nucleoside and the smallest gap possible between the stabilities of the matched and mismatched base pairs. From this assay, we predicted that two of our compounds, 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine, should be mutagenic. The second in vitro reverse transcription assay assesses DNA synthesis opposite nucleoside analogues inserted into a template strand and subsequent extension of the newly synthesized base pairs. Once again, only 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine are predicted to be efficient mutagens. The predictive potential of our fast and easy first line screens was confirmed by detailed analysis of the mutation spectrum induced by the compounds in cell culture because only compounds 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine were found to increase the mutation frequency by 3.1- and 3.4-fold, respectively.}, } @article {pmid25365338, year = {2014}, author = {Fodor, A and Segura, V and Denis, M and Neuenschwander, S and Fournier-Level, A and Chatelet, P and Homa, FA and Lacombe, T and This, P and Le Cunff, L}, title = {Genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e110436}, pmid = {25365338}, issn = {1932-6203}, mesh = {*Biodiversity ; Biological Evolution ; Breeding ; Computer Simulation ; Genetic Association Studies ; *Genome-Wide Association Study ; *Heterozygote ; Linkage Disequilibrium ; Models, Genetic ; Models, Statistical ; Phenotype ; Quantitative Trait Loci ; Quantitative Trait, Heritable ; Reproducibility of Results ; *Selection, Genetic ; Vitis/genetics ; }, abstract = {Nowadays, genome-wide association studies (GWAS) and genomic selection (GS) methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9) using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.}, } @article {pmid25356840, year = {2014}, author = {Handy, SM and Chizhikov, V and Yakes, BJ and Paul, SZ and Deeds, JR and Mossoba, MM}, title = {Microarray chip development using infrared imaging for the identification of catfish species.}, journal = {Applied spectroscopy}, volume = {68}, number = {12}, pages = {1365-1373}, doi = {10.1366/14-07505}, pmid = {25356840}, issn = {1943-3530}, mesh = {Animals ; Catfishes/*classification/*genetics ; DNA/analysis/*genetics ; Equipment Design ; Equipment Failure Analysis ; Oligonucleotide Array Sequence Analysis/*instrumentation ; Reproducibility of Results ; Sensitivity and Specificity ; Species Specificity ; Spectrophotometry, Infrared/*instrumentation ; }, abstract = {Several families of catfish species are extensively aquacultured around the world; however, only those from the family Ictaluridae can be labeled as catfish in the United States. Non-Ictalurid catfish species that are marketed as "catfish" in the USA are considered misbranded. Misbranding in general has led to an increased interest in developing deoxyribonucleic acid (DNA)-based methods such as DNA barcoding, polymerase chain reaction restriction fragment length polymorphism, and DNA microarrays with fluorescence detection for the identification of fish species. In this proof-of-concept study, DNA microarrays coupled with a newly developed mid-infrared imaging detection method were applied to the identification of seven species of catfish for the first time. Species-specific DNA probes targeting three regions per species of the cytochrome c oxidase 1 (barcoding) gene were developed and printed as microarrays on glass slides. Deoxyribonucleic acid targets labeled with biotin were hybridized to their complementary probes using a strategy that allowed the selective formation of a silver layer on hybridized spots needed for detection. Using this three-probe format, the seven species were all identified correctly, even when a limited number of false positive spots were observed. Raman spectroscopy was employed to further characterize the arrays.}, } @article {pmid25348174, year = {2015}, author = {Ruiz-García, M and Luengas-Villamil, K and Leguizamon, N and de Thoisy, B and Gálvez, H}, title = {Molecular phylogenetics and phylogeography of all the Saimiri taxa (Cebidae, Primates) inferred from mt COI and COII gene sequences.}, journal = {Primates; journal of primatology}, volume = {56}, number = {2}, pages = {145-161}, pmid = {25348174}, issn = {1610-7365}, mesh = {Animals ; Electron Transport Complex IV/genetics/metabolism ; *Hybridization, Genetic ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; *Phylogeny ; Phylogeography ; Saimiri/*genetics/metabolism ; Sequence Analysis, DNA ; South Africa ; }, abstract = {Some previous genetic studies have been performed to resolve the molecular phylogenetics of the squirrel monkeys (Saimiri). However, these studies did not show consensus in how many taxa are within this genus and what the relationships among them are. For this reason, we sequenced 2,237 base pairs of the mt COI and COII genes in 218 Saimiri individuals. All, less 12 S. sciureus sciureus from French Guyana, were sampled in the wild. These samples represented all the living Saimiri taxa recognized. There were four main findings of this study. (1) Our analysis detected 17 different Saimiri groups: albigena, cassiquiarensis, five polyphyletic macrodon groups, three polyphyletic ustus groups, sciureus, collinsi, boliviensis, peruviensis, vanzolinii, oerstedii and citrinellus. Four different phylogenetic trees showed the Central American squirrel monkey (S. oerstedii) as the most differentiated taxon. In contrast, albigena was indicated to be the most recent taxon. (2) There was extensive hybridization and/or historical introgression among albigena, different macrodon groups, peruviensis, sciureus and collinsi. (3) Different tests showed that our maximum likelihood tree was consistent with two species of Saimiri: S. oerstedii and S. sciureus. If no cases of hybridization were detected implicating S. vanzolinii, this could be a third recognized species. (4) We also estimated that the first temporal splits within this genus occurred around 1.4-1.6 million years ago, which indicates that the temporal split events within Saimiri were correlated with Pleistocene climatic changes. If the biological species concept is applied because, in this case, it is operative due to observed hybridization in the wild, the number of species within this genus is probably more limited than recently proposed by other authors. The Pleistocene was the fundamental epoch when the mitochondrial Saimiri diversification process occurred.}, } @article {pmid25337810, year = {2014}, author = {Alemán Resto, Y and Fernández Robledo, JA}, title = {Identification of MMV Malaria Box inhibitors of Perkinsus marinus using an ATP-based bioluminescence assay.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e111051}, pmid = {25337810}, issn = {1932-6203}, support = {R21 AI076797/AI/NIAID NIH HHS/United States ; 1R21AI076797-01A2/AI/NIAID NIH HHS/United States ; }, mesh = {Alveolata/*drug effects ; Animals ; Antiprotozoal Agents/*pharmacology ; Aquaculture ; Drug Discovery ; Inhibitory Concentration 50 ; Luminescent Measurements ; Ostreidae/*parasitology ; }, abstract = {"Dermo" disease caused by the protozoan parasite Perkinsus marinus (Perkinsozoa) is one of the main obstacles to the restoration of oyster populations in the USA. Perkinsus spp. are also a concern worldwide because there are limited approaches to intervention against the disease. Based on the phylogenetic affinity between the Perkinsozoa and Apicomplexa, we exposed Perkinsus trophozoites to the Medicines for Malaria Venture Malaria Box, an open access compound library comprised of 200 drug-like and 200 probe-like compounds that are highly active against the erythrocyte stage of Plasmodium falciparum. Using a final concentration of 20 µM, we found that 4 days after exposure 46% of the compounds were active against P. marinus trophozoites. Six compounds with IC50 in the µM range were used to compare the degree of susceptibility in vitro of eight P. marinus strains from the USA and five Perkinsus species from around the world. The three compounds, MMV666021, MMV665807 and MMV666102, displayed a uniform effect across Perkinsus strains and species. Both Perkinsus marinus isolates and Perkinsus spp. presented different patterns of response to the panel of compounds tested, supporting the concept of strain/species variability. Here, we expanded the range of compounds available for inhibiting Perkinsus proliferation in vitro and characterized Perkinsus phenotypes based on their resistance to six compounds. We also discuss the implications of these findings in the context of oyster management. The Perkinsus system offers the potential for investigating the mechanism of action of the compounds of interest.}, } @article {pmid25325751, year = {2014}, author = {Hui, C and McGeoch, MA}, title = {Zeta diversity as a concept and metric that unifies incidence-based biodiversity patterns.}, journal = {The American naturalist}, volume = {184}, number = {5}, pages = {684-694}, doi = {10.1086/678125}, pmid = {25325751}, issn = {1537-5323}, mesh = {*Biodiversity ; *Ecosystem ; Models, Theoretical ; Stochastic Processes ; }, abstract = {Patterns in species incidence and compositional turnover are central to understanding what drives biodiversity. Here we propose zeta (ζ) diversity, the number of species shared by multiple assemblages, as a concept and metric that unifies incidence-based diversity measures, patterns, and relationships. Unlike other measures of species compositional turnover, zeta diversity partitioning quantifies the complete set of diversity components for multiple assemblages, comprehensively representing the spatial structure of multispecies distributions. To illustrate the application and ecological value of zeta diversity, we show how it scales with sample number, grain, and distance. Zeta diversity reconciles several different biodiversity patterns, including the species accumulation curve, the species-area relationship, multispecies occupancy patterns, and scaling of species endemism. Exponential and power-law forms of zeta diversity are associated with stochastic versus niche assembly processes. Zeta diversity may provide new insights on biodiversity patterns, the processes driving them, and their response to environmental change.}, } @article {pmid25325742, year = {2014}, author = {Sobel, JM}, title = {Ecogeographic isolation and speciation in the genus Mimulus.}, journal = {The American naturalist}, volume = {184}, number = {5}, pages = {565-579}, doi = {10.1086/678235}, pmid = {25325742}, issn = {1537-5323}, mesh = {*Ecosystem ; *Genetic Speciation ; *Geography ; Mimulus/*genetics ; Phylogeny ; *Reproductive Isolation ; }, abstract = {Despite a long history of examining the geographic context of speciation, differences in geographic range have rarely been considered a legitimate isolating mechanism. This likely results from the complex relationship between historical and ecological processes in determining the spatial distribution of species. Ecogeographic isolation is the proportion of geographic isolation that results from genetically based ecological differences between taxa and should therefore be measured as an isolating mechanism under the biological species concept. In this study, species distribution modeling was used to evaluate the potential ranges of 12 recently diverged pairs of species in the genus Mimulus. Variation in the distribution models showed that these species differ significantly in the niches they occupy. These differences result in substantial ecogeographic isolation, with an average strength of 0.67, revealing that, on average, Mimulus species exhibit only 33% overlap in the extent of suitable habitat with their closest relatives. Because prezygotic barriers act early in the life cycle of organisms, this strong barrier has the potential to contribute greatly to the total isolation experienced between diverging species. Therefore, ecogeographic isolation appears to play an important role in Mimulus, and estimating the strength of this barrier is essential to our general understanding of speciation.}, } @article {pmid25292282, year = {2015}, author = {López-Sepúlveda, P and Takayama, K and Greimler, J and Crawford, DJ and Peñailillo, P and Baeza, M and Ruiz, E and Kohl, G and Tremetsberger, K and Gatica, A and Letelier, L and Novoa, P and Novak, J and Stuessy, TF}, title = {Progressive migration and anagenesis in Drimys confertifolia of the Juan Fernández Archipelago, Chile.}, journal = {Journal of plant research}, volume = {128}, number = {1}, pages = {73-90}, pmid = {25292282}, issn = {1618-0860}, support = {P 21723/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amplified Fragment Length Polymorphism Analysis ; Chile ; Drimys/*genetics ; *Genetic Speciation ; Genetic Variation ; Genetics, Population ; Geography ; *Islands ; Microsatellite Repeats/genetics ; Models, Biological ; Phylogeny ; }, abstract = {A common mode of speciation in oceanic islands is by anagenesis, wherein an immigrant arrives and through time transforms by mutation, recombination, and drift into a morphologically and genetically distinct species, with the new species accumulating a high level of genetic diversity. We investigate speciation in Drimys confertifolia, endemic to the two major islands of the Juan Fernández Archipelago, Chile, to determine genetic consequences of anagenesis, to examine relationships among populations of D. confertifolia and the continental species D. winteri and D. andina, and to test probable migration routes between the major islands. Population genetic analyses were conducted using AFLPs and nuclear microsatellites of 421 individuals from 42 populations from the Juan Fernández islands and the continent. Drimys confertifolia shows a wide genetic variation within populations on both islands, and values of genetic diversity within populations are similar to those found within populations of the continental progenitor. The genetic results are compatible with the hypothesis of high levels of genetic variation accumulating within anagenetically derived species in oceanic islands, and with the concept of little or no geographical partitioning of this variation over the landscape. Analysis of the probability of migration within the archipelago confirms colonization from the older island, Robinson Crusoe, to the younger island Alejandro Selkirk.}, } @article {pmid25283659, year = {2014}, author = {Hodda, M and Collins, SJ and Vanstone, VA and Hartley, D and Wanjura, W and Kehoe, M}, title = {Pratylenchus quasitereoides n. sp. from cereals in Western Australia.}, journal = {Zootaxa}, volume = {3866}, number = {2}, pages = {277-288}, doi = {10.11646/zootaxa.3866.2.6}, pmid = {25283659}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Body Size ; Edible Grain/parasitology ; Female ; Male ; Molecular Sequence Data ; Organ Size ; Phylogeny ; Plant Diseases/*parasitology ; Tylenchoidea/anatomy & histology/*classification/genetics/growth & development ; }, abstract = {Pratylenchus quasitereoides n. sp. is described from Western Australia. It is characterized by 2 external incisures in the head cuticle, 4 lateral incisures at mid body, stylet length 17 µm to 19 µm, V greater than 75%, PUS less than 2 body diameters long and crenate tail terminus. Molecular data confirm the separation of the new species from morphologically similar and sympatric congeners. The host range also differs from P. teres as well as the sympatric P. neglectus, P. thornei and P. penetrans. Reproduction rates on oat and lupin differed between the new species and P. neglectus. The species was originally described as P. teres, but the species concept of P. teres now encompasses a considerable range of different attributes spread over two described subspecies and three variant populations. The new species differs from all these subspecies and populations in at least two characters. It differs from all populations of P. teres teres most notably in having four rather than 6 lateral lines and a more posterior vulva. It differs from P. teres vandebergae in having a longer stylet and longer overlap of the intestine by the oesophageal glands. Characters which can be used under low magnification to separate the new species from the closest sympatric congeners (P. thornei and P. crenatus) are discussed.}, } @article {pmid25283058, year = {2015}, author = {Rodriguez-Cuenca, S and Barbarroja, N and Vidal-Puig, A}, title = {Dihydroceramide desaturase 1, the gatekeeper of ceramide induced lipotoxicity.}, journal = {Biochimica et biophysica acta}, volume = {1851}, number = {1}, pages = {40-50}, doi = {10.1016/j.bbalip.2014.09.021}, pmid = {25283058}, issn = {0006-3002}, support = {G0600717/MRC_/Medical Research Council/United Kingdom ; RG/12/13/29853/BHF_/British Heart Foundation/United Kingdom ; MC_UU_12012/2/MRC_/Medical Research Council/United Kingdom ; G0802051/MRC_/Medical Research Council/United Kingdom ; MC_UU_12012/5/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Ceramides/*metabolism ; Glycosphingolipids/*metabolism ; Humans ; Hypoxia/metabolism ; Inflammation/metabolism ; Oxidative Stress/physiology ; Oxidoreductases/*metabolism ; Sphingolipids/*metabolism ; }, abstract = {The pathogenic relevance of sphingolipid metabolism is increasingly being recognised. Here we elaborate on a new player within the sphingolipid field: the degs1 enzyme, a recently discovered enzyme that catalyses the final step in the de novo biosynthesis of ceramides controlling the step from dihydroceramides to ceramides. Here, we describe its function and dysregulation by factors such as oxidative stress, hypoxia and inflammation and provide evidence indicating that dihydroceramides constitute a biologically active molecule from the sphingolipid family with certain differential characteristics with respect to its delta-4 unsaturated counterparts, the ceramides. Finally we present pathophysiological scenarios characterised by specific increases in dihydroceramide that challenge the concept that "all ceramides species are the same". This article is part of a Special Issue entitled Linking transcription to physiology in lipodomics.}, } @article {pmid26988643, year = {2014}, author = {Niwa, K and Kobiyama, A}, title = {Speciation in the marine crop Pyropia yezoensis (Bangiales, Rhodophyta).}, journal = {Journal of phycology}, volume = {50}, number = {5}, pages = {897-900}, doi = {10.1111/jpy.12220}, pmid = {26988643}, issn = {1529-8817}, abstract = {In the marine red alga Pyropia yezoensis, commonly known in Japan as nori, sympatric occurrence of two cryptic species Pyropia sp. 2 and Pyropia sp. 3 on the same rock in a natural habitat has been confirmed by molecular analysis and detailed morphological observations. To confirm whether Pyropia sp. 2 and Pyropia sp. 3 were reproductively isolated in the sympatric population, 170 blades that had previously been studied using a maternally inherited plastid marker were examined with a nuclear gene marker. The results suggested that Pyropia sp. 2 and Pyropia sp. 3 with identical morphological features were reproductively isolated in the sympatric population and that they were different species based on the biological species concept. Although gametophytic blades of Pyropia were usually assumed to be haploid, 18 of 170 blades possessed both of the two genotypes derived from Pyropia sp. 2 and from Pyropia sp. 3. These results inferred that allodiploid blades were generated from the interspecific hybridization between these two cryptic species. The present findings provide insights for future studies on the speciation mechanism in seaweeds, particularly for genera that contain numerous species.}, } @article {pmid25264388, year = {2014}, author = {Morozova, OV and Noordeloos, ME and Vila, J}, title = {Entoloma subgenus Leptonia in boreal-temperate Eurasia: towards a phylogenetic species concept.}, journal = {Persoonia}, volume = {32}, number = {}, pages = {141-169}, pmid = {25264388}, issn = {0031-5850}, abstract = {This study reveals the concordance, or lack thereof, between morphological and phylogenetic species concepts within Entoloma subg. Leptonia in boreal-temperate Eurasia, combining a critical morphological examination with a multigene phylogeny based on nrITS, nrLSU and mtSSU sequences. A total of 16 taxa was investigated. Emended concepts of subg. Leptonia and sect. Leptonia as well as the new sect. Dichroi are presented. Two species (Entoloma percoelestinum and E. sublaevisporum) and one variety (E. tjallingiorum var. laricinum) are described as new to science. On the basis of the morphological and phylogenetical evidence E. alnetorum is reduced to a variety of E. tjallingiorum, and E. venustum is considered a variety of E. callichroum. Accordingly, the new combinations E. tjallingiorum var. alnetorum and E. callichroum var. venustum are proposed. Entoloma lepidissimum var. pauciangulatum is now treated as a synonym of E. chytrophilum. Neotypes for E. dichroum, E. euchroum and E. lampropus are designated.}, } @article {pmid25255272, year = {2014}, author = {Ashworth, J and Plaisier, CL and Lo, FY and Reiss, DJ and Baliga, NS}, title = {Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based prediction.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e107863}, pmid = {25255272}, issn = {1932-6203}, support = {P50 GM076547/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Archaeal Proteins/*chemistry/genetics/*metabolism ; Arginine/metabolism ; Binding Sites ; Computational Biology/*methods ; DNA, Archaeal/metabolism ; Gene Regulatory Networks ; Halobacterium salinarum/*genetics/*metabolism ; Molecular Sequence Data ; Operon/genetics ; Protein Binding ; Pyrimidines/metabolism ; Regulatory Sequences, Nucleic Acid/genetics ; Substrate Specificity ; Transcription Factors/chemistry/*metabolism ; }, abstract = {Widespread microbial genome sequencing presents an opportunity to understand the gene regulatory networks of non-model organisms. This requires knowledge of the binding sites for transcription factors whose DNA-binding properties are unknown or difficult to infer. We adapted a protein structure-based method to predict the specificities and putative regulons of homologous transcription factors across diverse species. As a proof-of-concept we predicted the specificities and transcriptional target genes of divergent archaeal feast/famine regulatory proteins, several of which are encoded in the genome of Halobacterium salinarum. This was validated by comparison to experimentally determined specificities for transcription factors in distantly related extremophiles, chromatin immunoprecipitation experiments, and cis-regulatory sequence conservation across eighteen related species of halobacteria. Through this analysis we were able to infer that Halobacterium salinarum employs a divergent local trans-regulatory strategy to regulate genes (carA and carB) involved in arginine and pyrimidine metabolism, whereas Escherichia coli employs an operon. The prediction of gene regulatory binding sites using structure-based methods is useful for the inference of gene regulatory relationships in new species that are otherwise difficult to infer.}, } @article {pmid25242540, year = {2014}, author = {Whatmore, AM and Davison, N and Cloeckaert, A and Al Dahouk, S and Zygmunt, MS and Brew, SD and Perrett, LL and Koylass, MS and Vergnaud, G and Quance, C and Scholz, HC and Dick, EJ and Hubbard, G and Schlabritz-Loutsevitch, NE}, title = {Brucella papionis sp. nov., isolated from baboons (Papio spp.).}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 12}, pages = {4120-4128}, pmid = {25242540}, issn = {1466-5034}, support = {P51 OD011133/OD/NIH HHS/United States ; P51 RR013986/RR/NCRR NIH HHS/United States ; 1C06RR014578/RR/NCRR NIH HHS/United States ; 1C06 RR015456/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bacterial Typing Techniques ; Brucella/*classification/genetics/isolation & purification ; DNA, Bacterial/genetics ; Female ; Genes, Bacterial ; Molecular Sequence Data ; Multilocus Sequence Typing ; Nucleic Acid Hybridization ; Papio/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Two Gram-negative, non-motile, non-spore-forming coccoid bacteria (strains F8/08-60(T) and F8/08-61) isolated from clinical specimens obtained from baboons (Papio spp.) that had delivered stillborn offspring were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA gene sequence similarities, both strains, which possessed identical sequences, were assigned to the genus Brucella. This placement was confirmed by extended multilocus sequence analysis (MLSA), where both strains possessed identical sequences, and whole-genome sequencing of a representative isolate. All of the above analyses suggested that the two strains represent a novel lineage within the genus Brucella. The strains also possessed a unique profile when subjected to the phenotyping approach classically used to separate species of the genus Brucella, reacting only with Brucella A monospecific antiserum, being sensitive to the dyes thionin and fuchsin, being lysed by bacteriophage Wb, Bk2 and Fi phage at routine test dilution (RTD) but only partially sensitive to bacteriophage Tb, and with no requirement for CO2 and no production of H2S but strong urease activity. Biochemical profiling revealed a pattern of enzyme activity and metabolic capabilities distinct from existing species of the genus Brucella. Molecular analysis of the omp2 locus genes showed that both strains had a novel combination of two highly similar omp2b gene copies. The two strains shared a unique fingerprint profile of the multiple-copy Brucella-specific element IS711. Like MLSA, a multilocus variable number of tandem repeat analysis (MLVA) showed that the isolates clustered together very closely, but represent a distinct group within the genus Brucella. Isolates F8/08-60(T) and F8/08-61 could be distinguished clearly from all known species of the genus Brucella and their biovars by both phenotypic and molecular properties. Therefore, by applying the species concept for the genus Brucella suggested by the ICSP Subcommittee on the Taxonomy of Brucella, they represent a novel species within the genus Brucella, for which the name Brucella papionis sp. nov. is proposed, with the type strain F8/08-60(T) (= NCTC 13660(T) = CIRMBP 0958(T)).}, } @article {pmid25225596, year = {2014}, author = {Witzany, G}, title = {Pragmatic turn in biology: From biological molecules to genetic content operators.}, journal = {World journal of biological chemistry}, volume = {5}, number = {3}, pages = {279-285}, pmid = {25225596}, issn = {1949-8454}, abstract = {Erwin Schrödinger's question "What is life?" received the answer for decades of "physics + chemistry". The concepts of Alain Turing and John von Neumann introduced a third term: "information". This led to the understanding of nucleic acid sequences as a natural code. Manfred Eigen adapted the concept of Hammings "sequence space". Similar to Hilbert space, in which every ontological entity could be defined by an unequivocal point in a mathematical axiomatic system, in the abstract "sequence space" concept each point represents a unique syntactic structure and the value of their separation represents their dissimilarity. In this concept molecular features of the genetic code evolve by means of self-organisation of matter. Biological selection determines the fittest types among varieties of replication errors of quasi-species. The quasi-species concept dominated evolution theory for many decades. In contrast to this, recent empirical data on the evolution of DNA and its forerunners, the RNA-world and viruses indicate cooperative agent-based interactions. Group behaviour of quasi-species consortia constitute de novo and arrange available genetic content for adaptational purposes within real-life contexts that determine epigenetic markings. This review focuses on some fundamental changes in biology, discarding its traditional status as a subdiscipline of physics and chemistry.}, } @article {pmid25225414, year = {2014}, author = {Violle, C and Reich, PB and Pacala, SW and Enquist, BJ and Kattge, J}, title = {The emergence and promise of functional biogeography.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {38}, pages = {13690-13696}, pmid = {25225414}, issn = {1091-6490}, mesh = {Biota/*physiology ; Phylogeography/*methods/*trends ; }, abstract = {Understanding, modeling, and predicting the impact of global change on ecosystem functioning across biogeographical gradients can benefit from enhanced capacity to represent biota as a continuous distribution of traits. However, this is a challenge for the field of biogeography historically grounded on the species concept. Here we focus on the newly emergent field of functional biogeography: the study of the geographic distribution of trait diversity across organizational levels. We show how functional biogeography bridges species-based biogeography and earth science to provide ideas and tools to help explain gradients in multifaceted diversity (including species, functional, and phylogenetic diversities), predict ecosystem functioning and services worldwide, and infuse regional and global conservation programs with a functional basis. Although much recent progress has been made possible because of the rising of multiple data streams, new developments in ecoinformatics, and new methodological advances, future directions should provide a theoretical and comprehensive framework for the scaling of biotic interactions across trophic levels and its ecological implications.}, } @article {pmid25223413, year = {2014}, author = {Meacham, D}, title = {Empathy and alteration: the ethical relevance of a phenomenological species concept.}, journal = {The Journal of medicine and philosophy}, volume = {39}, number = {5}, pages = {543-564}, doi = {10.1093/jmp/jhu030}, pmid = {25223413}, issn = {1744-5019}, mesh = {*Bioethics ; *Empathy ; *Ethics, Medical ; *Humanism ; Humans ; Morals ; *Personal Autonomy ; Philosophy, Medical ; }, abstract = {The debate over the ethics of radically, technologically altering the capacities and traditional form of the human body is rife with appeals to and dismissals of the importance of the integrity of the human species. Species-integrist arguments can be found in authors as varied as Annas, Fukuyama, Habermas, and Agar. However, the ethical salience of species integrity is widely contested by authors such as Buchanan, Daniels, Fenton, and Juengst. This article proposes a Phenomenological approach to the question of species-integrity, arguing in favor of a phenomenon of species-recognition that carries an ethical pull. Building on Husserl's Phenomenological account of empathy and the lived-body, as well as Schopenhauer's concept of compassion as an ethical urphenomenon, I develop a "Phenomenological species concept" (PSC), which I argue has the ethical significance that biological species concepts do not. The PSC reorients the debate over human alteration and species integrity.}, } @article {pmid25219384, year = {2014}, author = {Willems, M and Tahiri, N and Makarenkov, V}, title = {A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle.}, journal = {Journal of bioinformatics and computational biology}, volume = {12}, number = {5}, pages = {1450024}, doi = {10.1142/S0219720014500243}, pmid = {25219384}, issn = {1757-6334}, mesh = {*Algorithms ; Animals ; Biological Evolution ; Computational Biology ; Computer Simulation ; Culicidae/classification/genetics ; Databases, Genetic ; Diploidy ; *Hybridization, Genetic ; Least-Squares Analysis ; Models, Genetic ; *Phylogeny ; Plants/classification/genetics ; Polyploidy ; Software ; }, abstract = {Several algorithms and software have been developed for inferring phylogenetic trees. However, there exist some biological phenomena such as hybridization, recombination, or horizontal gene transfer which cannot be represented by a tree topology. We need to use phylogenetic networks to adequately represent these important evolutionary mechanisms. In this article, we present a new efficient heuristic algorithm for inferring hybridization networks from evolutionary distance matrices between species. The famous Neighbor-Joining concept and the least-squares criterion are used for building networks. At each step of the algorithm, before joining two given nodes, we check if a hybridization event could be related to one of them or to both of them. The proposed algorithm finds the exact tree solution when the considered distance matrix is a tree metric (i.e. it is representable by a unique phylogenetic tree). It also provides very good hybrids recovery rates for large trees (with 32 and 64 leaves in our simulations) for both distance and sequence types of data. The results yielded by the new algorithm for real and simulated datasets are illustrated and discussed in detail.}, } @article {pmid25185405, year = {2014}, author = {Bazsalovicsová, E and Králová-Hromadová, I and Brabec, J and Hanzelová, V and Oros, M and Scholz, T}, title = {Conflict between morphology and molecular data: a case of the genus Caryophyllaeus (Cestoda: Caryophyllidea), monozoic tapeworms of cyprinid fishes.}, journal = {Folia parasitologica}, volume = {61}, number = {4}, pages = {347-354}, pmid = {25185405}, issn = {0015-5683}, mesh = {Animals ; Cestoda/*classification/*genetics ; Cestode Infections/parasitology/*veterinary ; Cyprinidae ; DNA, Helminth/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics/metabolism ; Fish Diseases/*parasitology ; Gene Expression Regulation, Enzymologic ; Phylogeny ; }, abstract = {Molecular analysis of an extensive specimen collection of morphologically distinct tapeworms of the genus Caryophyllaeus Gmelin, 1790 (Cestoda: Caryophyllidea), parasites of cyprinid fishes in the Palaearctic Region, brought evidence of host-related plasticity in critical morphological characters widely used for species circumscription and classification of these tapeworms. The results obtained here do not support the traditionally used morphological concept of species-defining characters of the order Caryophyllidea Carus, 1863, especially due to high morphological plasticity of the scolex and the anterior end of the body. Several morphotypes within both Caryophyllaeus laticeps (Pallas, 1781) and Caryophyllaeus brachycollis Janiszewska, 1953 generally corresponding to different hosts and geographical regions, were recognised likely suggesting host- and geography-related intraspecific morphological variability. Genetic data confirmed euryxenous host specificity of both species, most profoundly C. laticeps, but did not support the existence of cryptic species. In fact, some of the fish hosts may harbour both of the congeneric species including several of their respective morphotypes. The pattern of morphological and genetic divergence observed in both cestode species studied indicates a scenario of possible host range extensions and subsequent parasite diversification. If molecular sequence variability and host-related morphological polymorphism are confirmed in other groups of monozoic cestodes, it may complicate species identification and straightforward classification of these parasites.}, } @article {pmid25176179, year = {2015}, author = {Randhawa, PK and Bali, A and Jaggi, AS}, title = {RIPC for multiorgan salvage in clinical settings: evolution of concept, evidences and mechanisms.}, journal = {European journal of pharmacology}, volume = {746}, number = {}, pages = {317-332}, doi = {10.1016/j.ejphar.2014.08.016}, pmid = {25176179}, issn = {1879-0712}, mesh = {Animals ; Arm/*blood supply/innervation ; Autonomic Nervous System/*metabolism ; Brain Ischemia/metabolism/therapy ; *Evidence-Based Medicine ; History, 20th Century ; History, 21st Century ; Humans ; Ischemic Preconditioning/*history/methods ; Kidney/blood supply/innervation ; Kidney Diseases/metabolism/therapy ; Leg/blood supply/innervation ; Mesenteric Ischemia/metabolism/therapy ; *Models, Biological ; Myocardial Ischemia/metabolism/therapy ; Peripheral Vascular Diseases/metabolism/therapy ; Reperfusion Injury/metabolism/*therapy ; Salvage Therapy/*history/methods ; }, abstract = {Ischemic preconditioning is an intrinsic process in which preconditioning ischemia (ischemia of shorter duration) protects the organs against the subsequent index ischemia (sustained ischemia). Remote ischemic preconditioning (RIPC) is an innovative treatment approach in which interspersed cycles of preconditioning ischemia followed by reperfusion to a remote organ (other than target organ) protect the target organ against index ischemia and reperfusion-induced injury. RIPC of various organs to provide multi-organ salvage became a successful approach in numerous species of animals. Consequently, the concept of RIPC evolved in clinical setups, and provided beneficial effects in alleviating ischemia-reperfusion-induced injury in various remote organs, including myocardium. Clinically, RIPC stimulus is generally delivered by inflating the blood pressure cuff tied on the upper arm 20 mm greater than the systolic blood pressure, rendering the forearm ischemic for 5 min, followed 5 min reperfusion by deflating the cuff. This cycle is repeated for 3-4 consecutive periods to precondition the tissue and improve the survival. The institution of RIPC is beneficial in mitigating myocardial injury in patients undergoing various surgical interventions including coronary artery bypass graft surgery, abdominal aortic aneurysm repair, percutaneous coronary intervention, heart valve surgery, drug-eluting stent implantation, kidney transplantation, elective decompression surgery. The involvement of hypoxia inducible factor-1α (HIF-1α), ATP-sensitive potassium channels, signal transducer and activator of transcription (STAT), matrix metalloproteinases, O-linked β-N-acetylglucosamine (O-GlcNAc) levels, autonomous nervous system in mediating RIPC-induced cardioprotective effects has been explored clinically. However, comprehensive studies are required to elucidate the other possible mechanisms responsible for producing multi-organ protection during RIPC.}, } @article {pmid25170177, year = {2014}, author = {Williamson, CJ and Brodie, J and Goss, B and Yallop, M and Lee, S and Perkins, R}, title = {Corallina and Ellisolandia (Corallinales, Rhodophyta) photophysiology over daylight tidal emersion: interactions with irradiance, temperature and carbonate chemistry.}, journal = {Marine biology}, volume = {161}, number = {9}, pages = {2051-2068}, pmid = {25170177}, issn = {0025-3162}, abstract = {The photophysiology of three geniculate coralline algal species (Corallina officinalis, C. caespitosa and Ellisolandia elongata) was determined in intertidal rock pools in the south-west UK at Combe Martin (51°12'31N 4°2'19W) and Heybrook Bay (50°31'66N 4°11'41W), at the start, middle and end of summer (September 1 and 2) and winter (February 9 and 10) daylight tidal emersion periods, in relation to prevailing irradiance, temperature and carbonate chemistry conditions. Algal photophysiology was assessed from rapid light curves performed using pulse amplitude modulation fluorometry. Corallina and Ellisolandia experienced significant fluctuations in irradiance, temperature and carbonate chemistry over seasonal and tidal cycles. Rock pool carbonate chemistry was predictable (R[2] = 0.82, P < 0.0001) by photodose (summed irradiance) plus water temperature, but not significantly related to photophysiology. In contrast, Corallina and Ellisolandia relative maximum electron transfer rate showed a significant negative relationship (R[2] = 0.65, P < 0.0001) with irradiance plus water temperature. At a seasonal resolution, photoacclimation to maximize both light harvesting during winter months and photoprotection during summer months was observed for all species. Dynamic photoinhibition was apparent over both summer and winter tidal emersion, in relation to irradiance fluctuations. More effective photoinhibition was apparent during summer months, with greater sensitivity to irradiance and slower recovery in Fv/Fm, observed during winter. With sustained high irradiance over tidal emersion, the establishment of high pH/low inorganic carbon conditions may impact photochemistry. This study represents the first assessment of C. officinalis, C. caespitosa and E. elongata photophysiology underpinned by clear species concepts and highlights their ability to adapt to the dramatically fluctuating conditions experienced in intertidal rock pools.}, } @article {pmid25156985, year = {2014}, author = {Burgess, MB and Cushman, KR and Doucette, ET and Talent, N and Frye, CT and Campbell, CS}, title = {Effects of apomixis and polyploidy on diversification and geographic distribution in Amelanchier (Rosaceae).}, journal = {American journal of botany}, volume = {101}, number = {8}, pages = {1375-1387}, doi = {10.3732/ajb.1400113}, pmid = {25156985}, issn = {1537-2197}, mesh = {*Apomixis ; *Biodiversity ; Chromosomes, Plant ; Ecosystem ; Endosperm ; *Genetic Speciation ; Genome, Plant ; North America ; *Plant Dispersal ; *Ploidies ; Pollen ; Polyploidy ; Reproduction/genetics ; Rosaceae/genetics/*physiology ; Seeds ; Species Specificity ; }, abstract = {UNLABELLED: •

PREMISE OF THE STUDY: Amelanchier polyploid apomicts differ from sexual diploids in their more complex diversification, greater species problems, and geographic distribution. To understand these differences, we investigated the occurrence of polyploidy and frequency of apomixis. This research helps clarify species delimitation in an evolutionarily complex genus.•

METHODS: We used flow cytometry to estimate genome size of 1355 plants. We estimated the frequency of apomixis from flow-cytometrically determined ploidy levels of embryo and endosperm and from a progeny study using RAPD markers. We explored relationships of triploids to other ploidy levels and of ploidy levels to latitude plus elevation.•

KEY RESULTS: Diploids (32% of sample) and tetraploids (62%) were widespread. Triploids (6%) mostly occurred in small numbers with diploids from two or more species or with diploids and tetraploids. Seeds from diploids were 2% apomictic, the first report of apomixis in Amelanchier diploids. Seeds from triploids were 75% apomictic. We documented potential triploid bridge and triploid block from unbalanced endosperm and low pollen viability. Seeds from tetraploids were 97% apomictic, and tetraploids often formed microspecies. We did not find strong evidence for geographical parthenogenesis in North American Amelanchier. Most currently recognized species contained multiple ploidy levels that were morphologically semicryptic.•

CONCLUSIONS: Documentation of numerous transitions from diploidy to polyploidy helps clarify diversification, geographic distribution, and the species problem in Amelanchier. Despite the infrequent occurrence of triploids, their retention of 25% sexuality and capacity for triploid bridge may be important steps between sexual diploids and predominantly apomictic tetraploids.}, } @article {pmid25141177, year = {2014}, author = {Romiguier, J and Gayral, P and Ballenghien, M and Bernard, A and Cahais, V and Chenuil, A and Chiari, Y and Dernat, R and Duret, L and Faivre, N and Loire, E and Lourenco, JM and Nabholz, B and Roux, C and Tsagkogeorga, G and Weber, AA and Weinert, LA and Belkhir, K and Bierne, N and Glémin, S and Galtier, N}, title = {Comparative population genomics in animals uncovers the determinants of genetic diversity.}, journal = {Nature}, volume = {515}, number = {7526}, pages = {261-263}, pmid = {25141177}, issn = {1476-4687}, mesh = {Animals ; Ecology ; *Evolution, Molecular ; Genetic Variation/*genetics ; *Genetics, Population ; Genome/*genetics ; *Genomics ; *Phylogeny ; }, abstract = {Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinants of this variation, and particularly the relative influences of species biology and ecology versus population history, are still largely mysterious. Here we show that the diversity of a species is predictable, and is determined in the first place by its ecological strategy. We investigated the genome-wide diversity of 76 non-model animal species by sequencing the transcriptome of two to ten individuals in each species. The distribution of genetic diversity between species revealed no detectable influence of geographic range or invasive status but was accurately predicted by key species traits related to parental investment: long-lived or low-fecundity species with brooding ability were genetically less diverse than short-lived or highly fecund ones. Our analysis demonstrates the influence of long-term life-history strategies on species response to short-term environmental perturbations, a result with immediate implications for conservation policies.}, } @article {pmid25127734, year = {2014}, author = {El-Sherry, S and Ogedengbe, ME and Hafeez, MA and Sayf-Al-Din, M and Gad, N and Barta, JR}, title = {Re-description of a genetically typed, single oocyst line of the turkey coccidium, Eimeria adenoeides Moore and Brown, 1951.}, journal = {Parasitology research}, volume = {113}, number = {11}, pages = {3993-4004}, pmid = {25127734}, issn = {1432-1955}, mesh = {Animals ; Cecum/pathology ; Coccidiosis/*veterinary ; Eimeria/*classification/*growth & development ; Ileum/pathology ; Ontario ; Oocysts ; Poultry Diseases/parasitology ; Turkeys/*parasitology ; }, abstract = {The Guelph strain of Eimeria adenoeides was obtained from a commercial turkey flock in Ontario, Canada, in 1985. Single oocyst derived lines of E. adenoeides were propagated, and one of them used to re-describe biological and morphological features of E. adenoeides in the turkey. Oocysts of this strain are within the lower size ranges in the original species description reported by Moore and Brown (1951); oocysts of the Guelph strain averaged 18.7 ± 1.4 μm (16.7-22.5) by 14.3 ± 0.9 μm (13-16.2, n = 30) with a shape index (SI) of 1.3 ± 0.1. It is possible that the original species description was based, at least in part, on a mixed culture of two or more Eimeria species. Immature first-generation meronts of E. adenoeides Guelph strain were observed histologically at 32 h post-infection in the ileum and cecal neck. Early studies reported only two asexual generations suggested that first asexual cycle observed at 32 h post-infection was overlooked. In the present study, three asexual generations were observed before the start of gametogony. The Guelph strain is also characterized by a prepatent period of 112 h. The Guelph strain of E. adenoeides is a highly pathogenic coccidium that forms classic cecal lesions, including prominent caseous cecal cores, during moderate to severe infections. The maximum output of oocysts (1.77 × 10(7) per bird) was obtained from birds inoculated with 1 × 10(3) oocysts; maximum fecundity (1.55 × 10(5) oocyst shed per oocyst inoculated) was obtained with an inoculation of 1 × 10(2) oocysts, but fecundity dropped dramatically as the inoculation dose increased. To promote stability of the E. adenoeides species concept, neotype specimens (a parahapantotype slides series and phototype) have been designated and deposited for future reference.}, } @article {pmid25115148, year = {2014}, author = {Breckheimer, I and Haddad, NM and Morris, WF and Trainor, AM and Fields, WR and Jobe, RT and Hudgens, BR and Moody, A and Walters, JR}, title = {Defining and evaluating the umbrella species concept for conserving and restoring landscape connectivity.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {28}, number = {6}, pages = {1584-1593}, doi = {10.1111/cobi.12362}, pmid = {25115148}, issn = {1523-1739}, mesh = {*Animal Distribution ; Animals ; Birds/*physiology ; Butterflies/*physiology ; Conservation of Natural Resources/*methods ; *Ecosystem ; *Endangered Species ; Forests ; Models, Biological ; North Carolina ; Ranidae/*physiology ; }, abstract = {Conserving or restoring landscape connectivity between patches of breeding habitat is a common strategy to protect threatened species from habitat fragmentation. By managing connectivity for some species, usually charismatic vertebrates, it is often assumed that these species will serve as conservation umbrellas for other species. We tested this assumption by developing a quantitative method to measure overlap in dispersal habitat of 3 threatened species-a bird (the umbrella), a butterfly, and a frog-inhabiting the same fragmented landscape. Dispersal habitat was determined with Circuitscape, which was parameterized with movement data collected for each species. Despite differences in natural history and breeding habitat, we found substantial overlap in the spatial distributions of areas important for dispersal of this suite of taxa. However, the intuitive umbrella species (the bird) did not have the highest overlap with other species in terms of the areas that supported connectivity. Nevertheless, we contend that when there are no irreconcilable differences between the dispersal habitats of species that cohabitate on the landscape, managing for umbrella species can help conserve or restore connectivity simultaneously for multiple threatened species with different habitat requirements.}, } @article {pmid25112259, year = {2014}, author = {Orr, MC and Koch, JB and Griswold, TL and Pitts, JP}, title = {Taxonomic utility of niche models in validating species concepts: A case study in Anthophora (Heliophila) (Hymenoptera: Apidae).}, journal = {Zootaxa}, volume = {3846}, number = {3}, pages = {411-429}, doi = {10.11646/zootaxa.3846.3.5}, pmid = {25112259}, issn = {1175-5334}, mesh = {Animals ; *Bees/anatomy & histology/classification/physiology ; *Ecosystem ; Female ; Male ; Phylogeography ; }, abstract = {Taxonomy has far-reaching effects throughout biology, and incorrect taxonomy can be detrimental in many ways. Polymorphic species complexes, many of which exist in the bee genus Anthophora Latreille, lend themselves to such difficulties. This study employs environmental niche mapping (ENM) and traditional morphological analyses to investigate the validity of the subjective synonymy of Anthophora (Heliophila) curta Provancher with the senior synonym A. squammulosa Dours. Eleven of fifty morphological characters consistently differentiate the two putative species, with an additional five characters sometimes separating them. Additionally, based on over 1000 georeferenced museum specimens, the geographic ranges of the two taxa do not overlap. The two entities also react differently to the bioclimatic variables based on correlation analysis. We further tested the two-species hypothesis by constructing ENMs with informative bioclimatic variables associated with locality records. Their modelled distributions overlapped less than 1%, suggesting discrete environmental boundaries. The variables which contributed most to each species' model also differed. These differences are explored in relation to their habitats. The combined morphological and biogeographic analysis indicates that A. curta and A. squammulosa are distinct species. Based on the accumulated evidence the synonymy is formally rejected and A. curta is recognized as a valid species. Five additional taxa (A. bispinosa Cockerell, A. franciscana Cockerell, A. usticauda Cockerell, A. u. cinerior Cockerell, A. zamoranella Cockerell) are newly synonymized with A. squammulosa and Anthophora curta var. melanops Cockerell is newly synonymized with A. curta. Implications outside of taxonomy are discussed.}, } @article {pmid25110113, year = {2014}, author = {Markham, J}, title = {Rare species occupy uncommon niches.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {6012}, pmid = {25110113}, issn = {2045-2322}, mesh = {*Biodiversity ; Grassland ; Models, Biological ; Poaceae/*growth & development ; Population Dynamics ; }, abstract = {The fact that temperate grasslands often contain upwards of 30 vascular plant species per m(2) yet these species seem to have relatively similar life histories and resource requirements has made explaining species coexistence in these communities a major focus of research. While the reduction of competition by disturbance has been a popular explanation for species coexistence, in tallgrass prairies any level of disturbance either has no effect, or decreases diversity, since it favors the dominant plants. Although there has long been speculation that grassland species could coexist by niche partitioning the concept received renewed interest when it was shown that soil hydrology could explain species coexistence. One aspect of community structure that has not been explained by niche partitioning is the rareness and commonness of species within communities. There are three classes of explanations for rareness: narrow habitat requirements, low competitive ability combined with frequency dependent fitness and, dispersal ability. However, evidence for these explanations tend to be anecdotal, focusing on particular species. Here I show that in tallgrass prairies common and rare species consistently occupy different parts of niche space, with rare species being restricted by the cover of common species and occupying the rare available niches.}, } @article {pmid25102811, year = {2014}, author = {Oren, A}, title = {Taxonomy of halophilic Archaea: current status and future challenges.}, journal = {Extremophiles : life under extreme conditions}, volume = {18}, number = {5}, pages = {825-834}, pmid = {25102811}, issn = {1433-4909}, mesh = {*Genome, Archaeal ; Halobacteriaceae/*classification/genetics/physiology ; *Phylogeny ; Salt Tolerance ; }, abstract = {Several groups of Archaea, all Euryarchaeota, develop in hypersaline environments (from >10% salt up to saturation). The cultured diversity of halophilic Archaea includes the family Halobacteriaceae of aerobic or facultative anaerobic, generally red-pigmented species (47 genera and 165 species as of February 2014) and seven representatives of four genera of methanogens, most of which obtain energy from methylated amines under anaerobic conditions. Metagenomic studies have identified an additional deep lineage of Archaea in salt lakes and ponds with brines approaching NaCl saturation. Genomic information is now available for representatives of these 'Nanohaloarchaea', but no members of this lineage have yet been cultured. Multilocus sequence analysis is becoming increasingly popular in taxonomic studies of the Halobacteriaceae, and such studies have demonstrated that recombination of genetic traits occurs at an extremely high frequency at least in some genera. Metagenomic studies in an Antarctic lake showed that large identical regions of up to 35 kb in length can be shared by members of different genera living together in the same environment. Such observations have important implications not only for the taxonomy of the Halobacteriaceae, but also for species concepts and questions on taxonomy and classification for prokaryotic microorganisms in general.}, } @article {pmid25083403, year = {2014}, author = {Crouch, JA}, title = {Colletotrichum caudatum s.l. is a species complex.}, journal = {IMA fungus}, volume = {5}, number = {1}, pages = {17-30}, pmid = {25083403}, issn = {2210-6340}, abstract = {Colletotrichum caudatum sensu lato is a widespread fungal pathogen of warm-season grasses. The fungus is easily differentiated from other Colletotrichum species through the presence of a unique filiform appendage at the apex of the conidium. Multi-locus phylogenetic analysis of four DNA sequence markers from 21 isolates of C. caudatum s.l. from six grass hosts recovered the morphospecies as a well-supported monophyletic group. Although closely related to other Colletotrichum species pathogenic to warm-season grasses (e.g. C. sublineola, C. falcatum, C. navitas, C. graminicola), the sister taxon placement of C. caudatum remained unclear. Four major subgroups and three monotypic lineages were identified from the C. caudatum s.l. isolates. Despite the presence of localized, taxon-specific incongruence between gene trees and evidence for recombination in the dataset, application of genealogical concordance species recognition criteria diagnosed the four subgroups as phylogenetic species. Traditional morphology-based species concept defines C. caudatum as one species with a broad host range; however, multi-locus phylogenetic analyses refuted this model. Instead, isolates from different hosts were mainly segregated into different lineages. In particular, isolates from the type locale and host (USA, Sorghastrum nutans) collected within a 400 km radius were divided into three distinct species that corresponded with the three sampling sites. These data established that traditional morphological and ecological features are not informative for recognition of taxa within C. caudatum s.l., although there is some evidence that some species may be host specific. To stabilize the application of the name C. caudatum, DNA sequence data from the lectotype was generated, an epitype strain consistent with the type was designated and illustrated, and an emended description of C. caudatum sensu stricto is provided. Colletotrichum alcornii, C. baltimorense, C. somersetense, and C. zoysiae are described as new morphologically cryptic species related to C. caudatum s.s.}, } @article {pmid25081433, year = {2014}, author = {Sartori, M}, title = {The concept of Compsoneuria Eaton, 1881 revisited in light of historical and new material from the Sunda Islands (Ephemeroptera: Heptageniidae: Ecdyonurinae).}, journal = {Zootaxa}, volume = {3835}, number = {1}, pages = {1-32}, doi = {10.11646/zootaxa.3835.1.1}, pmid = {25081433}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy & histology/growth & development ; Animals ; Body Size ; Ephemeroptera/anatomy & histology/*classification/growth & development ; Female ; Islands ; Male ; Organ Size ; Philippines ; }, abstract = {Based on re-examination of material belonging to the Museum of Zoology, Hamburg University, Germany, especially Georg Ulmer's collection, as well as newly collected specimens from the Sunda Islands, the genuine concept of Compsoneuria Eaton, 1881 is revised. The genus has had as junior synonyms Compsoneuriella Ulmer, 1939 (Oriental) and Notonurus Crass, 1947 (Afrotropical). A recent molecular study removed Notonurus from this synonymy. The type species of Compsoneuria, Compsoneuria spectabilis Eaton, 1881, is redescribed. A lectotype male imago is designated for Compsoneuriella thienemanni Ulmer, 1939, type species of Compsoneuriella. Based on egg morphology, nymphal stages of both Compsoneuria and Compsoneuriella are unequivocally attributed. The nymph of Compsoneuria spectabilis is described and corresponds in part to what Ulmer (1939) described as the nymph of Compsoneuriella thienemanni. The latter nymph is also redescribed from material collected recently in Sumatra. Due to the important number of morphological differences between these two species, Compsoneuriella stat. prop. is removed from its synonymy with Compsoneuria. Besides C. thienemanni, the genus Compsoneuriella encompasses C. langensis (Braasch & Boonsoong, 2010) comb. nov. from Thailand and C. tagbanua (Braasch & Freitag, 2008) comb. nov. from the Philippines (Palawan), which is partially redescribed. All other species under the combined concept of Compsoneuria/Compsoneuriella are mentioned and their generic placements are discussed. The new combination Afronurus taipokauensis (Tong & Dudgeon, 2003) comb. nov. from Hong Kong, China is proposed.}, } @article {pmid25079222, year = {2014}, author = {Rezaei-Matehkolaei, A and Mirhendi, H and Makimura, K and de Hoog, GS and Satoh, K and Najafzadeh, MJ and Shidfar, MR}, title = {Nucleotide sequence analysis of beta tubulin gene in a wide range of dermatophytes.}, journal = {Medical mycology}, volume = {52}, number = {7}, pages = {674-688}, doi = {10.1093/mmy/myu033}, pmid = {25079222}, issn = {1460-2709}, mesh = {Animals ; Arthrodermataceae/*classification/*genetics/isolation & purification ; Base Sequence ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; *Genetic Variation ; Humans ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Tubulin/*genetics ; }, abstract = {We investigated the resolving power of the beta tubulin protein-coding gene (BT2) for systematic study of dermatophyte fungi. Initially, 144 standard and clinical strains belonging to 26 species in the genera Trichophyton, Microsporum, and Epidermophyton were identified by internal transcribe spacer (ITS) sequencing. Subsequently, BT2 was partially amplified in all strains, and sequence analysis performed after construction of a BT2 database that showed length ranged from approximately 723 (T. ajelloi) to 808 nucleotides (M. persicolor) in different species. Intraspecific sequence variation was found in some species, but T. tonsurans, T. equinum, T. concentricum, T. verrucosum, T. rubrum, T. violaceum, T. eriotrephon, E. floccosum, M. canis, M. ferrugineum, and M. audouinii were invariant. The sequences were found to be relatively conserved among different strains of the same species. The species with the closest resemblance were Arthroderma benhamiae and T. concentricum and T. tonsurans and T. equinum with 100% and 99.8% identity, respectively; the most distant species were M. persicolor and M. amazonicum. The dendrogram obtained from BT2 topology was almost compatible with the species concept based on ITS sequencing, and similar clades and species were distinguished in the BT2 tree. Here, beta tubulin was characterized in a wide range of dermatophytes in order to assess intra- and interspecies variation and resolution and was found to be a taxonomically valuable gene.}, } @article {pmid25055940, year = {2014}, author = {Peterson, AT}, title = {Defining viral species: making taxonomy useful.}, journal = {Virology journal}, volume = {11}, number = {}, pages = {131}, pmid = {25055940}, issn = {1743-422X}, mesh = {Animals ; Classification/methods ; Humans ; Viruses/*classification ; }, abstract = {Virus taxonomy at present is best characterized as a categorization of convenience, without a firm basis in the principles of evolutionary biology. Specifically, virus species definitions appear to depend more on tradition and popular opinion among virologists than on firm, quantitative biological evidence. I suggest a series of changes to underlying species concepts that would shift the field from one that simply files viruses away in taxonomic boxes to one that can learn important biological lessons from its taxonomy.}, } @article {pmid25055023, year = {2014}, author = {Hällfors, MH and Vaara, EM and Hyvärinen, M and Oksanen, M and Schulman, LE and Siipi, H and Lehvävirta, S}, title = {Coming to terms with the concept of moving species threatened by climate change - a systematic review of the terminology and definitions.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102979}, pmid = {25055023}, issn = {1932-6203}, mesh = {Animals ; *Climate Change ; *Conservation of Natural Resources ; Ecosystem ; Endangered Species ; *Extinction, Biological ; *Terminology as Topic ; }, abstract = {Intentional moving of species threatened by climate change is actively being discussed as a conservation approach. The debate, empirical studies, and policy development, however, are impeded by an inconsistent articulation of the idea. The discrepancy is demonstrated by the varying use of terms, such as assisted migration, assisted colonisation, or managed relocation, and their multiple definitions. Since this conservation approach is novel, and may for instance lead to legislative changes, it is important to aim for terminological consistency. The objective of this study is to analyse the suitability of terms and definitions used when discussing the moving of organisms as a response to climate change. An extensive literature search and review of the material (868 scientific publications) was conducted for finding hitherto used terms (N = 40) and definitions (N = 75), and these were analysed for their suitability. Based on the findings, it is argued that an appropriate term for a conservation approach relating to aiding the movement of organisms harmed by climate change is assisted migration defined as follows: Assisted migration means safeguarding biological diversity through the translocation of representatives of a species or population harmed by climate change to an area outside the indigenous range of that unit where it would be predicted to move as climate changes, were it not for anthropogenic dispersal barriers or lack of time. The differences between assisted migration and other conservation translocations are also discussed. A wide adoption of the clear and distinctive term and definition provided would allow more focused research on the topic and enable consistent implementation as practitioners could have the same understanding of the concept.}, } @article {pmid25048948, year = {2014}, author = {Lindenmayer, DB and Lane, PW and Westgate, MJ and Crane, M and Michael, D and Okada, S and Barton, PS}, title = {An empirical assessment of the focal species hypothesis.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {28}, number = {6}, pages = {1594-1603}, doi = {10.1111/cobi.12330}, pmid = {25048948}, issn = {1523-1739}, mesh = {*Animal Distribution ; Animals ; *Biodiversity ; Birds/*physiology ; Conservation of Natural Resources/*methods ; *Forests ; New South Wales ; }, abstract = {Biodiversity surrogates and indicators are commonly used in conservation management. The focal species approach (FSA) is one method for identifying biodiversity surrogates, and it is underpinned by the hypothesis that management aimed at a particular focal species will confer protection on co-occurring species. This concept has been the subject of much debate, in part because the validity of the FSA has not been subject to detailed empirical assessment of the extent to which a given focal species actually co-occurs with other species in an assemblage. To address this knowledge gap, we used large-scale, long-term data sets of temperate woodland birds to select focal species associated with threatening processes such as habitat isolation and loss of key vegetation attributes. We quantified co-occurrence patterns among focal species, species in the wider bird assemblage, and species of conservation concern. Some, but not all, focal species were associated with high levels of species richness. One of our selected focal species was negatively associated with the occurrence of other species (i.e., it was an antisurrogate)-a previously undescribed property of nominated focal species. Furthermore, combinations of focal species were not associated with substantially elevated levels of bird species richness, relative to levels associated with individual species. Our results suggest that although there is some merit to the underpinning concept of the FSA, there is also a need to ensure that actions are sufficiently flexible because management tightly focused on a given focal species may not benefit some other species, including species of conservation concern, such of which might not occur in species-rich assemblages.}, } @article {pmid25039221, year = {2014}, author = {Bini, LM and Landeiro, VL and Padial, AA and Siqueira, T and Heino, J}, title = {Nutrient enrichment is related to two facets of beta diversity for stream invertebrates across the United States.}, journal = {Ecology}, volume = {95}, number = {6}, pages = {1569-1578}, doi = {10.1890/13-0656.1}, pmid = {25039221}, issn = {0012-9658}, mesh = {Animals ; *Biodiversity ; Demography ; Environment ; Invertebrates/*physiology ; *Rivers/chemistry ; United States ; }, abstract = {Beta diversity, the spatial or temporal variability of species composition, is a key concept in community ecology. However, our ability to predict the relative importance of the main drivers of beta diversity (e.g., environmental heterogeneity, dispersal limitation, and environmental productivity) remains limited. Using a comprehensive data set on stream invertebrate assemblages across the continental United States, we found a hump-shaped relationship between beta diversity and within-ecoregion nutrient concentrations. Within-ecoregion compositional dissimilarity matrices were mainly related to environmental distances in most of the 30 ecoregions analyzed, suggesting a stronger role for species-sorting than for spatial processes. The strength of these relationships varied considerably among ecoregions, but they were unrelated to within-ecoregion environmental heterogeneity or spatial extent. Instead, we detected a negative correlation between the strength of species sorting and nutrient concentrations. We suggest that eutrophication is a major mechanism disassembling invertebrate assemblages in streams at a continental scale.}, } @article {pmid25009440, year = {2014}, author = {Souza, IM and Funch, LS and de Queiroz, LP}, title = {Morphological analyses suggest a new taxonomic circumscription for Hymenaea courbaril L. (Leguminosae, Caesalpinioideae).}, journal = {PhytoKeys}, volume = {}, number = {38}, pages = {101-118}, pmid = {25009440}, issn = {1314-2011}, abstract = {Hymenaea is a genus of the Resin-producing Clade of the tribe Detarieae (Leguminosae: Caesalpinioideae) with 14 species. Hymenaea courbaril is the most widespread species of the genus, ranging from southern Mexico to southeastern Brazil. As currently circumscribed, Hymenaea courbaril is a polytypic species with six varieties: var. altissima, var. courbaril, var. longifolia, var. stilbocarpa, var. subsessilis, and var. villosa. These varieties are distinguishable mostly by traits related to leaflet shape and indumentation, and calyx indumentation. We carried out morphometric analyses of 14 quantitative (continuous) leaf characters in order to assess the taxonomy of Hymenaea courbaril under the Unified Species Concept framework. Cluster analysis used the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) based on Bray-Curtis dissimilarity matrices. Principal Component Analyses (PCA) were carried out based on the same morphometric matrix. Two sets of Analyses of Similarity and Non Parametric Multivariate Analysis of Variance were carried out to evaluate statistical support (1) for the major groups recovered using UPGMA and PCA, and (2) for the varieties. All analyses recovered three major groups coincident with (1) var. altissima, (2) var. longifolia, and (3) all other varieties. These results, together with geographical and habitat information, were taken as evidence of three separate metapopulation lineages recognized here as three distinct species. Nomenclatural adjustments, including reclassifying formerly misapplied types, are proposed.}, } @article {pmid24998346, year = {2014}, author = {Fromm, B and Burow, S and Hahn, C and Bachmann, L}, title = {MicroRNA loci support conspecificity of Gyrodactylus salaris and Gyrodactylus thymalli (Platyhelminthes: Monogenea).}, journal = {International journal for parasitology}, volume = {44}, number = {11}, pages = {787-793}, doi = {10.1016/j.ijpara.2014.05.010}, pmid = {24998346}, issn = {1879-0135}, mesh = {Animal Distribution ; Animals ; Genetic Variation ; MicroRNAs/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Helminth/*genetics ; Species Specificity ; Trematoda/*genetics/physiology ; }, abstract = {The monogenean flatworm Gyrodactylus salaris is a serious threat to wild and farmed Atlantic salmon stocks in Norway. Morphologically, the closely related but harmless Gyrodactylus thymalli on grayling can hardly be distinguished from G. salaris. Until now, molecular approaches could not resolve unambiguously whether G. salaris and G. thymalli represent just one polytypic species, two polytypic species or a complex of more than two species. In the first known genome-wide analysis utilizing 37 conserved microRNA loci, the genetic differentiation of seven populations of G. salaris and G. thymalli was assessed. The concatenated alignment spanned 21,742bp including 62 variable positions. A neighbor-joining cluster analysis did not support any host-based or mitochondrial haplotype-based grouping of strains. We conclude that a two species concept for G. salaris and G. thymalli does not reflect meaningful biological entities. Instead, G. salaris and G. thymalli are just one species comprising several pathogenic and non-pathogenic strains on various primary hosts. Following the International Code for Zoological Nomenclature, G. salaris Malmberg, 1957 is the valid species name with G. thymalli Žitňan, 1960 becoming the junior synonym. Accordingly, the range of G. salaris is significantly increased, given that formerly G. salaris-free countries such as e.g., Great Britain are now within the species' natural range. The synonymization of G. salaris and G. thymalli implies severe challenges to current disease management routines, which assume that G. salaris and G. thymalli are readily distinguishable. Protocols for reliable identification of pathogenic and non-pathogenic strains of G. salaris need to be developed.}, } @article {pmid24988775, year = {2014}, author = {Banks, JE and Stark, JD and Vargas, RI and Ackleh, AS}, title = {Deconstructing the surrogate species concept: a life history approach to the protection of ecosystem services.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {24}, number = {4}, pages = {770-778}, doi = {10.1890/13-0937.1}, pmid = {24988775}, issn = {1051-0761}, mesh = {Animals ; Arthropods/*physiology ; Conservation of Natural Resources/*methods ; *Ecosystem ; Environmental Monitoring/*methods ; Metamorphosis, Biological ; *Models, Biological ; }, abstract = {The use of the surrogate species concept is widespread in environmental risk assessment and in efforts to protect species that provide ecosystem services, yet there are no standard protocols for the choice of surrogates. Surrogates are often chosen on the basis of convenience or vague resemblances in physiology or life history to species of concern. Furthermore, our ability to predict how species of concern will fare when subjected to disturbances such as environmental contaminants or toxicants is often based on woefully misleading comparisons of static toxicity tests. Here we present an alternative approach that features a simple mathematical model parameterized with life history data applied to an assemblage of species that provide an important ecosystem service: a suite of parasitoid wasps that provide biological control of agricultural pests. Our results indicate that these parasitoid wasp species have different population responses to toxic insult--that is, we cannot predict how all four species will react to pesticide exposure simply by extrapolating from the response of any one species. Furthermore, sensitivity analysis of survivorship and reproduction demonstrates that the life stage most sensitive to pesticide disturbance varies among species. Taken together, our results suggest that the ability to predict the fate of a suite of species using the response of just one species (the surrogate species concept) is widely variable and potentially misleading.}, } @article {pmid24987126, year = {2014}, author = {Gazis, R and Skaltsas, D and Chaverri, P}, title = {Novel endophytic lineages of Tolypocladium provide new insights into the ecology and evolution of Cordyceps-like fungi.}, journal = {Mycologia}, volume = {106}, number = {6}, pages = {1090-1105}, doi = {10.3852/13-346}, pmid = {24987126}, issn = {0027-5514}, mesh = {Biological Evolution ; Cordyceps ; Ecology ; Endophytes ; Hevea/*microbiology ; Host Specificity ; Hypocreales/*classification/genetics/isolation & purification/physiology ; Phylogeny ; Sequence Analysis, DNA ; Spores, Fungal ; Symbiosis ; }, abstract = {The objective of this study was to identify a group of unknown endophytic fungal isolates from the living sapwood of wild and planted Hevea (rubber tree) populations. Three novel lineages of Tolypocladium are described based on molecular and morphological data. Findings from this study open a window for novel hypotheses regarding the ecology and role of endophytes within plant communities as well as trait evolution and potential forces driving diversification of Cordyceps-like fungi. This study stresses the importance of integrating asexual and sexual fungal states for a more complete understanding of the natural history of this diverse group. In addition, it highlights the study of fungi in the sapwood of tropical trees as habitat for the discovery of novel fungal lineages and substrate associations.}, } @article {pmid24987122, year = {2014}, author = {Mbenoun, M and Wilhelm de Beer, Z and Wingfield, MJ and Wingfield, BD and Roux, J}, title = {Reconsidering species boundaries in the Ceratocystis paradoxa complex, including a new species from oil palm and cacao in Cameroon.}, journal = {Mycologia}, volume = {106}, number = {4}, pages = {757-784}, doi = {10.3852/13-298}, pmid = {24987122}, issn = {0027-5514}, mesh = {Arecaceae/*microbiology ; Ascomycota/*classification/genetics/physiology/ultrastructure ; Base Sequence ; Cacao/*microbiology ; Cameroon ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Fungal Proteins/genetics ; Molecular Sequence Data ; Multilocus Sequence Typing ; Mycological Typing Techniques ; Peptide Elongation Factor 1/genetics ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, DNA ; Spores, Fungal ; Tubulin/genetics ; }, abstract = {The Ceratocystis paradoxa complex accommodates a group of fungal pathogens that have become specialized to infect mostly monocotyledonous plants. Four species currently are recognized in this group, including C. paradoxa, which has a widespread distribution and broad host range. In this study, multigene phylogenetic analyses involving sequences of the ITS, β-tubulin and TEF-1α gene loci, in combination with phenotypic and mating studies, were used to characterize purported C. paradoxa isolates from Cameroon and to compare them with isolates from elsewhere, including protologs and type specimens of known species. We show that the C. paradoxa complex comprises substantially greater species diversity than previously recognized. One new species in this group is described from Cameroon as Ceratocystis cerberus, while C. paradoxa sensu stricto (s. str.) and four other species are redefined. Lectotypes are designated for C. ethacetica and Endoconidium fragrans (synonym of C. ethacetica), while epitypes are designated for C. paradoxa s. str., C. ethacetica and C. musarum. A neotype is designated for Catenularia echinata (synonym of C. ethacetica) and two species, previously treated in Thielaviopsis, are transferred to Ceratocystis.}, } @article {pmid24982168, year = {2014}, author = {Lücking, R and Dal-Forno, M and Sikaroodi, M and Gillevet, PM and Bungartz, F and Moncada, B and Yánez-Ayabaca, A and Chaves, JL and Coca, LF and Lawrey, JD}, title = {A single macrolichen constitutes hundreds of unrecognized species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {30}, pages = {11091-11096}, pmid = {24982168}, issn = {1091-6490}, mesh = {Basidiomycota/*classification ; Lichens/*classification ; }, abstract = {The number of Fungi is estimated at between 1.5 and 3 million. Lichenized species are thought to make up a comparatively small portion of this figure, with unrecognized species richness hidden among little-studied, tropical microlichens. Recent findings, however, suggest that some macrolichens contain a large number of unrecognized taxa, increasing known species richness by an order of magnitude or more. Here we report the existence of at least 126 species in what until recently was believed to be a single taxon: the basidiolichen fungus Dictyonema glabratum, also known as Cora pavonia. Notably, these species are not cryptic but morphologically distinct. A predictive model suggests an even larger number, with more than 400 species. These results call into question species concepts in presumably well-known macrolichens and demonstrate the need for accurately documenting such species richness, given the importance of these lichens in endangered ecosystems such as paramos and the alarming potential for species losses throughout the tropics.}, } @article {pmid24956528, year = {2014}, author = {Ganji, SH and Kamanna, VS and Kashyap, ML}, title = {Niacin decreases leukocyte myeloperoxidase: mechanistic role of redox agents and Src/p38MAP kinase.}, journal = {Atherosclerosis}, volume = {235}, number = {2}, pages = {554-561}, doi = {10.1016/j.atherosclerosis.2014.05.948}, pmid = {24956528}, issn = {1879-1484}, mesh = {Apolipoprotein A-I/metabolism ; HL-60 Cells ; Humans ; Leukocytes/drug effects/enzymology ; NADPH Oxidases/antagonists & inhibitors ; Niacin/*pharmacology ; Peroxidase/*metabolism ; Reactive Oxygen Species/metabolism ; Tetradecanoylphorbol Acetate/pharmacology ; p38 Mitogen-Activated Protein Kinases/*metabolism ; src-Family Kinases/*metabolism ; }, abstract = {OBJECTIVES: Leukocyte myeloperoxidase (MPO) is a major player in the pathogenesis of various chronic diseases including atherosclerosis. This study proposes the novel concept that niacin, through reactive oxygen species (ROS)-mediated signaling, decreases neutrophil MPO release and its activity, protects apolipoprotein-AI (apo-AI) modification and improves HDL function.

METHODS: Human blood leukocytes and leukocytic cell line HL-60 cells were treated with niacin, and stimulated with phorbol myristate acetate (PMA). Cellular and released MPO activity in the medium was measured by assessing chlorination of MPO-specific substrate. MPO protein release in the medium and apo-AI degradation was measured by Western blot analysis. Monocyte adhesion to human aortic primary endothelial cells was measured to assess biological function of HDL/apo-AI.

RESULTS: PMA significantly increased leukocyte MPO activity in both intracellular extract and medium. Niacin (0.25-0.5 mM) decreased PMA-induced MPO activity (cellular and released in the media). Niacin also decreased MPO protein mass in the medium without affecting its mRNA expression. Increased NADPH oxidase and ROS production by PMA were also significantly inhibited by niacin. Studies with specific inhibitors suggest that ROS-dependent Src and p38MAP kinase mediate decreased MPO activity by niacin. Niacin blocked apo-AI degradation, and apo-AI from niacin treated cells decreased monocyte adhesion to aortic endothelial cells.

CONCLUSIONS: These findings identify niacin as a potent inhibitor of leukocyte MPO release and MPO-mediated formation of dysfunctional HDL. Niacin and niacin-related chemical entities may form important therapeutic agents for MPO-mediated inflammatory diseases.}, } @article {pmid24948670, year = {2014}, author = {Cornelissen, JH and Song, YB and Yu, FH and Dong, M}, title = {Plant traits and ecosystem effects of clonality: a new research agenda.}, journal = {Annals of botany}, volume = {114}, number = {2}, pages = {369-376}, pmid = {24948670}, issn = {1095-8290}, mesh = {Clone Cells ; *Ecosystem ; Plants/*metabolism ; *Quantitative Trait, Heritable ; *Reproduction, Asexual ; Soil ; }, abstract = {BACKGROUND: Clonal plants spread laterally by spacers between their ramets (shoot-root units); these spacers can transport and store resources. While much is known about how clonality promotes plant fitness, we know little about how different clonal plants influence ecosystem functions related to carbon, nutrient and water cycling.

APPROACH: The response-effect trait framework is used to formulate hypotheses about the impact of clonality on ecosystems. Central to this framework is the degree of correspondence between interspecific variation in clonal 'response traits' that promote plant fitness and interspecific variation in 'effect traits', which define a plant's potential effect on ecosystem functions. The main example presented to illustrate this concept concerns clonal traits of vascular plant species that determine their lateral extension patterns. In combination with the different degrees of decomposability of litter derived from their spacers, leaves, roots and stems, these clonal traits should determine associated spatial and temporal patterns in soil organic matter accumulation, nutrient availability and water retention.

CONCLUSIONS: This review gives some concrete pointers as to how to implement this new research agenda through a combination of (1) standardized screening of predominant species in ecosystems for clonal response traits and for effect traits related to carbon, nutrient and water cycling; (2) analysing the overlap between variation in these response traits and effect traits across species; (3) linking spatial and temporal patterns of clonal species in the field to those for soil properties related to carbon, nutrient and water stocks and dynamics; and (4) studying the effects of biotic interactions and feedbacks between resource heterogeneity and clonality. Linking these to environmental changes may help us to better understand and predict the role of clonal plants in modulating impacts of climate change and human activities on ecosystem functions.}, } @article {pmid24931730, year = {2014}, author = {Ruiz-García, M and Pinedo-Castro, M and Shostell, JM}, title = {How many genera and species of woolly monkeys (Atelidae, Platyrrhine, Primates) are there? The first molecular analysis of Lagothrix flavicauda, an endemic Peruvian primate species.}, journal = {Molecular phylogenetics and evolution}, volume = {79}, number = {}, pages = {179-198}, doi = {10.1016/j.ympev.2014.05.034}, pmid = {24931730}, issn = {1095-9513}, mesh = {Animals ; Atelinae/*classification/genetics ; *Genes, Mitochondrial ; *Genetic Speciation ; Genetic Variation ; Haplotypes ; Hybridization, Genetic ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {We sequenced COI and COII mitochondrial genes of 141 Neotropical woolly monkeys to provide new insights concerning their phylogeography and phylogenetic relationships. For the first time, eight individuals of the endemic and extremely rare Peruvian yellow-tailed woolly monkey (flavicauda) were sequenced at these genes and compared with other Lagothrix taxa (poeppigii, lagotricha, lugens and cana). There were four main results. (1) L. flavicauda showed a gene diversity of zero, whereas poeppigii and lugens showed high levels of gene diversity and lagotricha and cana showed more modest levels of gene diversity. The absence of gene diversity found for L. flavicauda strongly supports that it is one of the 25 more endangered primates on earth; (2) Our genetic distance and phylogenetic analyses, which included many cases of genetic introgression and recent hybridization, suggest that all woolly monkeys could be included in one unique genus, Lagotrix, divided into two species: L. flavicauda and L. lagotricha. The last species is divided into at least four subspecies. Our molecular results agree with Fooden's (1963) classification, but do not support the classification proposed by Groves (2001). (3) Poeppigii was the first taxon within L. lagotricha to experience a mitochondrial haplotype diversification, while cana and lagotricha experienced more recent mitochondrial haplotype diversification; (4) Poeppigii and lagotricha were the taxa which showed the greatest evidence of population expansions in different Pleistocene periods, whereas lugens experienced a population declination in the last 25,000 YA.}, } @article {pmid24903598, year = {2014}, author = {Vonk, J and Johnson-Ulrich, Z}, title = {Social and nonsocial category discriminations in a chimpanzee (Pan troglodytes) and American black bears (Ursus americanus).}, journal = {Learning & behavior}, volume = {42}, number = {3}, pages = {231-245}, pmid = {24903598}, issn = {1543-4508}, mesh = {Animals ; Behavior, Animal/physiology ; Choice Behavior/*physiology ; Female ; Male ; Pan troglodytes/*psychology ; *Social Behavior ; Transfer, Psychology/*physiology ; Ursidae/*psychology ; }, abstract = {One captive adult chimpanzee and 3 adult American black bears were presented with a series of natural category discrimination tasks on a touch-screen computer. This is the first explicit comparison of bear and primate abilities using identical tasks, and the first test of a social concept in a carnivore. The discriminations involved a social relationship category (mother/offspring) and a nonsocial category involving food items. The social category discrimination could be made using knowledge of the overarching mother/offspring concept, whereas the nonsocial category discriminations could be made only by using perceptual rules, such as "choose images that show larger and smaller items of the same type." The bears failed to show above-chance transfer on either the social or nonsocial discriminations, indicating that they did not use either the perceptual rule or knowledge of the overarching concept of mother/offspring to guide their choices in these tasks. However, at least 1 bear remembered previously reinforced stimuli when these stimuli were recombined, later. The chimpanzee showed transfer on a control task and did not consistently apply a perceptual rule to solve the nonsocial task, so it is possible that he eventually acquired the social concept. Further comparisons between species on identical tasks assessing social knowledge will help illuminate the selective pressures responsible for a range of social cognitive skills.}, } @article {pmid26988316, year = {2014}, author = {Manoylov, KM}, title = {Taxonomic identification of algae (morphological and molecular): species concepts, methodologies, and their implications for ecological bioassessment.}, journal = {Journal of phycology}, volume = {50}, number = {3}, pages = {409-424}, doi = {10.1111/jpy.12183}, pmid = {26988316}, issn = {1529-8817}, abstract = {Algal taxonomy is a key discipline in phycology and is critical for algal genetics, physiology, ecology, applied phycology, and particularly bioassessment. Taxonomic identification is the most common analysis and hypothesis-testing endeavor in science. Errors of identification are often related to the inherent problem of small organisms with morphologies that are difficult to distinguish without research-grade microscopes and taxonomic expertise in phycology. Proposed molecular approaches for taxonomic identification from environmental samples promise rapid, potentially inexpensive, and more thorough culture-independent identification of all algal species present in a sample of interest. Molecular identification has been used in biodiversity and conservation, but it also has great potential for applications in bioassessment. Comparisons of morphological and molecular identification of benthic algal communities are improved by the identification of more taxa; however, automated identification technology does not allow for the simultaneous analysis of thousands of samples. Currently, morphological identification is used to verify molecular taxonomic identities, but with the increased number of taxa verified in algal gene libraries, molecular identification will become a universal tool in biological studies. Thus, in this report, successful application of molecular techniques related to algal bioassessment is discussed.}, } @article {pmid24874921, year = {2014}, author = {Cruz, D and Suárez, JP and Kottke, I and Piepenbring, M}, title = {Cryptic species revealed by molecular phylogenetic analysis of sequences obtained from basidiomata of Tulasnella.}, journal = {Mycologia}, volume = {106}, number = {4}, pages = {708-722}, doi = {10.3852/12-386}, pmid = {24874921}, issn = {0027-5514}, mesh = {Base Sequence ; Basidiomycota/*genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Ecuador ; Germany ; Molecular Sequence Data ; Orchidaceae/*microbiology ; Phylogeny ; Sequence Analysis, DNA ; Spores, Fungal ; Trees ; }, abstract = {Delimitation of species and the search for a proper threshold for defining phylogenetic species in fungi are under discussion. In this study, morphological and molecular data are correlated to delimit species of Tulasnella, the most important mycobionts of Orchidaceae, which suffer from poor taxonomy. Resupinate basidiomata of Tulasnella species were collected in Ecuador and Germany, and 11 specimens (seven from Ecuador, four from Germany) were assigned to traditional species concepts by use of morphological keys. The specimens were compared by micro-anatomical examination with 75 specimens of Tulasnella borrowed from fungaria to obtain better insights on variation of characters. Sequences of the ITS region (127) were obtained after cloning from the fresh basidiomata and from pure cultures. Proportional variability of ITS sequences was analyzed within and among the cultures and the specimens designated to different morphospecies. Results suggested an intragenomic variation of less than 2%, an intraspecific variation of up to 4% and an interspecific divergence of more than 9% in Tulasnella. Cryptic species in Tulasnella, mostly from Ecuador, were revealed by phylogenetic analyses with 4% intraspecific divergence as a minimum threshold for delimiting species. Conventional diagnostic morphological characters appeared insufficient for species characterization. Arguments are presented for molecular delimitation of the established species Tulasnella albida, T. asymmetrica, T. eichleriana, T. cf. pinicola, T. tomaculum and T. violea.}, } @article {pmid24814699, year = {2014}, author = {Grattepanche, JD and Santoferrara, LF and McManus, GB and Katz, LA}, title = {Diversity of diversity: conceptual and methodological differences in biodiversity estimates of eukaryotic microbes as compared to bacteria.}, journal = {Trends in microbiology}, volume = {22}, number = {8}, pages = {432-437}, doi = {10.1016/j.tim.2014.04.006}, pmid = {24814699}, issn = {1878-4380}, mesh = {Bacteria/*classification/*genetics ; Computational Biology/methods ; Eukaryota/*classification/*genetics ; *Genetic Variation ; High-Throughput Nucleotide Sequencing/methods ; *Phylogeny ; }, abstract = {Recent advances such as high-throughput sequencing (HTS) have changed conceptions about the magnitude of diversity on Earth. This is especially true for microbial lineages, which have seen the discovery of great numbers of rare forms in places such as the human gut as well as diverse environments (e.g., freshwater, marine, and soil). Given the differences in perceptions of diversity for bacterial and eukaryotic microbes, including divergent species concepts, HTS tools used to eliminate errors and population-level variation in bacteria may not be appropriate for microbial eukaryotes and may eliminate valid species from the data. We discuss here how the nature of biodiversity varies among microbial groups and the extent to which HTS tools designed for bacteria are useful for eukaryotes.}, } @article {pmid24813385, year = {2014}, author = {Outlaw, DC and Ricklefs, RE}, title = {Species limits in avian malaria parasites (Haemosporida): how to move forward in the molecular era.}, journal = {Parasitology}, volume = {141}, number = {10}, pages = {1223-1232}, doi = {10.1017/S0031182014000560}, pmid = {24813385}, issn = {1469-8161}, mesh = {Animals ; Birds ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; Haemosporida/*genetics/isolation & purification ; Malaria, Avian/*parasitology ; Protozoan Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Delimiting species of malaria parasites (Haemosporida) has become increasingly problematic as new lineages of parasites are identified solely by molecular information, particularly mitochondrial cytochrome b sequence data. In this review, we highlight some of the issues, both historical and contemporary, that have hindered the development of objective criteria to diagnose, delimit and define species of haemosporidians. Defining species is not the focal interest of most researchers, most of whom merely wish to determine whether lineages identified in their samples match those of other researchers, and if so, where and in which host species. Rather than revisiting all the issues with respect to delimiting and naming species, we instead focus on finding a practical near-term resolution to the 'species problem' that utilizes the community's largest resource: mitochondrial cytochrome b DNA sequences. We recommend a standardized procedure to 'tag' these sequences, based on per cent sequence similarity, that will allow researchers to directly assess the novelty, known hosts and geographic distribution of avian malaria parasite lineages.}, } @article {pmid24806943, year = {2014}, author = {Powell, JR and Sikes, BA}, title = {Method or madness: does OTU delineation bias our perceptions of fungal ecology?.}, journal = {The New phytologist}, volume = {202}, number = {4}, pages = {1095-1097}, doi = {10.1111/nph.12823}, pmid = {24806943}, issn = {1469-8137}, mesh = {Fungi/*classification ; Mycorrhizae/*classification ; }, } @article {pmid24805963, year = {2014}, author = {Stroud, JL and Collins, RN}, title = {Improved detection of coastal acid sulfate soil hotspots through biomonitoring of metal(loid) accumulation in water lilies (Nymphaea capensis).}, journal = {The Science of the total environment}, volume = {487}, number = {}, pages = {500-505}, doi = {10.1016/j.scitotenv.2014.04.051}, pmid = {24805963}, issn = {1879-1026}, mesh = {Australia ; Environmental Monitoring/*methods ; Metalloids/*analysis ; Nymphaea/*chemistry ; Soil/*chemistry ; Soil Pollutants/*analysis ; Sulfates/*analysis ; }, abstract = {Anthropogenically disturbed coastal acid sulfate soils along the east coast of Australia, and worldwide, periodically result in the discharge of acid waters containing high concentrations of metals. Identifying priority sites (hotspots) within a catchment for acid sulfate soil remediation activities typically involves long-term monitoring of drainwater chemistry, including the capture of data on unpredictable rain-induced groundwater discharge events. To improve upon this monitoring approach, this study investigated using the water lily (Nymphaea capensis) as a biomonitor of drainage waters to identify hotspots in three acid sulfate soil impacted catchments (83 km(2)) in north-eastern New South Wales, Australia. In one catchment where the location of hotspots was known, water lily lamina concentrations of a suite of metal(loid)s were significantly (p<0.05) higher than plants collected from an unpolluted 'reference' drainage channel, thus validating the concept of using this species as a biomonitor. A catchment-scale water lily sampling program undertaken in catchments with unidentified hotspots revealed within catchment variation of plant metal concentrations up to 70-fold. High resolution maps produced from these results, therefore, provided strong evidence for the location of potential hotspots which were confirmed with measurements of drainwater chemistry during rain-induced groundwater discharge events. Median catchment lily accumulation was ca. 160 mg Al kg(-1) and 1,300 mg Fe kg(-1), with hotspots containing up to 6- and 10-fold higher Al and Fe concentrations. These findings suggest that biomonitoring with N. capensis can be an important tool to rapidly identify priority sites for remediation in acid sulfate soil impacted landscapes.}, } @article {pmid24790283, year = {2014}, author = {Stadler, M and Læssøe, T and Fournier, J and Decock, C and Schmieschek, B and Tichy, HV and Peršoh, D}, title = {A polyphasic taxonomy of Daldinia (Xylariaceae).}, journal = {Studies in mycology}, volume = {77}, number = {1}, pages = {1-143}, pmid = {24790283}, issn = {0166-0616}, abstract = {UNLABELLED: For a monograph based on a polythetic concept, several thousands of herbarium specimens, and several hundreds of freshly collected and cultured specimens of Daldinia and allied Xylariaceae, originating from around the world, were studied for morphological traits, including by SEM, and chemically by HPLC profiles using UV-visible and mass spectrometric detection. Emphasis was given to tropical material, and importantly, ancient specimens, including as many types as possible, were tracked and studied to review earlier taxonomic concepts. An epitype of D. eschscholtzii was selected as representative of the morphochemotype that is most widely distributed in the tropics. Six new species of Daldinia from the tropics and the southern Hemisphere are described. Daldinia asphalatum is resurrected, and D. cudonia is regarded as its synonym. In addition, the following binomials are epi-, iso-, neo- and/or lectotypified: Daldinia asphalatum, D. caldariorum, D. clavata, D. cuprea, D. durissima, D. eschscholtzii, D. grandis, D. loculata, and D. vernicosa. Annellosporium and Versiomyces are regarded as synonyms of Daldinia. Many new synonymies in Daldinia are proposed, and some previously published names are rejected. In total, 47 taxa in Daldinia are recognised and a key is provided. Their biogeography, chorology, and ecology, as well as the importance of their secondary metabolites, are also discussed. The previous definition of the genus is emended. The species concept is based mainly on morphological and other phenotype-derived characters because, despite diligent search, no molecular data or cultures of several of the accepted species could be obtained. Daldinia is segregated into five major groups, based on phenotypic characteristics. Some unnamed but aberrant specimens were not found in good condition and are therefore not formally described as new species. However, they are illustrated in detail in a hope that this will facilitate the discovery of fresh material in future. A preliminary molecular phylogeny based on 5.8S/ITS nrDNA including numerous representatives of all hitherto described taxa for which cultures are extant, was found basically in agreement with the above mentioned segregation of the genus, based on morphological and chemotaxonomic evidence. In the rDNA based phylogenetic tree, Daldinia appears clearly distinct from members of the genera Annulohypoxylon and Hypoxylon; nevertheless, representatives of small genera of predominantly tropical origin (Entonaema, Phylacia, Ruwenzoria, Rhopalostroma, Thamnomyces) appear to have evolved from daldinioid ancestors and are nested inside the Daldinia clade. Interestingly, these findings correlate with chemotaxonomic characters to a great extent, especially regarding the distribution of marker metabolites in their mycelial cultures. Hence, the current study revealed for the first time that fungal secondary metabolite profiles can have taxonomic value beyond the species rank and even coincide with phylogenetic data.

TAXONOMIC NOVELTIES: Daldinia andina sp. nov., D. australis sp. nov., D. hausknechtii sp. nov., D. rehmii sp. nov., D. starbaeckii sp. nov., D. theissenii sp. nov., D. cahuchosa comb. nov., D. nemorosa comb. nov.}, } @article {pmid24782502, year = {2014}, author = {Bubriski, R and Kennedy, P}, title = {A molecular and morphological analysis of the genus Rhizopogon subgenus Villosuli section Villosuli as a preface to ecological monitoring.}, journal = {Mycologia}, volume = {106}, number = {2}, pages = {353-361}, doi = {10.3852/106.2.353}, pmid = {24782502}, issn = {0027-5514}, mesh = {Basidiomycota/classification/*genetics/*growth & development/isolation & purification ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Molecular Sequence Data ; Mycorrhizae/classification/genetics/growth & development/isolation & purification ; Phylogeny ; }, abstract = {Rhizopogon (Boletales) represents a model genus for ecological studies of ectomycorrhizal fungi, but the identification of species in subgenus Villosuli section Villosuli has long been challenging due to variation in taxonomically informative morphological characters. Here we re-examine species concepts in this section using data from nuclear ribosomal internal transcribed spacer (ITS) and large subunit (LSU) sequences as well as spore measurements. Our phylogenetic analyses from 34 type and non-type collections of eight species, including the seven currently recognized in this section, found consistent support for only three species-level clades. Each of the clades had a significantly different combination of mean spore widths and Q ratios using digital-assisted measurements, which suggests both molecular and spore-based morphological approaches can be used to identify species in this section. Based on our analysis, we propose that only three species names be applied to future ecological studies: R. hawkerae, R. parksii and R. villosulus. We consider R. subareolatus and R. colossus as taxonomic synonyms of R. hawkerae and R. pseudovillosulus, R. rogersii, R. villescens and R. zelleri as taxonomic synonyms of R. villosulus.}, } @article {pmid24772276, year = {2014}, author = {Luo, S and Wu, Y and Chang, Q and Liu, Y and Yang, X and Zhang, Z and Zhang, M and Zhang, Q and Zou, F}, title = {Deep phylogeographic divergence of a migratory passerine in Sino-Himalayan and Siberian forests: the Red-flanked Bluetail (Tarsiger cyanurus) complex.}, journal = {Ecology and evolution}, volume = {4}, number = {7}, pages = {977-986}, pmid = {24772276}, issn = {2045-7758}, abstract = {Enormous mountainous forests in Sino-Himalayans and Siberia harbor important avian biodiversity in the Northern Hemisphere. Numerous studies in last two decades have been contributed to systematics and taxonomy of passerines birds in these regions and have revealed various and complex phylogeographic patterns. A passerine species Red-flanked Bluetail Tarsiger cyanurus provided a good system to manifest such evolutionary complexity. The subspecies T. c. cyanurus and T. c. rufilatus (or/and T. c. pallidior), divergent in morphology, acoustics, and migratory strategies are allopatric in Siberia and Sino-Himalayan forests, respectively. The two taxa most likely deserve full species status but rigorous genetic analysis is missing. In this study, multilocus phylogeography based on mitochondrial DNA and Z-linked DNA reveals that T. c. cyanurus and T. c. rufilatus are reciprocally monophyletic with significant statistical support and differ with a large number of diagnostic nucleotide sites resulting substantial genetic divergence. Our finding supports the proposed split of Tarsiger cyanurus s.l. that T. cyanurus and T. rufilatus should be treated as two full species. Whether "pallidior" is a subspecies or geographical form of T. rufilatus is still uncertain. Additionally, these two forest passerine species may have diverged 1.88 (3.25-1.30) Mya, which might be shaped by geographical vicariance due to grassland and desert steppe on the central Loess Plateau during the Pliocene. Taken together, this study and further suggests another independent example of North Palearctic-Sino-Himalayan phylogeographic pattern in Palearctic birds.}, } @article {pmid24768952, year = {2014}, author = {González-Casanova, A and Aguirre-von-Wobeser, E and Espín, G and Servín-González, L and Kurt, N and Spanò, D and Blath, J and Soberón-Chávez, G}, title = {Strong seed-bank effects in bacterial evolution.}, journal = {Journal of theoretical biology}, volume = {356}, number = {}, pages = {62-70}, doi = {10.1016/j.jtbi.2014.04.009}, pmid = {24768952}, issn = {1095-8541}, mesh = {Azotobacter vinelandii/*genetics ; *Evolution, Molecular ; Genome, Bacterial/*physiology ; *Models, Genetic ; }, abstract = {Bacterial genomes are mosaics with fragments showing distinct phylogenetic origins or even being unrelated to any other genetic information (ORFan genes). Thus the analysis of bacterial population genetics is in large part a collection of explanations for anomalies in relation to classical population genetic models such as the Wright-Fisher model and the Kingman coalescent that do not adequately describe bacterial population genetics, genomics or evolution. The concept of "species" as an evolutionary coherent biological group that is genetically isolated and shares genetic information through recombination among its members cannot be applied to any bacterial group. Recently, a simple probabilistic model considering the role of strong seed-bank effects in population genetics has been proposed by Blath et al. This model suggests the existence of a genetic pool with high diversity that is not subject to classical selection and extinction. We reason that certain bacterial population genetics anomalies could be explained by the prevalence of strong seed-bank effects among bacteria. To address this possibility we analyzed the genome of the bacterium Azotobacter vinelandii and show that genes that code for functions that are essential for the bacterium biology do not have a relation of ancestry with closely related bacteria, or are ORFan genes. The existence of essential genes that are not inherited from the most recent ancestor cannot be explained by classical population genetics models and is irreconcilable with the current view of genes acquired by horizontal transfer as being accessory or adaptive.}, } @article {pmid24761041, year = {2013}, author = {Morgado, LN and Noordeloos, ME and Lamoureux, Y and Geml, J}, title = {Multi-gene phylogenetic analyses reveal species limits, phylogeographic patterns, and evolutionary histories of key morphological traits in Entoloma (Agaricales, Basidiomycota).}, journal = {Persoonia}, volume = {31}, number = {}, pages = {159-178}, pmid = {24761041}, issn = {0031-5850}, abstract = {Species from Entoloma subg. Entoloma are commonly recorded from both the Northern and Southern Hemispheres and, according to literature, most of them have at least Nearctic-Palearctic distributions. However, these records are based on morphological analysis, and studies relating morphology, molecular data and geographical distribution have not been reported. In this study, we used phylogenetic species recognition criteria through gene genealogical concordance (based on nuclear ITS, LSU, rpb2 and mitochondrial SSU) to answer specific questions considering species limits in Entoloma subg. Entoloma and their geographic distribution in Europe, North America and Australasia. The studied morphotaxa belong to sect. Entoloma, namely species like the notorious poisonous E. sinuatum (E. lividum auct.), E. prunuloides (type-species of sect. Entoloma), E. nitidum and the red-listed E. bloxamii. With a few exceptions, our results reveal strong phylogeographical partitions that were previously not known. For example, no collection from Australasia proved to be conspecific with the Northern Hemisphere specimens. Almost all North American collections represent distinct and sister taxa to the European ones. And even within Europe, new lineages were uncovered for the red-listed E. bloxamii, which were previously unknown due to a broad morphological species concept. Our results clearly demonstrate the power of the phylogenetic species concept to reveal evolutionary units, to redefine the morphological limits of the species addressed and to provide insights into the evolutionary history of key morphological characters for Entoloma systematics. New taxa are described, and new combinations are made, including E. fumosobrunneum, E. pseudoprunuloides, E. ochreoprunuloides and E. caesiolamellatum. Epitypes are selected for E. prunuloides and E. bloxamii. In addition, complete descriptions are given of some other taxa used in this study for which modern descriptions are lacking, viz. E. subsinuatum, E. whiteae, E. flavifolium, E. luridum, E. bloxamii, E. madidum, E. corneri, E. callidermum and E. coeruleoviride.}, } @article {pmid24752890, year = {2014}, author = {Ellstrand, NC}, title = {Is gene flow the most important evolutionary force in plants?.}, journal = {American journal of botany}, volume = {101}, number = {5}, pages = {737-753}, doi = {10.3732/ajb.1400024}, pmid = {24752890}, issn = {1537-2197}, mesh = {Alleles ; *Biological Evolution ; *Gene Flow ; Genetic Drift ; Genomics ; *Plants ; Selection, Genetic ; }, abstract = {Although theory has demonstrated rather low levels of gene flow are sufficient to counteract opposing mutation, drift, and selection, widespread recognition of the evolutionary importance of gene flow has come slowly. The perceived role of gene flow as an evolutionary force has vacillated over the last century. In the last few decades, new methods and analyses have demonstrated that plant gene flow rates vary tremendously-from nil to very high-depending on the species and specific populations involved, and sometimes over time for individual populations. In many cases, the measured gene flow rates are evolutionarily significant at distances of hundreds and sometimes thousands of meters, occurring at levels sufficient to counteract drift, spread advantageous alleles, or thwart moderate levels of opposing local selection. Gene flow in plants is likely to often act as a cohesive force, uniting individual plant species into real evolutionary units. Also, gene flow can evolve under natural selection, decreasing or increasing. The fact of frequent, but variable, plant gene flow has important consequences for applied issues in which the presence or absence of gene flow might influence the outcome of a policy, regulatory, or management decision. Examples include the unintended spread of engineered genes, the evolution of invasiveness, and conservation. New data-rich genomic techniques allow closer scrutiny of the role of gene flow in plant evolution. Most plant evolutionists now recognize the importance of gene flow, and it is receiving increased recognition from other areas of plant biology as well.}, } @article {pmid24734911, year = {2014}, author = {Pawlowski, J and Esling, P and Lejzerowicz, F and Cedhagen, T and Wilding, TA}, title = {Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities.}, journal = {Molecular ecology resources}, volume = {14}, number = {6}, pages = {1129-1140}, doi = {10.1111/1755-0998.12261}, pmid = {24734911}, issn = {1755-0998}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Environmental Monitoring/*methods ; *Fisheries ; Foraminifera/*classification/*genetics ; Geologic Sediments/*parasitology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Salmon/growth & development ; Scotland ; }, abstract = {The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology-based identification of the macrobenthos demand highly trained specialists and are extremely time-consuming and costly, making it unsuitable for large-scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this laborious task by developing protist metabarcoding tools based on next-generation sequencing (NGS) of environmental DNA and RNA extracted from sediment samples. In this study, we analysed the response of benthic foraminiferal communities to the variation of environmental gradients associated with salmon farms in Scotland. We investigated the foraminiferal diversity based on ribosomal minibarcode sequences generated by the Illumina NGS technology. We compared the molecular data with morphospecies counts and with environmental gradients, including distance to cages and redox used as a proxy for sediment oxygenation. Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for species richness decrease in impacted sites, especially visible in the RNA data. We also detected some candidate bioindicator foraminiferal species. Based on this proof-of-concept study, we conclude that NGS metabarcoding using foraminifera and other protists has potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.}, } @article {pmid24693214, year = {2014}, author = {Kerr, PH}, title = {The Megophthalmidia (Diptera, Mycetophilidae) of North America including eight new species.}, journal = {ZooKeys}, volume = {}, number = {386}, pages = {29-83}, pmid = {24693214}, issn = {1313-2989}, abstract = {Megophthalmidia Dziedzicki is a small leiine genus (Mycetophilidae) with seven species described from the Neotropics and ten species from the Palearctic region. Two species of Megophthalmidia have been reported for North America. Recent collecting of Mycetophilidae in California and Arizona, however, shows current North American diversity of Megophthalmidia is at least on par to other regions of the world. Eight new species of Megophthalmidia are described here, increasing the number of Nearctic Megophthalmidia species to nine. Included is a particularly atypical member of the genus, M. saskia sp. n., which expands the genus concept of Megophthalmidia. Of the two species previously recorded for North America, only one actually belongs in the genus. Megophthalmidia occidentalis Johannsen, is fully described and illustrated. The other named species, M. marceda (Sherman) is illustrated and transferred to the genus Ectrepesthoneura Enderlein. A lectotype is designated for this species. A key to the species of Megophthalmidia of North America is provided. The biology of these flies is not yet known. Three of the new Megophthalmidia species - M. lenimenta, M. misericordia, and M. radiata - are only known to occur within small protected areas within the California State Park and UC Natural Reserve systems.}, } @article {pmid24685499, year = {2014}, author = {Sadowska-Deś, AD and Dal Grande, F and Lumbsch, HT and Beck, A and Otte, J and Hur, JS and Kim, JA and Schmitt, I}, title = {Integrating coalescent and phylogenetic approaches to delimit species in the lichen photobiont Trebouxia.}, journal = {Molecular phylogenetics and evolution}, volume = {76}, number = {}, pages = {202-210}, doi = {10.1016/j.ympev.2014.03.020}, pmid = {24685499}, issn = {1095-9513}, mesh = {Chlorophyta/*classification/*physiology ; Genetic Variation ; Lichens/*classification/*genetics/physiology ; *Phylogeny ; Reproduction, Asexual ; Sequence Analysis, DNA ; }, abstract = {The accurate assessment of species boundaries in symbiotic systems is a prerequisite for the study of speciation, co-evolution and selectivity. Many studies have shown the high genetic diversity of green algae from the genus Trebouxia, the most common photobiont of lichen-forming fungi. However, the phylogenetic relationships, and the amount of cryptic diversity of these algae are still poorly understood, and an adequate species concept for trebouxiophycean algae is still missing. In this study we used a multifaceted approach based on coalescence (GMYC, STEM) and phylogenetic relationships to assess species boundaries in the trebouxioid photobionts of the lichen-forming fungus Lasallia pustulata. We further investigated whether putative species of Trebouxia found in L. pustulata are shared with other lichen-forming fungi. We found that L. pustulata is associated with at least five species of Trebouxia and most of them are shared with other lichen-forming fungi, showing different patterns of species-to-species and species-to-community interactions. We also show that one of the putative Trebouxia species is found exclusively in association with L. pustulata and is restricted to thalli from localities with Mediterranean microclimate. We suggest that the species delimitation method presented in this study is a promising tool to address species boundaries within the heterogeneous genus Trebouxia.}, } @article {pmid24662681, year = {2014}, author = {Torstrom, SM and Pangle, KL and Swanson, BJ}, title = {Shedding subspecies: The influence of genetics on reptile subspecies taxonomy.}, journal = {Molecular phylogenetics and evolution}, volume = {76}, number = {}, pages = {134-143}, doi = {10.1016/j.ympev.2014.03.011}, pmid = {24662681}, issn = {1095-9513}, mesh = {Animals ; Classification/*methods ; *Genetic Speciation ; Phylogeny ; Reptiles/*classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The subspecies concept influences multiple aspects of biology and management. The 'molecular revolution' altered traditional methods (morphological traits) of subspecies classification by applying genetic analyses resulting in alternative or contradictory classifications. We evaluated recent reptile literature for bias in the recommendations regarding subspecies status when genetic data were included. Reviewing characteristics of the study, genetic variables, genetic distance values and noting the species concepts, we found that subspecies were more likely elevated to species when using genetic analysis. However, there was no predictive relationship between variables used and taxonomic recommendation. There was a significant difference between the median genetic distance values when researchers elevated or collapsed a subspecies. Our review found nine different concepts of species used when recommending taxonomic change, and studies incorporating multiple species concepts were more likely to recommend a taxonomic change. Since using genetic techniques significantly alter reptile taxonomy there is a need to establish a standard method to determine the species-subspecies boundary in order to effectively use the subspecies classification for research and conservation purposes.}, } @article {pmid24619315, year = {2014}, author = {Jones, SP and Farmahin, R and Kennedy, SW}, title = {Ethoxyresorufin-O-deethylase (EROD) induction by TCDD, PeCDF and PCB 126 in bobwhite quail hepatocytes.}, journal = {Ecotoxicology (London, England)}, volume = {23}, number = {5}, pages = {802-808}, pmid = {24619315}, issn = {1573-3017}, mesh = {Animals ; Benzofurans/*metabolism ; Cells, Cultured ; Colinus/*metabolism ; Cytochrome P-450 CYP1A1/*biosynthesis ; Enzyme Induction/drug effects ; Hepatocytes/*metabolism ; Polychlorinated Biphenyls/*metabolism ; Polychlorinated Dibenzodioxins/*metabolism ; }, abstract = {World Health Organization (WHO) toxic equivalency factors are used to calculate toxic equivalent (TEQ) concentrations of complex mixtures of dioxin-like compounds (DLCs), such as polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans and polychlorinated biphenyls (PCBs), for mammals, fish and birds. The TEQ concept assumes that all species of a taxa respond with similar sensitivity to individual DLCs, but several reports do not support this assumption for birds. Our laboratory is conducting research to attempt to uncover the fundamental mechanism(s) underlying the reasons why avian species differ in sensitivity to DLCs. The present study determined concentration-dependent effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 2,3,4,7,8-pentachlorodibenzofuran (PeCDF) and 3,3',4,4',5-pentachlorobiphenyl (PCB 126) on ethoxyresorufin-O-deethylase (EROD) activity in primary cultures of northern bobwhite quail (Colinus virginianus) hepatocytes. Bobwhite quail were studied because (1) this species is used in the laboratory for toxicity testing and (2) the amino acids at all locations within the ligand binding domain (LBD) of aryl hydrocarbon receptor 1 (AHR1) in bobwhite quail and ring necked pheasant (Phasianus colchicus) are identical. Because earlier work indicated the importance of the identity of amino acids at key sites within the AHR1 LBD, we hypothesized that bobwhite quail and ring necked pheasant hepatocytes should have similar sensitivity to EROD induction by DLCs. ECthreshold-based relative sensitivity of the bobwhite quail compared to chicken for TCDD, PeCDF and PCB 126 was 0.11, 0.17 and 0.02, respectively. The rank order of potency was PeCDF > TCDD > PCB 126. The results confirm that bobwhite quail and ring-necked pheasant hepatocytes have similar sensitivity to EROD induction by TCDD, PeCDF and PCB 126.}, } @article {pmid24616526, year = {2014}, author = {Ziemert, N and Lechner, A and Wietz, M and Millán-Aguiñaga, N and Chavarria, KL and Jensen, PR}, title = {Diversity and evolution of secondary metabolism in the marine actinomycete genus Salinispora.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {12}, pages = {E1130-9}, pmid = {24616526}, issn = {1091-6490}, support = {R01 GM086261/GM/NIGMS NIH HHS/United States ; R01 GM085770/GM/NIGMS NIH HHS/United States ; U01 TW007401/TW/FIC NIH HHS/United States ; U01-TW0007401/TW/FIC NIH HHS/United States ; GM086261/GM/NIGMS NIH HHS/United States ; GM085770/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/genetics/*metabolism ; Cluster Analysis ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Marine Biology ; Phylogeny ; }, abstract = {Access to genome sequence data has challenged traditional natural product discovery paradigms by revealing that the products of most bacterial biosynthetic pathways have yet to be discovered. Despite the insight afforded by this technology, little is known about the diversity and distributions of natural product biosynthetic pathways among bacteria and how they evolve to generate structural diversity. Here we analyze genome sequence data derived from 75 strains of the marine actinomycete genus Salinispora for pathways associated with polyketide and nonribosomal peptide biosynthesis, the products of which account for some of today's most important medicines. The results reveal high levels of diversity, with a total of 124 pathways identified and 229 predicted with continued sequencing. Recent horizontal gene transfer accounts for the majority of pathways, which occur in only one or two strains. Acquired pathways are incorporated into genomic islands and are commonly exchanged within and between species. Acquisition and transfer events largely involve complete pathways, which subsequently evolve by gene gain, loss, and duplication followed by divergence. The exchange of similar pathway types at the precise chromosomal locations in different strains suggests that the mechanisms of integration include pathway-level homologous recombination. Despite extensive horizontal gene transfer there is clear evidence of species-level vertical inheritance, supporting the concept that secondary metabolites represent functional traits that help define Salinispora species. The plasticity of the Salinispora secondary metabolome provides an effective mechanism to maximize population-level secondary metabolite diversity while limiting the number of pathways maintained within any individual genome.}, } @article {pmid24602986, year = {2014}, author = {Schuchert, P}, title = {High genetic diversity in the hydroid Plumularia setacea: a multitude of cryptic species or extensive population subdivision?.}, journal = {Molecular phylogenetics and evolution}, volume = {76}, number = {}, pages = {1-9}, doi = {10.1016/j.ympev.2014.02.020}, pmid = {24602986}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; Genes, Mitochondrial/genetics ; *Genetic Variation ; Haplotypes/genetics ; Hydrozoa/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The marine hydroid Plumularia setacea has a near-cosmopolitan distribution. As in other sessile invertebrates with limited dispersal abilities, the wide distribution could also be a taxonomic artefact and the species might in fact be a complex of sibling species. To investigate this, a set of worldwide samples of P. setacea and several closely related species was examined using the mitochondrial markers 16S and COI, as well as the nuclear marker ITS. The results suggest an even higher degree of genetic diversity than expected. Almost all sampled regions had only private haplotypes and the resulting trees split into a multitude of geographically delimited lineages, this both for the mitochondrial and nuclear markers. In the framework of a genealogical species concept, these lineages would qualify as cryptic species. Using alternative species concepts, the results could be reconciled with traditional taxonomy by regarding P. setacea as a single species with an extensive population subdivision. A rapid molecular clock, limited dispersal abilities, and localized clonal propagation are likely the factors that explain the high but dispersed genetic diversity within this species.}, } @article {pmid24593138, year = {2014}, author = {Stewart, JE and Timmer, LW and Lawrence, CB and Pryor, BM and Peever, TL}, title = {Discord between morphological and phylogenetic species boundaries: incomplete lineage sorting and recombination results in fuzzy species boundaries in an asexual fungal pathogen.}, journal = {BMC evolutionary biology}, volume = {14}, number = {1}, pages = {38}, pmid = {24593138}, issn = {1471-2148}, mesh = {Alternaria/*classification/cytology/genetics ; Citrus ; DNA, Fungal/genetics ; Microsatellite Repeats ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/microbiology ; Recombination, Genetic ; }, abstract = {BACKGROUND: Traditional morphological and biological species concepts are difficult to apply to closely related, asexual taxa because of the lack of an active sexual phase and paucity of morphological characters. Phylogenetic species concepts such as genealogical concordance phylogenetic species recognition (GCPSR) have been extensively used; however, methods that incorporate gene tree uncertainty into species recognition may more accurately and objectively delineate species. Using a worldwide sample of Alternaria alternata sensu lato, causal agent of citrus brown spot, the evolutionary histories of four nuclear loci including an endo-polygalacturonase gene, two anonymous loci, and one microsatellite flanking region were estimated using the coalescent. Species boundaries were estimated using several approaches including those that incorporate uncertainty in gene genealogies when lineage sorting and non-reciprocal monophyly of gene trees is common.

RESULTS: Coalescent analyses revealed three phylogenetic lineages strongly influenced by incomplete lineage sorting and recombination. Divergence of the citrus 2 lineage from the citrus 1 and citrus 3 lineages was supported at most loci. A consensus of species tree estimation methods supported two species of Alternaria causing citrus brown spot worldwide. Based on substitution rates at the endo-polygalacturonase locus, divergence of the citrus 2 and the 1 and 3 lineages was estimated to have occurred at least 5, 400 years before present, predating the human-mediated movement of citrus and associated pathogens out of SE Asia.

CONCLUSIONS: The number of Alternaria species identified as causing brown spot of citrus worldwide using morphological criteria has been overestimated. Little support was found for most of these morphospecies using quantitative species recognition approaches. Correct species delimitation of plant-pathogenic fungi is critical for understanding the evolution of pathogenicity, introductions of pathogens to new areas, and for regulating the movement of pathogens to enforce quarantines. This research shows that multilocus phylogenetic methods that allow for recombination and incomplete lineage sorting can be useful for the quantitative delimitation of asexual species that are morphologically indistinguishable. Two phylogenetic species of Alternaria were identified as causing citrus brown spot worldwide. Further research is needed to determine how these species were introduced worldwide, how they differ phenotypically and how these species are maintained.}, } @article {pmid24591142, year = {2014}, author = {Jolly, CJ}, title = {A Darwinian species definition and its implications.}, journal = {Evolutionary anthropology}, volume = {23}, number = {1}, pages = {36-38}, doi = {10.1002/evan.21396}, pmid = {24591142}, issn = {1520-6505}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; *Classification ; Knowledge ; Phylogeny ; }, abstract = {A review of the vast literature on the epistemology and ontology of "species" is far beyond the capacity of both the writer and the length-allotment of this essay, limiting it to a somewhat dogmatic presentation of personal opinions, few of them original. Also prohibited by the prescribed word limit is an account of species concepts considered but not adopted; in many cases, their omission does not do justice to their intellectual content.}, } @article {pmid24591139, year = {2014}, author = {Rosenberger, AL}, title = {Species: beasts of burden.}, journal = {Evolutionary anthropology}, volume = {23}, number = {1}, pages = {27-29}, doi = {10.1002/evan.21392}, pmid = {24591139}, issn = {1520-6505}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; *Classification ; Phenotype ; Primates/classification ; }, abstract = {Ernst Mayr (1904-2005) was the twentieth century's most influential writer to wrestle with the species problem. The following draws heavily on his work, albeit without presumptuously claiming to mirror his thinking or present any original ideas. As a personal meditation, I am thinking mostly of platyrrhines. Following Mayr, I adhere to what is commonly called the Biological Species Concept (BSC) as a way of thinking about a species in the real-world biosphere as a taxon. I also hold to the idea that the Linnaean category called species has the same function as other categories: a linguistic tool for organizing and retrieving information about biodiversity while embodying evolutionary hypotheses. In other words, alpha taxonomy, the area of systematics that involves identifying, naming, and classifying species, is not purely an exercise in either biology or inventory because it involves communication as well. The burdensome work of the species category stems partly from tension created by the several purposes associated with the concept: the objective observation and examination of a fundamental biological phenomenon, the collection and interpretation of data in a selective context of relevance, and the intention to deploy scientific decisions as a form of communication within a dynamic but highly structured language system.}, } @article {pmid24591138, year = {2014}, author = {Silcox, MT}, title = {A pragmatic approach to the species problem from a paleontological perspective.}, journal = {Evolutionary anthropology}, volume = {23}, number = {1}, pages = {24-26}, doi = {10.1002/evan.21386}, pmid = {24591138}, issn = {1520-6505}, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; Models, Biological ; *Paleontology ; *Phylogeny ; Primates/anatomy & histology/classification ; Tooth/anatomy & histology ; }, abstract = {The ideal scenario for paleontologists would be for the species they designate to be equivalent to the species recognized for modern animals, in the sense that they were formed as a result of the same evolutionary processes. This would mean, for example, that we could be confident that in combining extant and extinct taxa in phylogenetic analyses we would be dealing with equivalent operational taxonomic units. Notwithstanding the many thousands of pages that have been spent arguing over species concepts, the only concept that has won widespread acceptance for the designation of modern species is Mayr's Biological Species Concept (BSC).(1) In fact, whenever we complete a cladistic analysis, we assume reproductive isolation of our terminal taxa because otherwise their similarities could be the product of interbreeding rather than common ancestry. Fundamentally, we all behave as though the BSC is true.}, } @article {pmid24591136, year = {2014}, author = {Louis, EE and Lei, R}, title = {Defining species in an advanced technological landscape.}, journal = {Evolutionary anthropology}, volume = {23}, number = {1}, pages = {18-20}, doi = {10.1002/evan.21394}, pmid = {24591136}, issn = {1520-6505}, mesh = {Animals ; *Biological Evolution ; *Genetic Speciation ; *Genetics, Population ; *Genomics ; Lemur/genetics ; Madagascar ; Phylogeny ; }, abstract = {The answer to the proffered question, "What is a species?" is considered one of the fundamental issues of biological science, as well as one of the most polarizing and sometimes acrimonious problems. Dozens of species concepts have been defined, but none are universal for implementation across all taxa. Within the past thirty years, the ability to analyze DNA data has progressed to the point that multiple methodologies can be simultaneously applied to the same evolutionary questions. The use of restriction fragment length polymorphisms, microsatellites, and mitochondrial (mtDNA) and nuclear DNA (nucDNA) sequence data has unarguably changed how we look at diversity and intensified the concept debate through the proliferation of species descriptions. Over the past two decades, Madagascar's biodiversity has gone through a tremendous taxonomic expansion by the elevation of subspecies to species and through novel descriptions, especially within the nocturnal lemurs. With the tremendous continuous loss of habitat, exponential human population growth, and stochastic changes predicted over coming decades, elucidating the earth's biodiversity will never be more important than now. Here, we examine species concepts and their attendant criteria. We predict how technological advances will alter, improve and, we hope, fully consolidate the unity of thoughts related to this central topic of evolutionary biology and its numerous interconnected disciplines.}, } @article {pmid24591135, year = {2014}, author = {Yoder, AD}, title = {Gene flow happens.}, journal = {Evolutionary anthropology}, volume = {23}, number = {1}, pages = {15-17}, doi = {10.1002/evan.21397}, pmid = {24591135}, issn = {1520-6505}, mesh = {Animals ; Anthropology, Physical ; Cheirogaleidae ; *Evolution, Molecular ; *Gene Flow ; Humans ; }, abstract = {Debate over what is a species was already considered old hat when Darwin wrote his seminal abstract (as he called it) more than 150 years ago.(1) Endless papers, workshops, and symposia have been presented in an effort to "solve" the species problem. Yet, here we are, at it again. Has there been any progress? I believe that there has been, and that among the many advances enabled by the genomics revolution, progress on species concepts and species recognition is among them. To quote Feder and colleagues,(2) we are on the brink of a "unified theory of speciation genomics."}, } @article {pmid24591134, year = {2014}, author = {Zimmermann, E and Radespiel, U}, title = {Species concepts, diversity, and evolution in primates: lessons to be learned from mouse lemurs.}, journal = {Evolutionary anthropology}, volume = {23}, number = {1}, pages = {11-14}, doi = {10.1002/evan.21388}, pmid = {24591134}, issn = {1520-6505}, mesh = {Animals ; *Biological Evolution ; Cheirogaleidae/*anatomy & histology/*classification ; *Genetic Variation ; Species Specificity ; }, abstract = {Humans primarily rely on vision when categorizing the world. If you just look at the same-sized but strikingly differently colored Neotropical poison-dart frogs such as strawberry frogs (Fig.), you would be convinced that they must belong to different species. However, this is an excellent example of a polymorphic species, meaning that although these frogs look quite different, mating decisions are made based on their conspicuous and species-specific advertisements calls, which are not primarily linked to specific color pattern. The situation is quite different among nocturnal primates living in dense forest environments, such as the tiny nocturnal Malagasy mouse lemurs. In this case, even geographically isolated, well-accepted species look superficially quite similar and are therefore often termed cryptic species (Fig.). Some morphs are a bit larger than others or show minor phenotypic differences, but morph-specific differences are difficult to detect in living subjects. This phenomenon explains why, until the end of the last century, species diversity in mouse lemurs was assumed to be low, with only two morphologically distinct species. Over the last two decades, several international working groups, including our own, undertook a massive island-wide sampling effort, including DNA sequencing and phylogenetic analyses of mouse lemurs. These revealed a 10-fold higher species diversity, with 21 currently described species. Are these new species, mostly defined based on the phylogenetic species concept (sensu Cracraft), or independent evolutionary lineages or, perhaps, only artifacts of taxonomic inflation? What is a species? How can we identify primate species? How and why do species emerge during evolution?}, } @article {pmid24591133, year = {2014}, author = {Rylands, AB and Mittermeier, RA}, title = {Primate taxonomy: species and conservation.}, journal = {Evolutionary anthropology}, volume = {23}, number = {1}, pages = {8-10}, doi = {10.1002/evan.21387}, pmid = {24591133}, issn = {1520-6505}, mesh = {Animals ; *Anthropology, Physical ; Biological Evolution ; Primates/*classification ; Zoology ; }, abstract = {Primatology as a discrete branch of science involving the study of primate behavior and ecology took off in the 1960s after discovery of the importance of primates as models for biomedical research and the realization that primates provide insights into the evolutionary history of humans. Osman Hill's unfortunately incomplete monograph series on the comparative anatomy and taxonomy of the primates(1) and the Napiers' 1967 A Handbook of Living Primates(2) recorded the world's view of primate diversity at this time. This taxonomy remained the baseline for nearly three decades, with the diversity of each genus being represented by some species, but extensively as subspecies.}, } @article {pmid24591131, year = {2014}, author = {Groves, C}, title = {The species in primatology.}, journal = {Evolutionary anthropology}, volume = {23}, number = {1}, pages = {2-4}, doi = {10.1002/evan.21395}, pmid = {24591131}, issn = {1520-6505}, mesh = {Animals ; *Anthropology, Physical ; *Biological Evolution ; Primates/*classification ; *Zoology ; }, abstract = {Biologists of the late eighteenth and early nineteenth centuries all bandied about the term "species," but very rarely actually said what they meant by it. Often, however, one can get inside their thinking by piecing together some of their remarks. One of the most nearly explicit-appropriately, for the man who wrote a book called The Origin of Species - was Charles Darwin: "Practically, when a naturalist can unite two forms together by others having intermediate characters, he treats the one as a variety of the other… He later translated this into evolutionary terms: "Hereafter, we shall be compelled to acknowledge that the only distinction between species and well-marked varieties is, that the latter are known, or believed, to be connected at the present day by intermediate gradations, whereas species were formerly thus connected"(1:484-5.)}, } @article {pmid30708415, year = {2014}, author = {Ramírez-Suárez, A and Rosas-Hernández, L and Alcasio-Rangel, S and Powers, TO}, title = {First Report of the Root-Knot Nematode Meloidogyne enterolobii Parasitizing Watermelon from Veracruz, Mexico.}, journal = {Plant disease}, volume = {98}, number = {3}, pages = {428}, doi = {10.1094/PDIS-06-13-0636-PDN}, pmid = {30708415}, issn = {0191-2917}, abstract = {In early April 2012, a sampling of watermelon crop Citrullus lanatus (Thunb.) Matsum & Nakai, 1916 cv. Sunsugar took place as part of the National System of Epidemiological Phytosanitary Surveillance (SINAVEF-MEX). This sampling was conducted at Riachuelos locality, Tecolutla, Veracruz, located at the geographic coordinates: 20.42008° N and 96.9627° W, within 50 meters of the Gulf of Mexico. Plants showed yellowing, stunting, and high levels of infection expressed by extensive galling on the roots. These symptoms were reproduced in the greenhouse on watermelon cv. Sunsugar. Egg masses were extracted to obtain juveniles (J2). Female necks and perineal patterns were mounted as well as males and J2 to take measurements of selected morphometric characters. To determine the nematode identity based on a morphological species concept, the following characters were considered. Females: stylet length, DGO and perineal pattern; males: stylet length; J2: body, stylet, tail, and hyaline tail terminus length. The morphometric analysis showed that those values corresponded to the original description of the root-knot nematode Meloidogyne enterolobii Yang & Eisenback, 1983 (=M. mayaguensis Rammah & Hirschmann, 1988) (1,2,3,4). For confirmation of this finding, a molecular diagnosis was performed using markers located in rDNA and mtDNA by PCR amplification and DNA sequencing. The rDNA region analyzed was the expansion segments D2-D3 of the 28S gene (primers D2A and D3B). This produced an amplified product of 780 bp. With regard to mtDNA, an amplification of the marker located between the genes COII/16S (primers C2F3 and 1108) resulted in a fragment of 705 bp that is specific for M. enterolobii (1). Sequences of the amplified products were compared with sequences from GenBank (NCBI). The sequences of both markers exhibited 99 and 100% identity with sequences corresponding to M. enterolobii isolates from Florida, Puerto Rico, and China. Maximum likelihood phylogenetic trees of rDNA and mtDNA sequences demonstrated that the Mexican isolate of M. enterolobii grouped among other isolates exclusive of other Meloidogyne species. The detection of this nematode in Veracruz, Mexico, expands the previously known worldwide distribution. It represents a serious threat due to the high level of aggressiveness shown in watermelon, which was so severe that growers had to change to a different crop. To our knowledge, this is the first report of the root-knot nematode M. enterolobii infecting watermelon cv. Sunsugar in Veracruz, Mexico. References: (1) J. Brito et al. J. Nematol. 36:232, 2004. (2) G. Karssen et al. ZooKeys 181:67, 2012. (3) A. Rammah and H. Hirshmann. J. Nematol. 20:58, 1988. (4) B. Yang and J. Eisenback. J. Nematol. 15:381, 1983.}, } @article {pmid24576678, year = {2014}, author = {Tremmel, M and Müller, C}, title = {Diet dependent experience and physiological state shape the behavior of a generalist herbivore.}, journal = {Physiology & behavior}, volume = {129}, number = {}, pages = {95-103}, doi = {10.1016/j.physbeh.2014.02.030}, pmid = {24576678}, issn = {1873-507X}, mesh = {Adaptation, Psychological ; Animals ; Body Weight ; Brassicaceae ; Coleoptera/growth & development/*physiology ; Diapause, Insect ; Diet ; Exploratory Behavior ; *Feedback, Physiological ; *Feeding Behavior ; Female ; *Herbivory ; Larva/growth & development ; Male ; Motor Activity ; Plant Leaves ; }, abstract = {The performance of herbivorous insects depends on a balance of nutrient uptake and toxin avoidance. Whereas high concentrations of defensive plant metabolites impair both generalists and specialists, generalists are likely less adapted to particular hosts and thus more negatively affected by plant defense traits. Furthermore, resulting diet-dependent differences in the physiological state and the gained experience of an animal may shape its behavior. Here, we investigated the effects of life-long experience with leaves of different quality on the performance and various behavioral traits of the generalist leaf beetle Galeruca tanaceti. Rearing individuals continuously on three different diets [young leaves, old leaves, or leaves of different age of cabbage (Brassicaceae) in alternating order every other day], we found that relative growth rates (RGRs) of the larvae were higher when feeding on young leaves than when feeding on the other diets. Feeding on leaves of different age in alternating order reduced the performance of G. tanaceti, indicating costs involved in diet mixing. The experience gained by the respective food qualities shaped the preference behavior in adult beetles. Positive and negative feedbacks of animals reared on young or old leaves, respectively, led to a preference towards young leaves. In contrast, feedback was probably prevented for animals reared on alternating diet, which did not exhibit any preferences. Older adults did not show any diet-dependent differences in body mass due to physiological changes during adult development. A battery of behavioral tests with the older adults revealed that the behavior was consistent over context and partially over time but behaviors did not differ in dependence of the diet experience. We retrieved three personality dimensions for this species, namely boldness, activity, and exploration. The behavioral structure was very similar to earlier findings for another chrysomelid species, indicating a broader validity of the concept of personality dimensions in insects. Our results demonstrate the importance of both experience- and state-dependence when investigating behavioral phenotypes.}, } @article {pmid24565085, year = {2013}, author = {Wu, Q and Smith-Miles, K and Zhou, T and Tian, T}, title = {Stochastic modelling of biochemical systems of multi-step reactions using a simplified two-variable model.}, journal = {BMC systems biology}, volume = {7 Suppl 4}, number = {Suppl 4}, pages = {S14}, pmid = {24565085}, issn = {1752-0509}, mesh = {*Models, Biological ; RNA Stability ; RNA, Messenger/chemistry ; Ribosomal Proteins/genetics ; Stochastic Processes ; Systems Biology/*methods ; }, abstract = {BACKGROUND: A fundamental issue in systems biology is how to design simplified mathematical models for describing the dynamics of complex biochemical reaction systems. Among them, a key question is how to use simplified reactions to describe the chemical events of multi-step reactions that are ubiquitous in biochemistry and biophysics. To address this issue, a widely used approach in literature is to use one-step reaction to represent the multi-step chemical events. In recent years, a number of modelling methods have been designed to improve the accuracy of the one-step reaction method, including the use of reactions with time delay. However, our recent research results suggested that there are still deviations between the dynamics of delayed reactions and that of the multi-step reactions. Therefore, more sophisticated modelling methods are needed to accurately describe the complex biological systems in an efficient way.

RESULTS: This work designs a two-variable model to simplify chemical events of multi-step reactions. In addition to the total molecule number of a species, we first introduce a new concept regarding the location of molecules in the multi-step reactions, which is the second variable to represent the system dynamics. Then we propose a simulation algorithm to compute the probability for the firing of the last step reaction in the multi-step events. This probability function is evaluated using a deterministic model of ordinary differential equations and a stochastic model in the framework of the stochastic simulation algorithm. The efficiency of the proposed two-variable model is demonstrated by the realization of mRNA degradation process based on the experimentally measured data.

CONCLUSIONS: Numerical results suggest that the proposed new two-variable model produces predictions that match the multi-step chemical reactions very well. The successful realization of the mRNA degradation dynamics indicates that the proposed method is a promising approach to reduce the complexity of biological systems.}, } @article {pmid24561967, year = {2014}, author = {Wahlqvist, ML}, title = {Ecosystem Health Disorders - changing perspectives in clinical medicine and nutrition.}, journal = {Asia Pacific journal of clinical nutrition}, volume = {23}, number = {1}, pages = {1-15}, doi = {10.6133/apjcn.2014.23.1.20}, pmid = {24561967}, issn = {0964-7058}, mesh = {Agriculture/methods/trends ; Animals ; Clinical Medicine/*trends ; Conservation of Natural Resources ; Diet ; *Ecosystem ; Evidence-Based Practice ; Food Contamination ; Food Microbiology ; *Health Status ; Humans ; Inflammation/genetics ; Nutritional Requirements ; Nutritional Sciences/*trends ; Soil ; Sunlight ; Water ; }, abstract = {The inseparability of people from their ecosystem without biological change is increasingly clear. The discrete species concept is becoming more an approximation as the interconnectedness of all things, animate and inanimate, becomes more apparent. Yet this was evident even to our earliest Homo Sapiens sapiens ancestors as they hunted and gathered from one locality to another and migrated across the globe. During a rather short 150-200,000 years of ancestral history, we have changed the aeons-old planet and our ecology with dubious sustainability. As we have changed the ecosystems of which we are a part, with their opportunities for shelter, rest, ambulation, discourse, food, recreation and their sensory inputs, we have changed our shared biology and our health prospects. The rate of ecosystem change has increased quantitatively and qualitatively and so will that of our health patterns, depending on our resilience and how linear, non-linear or fractal-like the linkage. Our health-associated ecosystem trajectories are uncertain. The interfaces between us and our environment are blurred, but comprise time, biorhythms, prokaryotic organisms, sensory (auditory, visual, tactile, taste and smell), conjoint movement, endocrine with various external hormonal through food and contaminants, the reflection of soil and rock composition in the microbes, plants, insects and animals that we eat (our biogeology) and much more. We have sought ways to optimise our health through highly anthropocentric means, which have proven inadequate. Accumulated ecosystem change may now overwhelm our health. On these accounts, more integrative approaches and partnerships for health care practice are required.}, } @article {pmid24554969, year = {2013}, author = {Roche, B and Benbow, ME and Merritt, R and Kimbirauskas, R and McIntosh, M and Small, PL and Williamson, H and Guégan, JF}, title = {Identifying the Achilles' heel of multi-host pathogens: The concept of keystone "host" species illustrated by Mycobacterium ulcerans transmission.}, journal = {Environmental research letters : ERL [Web site]}, volume = {8}, number = {4}, pages = {045009}, pmid = {24554969}, issn = {1748-9326}, support = {R01 TW007550/TW/FIC NIH HHS/United States ; R03 AI062719/AI/NIAID NIH HHS/United States ; }, abstract = {Pathogens that use multiple host species are an increasing public health issue due to their complex transmission, which makes them difficult to mitigate. Here, we explore the possibility of using networks of ecological interactions among potential host species to identify the particular disease-source species to target to break down transmission of such pathogens. We fit a mathematical model on prevalence data of Mycobacterium ulcerans in western Africa and we show that removing the most abundant taxa for this category of pathogen is not an optimal strategy to decrease the transmission of the mycobacterium within aquatic ecosystems. On the contrary, we reveal that the removal of some taxa, especially Oligochaeta worms, can clearly reduce rates of pathogen transmission and should be considered as a keystone organism for its transmission because it leads to a substantial reduction in pathogen prevalence regardless of the network topology. Besides its potential application for the understanding of M. ulcerans ecology, we discuss about how networks of species interactions can modulate transmission of multi-host pathogens.}, } @article {pmid24549110, year = {2014}, author = {Daïnou, K and Mahy, G and Duminil, J and Dick, CW and Doucet, JL and Donkpégan, AS and Pluijgers, M and Sinsin, B and Lejeune, P and Hardy, OJ}, title = {Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae).}, journal = {Heredity}, volume = {113}, number = {1}, pages = {74-85}, pmid = {24549110}, issn = {1365-2540}, mesh = {Africa ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; DNA Primers/genetics ; Evolution, Molecular ; *Genetic Speciation ; Haplotypes/genetics ; Microsatellite Repeats/genetics ; Models, Genetic ; Molecular Sequence Data ; Moraceae/*anatomy & histology/*genetics ; Multigene Family/genetics ; *Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.}, } @article {pmid24548010, year = {2016}, author = {Kong, L and Wang, W and Cong, H and Son Nguyen, T and Yang, Q and Wu, Y and Li, Y}, title = {Molecular evidence revealed Lepus hainanus and L. peguensis have a conspecific relationship.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {265-269}, doi = {10.3109/19401736.2014.888550}, pmid = {24548010}, issn = {2470-1408}, mesh = {Animals ; Bayes Theorem ; Classification ; DNA, Mitochondrial/*genetics ; *Genetic Speciation ; Genetic Variation ; Hares/classification/*genetics ; Hybridization, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Accurate species delimitation in Lepus was often hindered by highly conserved morphology and frequent introgression. In this study, we used rigorous molecular species delimitation methods to evaluate the taxonomic status of Hainan hare (Lepus hainanus) which has been traditionally identified as a distinct species, or a subspecies of Burmese hare (L. peguensis). The genetic distance and phylogenetic network support L. hainanus and L. peguensis are conspecific. However, the phylogenetic species concept and Bayesian species delimitation analysis based on combined mtDNA supported they are different species. The discordance between different methods can be explained by different species criterion. By taking into account our conflict results, we hold the opinion that adoption of the phylogenetic species concept and Bayesian species delimitation analysis would increase the risk of taxonomic inflation of island biota or otherwise spatially isolated population. Conservatively, we suggest that L. hainanus and L. peguensis are conspecific based on the results of our genetic divergence and phylogenetic network exclusively.}, } @article {pmid24521299, year = {2014}, author = {Belema, M and Nguyen, VN and Bachand, C and Deon, DH and Goodrich, JT and James, CA and Lavoie, R and Lopez, OD and Martel, A and Romine, JL and Ruediger, EH and Snyder, LB and St Laurent, DR and Yang, F and Zhu, J and Wong, HS and Langley, DR and Adams, SP and Cantor, GH and Chimalakonda, A and Fura, A and Johnson, BM and Knipe, JO and Parker, DD and Santone, KS and Fridell, RA and Lemm, JA and O'Boyle, DR and Colonno, RJ and Gao, M and Meanwell, NA and Hamann, LG}, title = {Hepatitis C virus NS5A replication complex inhibitors: the discovery of daclatasvir.}, journal = {Journal of medicinal chemistry}, volume = {57}, number = {5}, pages = {2013-2032}, doi = {10.1021/jm401836p}, pmid = {24521299}, issn = {1520-4804}, mesh = {Animals ; Antiviral Agents/chemistry/pharmacokinetics/*pharmacology ; Area Under Curve ; Carbamates ; Dogs ; Drug Discovery ; Enzyme Inhibitors/chemistry/pharmacokinetics/*pharmacology ; Hepacivirus/*drug effects/enzymology/physiology ; Imidazoles/chemistry/pharmacokinetics/*pharmacology ; Magnetic Resonance Spectroscopy ; Pyrrolidines ; Rats ; Spectrometry, Mass, Electrospray Ionization ; Structure-Activity Relationship ; Valine/analogs & derivatives ; Viral Nonstructural Proteins/*antagonists & inhibitors ; Virus Replication/*drug effects ; }, abstract = {The biphenyl derivatives 2 and 3 are prototypes of a novel class of NS5A replication complex inhibitors that demonstrate high inhibitory potency toward a panel of clinically relevant HCV strains encompassing genotypes 1-6. However, these compounds exhibit poor systemic exposure in rat pharmacokinetic studies after oral dosing. The structure-activity relationship investigations that improved the exposure properties of the parent bis-phenylimidazole chemotype, culminating in the identification of the highly potent NS5A replication complex inhibitor daclatasvir (33) are described. An element critical to success was the realization that the arylglycine cap of 2 could be replaced with an alkylglycine derivative and still maintain the high inhibitory potency of the series if accompanied with a stereoinversion, a finding that enabled a rapid optimization of exposure properties. Compound 33 had EC50 values of 50 and 9 pM toward genotype-1a and -1b replicons, respectively, and oral bioavailabilities of 38-108% in preclinical species. Compound 33 provided clinical proof-of-concept for the NS5A replication complex inhibitor class, and regulatory approval to market it with the NS3/4A protease inhibitor asunaprevir for the treatment of HCV genotype-1b infection has recently been sought in Japan.}, } @article {pmid24509794, year = {2014}, author = {Kaczmarska, I and Mather, L and Luddington, IA and Muise, F and Ehrman, JM}, title = {Cryptic diversity in a cosmopolitan diatom known as Asterionellopsis glacialis (Fragilariaceae): Implications for ecology, biogeography, and taxonomy.}, journal = {American journal of botany}, volume = {101}, number = {2}, pages = {267-286}, doi = {10.3732/ajb.1300306}, pmid = {24509794}, issn = {1537-2197}, mesh = {Atlantic Ocean ; DNA/*analysis ; DNA, Ribosomal ; Diatoms/*genetics ; Ecology ; *Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Variation ; Pacific Ocean ; *Phylogeny ; Plastids/genetics ; RNA, Ribosomal, 18S ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {PREMISE OF THE STUDY: Diatoms have long been known as the most species-rich of algal groups, with a wide range of estimates for species number (20-200 k) due to differing species concepts. The fine valve structure in Asterionellopsis glacialis, a diatom believed cosmopolitan and eurytopic, has never been systematically examined using modern microscopy and is an excellent candidate to genetically test morphology-based conspecificity among its geographically distant culture isolates.

METHODS: Isolates from the Atlantic and Pacific Oceans that were morphologically delineated as A. glacialis were genetically characterized using three nuclear DNA regions (two 18S rDNA fragments and ITS region) and one plastidal (rbcL) and one mitochondrial gene (cox1) and related to SEM-based morphometrics.

KEY RESULTS: Five genetically distinct groupings were found, four of which are new to science. ITS2 RNA transcript secondary structure was species specific as were plastidal and mitochondrial genes, while the 18S gene fragments did not diverge sufficiently to segregate new species efficiently. We genetically circumscribed the A. glacialis epitype.

CONCLUSIONS: The morphological diversification of the species examined in this study lags behind their genetic divergence. The currently accepted 2% cutoff level of operational taxonomic unit (OTU) clustering in 18S rDNA environmental sequencing is too high to recognize genetic diversity in Asterionellopsis and very likely in many other species. Our results support the notion that a considerable number of species and diversity remain to be discovered among diatoms and that species number may be more in line with higher estimates. Molecular signatures of the species discovered here will aid in their globally consistent identification and ultimate understanding of their ecology.}, } @article {pmid24505070, year = {2014}, author = {Kurtzman, CP}, title = {Use of gene sequence analyses and genome comparisons for yeast systematics.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 2}, pages = {325-332}, doi = {10.1099/ijs.0.054197-0}, pmid = {24505070}, issn = {1466-5034}, mesh = {Classification/*methods ; DNA, Fungal/genetics ; Genome, Fungal ; Genomics/*methods ; *Phylogeny ; Sequence Analysis, DNA/*methods ; Yeasts/*classification/genetics ; }, abstract = {Detection, identification and classification of yeasts have undergone a major transformation in the past decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined gene sequences from domains 1 and 2 (D1/D2) of large subunit rRNA and from the internal transcribed spacer (ITS) now permits many laboratories to identify species accurately and this has led to a doubling in the number of known species of yeasts over the past decade. Phylogenetic analysis of gene sequences has resulted in major revision of yeast systematics, resulting in redefinition of nearly all genera. Future work calls for application of genomics to refine our understanding of the species concept and to provide a better understanding of the boundaries of genera and higher levels of classification. This increased understanding of phylogeny is expected to allow prediction of the genetic potential of various clades and species for biotechnological applications and adaptation to environmental changes.}, } @article {pmid28040099, year = {2014}, author = {Wang, L and Zhuang, Y and Zhang, H and Lin, X and Lin, S}, title = {DNA barcoding species in Alexandrium tamarense complex using ITS and proposing designation of five species.}, journal = {Harmful algae}, volume = {31}, number = {}, pages = {100-113}, doi = {10.1016/j.hal.2013.10.013}, pmid = {28040099}, issn = {1878-1470}, abstract = {Alexandrium species can be very difficult to identify, with A. catenella, A. tamarense, and A. fundyense that compose "Alexandrium tamarense species complex" (Atama complex) as a distinct example. DNA barcoding is promising to offer a solution but remains to be established. In this study, we examined the utility of ITS in resolving the Atama species complex, by analyzing previously studied strains plus unstudied Chinese strains within the LSU- and SSU-rDNA based group/clade frameworks recently established. We further investigated the presence of intragenomic polymorphism and its implications in species delimitation. Similar to the previous SSU and LSU results, our ITS-based phylogenies divided the complex to five clusters, but with longer and evener branch lengths between the clusters. Based on the ITS region, the inter-cluster genetic distances (p=0.134-0.216) were consistently and substantially greater than intra-cluster genetic distances (p=0.000-0.066), with an average inter-cluster (species) distance (p=0.167) 7.6-fold of the average intraspecific difference (p=0.022), qualifying the approximately 510-520bp ITS as a DNA barcode for Atama complex. We detected varying levels of intragenomic polymorphism in ITS but found that this did not impact the taxon-resolving power of this gene. With this DNA barcode, the new East and South China Sea strains and one Antarctic strain were placed in Clade IIC/Group IV, even though there were 7-10 polymorphic sites in their ITS, in contrast to none in SSU. Furthermore, our results suggest that the five clusters are recognizable as distinct species according to the phylogenetic species concept. Based on the phylogenetic placements of the type-locality strains of the existing three morphospecies and the dominant localities of other strains, we propose that Group I/Clade I be designated as A. fundyense, Group III/Clade IIB as A. tamarense, Group IV/Clade IIC as A. catenella, Group II/Clade IIA as A. mediterranis, and Group V/Clade IID as A. australis.}, } @article {pmid27007320, year = {2013}, author = {Guidone, M and Thornber, C and Wysor, B and O'Kelly, CJ}, title = {Molecular and morphological diversity of Narragansett Bay (RI, USA) Ulva (Ulvales, Chlorophyta) populations.}, journal = {Journal of phycology}, volume = {49}, number = {5}, pages = {979-995}, doi = {10.1111/jpy.12108}, pmid = {27007320}, issn = {0022-3646}, abstract = {Macroalgal bloom-forming species occur in coastal systems worldwide. However, due to overlapping morphologies in some taxa, accurate taxonomic assessment and classification of these species can be quite challenging. We investigated the molecular and morphological characteristics of 153 specimens of bloom-forming Ulva located in and around Narragansett Bay, RI, USA. We analyzed sequences of the nuclear internal transcribed spacer 1 region (ITS1) and the chloroplast-encoded rbcL; based on the ITS1 data, we grouped the specimens into nine operational taxonomic units (OTUs). Eight of these OTUs have been previously reported to exist, while one is novel. Of the eight OTUs, all shared sequence identity with previously published sequences or differed by less than 1.5% sequence divergence for two molecular markers. Previously, 10 species names were reported for Ulva in Rhode Island (one blade and nine tube-forming species) based upon morphological classification alone. Of our nine OTUs, three contained blade-forming specimens (U. lactuca, U. compressa, U. rigida), one OTU had a blade with a tubular stipe, and six contained unbranched and/or branched tubular morphologies (one of these six, U. compressa, had both a blade and a tube morphology). While the three blade-forming OTUs in Narragansett Bay can frequently be distinguished by careful observations of morphological characteristics, and spatial/temporal distribution, it is much more difficult to distinguish among the tube-forming specimens based upon morphology or distribution alone. Our data support the molecular species concept for Ulva, and indicate that molecular-based classifications of Ulva species are critical for proper species identification, and subsequent ecological assessment or mitigation of Ulva blooms.}, } @article {pmid26462580, year = {2013}, author = {Argôlo-Filho, RC and Loguercio, LL}, title = {Bacillus thuringiensis Is an Environmental Pathogen and Host-Specificity Has Developed as an Adaptation to Human-Generated Ecological Niches.}, journal = {Insects}, volume = {5}, number = {1}, pages = {62-91}, pmid = {26462580}, issn = {2075-4450}, abstract = {Bacillus thuringiensis (Bt) has been used successfully as a biopesticide for more than 60 years. More recently, genes encoding their toxins have been used to transform plants and other organisms. Despite the large amount of research on this bacterium, its true ecology is still a matter of debate, with two major viewpoints dominating: while some understand Bt as an insect pathogen, others see it as a saprophytic bacteria from soil. In this context, Bt's pathogenicity to other taxa and the possibility that insects may not be the primary targets of Bt are also ideas that further complicate this scenario. The existence of conflicting research results, the difficulty in developing broader ecological and genetics studies, and the great genetic plasticity of this species has cluttered a definitive concept. In this review, we gathered information on the aspects of Bt ecology that are often ignored, in the attempt to clarify the lifestyle, mechanisms of transmission and target host range of this bacterial species. As a result, we propose an integrated view to account for Bt ecology. Although Bt is indeed a pathogenic bacterium that possesses a broad arsenal for virulence and defense mechanisms, as well as a wide range of target hosts, this seems to be an adaptation to specific ecological changes acting on a versatile and cosmopolitan environmental bacterium. Bt pathogenicity and host-specificity was favored evolutionarily by increased populations of certain insect species (or other host animals), whose availability for colonization were mostly caused by anthropogenic activities. These have generated the conditions for ecological imbalances that favored dominance of specific populations of insects, arachnids, nematodes, etc., in certain areas, with narrower genetic backgrounds. These conditions provided the selective pressure for development of new hosts for pathogenic interactions, and so, host specificity of certain strains.}, } @article {pmid26185855, year = {2013}, author = {Borovec, R and Oberprieler, RG}, title = {Afrophloeus, a new genus of African weevils of the tribe Embrithini (Coleoptera: Curculionidae: Entiminae), with description of a new species and notes on the composition of Embrithini.}, journal = {Zootaxa}, volume = {3693}, number = {}, pages = {365-378}, doi = {10.11646/zootaxa.3693.3.7}, pmid = {26185855}, issn = {1175-5326}, mesh = {Animal Distribution/*physiology ; Animals ; Female ; Male ; South Africa ; South Australia ; Species Specificity ; Weevils/*anatomy & histology/*classification/physiology ; }, abstract = {A new genus, Afrophloeus gen. n., is described for three South African weevil species assigned to the tribe Embrithini Marshall: Trachyphloeus spathulatus Boheman (type species), T. squamifer Boheman and Afrophloeus dilaticornis sp. n. Afrophloeus squamifer has been introduced to Australia in 1992 and become an agricultural pest in South Australia in recent years. All three species are illustrated and keyed. The concept and composition of Embrithini is discussed and revised. Thirteen genera are newly transferred to Embrithini: Bryochaeta Pascoe, Cosmorhinus Schoenherr, Cycliscus Schoenherr, Glyptosomus Schoenherr, Porpacus Schoenherr and Syntaphocerus J. Thomson from the tribe Oosomini Lacordaire and Bicodes Marshall, Goniorhinus Faust, Holorygma Marshall, Lecanophora Aurivillius, Neobicodes Hustache, Sympiezorhynchus Schoenherr and Zeugorygma Marshall from the tribe Myorhinini Marseul. Two genera are excluded from Embrithini, Epibrithus Marshall and Rhyncholobus Gahan, left without tribal assignment in Entiminae. In its revised concept the tribe Embrithini includes 67 genera of African Entiminae.}, } @article {pmid26120714, year = {2013}, author = {Lee, MY and Munroe, TA and Shao, KT}, title = {Symphurus orientalis (Bleeker) redefined based on morphological and molecular characters (Pleuronectiformes: Cynoglossidae).}, journal = {Zootaxa}, volume = {3620}, number = {}, pages = {379-403}, doi = {10.11646/zootaxa.3620.3.3}, pmid = {26120714}, issn = {1175-5326}, mesh = {Animal Distribution ; Animals ; Electron Transport Complex IV/genetics ; Female ; Fish Proteins/*genetics ; Flatfishes/*anatomy & histology/classification/*genetics/physiology ; Japan ; Male ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Taiwan ; }, abstract = {Aphoristia (= Symphurus) orientalis Bleeker 1879, collected from an unspecified depth and location in Japanese waters, is the first described species of symphurine tonguefish from Indo-Pacific waters. The original description with accompanying illustration is based on the unique holotype specimen and provides limited diagnostic characters for this taxon. Subsequent to its description, the holotype of A. orientalis has been lost. Limited diagnostic information and loss of the holotype have caused considerable confusion to subsequent systematic studies regarding the identity of this and similar tonguefish species occurring in the Indo-West Pacific region. Several, often-cited, taxonomic accounts purportedly redescribing S. orientalis are erroneous because they include more than one species in these redescriptions. These erroneous redescriptions not only confused the species concept of S. orientalis (Bleeker), but also confounded the systematics of similar Indo-West Pacific tonguefishes. Symphurus novemfasciatus Shen and Lin, described on two specimens collected in southern Taiwan, shares many morphological and pigmentation features similar to those of S. orientalis. Morphological data from a large series of tonguefishes collected in Taiwanese and Japanese waters, as well as molecular data from a smaller number of specimens from these locations, including the type locality of S. novemfasciatus, confirm the presence of only one species, S. orientalis (Bleeker), among these specimens. Symphurus novemfasciatus Shen and Lin is therefore regarded as ajunior subjective synonym of S. orientalis. Symphurus orientalis is redefined based on a large series of specimens identified by a consistent set of morphological criteria, and a neotype is designated to stabilize nomenclature and systematics of this species. Symphurus orientalis differs from congeners by its combination of: a predominant 1-2-2-2-2 pattern of interdigitation of proximal dorsal-fin pterygiophores and neural spines, 12 caudal-fin rays, 9 abdominal and 52-55 total vertebrae, four hypurals, 96-101 dorsal-fin rays, 82-89 anal-fin rays, 87-99 longitudinal scale rows, 37-42 transverse scales, 5-11 (usually) distinct, complete or incomplete, blackish-brown crossbands on the ocular side, uniformly white blind side, and conspicuous bluish-black peritoneum. Documenting morphological variation for S. orientalis represents the most important step towards clarification of the identity of this and other symphurine tonguefish species from this region. Reliable identification of specimens of S. orientalis also provides the foundation for evaluating the status of several other, poorly-known, nominal species of Indo-West Pacific tonguefishes that have features similar to those of S. orientalis. Improved identifications will lead to better knowledge on the geographic distribution of S. orientalis and these other species, as well as to improve estimates of biodiversity and the biogeography of Indo-West Pacific symphurine tonguefishes.}, } @article {pmid25780574, year = {2013}, author = {Borday, C and Merlet, J and Racine, C and Habert, R}, title = {Expression and localization of aromatase during fetal mouse testis development.}, journal = {Basic and clinical andrology}, volume = {23}, number = {}, pages = {12}, pmid = {25780574}, issn = {2051-4190}, abstract = {BACKGROUND: Both androgens and estrogens are necessary to ensure proper testis development and function. Studies on endocrine disruptors have highlighted the importance of maintaining the balance between androgens and estrogens during fetal development, when testis is highly sensitive to environmental disturbances. This balance is regulated mainly through an enzymatic cascade that converts irreversibly androgens into estrogens. The most important and regulated component of this cascade is its terminal enzyme: the cytochrome p450 19A1 (aromatase hereafter). This study was conducted to improve our knowledge about its expression during mouse testis development.

FINDINGS: By RT-PCR and western blotting, we show that full-length aromatase is expressed as early as 12.5 day post-coitum (dpc) with maximal expression at 17.5 dpc. Two additional truncated transcripts were also detected by RT-PCR. Immunostaining of fetal testis sections and of gonocyte-enriched cell cultures revealed that aromatase is strongly expressed in fetal Leydig cells and at variable levels in gonocytes. Conversely, it was not detected in Sertoli cells.

CONCLUSIONS: This study shows for the first time that i) aromatase is expressed from the early stages of fetal testis development, ii) it is expressed in mouse gonocytes suggesting that fetal germ cells exert an endocrine function in this species and that the ratio between estrogens and androgens may be higher inside gonocytes than in the interstitial fluid. Furthermore, we emphasized a species-specific cell localization. Indeed, previous works found that in the rat aromatase is expressed both in Sertoli and Leydig cells. We propose to take into account this species difference as a new concept to better understand the changes in susceptibility to Endocrine Disruptors from one species to another.}, } @article {pmid25250433, year = {2013}, author = {Wright, SG and Skevington, JH}, title = {Revision of the subgenus Episyrphus (Episyrphus) Matsumura (Diptera: Syrphidae) in Australia.}, journal = {Zootaxa}, volume = {3683}, number = {}, pages = {51-64}, doi = {10.11646/zootaxa.3683.1.3}, pmid = {25250433}, issn = {1175-5326}, mesh = {Animals ; Australia ; Diptera/*anatomy & histology/*classification/genetics ; Electron Transport Complex IV/genetics ; Female ; Insect Proteins/genetics ; Larva ; Male ; Molecular Sequence Data ; Phylogeny ; Pupa ; Sequence Analysis, DNA ; Species Specificity ; Temperature ; }, abstract = {Three species of Episyrphus (Episyrphus) Matsumura, 1917 are here recorded in Australia: E. (E.) viridaureus (Wiedemann, 1824) and two new species E. (E.) oliviae Wright sp. nov. and E. (E.) glaber Wright sp. nov. A key to Australian Episyrphus (Episyrphus) species is provided, important taxonomic characters are illustrated and distributions of the three species are mapped. The distribution of E. (E.) viridaureus is extended to include Australia. Mitochondrial cytochrome c oxidase subunit I (COI) data are provided from some Episyrphus species to test morphological species concepts.}, } @article {pmid25113703, year = {2013}, author = {Cardozo-de-Almeida, M and Castro-de-Souza, S and De Oliveira, ML and De Almeida, SA and Gonçalves, TC and Dos Santos-Mallet, JR}, title = {Ultrastructure and morphometry of eggs of Triatoma rubrovaria (Blanchard, 1843), Triatoma carcavalloi Juberg, Rocha & Lent, 1998 and Triatoma circummaculata (Stål, 1859) (Hemiptera-Reduviidae-Triatominae).}, journal = {Zootaxa}, volume = {3750}, number = {}, pages = {348-356}, doi = {10.11646/zootaxa.3750.4.3}, pmid = {25113703}, issn = {1175-5326}, mesh = {Animals ; Cell Size ; Female ; Male ; Ovum/cytology/*ultrastructure ; Triatoma/anatomy & histology/*ultrastructure ; }, abstract = {This study analyzed the body and the operculum of eggs of Triatoma rubrovaria, T. carcavalloi and T. circummaculata, considered sylvatic species that live in sympatry.Triatoma rubrovaria is currently considered the most important vector of Trypanosoma cruzi in the rural areas of the state of Rio Grande do Sul, followed by T.circummaculata. Significant differences other than morphometry have been observed in the egg structures of the three species using traditional microscopy and scanning electron microscopy. Triatoma circummaculata eggs are smaller than those of T.rubrovaria and T. carcavalloi. The average number of perforations in corionic cells in the egg body is higher for the T. rubrovaria. The average number of perforations in the operculum cell is higher in T. circummaculata. This is the first morpho-structural description of T. carcavalloi eggs. These results widen the concept of these three species and create new subsidies for the entomological monitoring in areas in which these vectors may infest human living quarters.}, } @article {pmid27008273, year = {2012}, author = {Lajeunesse, TC and Parkinson, JE and Reimer, JD}, title = {A genetics-based description of Symbiodinium minutum sp. nov. and S. psygmophilum sp. nov. (Dinophyceae), two dinoflagellates symbiotic with cnidaria.}, journal = {Journal of phycology}, volume = {48}, number = {6}, pages = {1380-1391}, doi = {10.1111/j.1529-8817.2012.01217.x}, pmid = {27008273}, issn = {0022-3646}, abstract = {Traditional approaches for describing species of morphologically cryptic and often unculturable forms of endosymbiotic dinoflagellates are problematic. Two new species in the genus Symbiodinium Freudenthal 1962 are described using an integrative evolutionary genetics approach: Symbiodinium minutum sp. nov. are harbored by widespread tropical anemones in the genus Aiptasia; and Symbiodinium psygmophilum sp. nov. are harbored by subtropical and temperate stony corals (e.g., Astrangia, Cladocora, and Oculina) from the Atlantic Ocean and Mediterranean Sea. Both new species are readily distinguished from each other by phylogenetic disparity and reciprocal monophyly of several nucleic acid sequences including nuclear ribosomal internal transcribed spacers 1 and 2, single copy microsatellite flanker Sym15, mitochondrial cytochrome b, and the chloroplast 23S rRNA gene. Such molecular evidence, combined with well-defined differences in cell size, physiology (thermal tolerance), and ecology (host compatibility) establishes these organisms as distinct species. Future descriptions of Symbiodinium spp. will need to emphasize genetics-based descriptions because significant morphological overlap in this group obscures large differences in ecology and evolutionary divergence. By using molecular evidence based on conserved and rapidly evolving genes analyzed from a variety of samples, species boundaries are defined under the precepts of Evolutionary and Biological Species Concepts without reliance on an arbitrary genetic distance metric. Because ecological specialization arises through genetic adaptations, the Ecological Species Concept can also serve to delimit many host-specific Symbiodinium spp.}, } @article {pmid27011267, year = {2012}, author = {Guiry, MD}, title = {HOW MANY SPECIES OF ALGAE ARE THERE?.}, journal = {Journal of phycology}, volume = {48}, number = {5}, pages = {1057-1063}, doi = {10.1111/j.1529-8817.2012.01222.x}, pmid = {27011267}, issn = {0022-3646}, abstract = {Algae have been estimated to include anything from 30,000 to more than 1 million species. An attempt is made here to arrive at a more accurate estimate using species numbers in phyla and classes included in the on-line taxonomic database AlgaeBase (http://www.algaebase.org). Despite uncertainties regarding what organisms should be included as algae and what a species is in the context of the various algal phyla and classes, a conservative approach results in an estimate of 72,500 algal species, names for 44,000 of which have probably been published, and 33,248 names have been processed by AlgaeBase to date (June 2012). Some published estimates of diatom numbers are of over 200,000 species, which would result in four to five diatom species for every other algal species. Concern is expressed at the decline and potential extinction of taxonomists worldwide capable of improving and completing the necessary systematic studies.}, } @article {pmid32480758, year = {2012}, author = {Turnbull, MH and Pharis, RP and Kurepin, LV and Sarfati, M and Mander, LN and Kelly, D}, title = {Flowering in snow tussock (Chionochloa spp.) is influenced by temperature and hormonal cues.}, journal = {Functional plant biology : FPB}, volume = {39}, number = {1}, pages = {38-50}, doi = {10.1071/FP11116}, pmid = {32480758}, issn = {1445-4416}, abstract = {Snow tussocks (Chionochloa spp.) in New Zealand exhibit extreme mast (episodic) seeding which has important implications for plant ecology and plant-insect interactions. Heavy flowering appears to be triggered by very warm/dry summers in the preceding year. In order to investigate the physiological basis for mast flowering, mature snow tussock plants in the field and younger plants in a glasshouse and shadehouse were subjected to a range of manipulative treatments. Field treatments included combinations of warming, root pruning and applications of two native gibberellins (GAs) GA3, which is known to be highly floral inductive and GA4, which is associated with continued floral apex development in another long-day grass. Warming, GA3 alone and especially warming+GA3, significantly promoted flowering, as did applications of GA4 alone and GA4+CCC (2-chloroethyltrimethylammonium chloride, which is a known synergist of GA3-induced flowering in the annual grass, Lolium temulentum L.). Our results provide support for the concept that mast flowering events in tussock species are causally related to high temperature-induced increases in endogenous gibberellin levels. It is likely that GAs (endogenous or applied) promote the continued development of a previously long-day induced floral apex. In addition to the promotion of flowering, applied GA3 also disturbed the plant's innate resource threshold requirements, as shown by the death, over winter, of many non-flowering tillers. Applied GA4 did not show this effect, likely due to its rapid catabolic metabolism to an inactive form. High temperature-induced flowering mediated by elevated levels of endogenous floral-promotive GAs could have important implications for regulating the evolutionary interaction between these masting plants and their seed predators.}, } @article {pmid27020024, year = {2011}, author = {Tellier, F and Tapia, J and Faugeron, S and Destombe, C and Valero, M}, title = {THE LESSONIA NIGRESCENS SPECIES COMPLEX (LAMINARIALES, PHAEOPHYCEAE) SHOWS STRICT PARAPATRY AND COMPLETE REPRODUCTIVE ISOLATION IN A SECONDARY CONTACT ZONE(1).}, journal = {Journal of phycology}, volume = {47}, number = {4}, pages = {894-903}, doi = {10.1111/j.1529-8817.2011.01019.x}, pmid = {27020024}, issn = {0022-3646}, abstract = {During secondary contact between phylogenetically closely related species (sibling species) having diverged in allopatry, the maintenance of species integrity depends on intrinsic and extrinsic reproductive barriers. In kelps (Phaeophyceae), the observations of hybrids in laboratory conditions suggest that reproductive isolation is incomplete. However, not all interspecific crosses are successful, and very few hybrids have been observed in nature, despite the co-occurrence of many kelp species in sympatry. This suggests that there are reproductive barriers that maintain species integrity. In this study, we characterized the fine genetic structure of a secondary contact zone to clarify the extent of reproductive isolation between two sister species. In Lessonia nigrescens Bory (Laminariales, Phaeophyta) species complex, two cryptic species have been recently found out from gene phylogenies, and-waiting for a formal taxonomic description-we used their geographic distribution to name them (northern and southern species). We studied 12 populations, distributed along 50 km of coastline, and employed two molecular approaches, assigning individuals to phylogenetic species according to a diagnostic mitochondrial marker (351 individuals analyzed) and quantifying interspecific gene flow with four microsatellite markers (248 individuals analyzed). No hybridization or introgression was revealed, indicating complete reproductive isolation in natural conditions. Unexpectedly, our study demonstrated that the two species were strictly segregated in space. This absence of co-occurrence along the contact zone can partially explain the lack of hybridization, raising new interesting questions as to the mechanisms that limit sympatry at small spatial scales.}, } @article {pmid27021867, year = {2011}, author = {Lin, SM and Yang, SY and Huisman, JM}, title = {SYSTEMATIC REVISION OF THE GENERA LIAGORA AND IZZIELLA (LIAGORACEAE, RHODOPHYTA) FROM TAIWAN BASED ON MOLECULAR ANALYSES AND CARPOSPOROPHYTE DEVELOPMENT, WITH THE DESCRIPTION OF TWO NEW SPECIES(1).}, journal = {Journal of phycology}, volume = {47}, number = {2}, pages = {352-365}, doi = {10.1111/j.1529-8817.2011.00965.x}, pmid = {27021867}, issn = {0022-3646}, abstract = {Some Liagora and Izziella distributed in Taiwan display a wide range of morphological variation and can be difficult to distinguish. To clarify species concepts, we applied DNA sequence analyses and examined carposporophyte development in detail. These studies revealed two new species, which are described herein as Izziella hommersandii sp. nov. and Izziella kuroshioensis sp. nov. I. kuroshioensis superficially resembles Izziella formosana and Izziella orientalis in that its involucral filaments subtend rather than surround the lower portion of the gonimoblast mass (= Izziella type) and a fusion cell is formed from cells of the carpogonial branch, but it can be separated by differences in the cell numbers and branching pattern of the involucral filaments, as well as thallus morphology. In contrast to other species that also bear short lateral branchlets, I. hommersandii is unique in possessing a mixture of short and long involucral filaments, a phenomenon not reported before. The length of the involucral filaments is species specific among species of Izziella and contrasts to the behavior of the involucral filaments after fertilization in species such as "Liagora"setchellii [= Titanophycus setchellii comb. nov.], in which the filaments completely envelop the gonimoblast. In addition, the cells of the carpogonial branch in Titanophycus do not fuse after fertilization to form a fusion cell. Thus, a combination of characters with respect to the behavior of the carpogonial branch and the involucral filaments after fertilization is very useful for delineating species boundaries in Izziella and for separating Titanophycus from Izziella and Liagora.}, } @article {pmid34969199, year = {2011}, author = {Ereshefsky, M}, title = {Mystery of mysteries: Darwin and the species problem.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {27}, number = {1}, pages = {67-79}, doi = {10.1111/j.1096-0031.2010.00311.x}, pmid = {34969199}, issn = {1096-0031}, abstract = {Darwin offered an intriguing answer to the species problem. He doubted the existence of the species category as a real category in nature, but he did not doubt the existence of those taxa called "species". And despite his scepticism of the species category, Darwin continued using the word "species". Many have said that Darwin did not understand the nature of species. Yet his answer to the species problem is both theoretically sound and practical. On the theoretical side, Darwin's answer is confirmed by contemporary biology, and it offers a more satisfactory answer to the species problem than recent attempts to save the species category. On the practical side, Darwin's answer frees us from the search for the correct theoretical definition of "species". But at the same time it does not require that we banish the word "species" from biology as some recent sceptics of the species category advocate. © The Willi Hennig Society 2010.}, } @article {pmid26467499, year = {2011}, author = {Kawakami, T and Butlin, RK and Cooper, SJ}, title = {Chromosomal Speciation Revisited: Modes of Diversification in Australian Morabine Grasshoppers (Vandiemenella, viatica Species Group).}, journal = {Insects}, volume = {2}, number = {1}, pages = {49-61}, pmid = {26467499}, issn = {2075-4450}, abstract = {Chromosomal rearrangements can alter the rate and patterns of gene flow within or between species through a reduction in the fitness of chromosomal hybrids or by reducing recombination rates in rearranged areas of the genome. This concept, together with the observation that many species have structural variation in chromosomes, has led to the theory that the rearrangements may play a direct role in promoting speciation. Australian morabine grasshoppers (genus Vandiemenella, viatica species group) are an excellent model for studying the role of chromosomal rearrangement in speciation because they show extensive chromosomal variation, parapatric distribution patterns, and narrow hybrid zones at their boundaries. This species group stimulated development of one of the classic chromosomal speciation models, the stasipatric speciation model proposed by White in 1968. Our population genetic and phylogeographic analyses revealed extensive non-monophyly of chromosomal races along with historical and on-going gene introgression between them. These findings suggest that geographical isolation leading to the fixation of chromosomal variants in different geographic regions, followed by secondary contact, resulted in the present day parapatric distributions of chromosomal races. The significance of chromosomal rearrangements in the diversification of the viatica species group can be explored by comparing patterns of genetic differentiation between rearranged and co-linear parts of the genome.}, } @article {pmid30743628, year = {2010}, author = {Lembicz, M and Górzyńska, K and Leuchtmann, A}, title = {Choke Disease Caused by Epichloë bromicola in the Grass Agropyron repens in Poland.}, journal = {Plant disease}, volume = {94}, number = {11}, pages = {1372}, doi = {10.1094/PDIS-12-09-0810}, pmid = {30743628}, issn = {0191-2917}, abstract = {Agropyron repens (synonym Elymus repens, couch grass) is a species native to Europe and Asia. In Poland, it is a common weed of crop fields. In May 2008, we noticed for the first time symptoms of choke disease (caused by Epichloë spp.) on A. repens at two localities in central Poland. The localities, Pakość (52°47.531'N, 18°06.118'E) and Dulsk (52°45.329'N, 18°20.518'E), are located 16 km apart from each other. The following year, we confirmed the occurrence of choke disease on couch grass at these localities. Stromata were formed on reproductive stems that did not produce inflorescences. They ranged from 16 to 31 mm long and were covered with perithecia 520 to 560 × 160 to 250 μm at a density of 35 to 45 per mm[2]. Asci measured 270 to 310 × 5.2 to 6.5 μm and ascospores were 225 to 275 × 1.5 to 1.7 μm (specimen deposited in ZT). Morphological characters match with the original description of Epichloë bromicola (4). One strain was isolated from stromatal tissue and the partial DNA sequence of tubB including introns 1 to 3 was obtained as previously described (2). In a phylogenetic analysis, the isolate (GenBank Accession No. GU325782) grouped with Epichloë isolates from other Agropyron spp. from Poland (A. intermedium) and Japan (A. ciliare and A. tsukushiense) and with an isolate from a Roegneria sp. (from China). Experimental mating tests involving isolates from A. intermedium and a Roegneria sp. indicated that these isolates were sexually compatible with Epichloë bromicola from Bromus erectus. Similarly, E. yangsii was compatible with E. bromicola. This suggests that Epichloë isolates from Agropyron, Roegneria, and Bromus hosts form a common mating population, and implies that under a biological species concept the phylogenetic definition of E. bromicola has to be broadened. Epichloë on A. repens has been previously found in Poland (1), Germany (3), Hungary, and Romania (specimen deposited in herbarium of ETH Zurich, ZT) based on incidental records or on herbarium specimens that have been listed under E. typhina. Our study, based on morphology, tubB sequence similarity, and mating compatibility, suggests that the fungus infecting A. repens in Poland is E. bromicola. References: (1) I. Adamska. Acta Mycol. 36:31, 2001. (2) D. Brem and A. Leuchtmann. Evolution 57:37, 2003. (3) J. Kohlmeyer and E. Kohlmeyer. Mycologia 66:77, 1974. (4) A. Leuchtmann and C. L. Schardl. Mycol. Res. 102:1169, 1998.}, } @article {pmid34879593, year = {2009}, author = {Reydon, TAC}, title = {Species and kinds: a critique of Rieppel's "one of a kind" account of species.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {25}, number = {6}, pages = {660-667}, doi = {10.1111/j.1096-0031.2009.00266.x}, pmid = {34879593}, issn = {1096-0031}, abstract = {A major issue in philosophical debates on the species problem concerns the opposition between two seemingly incompatible views of the metaphysics of species: the view that species are individuals and the view that species are natural kinds. In two recent papers in this journal, Olivier Rieppel suggested that this opposition is much less deep than it seems at first sight. Rieppel used a recently developed philosophical account of natural kindhood, namely Richard Boyd's "homeostatic property cluster" theory, to argue that every species taxon can be conceived of as an individual that constitutes the single member of its own specific natural kind. In this paper I criticize Rieppel's approach and argue that it does not deliver what it is supposed to, namely an account of species as kinds about which generalized statements can be made.}, } @article {pmid34879613, year = {2009}, author = {Rieppel, O}, title = {Hennig's enkaptic system.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {25}, number = {3}, pages = {311-317}, doi = {10.1111/j.1096-0031.2009.00260.x}, pmid = {34879613}, issn = {1096-0031}, abstract = {Hennig's phylogenetic system is characterized by an asymmetry between (sexually reproducing) species that form tokogenetic systems, versus monophyletic taxa that form a phylogenetic system. This was claimed to reflect a conflict between two hierarchies, i.e. the hierarchy of species-lineages splitting and splitting again as opposed to the phylogenetic hierarchy of groups within groups. Some cladists have sought the unification of the phylogenetic system by abandoning the species concept. In contrast, contemporary commentators (Klaus Günther, Walter Zimmermann) characterized Hennig's system as an enkaptic hierarchy. This paper explores the concept of enkapsis, and the way Hennig used it as a basis for the unification of his phylogenetic system. © The Willi Hennig Society 2009.}, } @article {pmid27033660, year = {2009}, author = {Won, BY and Cho, TO and Fredericq, S}, title = {MORPHOLOGICAL AND MOLECULAR CHARACTERIZATION OF SPECIES OF THE GENUS CENTROCERAS (CERAMIACEAE, CERAMIALES), INCLUDING TWO NEW SPECIES(1).}, journal = {Journal of phycology}, volume = {45}, number = {1}, pages = {227-250}, doi = {10.1111/j.1529-8817.2008.00620.x}, pmid = {27033660}, issn = {0022-3646}, abstract = {Centroceras clavulatum (C. Agardh) Montagne is widely reported as being a prime example of a cosmopolitan red algal species. Instead, C. clavulatum is here determined as restricted to northern Chile, Peru, southern California, southern Australia, and New Zealand. Specimens identified using the current species concept for "C. clavulatum" fall into nine morphological groups that correspond to highly supported clades in phylogenetic analyses. Three of these clades correspond to the resurrected species Centroceras gasparrinii (Meneghini) Kützing, C. hyalacanthum Kützing, and C. micracanthum Kützing. Two others are recognized as new species: Centroceras rodmanii sp. nov. from southern Chile, which is characterized by hooked spines arranged in a whorl at the node, a spine or flattened gland cell cut off from the first cortical initials, and a single acropetal cortical cell issued from the second cortical initials; and C. tetrachotomum sp. nov. from South Africa, which has a tetrachotomous branching pattern, straight spines in a whorl, an acropetal cortical cell and a spine or a flattened gland cell cut off from the first cortical initials, and a two-celled acropetal filament cut off from the second cortical initials. Three additional species from South Africa are also recognized as distinct species. All phylogenetic analyses of the rbcL gene, LSU rDNA, and SSU rDNA were consistent with the vegetative and tetrasporangial morphological distinctions, thus supporting the resurrection of three species and the description of two new species.}, } @article {pmid27041055, year = {2008}, author = {Sluiman, HJ and Guihal, C and Mudimu, O}, title = {ASSESSING PHYLOGENETIC AFFINITIES AND SPECIES DELIMITATIONS IN KLEBSORMIDIALES (STREPTOPHYTA): NUCLEAR-ENCODED rDNA PHYLOGENIES AND ITS SECONDARY STRUCTURE MODELS IN KLEBSORMIDIUM, HORMIDIELLA, AND ENTRANSIA(1).}, journal = {Journal of phycology}, volume = {44}, number = {1}, pages = {183-195}, doi = {10.1111/j.1529-8817.2007.00442.x}, pmid = {27041055}, issn = {0022-3646}, abstract = {Nuclear-encoded SSU, group I intron, and internal transcribed spacer (ITS) rDNA sequences were obtained for 16 strains of green algae representing species of Klebsormidium, Hormidiella attenuata, and Entransia fimbriata (for taxonomic authorities, see Table S1 in the supplementary material). The SSU phylogeny resolved a well-supported clade Klebsormidiales in the Streptophyta that comprised authentic Klebsormidium isolates described recently in a monograph by G. M. Lokhorst and various strains from culture collections. The H. attenuata and En. fimbriata pair was the sister group of Klebsormidium. Certain isolates from culture collections previously identified as "Klebsormidium" emerged as Trebouxiophyceae. Strains assigned to Koliella, Gloeotila, and Stichococcus previously allied with Klebsormidium because of shared morphological and ultrastructural characteristics also belonged to Trebouxiophyceae. Group I introns inserted at Escherichia coli position 516 were found in K. nitens and SAG strain 384-1, and at position 1506 in H. attenuata and En. fimbriata. Introns were not observed in other Klebsormidiales. Unambiguous alignment of ITS regions of Klebsormidiales was only possible after thermodynamic folding had predicted eight conserved helical domains. The ITS phylogeny provided support for five of the morphospecies recognized by Lokhorst (K. flaccidum, K. elegans, K. bilatum, K. crenulatum, K. mucosum), but the sequences of K. dissectum, K. fluitans, and K. nitens formed an unresolved clade. The species with the earliest origin in the Klebsormidium phylogeny was K. flaccidum. The incongruence between Lokhorst's morphology-based cladograms and the ITS phylogenies demonstrated the need for a critical reappraisal of the taxonomy and the morphological and molecular species concept in Klebsormidium on the basis of a more extensive taxonomic and geographic sampling strategy.}, } @article {pmid30408897, year = {2006}, author = {Samson, RA and Hong, SB and Frisvad, JC}, title = {Old and new concepts of species differentiation in Aspergillus.}, journal = {Medical mycology}, volume = {44}, number = {Supplement_1}, pages = {S133-S148}, doi = {10.1080/13693780600913224}, pmid = {30408897}, issn = {1460-2709}, abstract = {The classification of the genus Aspergillus has been studied by many taxonomists. The most important monograph on which most taxonomies are derived from is strictly based on phenotypical characters. Later revisions of certain Aspergillus sections have been predominantly nomenclatural changes and primarily used morphological criteria. Many new taxa were added particularly in the genera Emericella and Neosartorya. Identification of the most common and often important species remains problematic due to the variability in the phenotypic characters. This has caused errors in the literature, especially concerning the links to mycotoxin formation. The new taxonomies are based on a polyphasic approach using phenotypical characters together with multigene DNA sequences. In a polyphasic approach micro- and macromorphology, physiology, metabolites produced and molecular data are all important, and in principle no particular method should be overemphasized. In particular extrolite profiles have proven to be specific for the taxa and this has contributed to a stable species concept, but DNA sequence data have also been very valuable in critical revisions of species and their taxonomy and phylogeny. Examples of new classifications for species in section Circumdati, Flavi,Fumigati and Nigri are presented. Although the polyphasic approach might reveal clear cut species, problems may arise for some species if they are to be separated based only on their microscopic features and few physiological features. Suggestions for new methods in order to carry out more fast and precise identifications will be discussed. Full genome sequencing and DNA arrays offers exciting new bases for identifying the Aspergilli, but recent methods based on image analysis of accurately fingerprinted phenotypes are also very promising. However both methods require a stable and well resolved taxonomy and nomenclature. Validated careful phenotypic classification (taxonomy) together with phylogenetic treatment of DNA sequence data is a prerequisite for reliable rapid identification methods and database formation. Concerning identification, DNA bar coding will be possible in the future, either based on molecular methods or certain phenotypic features.}, } @article {pmid34892973, year = {2004}, author = {Grant, T and Kluge, AG}, title = {Transformation Series as an Ideographic Character Concept.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {20}, number = {1}, pages = {23-31}, pmid = {34892973}, issn = {1096-0031}, abstract = {An ideographic concept of character is indispensable to phylogenetic inference. Hennig proposed that characters be conceptualized as "transformation series", a proposal that is firmly grounded in evolutionary theory and consistent with the method of inferring transformation events as evidence of phylogenetic propinquity. Nevertheless, that concept is usually overlooked or rejected in favor of others based on similarity. Here we explicate Hennig's definition of character as an ideographic concept in the science of phylogenetic systematics. As transformation series, characters are historical individuals akin to species and clades. As such, the related concept of homology refers to a historical identity relation and is not equivalent to or synonymous with synapomorphy. The distinction between primary and secondary homology is dismissed on the grounds that it conflates the concept of homology with the discovery operations used to detect instances of that concept. Although concern for character dependence is generally valid, it is often misplaced, focusing on functional or developmental correlation (both of which are irrelevant in phylogenetic systematics but may be valid in other fields) instead of the historical/transformational independence relevant to phylogenetic inference. As an ideographic science concerned with concrete objects and events (i.e. individuals), intensionally and extensionally defined properties are inconsistent with the individuation of characters for phylogenetic analysis, the utility of properties being limited to communicating results and facilitating future rounds of testing.}, } @article {pmid34905853, year = {2003}, author = {Willmann, R}, title = {From Haeckel to Hennig: the early development of phylogenetics in German-speaking Europe.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {19}, number = {6}, pages = {449-479}, doi = {10.1111/j.1096-0031.2003.tb00383.x}, pmid = {34905853}, issn = {1096-0031}, abstract = {An outline of the development of phylogenetic thinking and methodology in German literature published between 1862 and 1942 is presented. Central European biologists and palaeontologists of the first post-Darwinian generation of biologists holding evolutionary views were directly stimulated by Darwin. Members of the second generation, mostly born after 1850, were largely influenced also by colleagues of the first post-Darwinian generation, mainly by Haeckel. Among them were O. Abel, V. Franz, R. Hertwig, A. Naef, L. Plate, and R. v. Wettstein. Opinions on the relationship between systematics and phylogeny differed considerably. Many authors admitted that phylogeny must be mirrored in systematics but at the same time shared Haeckel's views on classification, which permitted paraphyletic groupings. Particularly Abel and Naef took systematics several steps further, and many important elements of phylogenetic systematics were developed several decades before Hennig. Naef presented a definition of a phylogenetic group that exactly matches Hennig's definition of monophyly. He also formulated a species concept that was implicitly based on reproductive isolation. This was an important presupposition for viewing speciation as the splitting of a stem species into daughter species. However, many authors of the first half of the 20th century repeated old, but established views on phylogenetics, while others overlooked or misunderstood earlier progressive views thus causing slow development of phylogenetic systematics in Central Europe. Its development almost stopped between 1925 and 1950, because of a widespread shift towards typology and extreme idealistic morphology. During that time very few persons such as W. Zimmermann and W. Hennig assembled elements of phylogenetic systematics and combined them with their own thoughts to create a sound theory and methodology.}, } @article {pmid33873326, year = {2001}, author = {Clapp, JP and Rodriguez, A and Dodd, JC}, title = {Inter- and intra-isolate rRNA large subunit variation in Glomus coronatum spores.}, journal = {The New phytologist}, volume = {149}, number = {3}, pages = {539-554}, doi = {10.1046/j.1469-8137.2001.00060.x}, pmid = {33873326}, issn = {1469-8137}, abstract = {• High levels of variation are reported in the large subunit (LSU) rRNA gene, D2 region of Glomus coronatum, a well characterized species of arbuscular mycorrhizal fungus (AMF). • Clones (435) containing the D2 regions from 7 isolates of G. coronatum were investigated for intra- and inter-isolate sequence variation using PCR-single-strand conformational polymorphism (PCR-SSCP) as a prescreen before sequencing. Isolates of G. mosseae, G. constrictum and G. geosporum, three species of AMF with similar spore ontogeny and morphology, were also analysed. • Analysis of 138 representative sequences indicated that most were unique; this variation could not be attributed to DNA polymerase or cloning artefacts. Only 13 sequences were found in more than one isolate. Neighbour-joining analysis showed that most sequences from G. coronatum formed a main group although several sequences from G. mosseae and G. constrictum clustered with G. coronatum. • There was greater than expected variation in the LSU D2 region sequences from G. coronatum. The four Glomus species, closely related by spore morphology, might represent part of a genetic continuum. Implications for the concept of species in AMF, the use of rRNA sequences to estimate biodiversity and in situ detection in field ecology are discussed.}, } @article {pmid35701949, year = {2000}, author = {Kotliar, NB}, title = {Application of the New Keystone-Species Concept to Prairie Dogs: How Well Does It Work?.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {14}, number = {6}, pages = {1715-1721}, doi = {10.1111/j.1523-1739.2000.98384.x}, pmid = {35701949}, issn = {1523-1739}, abstract = {It has been suggested that the keystone-species concept should be dropped from ecology and conservation, primarily because the concept is poorly defined. This prompted Power et al. (1996) to refine the definition: keystone species have large effects on community structure or ecosystem function (i.e., high overall importance), and this effect should be large relative to abundance (i.e., high community importance). Using prairie dogs (Cynomys spp.) as an example, I review operational and conceptual difficulties encountered in applying this definition. As applied to prairie dogs, the implicit assumption that overall importance is a linear function of abundance is invalid. In addition, community importance is sensitive to abundance levels, the definition of community, and sampling scale. These problems arise largely from the equation for community importance, as used in conjunction with removal experiments at single abundance levels. I suggest that we shift from the current emphasis on the dualism between keystone and nonkeystone species and instead examine how overall and community importance vary (1) with abundance, (2) across spatial and temporal scales, and (3) under diverse ecological conditions. In addition, I propose that a third criterion be incorporated into the definition: keystone species perform roles not performed by other species or processes. Examination of how these factors vary among populations of keystone species should help identify the factors contributing to, or limiting, keystone-level functions, thereby increasing the usefulness of the keystone-species concept in ecology and conservation. Although the quantitative framework of Power et al. falls short of being fully operational, my conceptual guidelines may improve the usefulness of the keystone-species concept. Careful attention to the factors that limit keystone function will help avoid misplaced emphasis on keystone species at the expense of other species.}, } @article {pmid34902901, year = {2000}, author = {Goldstein, PZ and DeSalle, R}, title = {Phylogenetic Species, Nested Hierarchies, and Character Fixation.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {16}, number = {4}, pages = {364-384}, doi = {10.1111/j.1096-0031.2000.tb00356.x}, pmid = {34902901}, issn = {1096-0031}, abstract = {Cladistic mechanics and ramifications of various species concepts rooted in phylogenetic theory are explored. Published discussions of the phylogenetic species concept (PSC) have been hampered by persistent misconceptions surrounding its ontology and applicability, and by confusion of various incompatible versions of species concepts claiming to follow from Hennig's (1966), Phylogenetic Systematics, Univ. of Illinois Press, Urbana work. Especially problematic are topology- or tree-based versions of species diagnosis, which render diagnoses dependent on relationships depicted as hierarchically structured regardless of any lack of underlying hierarchy. Because the applicability of concepts such as monophyly, paraphyly, and polyphyly rests ultimately on the underlying hierarchical distribution of characters, representations of tokogenetic or reticulating systems as nested hierarchies are necessarily inaccurate. And since hierarchical representations-even if accurate-of nonrecombining genetic elements need not coincide with the organisms that bear them, tree-based diagnoses are further hampered, except potentially as retrospective tools. The relationship between tree-based species delineations and the criterion of character fixation is explored. Fixation of characters by which one identifies phylogenetic species is further distinguished from the fixation of character state differences, and the implications of that distinction are explored with reference to the interpretation of speciation events. It is demonstrated that character fixation in alternative species need not coincide with the achievement of reciprocal monophyly. While the PSC retains shortcomings, some of the more frequently criticized aspects of the PSC are functions of sampling that are no more problematic than for any basic systematic endeavor.}, } @article {pmid28308280, year = {2000}, author = {Schwartz, MW and Brigham, CA and Hoeksema, JD and Lyons, KG and Mills, MH and van Mantgem, PJ}, title = {Linking biodiversity to ecosystem function: implications for conservation ecology.}, journal = {Oecologia}, volume = {122}, number = {3}, pages = {297-305}, doi = {10.1007/s004420050035}, pmid = {28308280}, issn = {1432-1939}, abstract = {We evaluate the empirical and theoretical support for the hypothesis that a large proportion of native species richness is required to maximize ecosystem stability and sustain function. This assessment is important for conservation strategies because sustenance of ecosystem functions has been used as an argument for the conservation of species. If ecosystem functions are sustained at relatively low species richness, then arguing for the conservation of ecosystem function, no matter how important in its own right, does not strongly argue for the conservation of species. Additionally, for this to be a strong conservation argument the link between species diversity and ecosystem functions of value to the human community must be clear. We review the empirical literature to quantify the support for two hypotheses: (1) species richness is positively correlated with ecosystem function, and (2) ecosystem functions do not saturate at low species richness relative to the observed or experimental diversity. Few empirical studies demonstrate improved function at high levels of species richness. Second, we analyze recent theoretical models in order to estimate the level of species richness required to maintain ecosystem function. Again we find that, within a single trophic level, most mathematical models predict saturation of ecosystem function at a low proportion of local species richness. We also analyze a theoretical model linking species number to ecosystem stability. This model predicts that species richness beyond the first few species does not typically increase ecosystem stability. One reason that high species richness may not contribute significantly to function or stability is that most communities are characterized by strong dominance such that a few species provide the vast majority of the community biomass. Rapid turnover of species may rescue the concept that diversity leads to maximum function and stability. The role of turnover in ecosystem function and stability has not been investigated. Despite the recent rush to embrace the linkage between biodiversity and ecosystem function, we find little support for the hypothesis that there is a strong dependence of ecosystem function on the full complement of diversity within sites. Given this observation, the conservation community should take a cautious view of endorsing this linkage as a model to promote conservation goals.}, } @article {pmid28565467, year = {1999}, author = {Wiens, JJ and Reeder, TW and Oca, ANM}, title = {MOLECULAR PHYLOGENETICS AND EVOLUTION OF SEXUAL DICHROMATISM AMONG POPULATIONS OF THE YARROW'S SPINY LIZARD (SCELOPORUS JARROVII).}, journal = {Evolution; international journal of organic evolution}, volume = {53}, number = {6}, pages = {1884-1897}, doi = {10.1111/j.1558-5646.1999.tb04570.x}, pmid = {28565467}, issn = {1558-5646}, abstract = {Understanding evolution of geographic variation in sexually dimorphic traits is critical for understanding the role that sexual selection may play in speciation. We performed a phylogenetic analysis of geographic variation in sexual dichromatism in the Yarrow's spiny lizard (Sceloporus jarrovii), a taxon that exhibits remarkable diversity in male coloration among populations (e.g., black, red, green, yellow, blue, brown). An mtDNA phylogeny based on approximately 880 bp from the 12S ribosomal RNA gene and 890 bp from the ND4 gene was reconstructed for 30 populations of S. jarrovii and eight other species of the torquatus species group using maximum-likelihood and parsimony methods. The phylogeny suggests that S. jarrovii consists of at least five evolutionary species, none of which are sister taxa. Although intraspecific diversity in male coloration is less than indicated by previous taxonomy, two species formerly referred to as S. jarrovii exhibit impressive geographic variation in sexual dichromatism. In one of these species, the phylogeny shows the independent evolution of a distinctive blue color morph in different parts of the species range. This pattern suggests that sexual selection may lead to striking phenotypic divergence among conspecific populations and striking convergence. Results also demonstrate the importance of a phylogenetic perspective in studies of evolutionary processes within nominal species and the problematic nature of "polytypic" species recognized under the biological species concept.}, } @article {pmid30845544, year = {1999}, author = {Costa, JLDS and de Oliveira, VC}, title = {Occurrence of Smut Caused by a Ustilago sp. on Dry-Beans.}, journal = {Plant disease}, volume = {83}, number = {5}, pages = {486}, doi = {10.1094/PDIS.1999.83.5.486A}, pmid = {30845544}, issn = {0191-2917}, abstract = {In September 1997, after the tropical winter season and following a long warm (28 to 33°C) and rainy (27 mm) period, smut symptoms were observed on two dry-bean (Phaseolus vulgaris) fields in Brazil. Brownish to blackish powdery masses of spores were observed on stems, pods, and roof green and senescent plants. No galls were observed. Hyphae in infected tissue were intercellular; no clamp connections were observed. Typical globose teliospores were observed that measured 7 to 11 μm. Spores were uninucleate or binucleate; predominantly brownish with flattened poles and equatorial band; the exospore wall was thick and surface ornamented (echinulate-type). Teliospores incubated in water drops generated transversely septate promycelia, unbranched, producing terminal and lateral basidiospores. The fungus did not grow well on potato dextrose agar (PDA) medium, generating yeastlike colonies. To confirm pathogenicity of a Ustilago sp., spores collected from field-infected plants were inoculated on 8- and 20-day old seedlings of dry-bean cultivars Rosinha and Perola. Spore suspensions of 10[5] teliospores were sprayed all over the plants. After inoculation, plants were kept in a moist chamber (relative humidity [RH] 100%) for 2 days. At the third day, inoculated plants were covered with clear polyethylene bags and transferred to the greenhouse (RH 50%, temperature 25 ± 2°C). Noninoculated controls were included for comparisons. Within 2 weeks, all inoculated plants reproduced field symptoms of darkened tissues covered by profuse sori containing teliospores and basidiospores. Eight-day-old plants died 2 weeks after inoculation. Noninoculated plants did not develop any symptoms. Teliospores obtained from dead plants were identical to those used for inoculation, thus completing Koch's postulates. Fischer (1), and later Fischer and Shaw (2), proposed a species concept for Ustilago based on morphology (primarily of the teliospore), symptomatology, and host specialization at the host-family level. Although the teliospores found on dry-beans, in Brazil, are much like those of Ustilago maydis, the fungus did not cause galls on plants, was able to infect roots and kill seedlings. and is very well adapted to a legume plant. Cross inoculation tests indicated that spores from dry-beans cannot cause disease symptoms on maize. We therefore regard the bean smut as a new species. We are not aware of any other Ustilago sp. being reported on a legume host. References: (1) G. W. Fischer. 1953. Manual of the North America Smut Fungi. (2) G. W. Fischer and C. G. Shaw. Phytopathology 43:181, 1953.}, } @article {pmid28308062, year = {1998}, author = {Guehl, JM and Domenach, AM and Bereau, M and Barigah, TS and Casabianca, H and Ferhi, A and Garbaye, J}, title = {Functional diversity in an Amazonian rainforest of French Guyana: a dual isotope approach (δ[15]N and δ[13]C).}, journal = {Oecologia}, volume = {116}, number = {3}, pages = {316-330}, doi = {10.1007/s004420050593}, pmid = {28308062}, issn = {1432-1939}, abstract = {Functional aspects of biodiversity were investigated in a lowland tropical rainforest in French Guyana (5°2'N, annual precipitation 2200 mm). We assessed leaf δ[15]N as a presumptive indicator of symbiotic N2 fixation, and leaf and wood cellulose δ[13]C as an indicator of leaf intrinsic water-use efficiency (CO2 assimilation rate/leaf conductance for water vapour) in dominant trees of 21 species selected for their representativeness in the forest cover, their ecological strategy (pioneers or late successional stage species, shade tolerance) or their potential ability for N2 fixation. Similar measurements were made in trees of native species growing in a nearby plantation after severe perturbation (clear cutting, mechanical soil disturbance). Bulk soil δ[15]N was spatially quite uniform in the forest (range 3-5‰), whereas average leaf δ[15]N ranged from -0.3‰ to 3.5‰ in the different species. Three species only, Diplotropis purpurea, Recordoxylon speciosum (Fabaceae), and Sclerolobium melinonii (Caesalpiniaceae), had root bacterial nodules, which was also associated with leaf N concentrations higher than 20 mg g[-1]. Although nodulated trees displayed significantly lower leaf δ[15]N values than non-nodulated trees, leaf δ[15]N did not prove a straightforward indicator of symbiotic fixation, since there was a clear overlap of δ[15]N values for nodulated and non-nodulated species at the lower end of the δ[15]N range. Perturbation did not markedly affect the difference δ[15]Nsoil - δ[15]Nleaf, and thus the isotopic data provide no evidence of an alteration in the different N acquisition patterns. Extremely large interspecific differences in sunlit leaf δ[13]C were observed in the forest (average values from -31.4 to -26.7‰), corresponding to intrinsic water-use efficiencies (ratio CO2 assimilation rate/leaf conductance for water vapour) varying over a threefold range. Wood cellulose δ[13]C was positively related to total leaf δ[13]C, the former values being 2-3‰ higher than the latter ones. Leaf δ[13]C was not related to leaf δ[15]N at either intraspecific or interspecific levels. δ[13]C of sunlit leaves was highest in shade hemitolerant emergent species and was lower in heliophilic, but also in shade-tolerant species. For a given species, leaf δ[13]C did not differ between the pristine forest and the disturbed plantation conditions. Our results are not in accord with the concept of existence of functional types of species characterized by common suites of traits underlying niche differentiation; rather, they support the hypothesis that each trait leads to a separate grouping of species.}, } @article {pmid28565231, year = {1998}, author = {Gleason, JM and Griffith, EC and Powell, JR}, title = {A MOLECULAR PHYLOGENY OF THE DROSOPHILA WILLISTONI GROUP: CONFLICTS BETWEEN SPECIES CONCEPTS?.}, journal = {Evolution; international journal of organic evolution}, volume = {52}, number = {4}, pages = {1093-1103}, doi = {10.1111/j.1558-5646.1998.tb01836.x}, pmid = {28565231}, issn = {1558-5646}, abstract = {The six sibling species of the Neotropical Drosophila willistoni group have a long history in studies of evolutionary biology, yet to date only one molecular study, which used allozymes, has been published on the phylogeny of the group. Here we present a phylogeny of the siblings based on the sequences of two nuclear genes, period (per) and Alcohol dehydrogenase (Adh), as well as the mitochondrial gene Cytochrome oxidase I (COI). Taken individually, only per has a strong phylogenetic signal supporting a well-resolved phylogeny of the group, and this phylogeny is different from that obtained using allozymes. The COI dataset by itself produces trees that disagree with per, and neither that data nor the Adh data have a strong phylogenetic signal, as indicated by low bootstrap values for all analyses. Combining the Adh and COI datasets results in the same tree as per alone. Combining all three genes results in the same topology, which is strongly supported. Two problematic taxa, D. pavlovskiana and a "Carmody strain," which were identified as potentially separate species based on reproductive isolation, clearly cluster in the phylogenetic analyses within D. paulistorum and D. equinoxialis, respectively. Thus, there appears to be a conflict between the biological species concept and the phylogenetic species concept.}, } @article {pmid28565219, year = {1998}, author = {Johns, GC and Avise, JC}, title = {TESTS FOR ANCIENT SPECIES FLOCKS BASED ON MOLECULAR PHYLOGENETIC APPRAISALS OF SEBASTES ROCKFISHES AND OTHER MARINE FISHES.}, journal = {Evolution; international journal of organic evolution}, volume = {52}, number = {4}, pages = {1135-1146}, doi = {10.1111/j.1558-5646.1998.tb01840.x}, pmid = {28565219}, issn = {1558-5646}, abstract = {The concept of species flocks has been central to previous interpretations of patterns and processes of explosive species radiations within several groups of freshwater fishes. Here, molecular phytogenies of species-rich Sebastes rockfishes from the northeastern Pacific Ocean were used to test predictions of null theoretical models that assume random temporal placements of phylogenetic nodes. Similar appraisals were conducted using molecular data previously published for particular cichlid fishes in Africa that epitomize, by virtue of a rapid and recent radiation of species, the traditional concept of an intralacustrine "species flock." As gauged by the magnitudes of genetic divergence in cytochrome b sequences from mitochondrial DNA, as well as in allozymes, most speciation events in the Sebastes complex were far more ancient than those in the cichlids. However, statistical tests of the nodal placements in the Sebastes phylogeny suggest that speciation events in the rockfishes were temporally nonrandom, with significant clustering of cladogenetic events in time. Similar conclusions also apply to an ancient complex of icefishes (within the Notothenioidei) analyzed in the same fashion. Thus, the rockfishes (and icefishes) may be interpreted as ancient species flocks in the marine realm. The analyses exemplified in this report introduce a conceptual and operational approach for extending the concept of species flocks to additional environmental settings and evolutionary timescales.}, } @article {pmid34920636, year = {1997}, author = {Zrzavý, J and Nedved, O}, title = {Phylogeny of the New World Dysdercus (Insecta: Hemiptera: Pyrrhocoridae) and Evolution of their Colour Patterns.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {13}, number = {1-2}, pages = {109-123}, doi = {10.1111/j.1096-0031.1997.tb00245.x}, pmid = {34920636}, issn = {1096-0031}, abstract = {Evolution of colour patterns is reconstructed in the case of the New World species of Dysdercus (Hemiptera: Pyrrhocoridae). The phylogenetic species concept was applied to this group, elevating five subspecific taxa to specific rank (D. capitatus, D. discolor, D. fervidus, D. luteus, and D. neglectus), and the resulting 41 phylogenetic species were analysed cladistically. Using optimization methods, evolution of colour patterns of the group is hypothesized, and possible developmental mechanisms of colour-pattern evolutionary changes are inferred.}, } @article {pmid28307844, year = {1996}, author = {Connolly, J and Wayne, P}, title = {Asymmetric competition between plant species.}, journal = {Oecologia}, volume = {108}, number = {2}, pages = {311-320}, pmid = {28307844}, issn = {1432-1939}, abstract = {Despite extensive interest in the role of plant size in competition, few formal attempts have been made to quantify the magnitude of asymmetric competition, particularly for interactions between members of different species. This paper introduces the concept of asymmetric interspecific competition at the population livel (i.e. mean plant performance) in mixtures of species. It proposes an index of interspecific competitive asymmetry which allows for a progressively greater asymmetric effect as the average size differences between competing species increase, and allows for such an effect whether individuals of focal species are larger or smaller, on average, than competitors. This index of competitive asymmetry is evaluated in the study of interactions between two widely coexisting annuals of disturbed habitats, Stellaria media and Poa annua. An experiment was conducted in which the density, relative frequency and relative seedling sizes (emergence times) of Poa and Stellaria individuals were varied. The relative growth rate (RGR) for both species was measured over a 22-day period. An inverse linear model was fitted for each species, relating the RGR of the focal species to the initial biomass of each species. Each response model included an asymmetry coefficient (β) to assess whether the impact of a unit of initial biomass of the associate species changed with the relative sizes of seedlings of the two species. A zero value of β implies symmetric competition between the two populations; i.e. the competitive effect of a unit of associate species biomass does not change with its initial seedling size. If β is positive the smaller the initial relative size of seedlings of the associate species, the smaller their per unit biomass effect on the response of the focal species. The model fitted our data for Stellaria and Poa well and was validated by an alternative modelling approach. Asymmetry coefficients were estimated as 0.508 (P<0.05) for the effect of Poa in the Stellaria model, and 0.0001 (NS) for the effect of Stellaria in the Poa model; i.e. the effect of Poa on Stellaria was asymmetric while the effect of Stellaria on Poa was symmetric. Differences in interspecific species asymmetric competitive effects are discussed within the context of shoot architecture, and the relative importance of competition for light versus soil resources. Finally, we discuss the relationship of this model to earlier models of competitive asymmetry, and consider the implications of interspecific competitive asymmetry for a number of current theories of plant competition and community organisation.}, } @article {pmid28593680, year = {1995}, author = {Cohan, FM}, title = {DOES RECOMBINATION CONSTRAIN NEUTRAL DIVERGENCE AMONG BACTERIAL TAXA?.}, journal = {Evolution; international journal of organic evolution}, volume = {49}, number = {1}, pages = {164-175}, doi = {10.1111/j.1558-5646.1995.tb05968.x}, pmid = {28593680}, issn = {1558-5646}, abstract = {A coalescence model for predicting the fate of neutral divergence among closely related taxa distinguishable as separate DNA sequence clusters is presented here. The model simulates iteratively the positive feedback between sequence divergence and sexual isolation among taxa, where increases in sequence divergence result in reduced recombination, and reduced recombination results in increased sequence divergence. Iteration of this feedback is continued until sequence divergence either converges on a steady state or reaches a runaway process. The eventual outcome of sequence divergence was shown to depend on four estimable population-genetic parameters: the expected intrataxon sequence diversity, the baseline rate of intertaxon recombination, the sensitivity of the recombination rate to sequence divergence, and the neutral mutation rate. The model can be used to determine whether neutral divergence among actual taxa is destined to stop at an equilibrium level, or whether neutral divergence will reach a runaway process. Application of the model to the group of taxa containing Bacillus subtilis and its closest relatives showed these taxa to be on a trajectory of unbounded neutral divergence from one another.}, } @article {pmid28564903, year = {1993}, author = {Mercure, A and Ralls, K and Koepfli, KP and Wayne, RK}, title = {GENETIC SUBDIVISIONS AMONG SMALL CANIDS: MITOCHONDRIAL DNA DIFFERENTIATION OF SWIFT, KIT, AND ARCTIC FOXES.}, journal = {Evolution; international journal of organic evolution}, volume = {47}, number = {5}, pages = {1313-1328}, doi = {10.1111/j.1558-5646.1993.tb02157.x}, pmid = {28564903}, issn = {1558-5646}, abstract = {Gene flow can effectively suppress genetic divergence among widely separated populations in highly mobile species. However, the same may not be true of species that typically disperse over shorter distances. Using mtDNA restriction-site and sequence analyses, we evaluate the extent of divergence among populations of two small relatively sedentary North American canids, the kit and swift foxes (genus Vulpes). We determine the significance of genetic differentiation among populations separated by distance and those separated by discrete topographic barriers. Our results show the among-population component of genetic variation in kit and swift foxes is large and similar to that of small rodents with limited dispersal ability. In addition, we found two distinct groupings of genotypes, separated by the Rocky Mountains, corresponding to the traditional division between kit and swift fox populations. Previous workers have characterized these morphologically similar populations either as separate species or subspecies. Our mtDNA data also suggest that kit and swift fox populations hybridize over a limited geographic area. However, the sequence divergence between kit and swift foxes is similar to that between these taxa and the arctic fox (Alopex lagopus), a morphologically distinct species commonly placed in a separate genus. This result presents a dilemma for species concepts, and we conclude that kit and swift foxes should be recognized as separate species.}, } @article {pmid34929952, year = {1992}, author = {Cracraft, J}, title = {THE SPECIES OF THE BIRDS-OF-PARADISE (PARADISAEIDAE): APPLYING THE PHYLOGENETIC SPECIES CONCEPT TO A COMPLEX PATTERN OF DIVERSIFICATION.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {8}, number = {1}, pages = {1-43}, doi = {10.1111/j.1096-0031.1992.tb00049.x}, pmid = {34929952}, issn = {1096-0031}, abstract = {The phylogenetic species concept is applied for the first time to a major radiation of birds, the birds-of-paradise (Paradisaeidae) of Australasia. Using the biological species concept, previous workers have postulated approximately 40-42 species in the family. Of these, approximately 13 are monotypic and 27 are polytypic with about 100 subspecies. Phylogenetic species are irreducible (basal) clusters of organisms (terminal taxa) that are diagnosably distinct from other such clusters. Within the context of this concept, approximately 90 species of paradisaeids are postulated to have diversified within Australasia. The phylogenetic species concept more accurately describes evolutionary diversity within the family and provides a better theoretical and empirical framework for analysing speciation, historical biogeography and patterns of morphological, behavioral and ecological diversification within this group than does the biological species concept.}, } @article {pmid34929949, year = {1992}, author = {Vrana, P and Wheeler, W}, title = {INDIVIDUAL ORGANISMS AS TERMINAL ENTITIES: LAYING THE SPECIES PROBLEM TO REST.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {8}, number = {1}, pages = {67-72}, doi = {10.1111/j.1096-0031.1992.tb00051.x}, pmid = {34929949}, issn = {1096-0031}, } @article {pmid28312496, year = {1991}, author = {Green, TG and Kilian, E and Lange, OL}, title = {Pseudocyphellaria dissimilis: a desiccation-sensitive, highly shade-adapted lichen from New Zealand.}, journal = {Oecologia}, volume = {85}, number = {4}, pages = {498-503}, pmid = {28312496}, issn = {1432-1939}, abstract = {Pseudocyphellaria dissimilis, a foliose, cyanobacterial lichen, is shown not to fit into the normal ecological concept of lichens. This species is both extremely shade-tolerant and also more intolerant to drying than aquatic lichens previously thought to be the most desiccation-sensitive of lichens. Samples of P. dissimilis from a humid rain-forest site in New Zealand were transported in a moist state to Germany. Photosynthesis response curves were generated. The effect of desiccation was measured by comparing CO2 exchange before and after a standard 20-h drying routine. Lichen thalli could be equilibrated at 15° C to relative humidities (RH) from 5% to almost 100%. Photosynthesis was saturated at a photosynthetically active radiation (PAR) level of 20 μmol m[-2] s[-1] (350 μbar CO2) and PAR compensation was a very low 1 μmol m[-2] s[-1]. Photosynthesis did not saturate until 1500 μbar CO2. Net photosynthesis was relatively unaffected by temperature between 10° C and 30° C with upper compensation at over 40° C. Temporary depression of photosynthesis occurred after a drying period of 20 h with equilibration at 45-65% relative humidity (RH). Sustained damage occurred at 15-25% RH and many samples died after equilibration at 5-16% RH. Microclimate studies of the lichen habitat below the evergreen, broadleaf forest canopy revealed consistently low PAR (normally below 10-20 μmol m[-2] s[-1]) and high humidities (over 80% RH even during the day time). The species shows many features of an extremely deep shade-adapted plant including low PAR saturation and compensation, low photosynthetic and respiratory rates and low dry weight per unit area.}, } @article {pmid34933512, year = {1990}, author = {Lidén, M}, title = {REPLICATORS, HIERARCHY, AND THE SPECIES PROBLEM.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {6}, number = {2}, pages = {183-186}, doi = {10.1111/j.1096-0031.1990.tb00535.x}, pmid = {34933512}, issn = {1096-0031}, } @article {pmid34933475, year = {1990}, author = {Wheeler, QD and Nixon, KC}, title = {ANOTHER WAY OF LOOKING AT THE SPECIES PROBLEM: A REPLY TO DE QUEIROZ AND DONOGHUE.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {6}, number = {1}, pages = {77-81}, doi = {10.1111/j.1096-0031.1990.tb00526.x}, pmid = {34933475}, issn = {1096-0031}, } @article {pmid28564509, year = {1989}, author = {Wagner, GP}, title = {THE ORIGIN OF MORPHOLOGICAL CHARACTERS AND THE BIOLOGICAL BASIS OF HOMOLOGY.}, journal = {Evolution; international journal of organic evolution}, volume = {43}, number = {6}, pages = {1157-1171}, doi = {10.1111/j.1558-5646.1989.tb02566.x}, pmid = {28564509}, issn = {1558-5646}, abstract = {A homolog is a part of the phenotype that is homologous to equivalent parts in other species. A biological homology concept is expected to explain three properties of homologs: 1) the conservation of those features that are used to define a homolog, 2) the individualization of the homolog with regard to the rest of the body, and 3) the uniqueness of homologs, i.e., their specificity for monophyletic groups. The main obstacle to describing a mechanistic basis for homology is the variability of the developmental pathways of undoubtedly homologous characters. However, not all aspects of the developmental pathway are of equal importance. The only organizational features of the developmental system that matter are those that have been historically acquired and cause developmental constraints on the further evolutionary modification of the characters. Two main factors contribute to historically acquired developmental constraints: generative rules of pattern formation and ontogenetic networks. In particular, hierarchical and cyclical inductive networks have the required properties to explain homology. How common such networks are is an open empirical question. The development and variation of pectoral fin hooks in blenniid fishes is presented as a model for the study of a simple ontogenetic network.}, } @article {pmid34949064, year = {1988}, author = {de Queiroz, K and Donoghue, MJ}, title = {PHYLOGENETIC SYSTEMATICS AND THE SPECIES PROBLEM.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {4}, number = {4}, pages = {317-338}, doi = {10.1111/j.1096-0031.1988.tb00518.x}, pmid = {34949064}, issn = {1096-0031}, abstract = {Abstract- A tension has arisen over the primacy of interbreeding versus monophyly in defining the species category. Manifestations of this tension include unnecessary restriction of the concept of monophyly as well as inappropriate attribution of "species" properties, to "higher taxa", and vice versa. Distinctions between systems (wholes) deriving their existence from different underlying. processes have been obscured by failure to acknowledge different interpretations of the concept of individuality. We identify interbreeding (resulting in populations) and evolutionary descent (resulting in monophyletic groups) as two processes of interest to phylogenetic systematists, and explore the relations between the systems resulting from these processes. In the case of sexual reproduction, populations of interbreeding organisms (regardless of whether they are monophyletic) exist as cohesive wholes and play a special role in phylogenetic systematics, being the least inclusive entities appropriate for use as terminal units in phylogenetic analysis of organismal relationships. Both sexual and asexual organisms form monophyletic groups. Accepting the reality and significance of both interbreeding and monophyly emphasizes that a conscious decision must be made regarding which phenomenon should be used to define the species category. Examination of species concepts that focus either on interbreeding or on common descent leads us to conclude that several alternatives are acceptable from the standpoint of phylogenetic systematics but that no one species concept can meet the needs of all comparative biologists.}, } @article {pmid28563413, year = {1987}, author = {Natvig, DO and Jackson, DA and Taylor, JW}, title = {RANDOM-FRAGMENT HYBRIDIZATION ANALYSIS OF EVOLUTION IN THE GENUS NEUROSPORA: THE STATUS OF FOUR-SPORED STRAINS.}, journal = {Evolution; international journal of organic evolution}, volume = {41}, number = {5}, pages = {1003-1021}, doi = {10.1111/j.1558-5646.1987.tb05873.x}, pmid = {28563413}, issn = {1558-5646}, abstract = {A random-fragment hybridization method employing nuclear DNA has been developed to explore phylogenetic relationships in the genus Neurospora. Four cloned fragments and repetitive rDNA sequences were examined for restriction-fragment polymorphisms among 14 strains representing four species. The findings demonstrate that variation among randomly selected nuclear fragments can be employed to group related taxa with a higher degree of resolution than has been obtained with other DNA hybridization methods, isozyme electrophoresis, or restriction analysis of repetitive DNA. Based on our analysis of cloned fragments, we conclude that four-spored, secondarily-homothallic strains collected worldwide represent a monophyletic group. Trees constructed on the basis of restriction-fragment cataloging and coarse-structure restriction-site maps are for the most part consistent with the present mating-based species concept. We are encouraged that this method will provide an additional important experimental tool for evolutionary studies.}, } @article {pmid34949080, year = {1987}, author = {Loevtrup, S}, title = {ON SPECIES and OTHER TAXA.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {3}, number = {2}, pages = {157-177}, doi = {10.1111/j.1096-0031.1987.tb00504.x}, pmid = {34949080}, issn = {1096-0031}, abstract = {Abstract- It is argued that taxa, whether Linnaean or phylogenetic, belong to Popper's worlds 2 and 3, the worlds of knowledge, but that they represent entities residing in world 1, the world of objects, namely, classes of living beings. The Linnaean taxa are concepts, and thus untestable, whereas phylogenetic taxa are statements, the monophyletic taxa being true, and the paraphyletic and polyphyletic ones false statements. The taxa are neither strictly nor numerically universal statements, but probabilistic ones which cannot be falsified by single observations. It is suggested that the classical "species problem" is due to the fact that "species" has been used in three different senses. First, traditionally it has been assumed that the specific "essence" of an organism is that by which it is what it is. When we know the species, we know the organism. Second, the species are terminal taxa in the phylogenetic hierarchy. This implies that it is only a very small part of the "essence" of the organism which distinguishes the species. The remaining part characterizes the succession of superior taxa in the phylogenetic lineage which ends with the species in question. Third, the species has been regarded to be the "evolutionary unit." This idea may be refuted for two reasons: (1) since concepts and statements cannot evolve, species cannot evolve either, and (2) it is generally in very small isolated populations that evolutionary innovations are first established. In Linnean systematics the superior taxa are allotted categorical rank. The fact that the classification is constrained by this conventional stipulation implies that the superior taxa are often man-made artifacts. In the phylogenetic hierarchy, composed of monophyletic taxa, the ontological states of the taxa is completely independent of their numerical rank; the kingdom is as "real" as the species.}, } @article {pmid31973509, year = {1987}, author = {Horn, AD}, title = {Taxonomic assessment of the allopatric gray-cheeked mangabey (Cercocebus albigena) and black mangabey (C. aterrimus): Comparative socioecological data and the species concept.}, journal = {American journal of primatology}, volume = {12}, number = {2}, pages = {181-187}, doi = {10.1002/ajp.1350120205}, pmid = {31973509}, issn = {1098-2345}, abstract = {A brief review of past taxonomic assessments of the allopatric gray-cheeked mangabey (Cercocebus albigena) and the black mangabey (Cercocebus aterrimus) is presented. On the basis of pelage, cranial, and biomolecular morphology, aterrimus and albigena have been lumped together in the same species-group, superspecies, subgenus, or species by various systematists over the years. A comparison of the available socioecological data on the two forms supports their close taxonomic association, as they are found to be very similar in socioecological traits. After a brief review of current species concepts, the author, on the basis of the socioecological commonalities, tentatively supports Groves' [1978] conspecific designation of albigena and aterrimus and suggests further tests for this proposal and for the species concept, from the points of view of both taxonomic and evolutionary theory.}, } @article {pmid34965679, year = {1985}, author = {Ax, P}, title = {STEM SPECIES AND THE STEM LINEAGE CONCEPT.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {1}, number = {3}, pages = {279-287}, doi = {10.1111/j.1096-0031.1985.tb00428.x}, pmid = {34965679}, issn = {1096-0031}, } @article {pmid28310040, year = {1980}, author = {Roberts, SW and Strain, BR and Knoerr, KR}, title = {Seasonal patterns of leaf water relations in four co-occurring forest tree species: Parameters from pressure-volume curves.}, journal = {Oecologia}, volume = {46}, number = {3}, pages = {330-337}, pmid = {28310040}, issn = {1432-1939}, abstract = {Leaf water relationships were studied in four widespread forest tree species (Ilex opaca Ait., Cornus florida L., Acer rubrum L., and Liriodendron tulipifera L.). The individuals studied all occurred on the same site and were selected to represent a range of growth forms and water relationships in some of the principal tree species of the region. The water relations of the species were analyzed using the concept of the water potential-water content relationship. The pressure-volume method was used to measure this relationship using leaf material sampled from naturally occurring plants in the field. Water potential components (turgor, osmotic, and matric) were obtained by analysis of the pressure-volume curves.Initial osmotic potentials (the value of the osmotic component at full turgidity) were highest (least negative) at the start of the growing season. They decreased (becoming progressively more negative) as the season progressed through a drought period. Following a period of precipitation at the end of the drought period, initial osmotic potentials increased toward the values measured earlier in the season.Seasonal osmotic adjustments were sufficient in all species to allow maintenance of leaf turgor through the season, with one exception: Acer appeared to undergo some midday turgor loss during the height of the July drought period.In addition to environmental influences, tissue stage of development played a role; young Ilex leaves had higher early season initial osmotic potentials than overwintering leaves from the same tree.The seasonal pattern of initial osmotic potential in Liriodendron and the observed pattern of leaf mortality suggested a possible role of osmotic potentials in the resistance of those leaves to drought conditions. The fraction of total leaf water which is available to affect osmotic potentials, called the osmotic water fraction in this study, was greatest in young tissue early in the season and declined as the season progressed.The results of this study showed that the water potential-water content relationship represents a dynamic mechanism by which plant internal water relations may vary in response to a changing external water-availability regime. The measured water relationships confirmed the relative positions of the species along a water-availability gradient, with Cornus at the wettest end and Ilex at the driest end of the gradient. Acer and Liriodendron were intermediate in their water relations. The spread of these species along a water-availability gradient on the same site suggested that coexistence is partially based on differential water use patterns.}, } @article {pmid28309107, year = {1976}, author = {Enright, JT}, title = {Climate and population regulation : The biogeographer's dilemma.}, journal = {Oecologia}, volume = {24}, number = {4}, pages = {295-310}, doi = {10.1007/BF00381136}, pmid = {28309107}, issn = {1432-1939}, abstract = {Based upon a conceptual dichotomy between those environmental influences on a population which vary in their effect with population density, and those which do not, it is widely held that only density-dependent factors can determine equilibrium abundance or "carrying capacity" for a population under field conditions. Since the direct effects of climate on mortality and birth rates are commonly thought to be independent of density, that interpretation means that correlations between climatic factors and long-term average population density are presumed to reflect only indirect effects of climate, acting, for example, on resource availability. When density-dependent and density-independent processes are carefully defined, however, and their expected consequences derived, it becomes clear that the equilibrium abundance for a species can usually be altered by any environmental factor which has a consistent effect on either birth rate or mortality rate, regardless of whether that action itself depends upon density of the species. This implies that the concept of "carrying capacity" must be extended, to include possible direct, density-independent effects of climate on birth and death rates; these conclusions follow from a very simple model which appears to be extremely robust. Hence, geographic trends in average population density, which are so familiar to the biographer, may well be due in a straight-forward manner to the influences of climate, even if climate were to act only in a densityindependent manner.}, } @article {pmid28309244, year = {1975}, author = {van Andel, J}, title = {A study on the population dynamics of the perennial plant species Chamaenerion angustifolium (L.) scop.}, journal = {Oecologia}, volume = {19}, number = {4}, pages = {329-337}, pmid = {28309244}, issn = {1432-1939}, abstract = {From a study of differently aged populations of the perennial plant species Chamaenerion angustifolium a concept was deduced concerning the population dynamics of the species. The age structure was determined by counting the rings of periderm in the roots. After the establishment of seedlings vegetative propagation is the main factor in population development. The longevity of populations depends on exogenic factors, since older root samples-if isolated from the population-appeared to be as viable as were younger specimens. The oldest population studied had been able to persist for about thirty years due to the mineral cycle brought about by the population itself. In still developing populations a greater number of shoots tend to sprout from younger roots than from older roots, when compared per unit root weight. The shoot density in full-grown populations (in which further root expansion does not occur) is related to the root biomass per unit area. It was suggested that the allocation of reserve assimilates within the roots is an endogenic factor determining the shoot density. After the early sprouting phase the shoot development depends mainly on environmental factors.}, } @article {pmid28973811, year = {1971}, author = {Hurlbert, SH}, title = {The Nonconcept of Species Diversity: A Critique and Alternative Parameters.}, journal = {Ecology}, volume = {52}, number = {4}, pages = {577-586}, doi = {10.2307/1934145}, pmid = {28973811}, issn = {0012-9658}, abstract = {The recent literature on species diversity contains many semantic, conceptual, and technical problems. It is suggested that, as a result of these problems, species diversity has become a meaningless concept, that the term be abandoned, and that ecologists take a more critical approach to species-number relations and rely less on information theoretic and other analogies. As multispecific collections of organisms possess numerous statistical properties which conform to the conventional criteria for diversity indices, such collections are not intrinsically arrangeable in linear order along some diversity scale. Several such properties or "species composition parameters" having straightforward biological interpretations are presented as alternatives to the diversity approach. The two most basic of these are simply ▵1 =[n/n-1][[1][-][Σ]i ([N] _i/_N)[2] ] =the proportion of potential interindividual encounters which is interspecific (as opposed to intraspecific), assuming every individual in the collection can encounter all other individuals, E(Sn) = [Σ]i [1-([N][-][N]in)/([N]n)] =the expected number of species in a sample of n individuals selected at random from a collection containing N individuals, S species, and Ni individuals in the ith species.}, } @article {pmid24478720, year = {2014}, author = {Turner, EE and Cox, TC}, title = {Genetic evidence for conserved non-coding element function across species-the ears have it.}, journal = {Frontiers in physiology}, volume = {5}, number = {}, pages = {7}, pmid = {24478720}, issn = {1664-042X}, support = {R01 DE022561/DE/NIDCR NIH HHS/United States ; }, abstract = {Comparison of genomic sequences from diverse vertebrate species has revealed numerous highly conserved regions that do not appear to encode proteins or functional RNAs. Often these "conserved non-coding elements," or CNEs, can direct gene expression to specific tissues in transgenic models, demonstrating they have regulatory function. CNEs are frequently found near "developmental" genes, particularly transcription factors, implying that these elements have essential regulatory roles in development. However, actual examples demonstrating CNE regulatory functions across species have been few, and recent loss-of-function studies of several CNEs in mice have shown relatively minor effects. In this Perspectives article, we discuss new findings in "fancy" rats and Highland cattle demonstrating that function of a CNE near the Hmx1 gene is crucial for normal external ear development and when disrupted can mimic loss-of function Hmx1 coding mutations in mice and humans. These findings provide important support for conserved developmental roles of CNEs in divergent species, and reinforce the concept that CNEs should be examined systematically in the ongoing search for genetic causes of human developmental disorders in the era of genome-scale sequencing.}, } @article {pmid24477002, year = {2014}, author = {Sayin, VI and Ibrahim, MX and Larsson, E and Nilsson, JA and Lindahl, P and Bergo, MO}, title = {Antioxidants accelerate lung cancer progression in mice.}, journal = {Science translational medicine}, volume = {6}, number = {221}, pages = {221ra15}, doi = {10.1126/scitranslmed.3007653}, pmid = {24477002}, issn = {1946-6242}, mesh = {Acetylcysteine/adverse effects ; Animals ; Antioxidants/*adverse effects ; Cell Line, Tumor ; Cell Proliferation/drug effects ; DNA Damage ; Disease Models, Animal ; *Disease Progression ; Fibroblasts/drug effects/metabolism ; Humans ; Lung Neoplasms/*pathology ; Mice ; Reactive Oxygen Species/metabolism ; Solubility ; Tumor Suppressor Protein p53/metabolism ; Vitamin E/adverse effects/analogs & derivatives ; }, abstract = {Antioxidants are widely used to protect cells from damage induced by reactive oxygen species (ROS). The concept that antioxidants can help fight cancer is deeply rooted in the general population, promoted by the food supplement industry, and supported by some scientific studies. However, clinical trials have reported inconsistent results. We show that supplementing the diet with the antioxidants N-acetylcysteine (NAC) and vitamin E markedly increases tumor progression and reduces survival in mouse models of B-RAF- and K-RAS-induced lung cancer. RNA sequencing revealed that NAC and vitamin E, which are structurally unrelated, produce highly coordinated changes in tumor transcriptome profiles, dominated by reduced expression of endogenous antioxidant genes. NAC and vitamin E increase tumor cell proliferation by reducing ROS, DNA damage, and p53 expression in mouse and human lung tumor cells. Inactivation of p53 increases tumor growth to a similar degree as antioxidants and abolishes the antioxidant effect. Thus, antioxidants accelerate tumor growth by disrupting the ROS-p53 axis. Because somatic mutations in p53 occur late in tumor progression, antioxidants may accelerate the growth of early tumors or precancerous lesions in high-risk populations such as smokers and patients with chronic obstructive pulmonary disease who receive NAC to relieve mucus production.}, } @article {pmid24473222, year = {2014}, author = {Ernst, S and Norman, SE and Hardacre, C and Compton, RG}, title = {The electrochemical reduction of 1-bromo-4-nitrobenzene at zinc electrodes in a room-temperature ionic liquid: a facile route for the formation of arylzinc compounds.}, journal = {Physical chemistry chemical physics : PCCP}, volume = {16}, number = {10}, pages = {4478-4482}, doi = {10.1039/c3cp54861a}, pmid = {24473222}, issn = {1463-9084}, abstract = {The electrochemical reduction of 1-bromo-4-nitrobenzene (p-BrC6H4NO2) at zinc microelectrodes in the [C4mPyrr][NTf2] ionic liquid was investigated via cyclic voltammetry. The reduction was found to occur via an EC type mechanism, where p-BrC6H4NO2 is first reduced by one electron, quasi-reversibly, to yield the corresponding radical anion. The radical anions then react with the Zn electrode to form arylzinc products. Introduction of carbon dioxide into the system led to reaction with the arylzinc species, fingerprinting the formation of the latter. This method thus demonstrates a proof-of-concept of the formation of functionalised arylzinc species.}, } @article {pmid24453553, year = {2013}, author = {Breugelmans, K and Jordaens, K and Adriaens, E and Remon, JP and Cardona, JQ and Backeljau, T}, title = {DNA barcodes and phylogenetic affinities of the terrestrial slugs Arion gilvus and A. ponsi (Gastropoda, Pulmonata, Arionidae).}, journal = {ZooKeys}, volume = {}, number = {365}, pages = {83-104}, pmid = {24453553}, issn = {1313-2989}, abstract = {The Iberian Peninsula is a region with a high endemicity of species of the terrestrial slug subgenus Mesarion. Many of these species have been described mainly on subtle differences in their proximal genitalia. It therefore remains to be investigated 1) whether these locally diverged taxa also represent different species under a phylogenetic species concept as has been shown for other Mesarion species outside the Iberian Peninsula, and 2) how these taxa are phylogenetically related. Here, we analysed DNA sequence data of two mitochondrial (COI and 16S) genes, and of the nuclear ITS1 region, to explore the phylogenetic affinities of two of these endemic taxa, viz. Arion gilvus Torres Mínguez, 1925 and A. ponsi Quintana Cardona, 2007. We also evaluated the use of these DNA sequence data as DNA barcodes for both species. Our results showed that ITS did not allow to differentiate among most of the Mesarion molecular operational taxonomic units (MOTUs) / morphospecies in Mesarion. Yet, the overall mean p-distance among the Mesarion MOTUs / morphospecies for both mtDNA fragments (16.7% for COI, 13% for 16S) was comparable to that between A. ponsi and its closest relative A. molinae (COI: 14.2%; 16S: 16.2%) and to that between A. gilvus and its closest relative A. urbiae (COI: 14.4%; 16S: 13.4%). Hence, with respect to mtDNA divergence, both A. ponsi and A. gilvus, behave as other Mesarion species or putative species-level MOTUs and thus are confirmed as distinct 'species'.}, } @article {pmid24427149, year = {2014}, author = {Dresler, M and Eibl, L and Fischer, CF and Wehrle, R and Spoormaker, VI and Steiger, A and Czisch, M and Pawlowski, M}, title = {Volitional components of consciousness vary across wakefulness, dreaming and lucid dreaming.}, journal = {Frontiers in psychology}, volume = {4}, number = {}, pages = {987}, pmid = {24427149}, issn = {1664-1078}, abstract = {Consciousness is a multifaceted concept; its different aspects vary across species, vigilance states, or health conditions. While basal aspects of consciousness like perceptions and emotions are present in many states and species, higher-order aspects like reflective or volitional capabilities seem to be most pronounced in awake humans. Here we assess the experience of volition across different states of consciousness: 10 frequent lucid dreamers rated different aspects of volition according to the Volitional Components Questionnaire for phases of normal dreaming, lucid dreaming, and wakefulness. Overall, experienced volition was comparable for lucid dreaming and wakefulness, and rated significantly higher for both states compared to non-lucid dreaming. However, three subscales showed specific differences across states of consciousness: planning ability was most pronounced during wakefulness, intention enactment most pronounced during lucid dreaming, and self-determination most pronounced during both wakefulness and lucid dreaming. Our data confirm the multifaceted nature of consciousness: different higher-order aspects of consciousness are differentially expressed across different conscious states.}, } @article {pmid24408951, year = {2014}, author = {Tindall, BJ}, title = {The correct name of the taxon that contains the type strain of Rhodococcus equi.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {64}, number = {Pt 1}, pages = {302-308}, doi = {10.1099/ijs.0.059584-0}, pmid = {24408951}, issn = {1466-5034}, mesh = {Rhodococcus equi/*classification ; *Terminology as Topic ; }, abstract = {Based on a nomenclatural point of view, the name Rhodococcus equi is associated, as required by the Bacteriological Code, with a defined position, rank and circumscription. A search of the literature indicates that the name Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 has also been shown to be a synonym of Corynebacterium equi Magnusson 1923, Corynebacterium hoagii (Morse 1912) Eberson 1918 and Nocardia restricta (Turfitt 1944) McClung 1974. Application of the rules of the Bacteriological Code together with the currently inferred taxonomic concept associated with the species bearing the name Rhodococcus equi indicates that this is not the correct name of this taxon and the use of that name in the context of a circumscription that includes the type strain of the species Corynebacterium hoagii is contrary to the Rules of the Code.}, } @article {pmid24401083, year = {2014}, author = {Tripathi, A and Schofield, MM and Chlipala, GE and Schultz, PJ and Yim, I and Newmister, SA and Nusca, TD and Scaglione, JB and Hanna, PC and Tamayo-Castillo, G and Sherman, DH}, title = {Baulamycins A and B, broad-spectrum antibiotics identified as inhibitors of siderophore biosynthesis in Staphylococcus aureus and Bacillus anthracis.}, journal = {Journal of the American Chemical Society}, volume = {136}, number = {4}, pages = {1579-1586}, pmid = {24401083}, issn = {1520-5126}, support = {T32 GM008353/GM/NIGMS NIH HHS/United States ; U01 TW007404/TW/FIC NIH HHS/United States ; U54 AI057153/AI/NIAID NIH HHS/United States ; U54 AI57153/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/chemistry/isolation & purification/*pharmacology ; Bacillus anthracis/chemistry/*drug effects/metabolism ; Biological Products/chemistry/isolation & purification/*pharmacology ; Daunorubicin/*analogs & derivatives/chemical synthesis/chemistry/pharmacology ; Dose-Response Relationship, Drug ; Escherichia coli/*drug effects ; High-Throughput Screening Assays ; Microbial Sensitivity Tests ; Molecular Conformation ; Siderophores/*antagonists & inhibitors/biosynthesis ; Staphylococcus aureus/chemistry/*drug effects/metabolism ; Structure-Activity Relationship ; }, abstract = {Siderophores are high-affinity iron chelators produced by microorganisms and frequently contribute to the virulence of human pathogens. Targeted inhibition of the biosynthesis of siderophores staphyloferrin B of Staphylococcus aureus and petrobactin of Bacillus anthracis hold considerable potential as a single or combined treatment for methicillin-resistant S. aureus (MRSA) and anthrax infection, respectively. The biosynthetic pathways for both siderophores involve a nonribosomal peptide synthetase independent siderophore (NIS) synthetase, including SbnE in staphyloferrin B and AsbA in petrobactin. In this study, we developed a biochemical assay specific for NIS synthetases to screen for inhibitors of SbnE and AsbA against a library of marine microbial-derived natural product extracts (NPEs). Analysis of the NPE derived from Streptomyces tempisquensis led to the isolation of the novel antibiotics baulamycins A (BmcA, 6) and B (BmcB, 7). BmcA and BmcB displayed in vitro activity with IC50 values of 4.8 μM and 19 μM against SbnE and 180 μM and 200 μM against AsbA, respectively. Kinetic analysis showed that the compounds function as reversible competitive enzyme inhibitors. Liquid culture studies with S. aureus , B. anthracis , E. coli , and several other bacterial pathogens demonstrated the capacity of these natural products to penetrate bacterial barriers and inhibit growth of both Gram-positive and Gram-negative species. These studies provide proof-of-concept that natural product inhibitors targeting siderophore virulence factors can provide access to novel broad-spectrum antibiotics, which may serve as important leads for the development of potent anti-infective agents.}, } @article {pmid24393294, year = {2014}, author = {Rosas-Guerrero, V and Aguilar, R and Martén-Rodríguez, S and Ashworth, L and Lopezaraiza-Mikel, M and Bastida, JM and Quesada, M}, title = {A quantitative review of pollination syndromes: do floral traits predict effective pollinators?.}, journal = {Ecology letters}, volume = {17}, number = {3}, pages = {388-400}, doi = {10.1111/ele.12224}, pmid = {24393294}, issn = {1461-0248}, mesh = {*Adaptation, Biological ; *Biological Evolution ; Flowers/*anatomy & histology ; Geography ; Magnoliopsida/genetics/*physiology ; *Phylogeny ; Pollination/*physiology ; Species Specificity ; Symbiosis/*physiology ; }, abstract = {The idea of pollination syndromes has been largely discussed but no formal quantitative evaluation has yet been conducted across angiosperms. We present the first systematic review of pollination syndromes that quantitatively tests whether the most effective pollinators for a species can be inferred from suites of floral traits for 417 plant species. Our results support the syndrome concept, indicating that convergent floral evolution is driven by adaptation to the most effective pollinator group. The predictability of pollination syndromes is greater in pollinator-dependent species and in plants from tropical regions. Many plant species also have secondary pollinators that generally correspond to the ancestral pollinators documented in evolutionary studies. We discuss the utility and limitations of pollination syndromes and the role of secondary pollinators to understand floral ecology and evolution.}, } @article {pmid24387692, year = {2014}, author = {Tovar-Méndez, A and Kumar, A and Kondo, K and Ashford, A and Baek, YS and Welch, L and Bedinger, PA and McClure, BA}, title = {Restoring pistil-side self-incompatibility factors recapitulates an interspecific reproductive barrier between tomato species.}, journal = {The Plant journal : for cell and molecular biology}, volume = {77}, number = {5}, pages = {727-736}, doi = {10.1111/tpj.12424}, pmid = {24387692}, issn = {1365-313X}, mesh = {Flowers/*physiology ; Genes, Plant ; Lycopersicon esculentum/*physiology ; Plant Proteins/metabolism ; Ribonucleases/metabolism ; *Self-Incompatibility in Flowering Plants ; }, abstract = {Interspecific reproductive barriers are poorly understood, but are central to the biological species concept. The pre-zygotic barriers between red- and green-fruited species in the tomato clade of the genus Solanum provide a model to better understand these barriers in plants. Compatibility usually follows the SI x SC rule: pollen from self-compatible (SC) red-fruited species is rejected on pistils of the predominantly self-incompatible (SI) green-fruited species, but the reciprocal crosses are compatible. This suggests that the interspecific reproductive barrier may be linked to the intraspecific SI mechanism. However, pollen from the SC red-fruited species is also rejected by SC accessions of green-fruited species that lack S-RNase, a key protein expressed in pistils of SI Solanum species. Thus, multiple mechanisms may contribute to the barrier between red- and green-fruited species. We tested whether an S-RNase-dependent barrier is sufficient for rejection of pollen from red-fruited species by introducing functional S-RNase, HT-A and HT-B genes from SI species into Solanum lycopersicum (cultivated tomato). We found that expressing S-RNase in combination with either HT-A or HT-B in the pistil is sufficient to cause rejection of pollen from all four red-fruited species. Thus, redundant mechanisms must operate side by side to prevent crosses between red- and green-fruited species in the clade, underlining the complexity of interspecific pollination barriers. Our results also have implications for mating system transitions. We suggest that these transitions must occur in a specific sequence, and that the transition from SI to SC also affects interspecific compatibility.}, } @article {pmid24386104, year = {2013}, author = {Montenegro-Miranda, PS and Pañeda, A and ten Bloemendaal, L and Duijst, S and de Waart, DR and Gonzalez- Aseguinolaza, G and Bosma, PJ}, title = {Adeno-associated viral vector serotype 5 poorly transduces liver in rat models.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82597}, pmid = {24386104}, issn = {1932-6203}, mesh = {Animals ; *Dependovirus ; Genetic Therapy/methods ; Genetic Vectors ; Glucuronosyltransferase/genetics/metabolism ; Liver/*virology ; Rats ; }, abstract = {Preclinical studies in mice and non-human primates showed that AAV serotype 5 provides efficient liver transduction and as such seems a promising vector for liver directed gene therapy. An advantage of AAV5 compared to serotype 8 already shown to provide efficient correction in a phase 1 trial in patients suffering from hemophilia B, is its lower seroprevalence in the general population. Our goal is liver directed gene therapy for Crigler-Najjar syndrome type I, inherited severe unconjugated hyperbilirubinemia caused by UGT1A1 deficiency. In a relevant animal model, the Gunn rat, we compared the efficacy of AAV 5 and 8 to that of AAV1 previously shown to be effective. Ferrying a construct driving hepatocyte specific expression of UGT1A1, both AAV8 and AAV1 provided an efficient correction of hyperbilirubinemia. In contrast to these two and to other animal models AAV5 failed to provide any correction. To clarify whether this unexpected finding was due to the rat model used or due to a problem with AAV5, the efficacy of this serotype was compared in a mouse and two additional rat strains. Administration of an AAV5 vector expressing luciferase under the control of a liver specific promoter confirmed that this serotype poorly performed in rat liver, rendering it not suitable for proof of concept studies in this species.}, } @article {pmid24378641, year = {2014}, author = {Stoffel, W and Hammels, I and Jenke, B and Binczek, E and Schmidt-Soltau, I and Brodesser, S and Odenthal, M and Thevis, M}, title = {Obesity resistance and deregulation of lipogenesis in Δ6-fatty acid desaturase (FADS2) deficiency.}, journal = {EMBO reports}, volume = {15}, number = {1}, pages = {110-120}, pmid = {24378641}, issn = {1469-3178}, mesh = {Adipocytes, White/pathology ; Adipose Tissue, White/pathology ; Animals ; Arachidonic Acid/metabolism ; Cell Size ; Disease Resistance ; Docosahexaenoic Acids/metabolism ; Fatty Liver/enzymology ; Female ; Linoleic Acid/metabolism ; Linoleoyl-CoA Desaturase/*deficiency/genetics ; *Lipogenesis ; Liver/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Obesity/*enzymology/genetics ; Phospholipids/metabolism ; Transcriptome ; Weight Gain ; }, abstract = {Δ-6-fatty acid desaturase (FADS2) is the key enzyme in the biosynthesis of polyunsaturated fatty acids (PUFAs), the essential structural determinants of mammalian membrane lipid-bilayers. We developed the auxotrophic fads2(-/-) mouse mutant to assess the enigmatic role of ω3- and ω6-PUFAs in lipid homeostasis, membrane structure and function. Obesity resistance is another major phenotype of the fads2(-/-) mutant, the molecular basis of which is unknown. Phospholipidomic profiling of membrane systems of fads2(-/-)mice revealed diacylglycerol-structures, deprived of PUFAs but substituted with surrogate eicosa-5,11,14-trienoic acid. ω6-Arachidonic (AA) and ω3-docosahexaenoic acid (DHA) supplemented diets transformed fads2(-/-) into AA-fads2(-/-) and DHA-fads2(-/-) mutants. Severely altered phospholipid-bilayer structures of subcellular membranes of fads2(-/-) liver specifically interfered with maturation of transcription factor sterol-regulatory-element-binding protein, the key regulator of lipogenesis and lipid homeostasis. This study strengthens the concept that specific PUFA-substituted membrane phospholipid species are critical constituents of the structural platform operative in lipid homeostasis in normal and disease conditions.}, } @article {pmid24376533, year = {2013}, author = {Huang, J and Zhang, A and Mao, S and Huang, Y}, title = {DNA barcoding and species boundary delimitation of selected species of Chinese Acridoidea (Orthoptera: Caelifera).}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82400}, pmid = {24376533}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; China ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Haplotypes/genetics ; Molecular Sequence Data ; Orthoptera/*classification ; *Phylogeny ; Sequence Alignment ; Species Specificity ; }, abstract = {We tested the performance of DNA barcoding in Acridoidea and attempted to solve species boundary delimitation problems in selected groups using COI barcodes. Three analysis methods were applied to reconstruct the phylogeny. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. "Best match (BM)", "best close match (BCM)", "all species barcodes (ASB)" and "back-propagation neural networks (BP-based method)" were utilized to test the success rate of species identification. Phylogenetic species concept and network analysis were employed to delimitate the species boundary in eight selected species groups. The results demonstrated that the COI barcode region performed better in phylogenetic reconstruction at genus and species levels than at higher-levels, but showed a little improvement in resolving the higher-level relationships when the third base data or both first and third base data were excluded. Most overlaps and incorrect identifications may be due to imperfect taxonomy, indicating the critical role of taxonomic revision in DNA barcoding study. Species boundary delimitation confirmed the presence of oversplitting in six species groups and suggested that each group should be treated as a single species.}, } @article {pmid24374376, year = {2014}, author = {Schnug, L and Leinaas, HP and Jensen, J}, title = {Synergistic sub-lethal effects of a biocide mixture on the springtail Folsomia fimetaria.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {186}, number = {}, pages = {158-164}, doi = {10.1016/j.envpol.2013.12.004}, pmid = {24374376}, issn = {1873-6424}, mesh = {Acrylates/toxicity ; Animals ; Arthropods/drug effects ; Disinfectants/*toxicity ; Drug Synergism ; Nitriles/toxicity ; Pyrethrins/toxicity ; Pyridines/toxicity ; Reproduction/drug effects ; Risk Assessment ; Soil Pollutants/*toxicity ; Strobilurins ; Triclosan/toxicity ; }, abstract = {The toxicity of three biocides, esfenvalerate, picoxystrobin and triclosan, on adult survival and recruitment of juveniles was studied in the springtail Folsomia fimetaria, both in single and mixture experiments. Recruitment of juveniles was more sensitive to biocide exposure than adult survival. The concepts of concentration addition and independent action returned almost identical toxicity predictions, though both models failed to predict the observed toxicity due to synergistic deviations at high exposure concentrations. A comparison with a similar study on earthworms showed that response-patterns were species-specific. Consequently, there is no single reference concept which is applicable for all species of one ecosystem, which in turn questions the usefulness of such mixture prediction concepts in ecological risk assessment.}, } @article {pmid24371162, year = {2013}, author = {Pandit, A and Vadlamudi, J and Sinha, S}, title = {Analysis of dinucleotide signatures in HIV-1 subtype B genomes.}, journal = {Journal of genetics}, volume = {92}, number = {3}, pages = {403-412}, pmid = {24371162}, issn = {0973-7731}, mesh = {Base Composition ; Evolution, Molecular ; Genetic Variation ; *Genome, Viral ; HIV Infections/*virology ; HIV-1/*genetics ; Humans ; Models, Genetic ; Sequence Analysis, DNA ; }, abstract = {Dinucleotide usage is known to vary in the genomes of organisms. The dinucleotide usage profiles or genome signatures are similar for sequence samples taken from the same genome, but are different for taxonomically distant species. This concept of genome signatures has been used to study several organisms including viruses, to elucidate the signatures of evolutionary processes at the genome level. Genome signatures assume greater importance in the case of host-pathogen interactions, where molecular interactions between the two species take place continuously, and can influence their genomic composition. In this study, analyses of whole genome sequences of the HIV-1 subtype B, a retrovirus that caused global pandemic of AIDS, have been carried out to analyse the variation in genome signatures of the virus from 1983 to 2007. We show statistically significant temporal variations in some dinucleotide patterns highlighting the selective evolution of the dinucleotide profiles of HIV-1 subtype B, possibly a consequence of host specific selection.}, } @article {pmid24340131, year = {2013}, author = {Villarreal, LP and Witzany, G}, title = {Rethinking quasispecies theory: From fittest type to cooperative consortia.}, journal = {World journal of biological chemistry}, volume = {4}, number = {4}, pages = {79-90}, pmid = {24340131}, issn = {1949-8454}, abstract = {Recent investigations surprisingly indicate that single RNA "stem-loops" operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops (not individuals) are the basic players. We thus redefine quasispecies as RNA quasispecies consortia (qs-c) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competence-not error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity (immunity) functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs.}, } @article {pmid24329302, year = {2013}, author = {Markham, DC and Simpson, MJ and Maini, PK and Gaffney, EA and Baker, RE}, title = {Incorporating spatial correlations into multispecies mean-field models.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {88}, number = {5}, pages = {052713}, doi = {10.1103/PhysRevE.88.052713}, pmid = {24329302}, issn = {1550-2376}, mesh = {*Models, Theoretical ; Movement ; *Spatial Analysis ; }, abstract = {In biology, we frequently observe different species existing within the same environment. For example, there are many cell types in a tumour, or different animal species may occupy a given habitat. In modeling interactions between such species, we often make use of the mean-field approximation, whereby spatial correlations between the locations of individuals are neglected. Whilst this approximation holds in certain situations, this is not always the case, and care must be taken to ensure the mean-field approximation is only used in appropriate settings. In circumstances where the mean-field approximation is unsuitable, we need to include information on the spatial distributions of individuals, which is not a simple task. In this paper, we provide a method that overcomes many of the failures of the mean-field approximation for an on-lattice volume-excluding birth-death-movement process with multiple species. We explicitly take into account spatial information on the distribution of individuals by including partial differential equation descriptions of lattice site occupancy correlations. We demonstrate how to derive these equations for the multispecies case and show results specific to a two-species problem. We compare averaged discrete results to both the mean-field approximation and our improved method, which incorporates spatial correlations. We note that the mean-field approximation fails dramatically in some cases, predicting very different behavior from that seen upon averaging multiple realizations of the discrete system. In contrast, our improved method provides excellent agreement with the averaged discrete behavior in all cases, thus providing a more reliable modeling framework. Furthermore, our method is tractable as the resulting partial differential equations can be solved efficiently using standard numerical techniques.}, } @article {pmid24306768, year = {2014}, author = {Oren, A and Garrity, GM}, title = {Then and now: a systematic review of the systematics of prokaryotes in the last 80 years.}, journal = {Antonie van Leeuwenhoek}, volume = {106}, number = {1}, pages = {43-56}, doi = {10.1007/s10482-013-0084-1}, pmid = {24306768}, issn = {1572-9699}, mesh = {Bacteria/*classification/genetics/*isolation & purification ; History, 20th Century ; History, 21st Century ; Microbiology/*history ; Prokaryotic Cells/*classification ; Systems Biology/*history ; }, abstract = {In the 80 years that have passed since the first issue of Antonie van Leeuwenhoek was published, the field of prokaryote systematics has changed dramatically. The 4th edition of Bergey's Manual of Determinative Bacteriology (1934) described 132 genera and 2,703 species. The numbers of genera and species with names with standing in the nomenclature in August 2013 were 2,390 and 11,482, respectively, including no more than 75 genera and 250 species that were recognized in 1934. In the years 2006-2012, on average 624 new species were added annually, most of which were described by scientists in Asian countries. We review the past and current species concept for the prokaryotes and the current requirements for the description of new species, based on a 'polyphasic' approach. We discuss the impact of genomics and metagenomics and other new trends toward revitalization of prokaryote systematics, and provide some ideas and speculations on possible future developments in the field.}, } @article {pmid24295919, year = {2013}, author = {Goldmann, L and Weir, A and Rossi, W}, title = {Molecular analysis reveals two new dimorphic species of Hesperomyces (Ascomycota, Laboulbeniomycetes) parasitic on the ladybird Coleomegilla maculata (Coleoptera, Coccinellidae).}, journal = {Fungal biology}, volume = {117}, number = {11-12}, pages = {807-813}, doi = {10.1016/j.funbio.2013.10.004}, pmid = {24295919}, issn = {1878-6146}, mesh = {Animals ; Ascomycota/*classification/cytology/genetics/*isolation & purification ; Cluster Analysis ; Coleoptera/*microbiology ; Costa Rica ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Ecuador ; Genes, rRNA ; Microscopy ; Molecular Sequence Data ; Phylogeny ; RNA, Fungal/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {Four morphotypes of Hesperomyces (Ascomycota, Laboulbeniomycetes) were found on the ladybird Coleomegilla maculata (Coleoptera, Coccinellidae) from Costa Rica and Ecuador. Partial SSU and ITS rDNA sequence analysis revealed that these belong to two phylogenetic species, each with a pair of morphotypes displaying position specificity. Confirmation of dimorphism in Laboulbeniales highlights the need for a thorough systematic revision of species concepts within the order. The theory of 'position specificity' also needs to be revisited.}, } @article {pmid24278356, year = {2013}, author = {Clavel, J and Poulet, N and Porcher, E and Blanchet, S and Grenouillet, G and Pavoine, S and Biton, A and Seon-Massin, N and Argillier, C and Daufresne, M and Teillac-Deschamps, P and Julliard, R}, title = {A new freshwater biodiversity indicator based on fish community assemblages.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80968}, pmid = {24278356}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; Databases, Factual ; Datasets as Topic ; Ecosystem ; *Fishes ; France ; *Fresh Water ; Humans ; Spatio-Temporal Analysis ; }, abstract = {Biodiversity has reached a critical state. In this context, stakeholders need indicators that both provide a synthetic view of the state of biodiversity and can be used as communication tools. Using river fishes as model, we developed community indicators that aim at integrating various components of biodiversity including interactions between species and ultimately the processes influencing ecosystem functions. We developed indices at the species level based on (i) the concept of specialization directly linked to the niche theory and (ii) the concept of originality measuring the overall degree of differences between a species and all other species in the same clade. Five major types of originality indices, based on phylogeny, habitat-linked and diet-linked morphology, life history traits, and ecological niche were analyzed. In a second step, we tested the relationship between all biodiversity indices and land use as a proxy of human pressures. Fish communities showed no significant temporal trend for most of these indices, but both originality indices based on diet- and habitat- linked morphology showed a significant increase through time. From a spatial point of view, all indices clearly singled out Corsica Island as having higher average originality and specialization. Finally, we observed that the originality index based on niche traits might be used as an informative biodiversity indicator because we showed it is sensitive to different land use classes along a landscape artificialization gradient. Moreover, its response remained unchanged over two other land use classifications at the global scale and also at the regional scale.}, } @article {pmid24260686, year = {2013}, author = {Venu, G and Venkatachalaiah, G}, title = {Chromosomal homology of Uraeotyphlus oxyurus group of species (Amphibia, Gymnophiona, Ichthyophiidae).}, journal = {Comparative cytogenetics}, volume = {7}, number = {1}, pages = {11-23}, pmid = {24260686}, issn = {1993-0771}, abstract = {Uraeotyphlus oxyurus (Dumeril et Bibron, 1841), Uraeotyphlus interruptus Pillai et Ravichandran, 1999, Uraeotyphlus narayani Seshachar, 1939 and Uraeotyphlus menoni Annandale, 1913 were cytogenetically analysed following conventional and differential staining techniques. These species show similar karyotypes with 2n=36 (FN=58). There were no traces of species-specific features in regard to C-banding and NOR staining. The comparative study of karyotypes shows chromosomal homologies among the four species. Chromosomal data seem to support the concept that two species groups exist in the genus Uraeotyphlus.}, } @article {pmid24244043, year = {2013}, author = {Kowalczyk, R and Krasińska, M and Kamiński, T and Górny, M and Struś, P and Hofman-Kamińska, E and Krasiński, ZA}, title = {Movements of European bison (Bison bonasus) beyond the Białowieża Forest (NE Poland): range expansion or partial migrations?.}, journal = {Acta theriologica}, volume = {58}, number = {4}, pages = {391-401}, pmid = {24244043}, issn = {0001-7051}, abstract = {The European bison is the largest terrestrial mammal in Europe. After extinction in the wild at the beginning of the twentieth century, it was re-introduced to Białowieża Forest and other woodlands in Eastern Europe. In this paper, we analysed the movements of European bison beyond the continuous woodlands of the Białowieża Forest (NE Poland) between 1964 and 2010. In total, 1,117 direct observations of bison were collected. The number of males moving out of the forest fluctuated during the study period, whilst the number of females steadily increased. The number of male observations outside of the forest per annum was dependent on the population size and snow depth, whilst the number of cows in mixed groups moving outside of the forest was correlated with the population size only. Males were observed mainly alone (50 % of observations) or in small groups of two to three individuals (25 %); however, distribution of group size differed from those observed in the population. There was a significant difference between the direction of movement of males and females out of the forest-males moved mainly west and southwest, whilst females moved to the north. This was also significantly different from the expected movement direction. The mean distance of bison observations from the forest border was 1.8 ± 0.13 km and did not differ significantly between sexes. After 1990, males were observed significantly farther away from the forest (2.2 km) than in the previous years (0.9 km). Most observations (94 % of bulls and 93 % of cows) were up to 5 km from the forest edge. The range of bison in the vicinity of the Białowieża Forest was strictly seasonal. Most observations (78 % in males and 88 % in females) were recorded from November to April. Increasing utilisation of areas beyond the forest habitats may be driven by different factors but most probably it is related to range expansion and the bison's preference for open habitats. The strong seasonal pattern of bison movements indicate that the partial seasonal migrations were initiated in the Białowieża population.}, } @article {pmid24223279, year = {2013}, author = {Stålstedt, J and Bergsten, J and Ronquist, F}, title = {"Forms" of water mites (Acari: Hydrachnidia): intraspecific variation or valid species?.}, journal = {Ecology and evolution}, volume = {3}, number = {10}, pages = {3415-3435}, pmid = {24223279}, issn = {2045-7758}, abstract = {In many groups of organisms, especially in the older literature, it has been common practice to recognize sympatrically occurring phenotypic variants of a species as "forms". However, what these forms really represent often remains unclear, especially in poorly studied groups. With new algorithms for DNA-based species delimitation, the status of forms can be explicitly tested with molecular data. In this study, we test a number of what is now recognized as valid species of water mites (Hydrachnidia), but have in the past been treated as forms sympatrically occurring with their nominate species. We also test a form without prior taxonomical status, using DNA and morphometrics. The barcoding fragment of COI, nuclear 28S and quantitative analyses of morphological data were used to test whether these taxa merit species status, as suggested by several taxonomists. Our results confirm valid species. Genetic distances between the form and nominate species (Piona dispersa and Piona variabilis, COI 11%), as well as likelihood ratio tests under the general mixed-Yule coalescent model, supported that these are separately evolving lineages as defined by the unified species concept. In addition, they can be diagnosed with morphological characters. The study also reveals that some taxa genetically represent more than one species. We propose that P. dispersa are recognized as valid taxa at the species level. Unionicola minor (which may consist of several species), Piona stjordalensis, P. imminuta s. lat., and P. rotundoides are confirmed as species using this model. The results also imply that future studies of other water mite species complexes are likely to reveal many more genetically and morphologically distinct species.}, } @article {pmid24219357, year = {2013}, author = {Khelifa, R and Zebsa, R and Moussaoui, A and Kahalerras, A and Bensouilah, S and Mahdjoub, H}, title = {Niche partitioning in three sympatric congeneric species of dragonfly, Orthetrum chrysostigma, O. coerulescens anceps, and O. nitidinerve: the importance of microhabitat.}, journal = {Journal of insect science (Online)}, volume = {13}, number = {}, pages = {71}, pmid = {24219357}, issn = {1536-2442}, mesh = {Algeria ; Animals ; *Ecosystem ; Female ; Male ; Odonata/*physiology ; Reproduction ; Species Specificity ; }, abstract = {Habitat heterogeneity has been shown to promote co-existence of closely related species. Based on this concept, a field study was conducted on the niche partitioning of three territorial congeneric species of skimmers (Anisoptera: Libellulidae) in Northeast Algeria during the breeding season of 2011. According to their size, there is a descending hierarchy between Orthetrum nitidinerve Sélys, O. chrysostigma (Burmeister), and O. coerulescens anceps (Schneider). After being marked and surveyed, the two latter species had the same breeding behavior sequence. Knowing that they had almost the same size, such species could not co-occur in the same habitat according to the competitive exclusion principle. The spatial distribution of the three species was investigated at two different microhabitats, and it was found that these two species were actually isolated at this scale. O. chrysostigma and O. nitidinerve preferred open areas, while O. c. anceps occurred in highly vegetated waters. This study highlights the role of microhabitat in community structure as an important niche axis that maintains closely related species in the same habitat.}, } @article {pmid24204671, year = {2013}, author = {Meleg, IN and Zakšek, V and Fišer, C and Kelemen, BS and Moldovan, OT}, title = {Can environment predict cryptic diversity? The case of Niphargus inhabiting Western Carpathian groundwater.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76760}, pmid = {24204671}, issn = {1932-6203}, mesh = {Amphipoda/classification/*genetics ; Animals ; Arthropod Proteins/genetics ; Bayes Theorem ; Ecosystem ; Electron Transport Complex IV/genetics ; *Environment ; Female ; *Genetic Variation ; Geography ; Groundwater/*parasitology ; Histones/genetics ; Male ; Molecular Sequence Data ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 28S/genetics ; Romania ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {In the last decade, several studies have shown that subterranean aquatic habitats harbor cryptic species with restricted geographic ranges, frequently occurring as isolated populations. Previous studies on aquatic subterranean species have implied that habitat heterogeneity can promote speciation and that speciation events can be predicted from species' distributions. We tested the prediction that species distributed across different drainage systems and karst sectors comprise sets of distinct species. Amphipods from the genus Niphargus from 11 caves distributed along the Western Carpathians (Romania) were investigated using three independent molecular markers (COI, H3 and 28S). The results showed that: 1) the studied populations belong to eight different species that derive from two phylogenetically unrelated Niphargus clades; 2) narrow endemic species in fact comprise complexes of morphologically similar species that are indistinguishable without using a molecular approach. The concept of monophyly, concordance between mitochondrial and nuclear DNA, and the value of patristic distances were used as species delimitation criteria. The concept of cryptic species is discussed within the framework of the present work and the contribution of these species to regional biodiversity is also addressed.}, } @article {pmid24198939, year = {2013}, author = {Bevilacqua, S and Claudet, J and Terlizzi, A}, title = {Best Practicable Aggregation of Species: a step forward for species surrogacy in environmental assessment and monitoring.}, journal = {Ecology and evolution}, volume = {3}, number = {11}, pages = {3780-3793}, pmid = {24198939}, issn = {2045-7758}, abstract = {The available taxonomic expertise and knowledge of species is still inadequate to cope with the urgent need for cost-effective methods to quantifying community response to natural and anthropogenic drivers of change. So far, the mainstream approach to overcome these impediments has focused on using higher taxa as surrogates for species. However, the use of such taxonomic surrogates often limits inferences about the causality of community patterns, which in turn is essential for effective environmental management strategies. Here, we propose an alternative approach to species surrogacy, the "Best Practicable Aggregation of Species" (BestAgg), in which surrogates exulate from fixed taxonomic schemes. The approach uses null models from random aggregations of species to minimizing the number of surrogates without causing significant losses of information on community patterns. Surrogate types are then selected in order to maximize ecological information. We applied the approach to real case studies on natural and human-driven gradients from marine benthic communities. Outcomes from BestAgg were also compared with those obtained using classic taxonomic surrogates. Results showed that BestAgg surrogates are effective in detecting community changes. In contrast to classic taxonomic surrogates, BestAgg surrogates allow retaining significantly higher information on species-level community patterns than what is expected to occur by chance and a potential time saving during sample processing up to 25% higher. Our findings showed that BestAgg surrogates from a pilot study could be used successfully in similar environmental investigations in the same area, or for subsequent long-term monitoring programs. BestAgg is virtually applicable to any environmental context, allowing exploiting multiple surrogacy schemes beyond stagnant perspectives strictly relying on taxonomic relatedness among species. This prerogative is crucial to extend the concept of species surrogacy to ecological traits of species, thus leading to ecologically meaningful surrogates that, while cost effective in reflecting community patterns, may also contribute to unveil underlying processes. A specific R code for BestAgg is provided.}, } @article {pmid24159931, year = {2013}, author = {Markolf, M and Rakotonirina, H and Fichtel, C and von Grumbkow, P and Brameier, M and Kappeler, PM}, title = {True lemurs…true species - species delimitation using multiple data sources in the brown lemur complex.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {233}, pmid = {24159931}, issn = {1471-2148}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; Female ; Lemur/anatomy & histology/*classification/*genetics ; Lemuridae/genetics ; Madagascar ; Male ; Phylogeny ; Principal Component Analysis ; Vocalization, Animal ; }, abstract = {BACKGROUND: Species are the fundamental units in evolutionary biology. However, defining them as evolutionary independent lineages requires integration of several independent sources of information in order to develop robust hypotheses for taxonomic classification. Here, we exemplarily propose an integrative framework for species delimitation in the "brown lemur complex" (BLC) of Madagascar, which consists of seven allopatric populations of the genus Eulemur (Primates: Lemuridae), which were sampled extensively across northern, eastern and western Madagascar to collect fecal samples for DNA extraction as well as recordings of vocalizations. Our data base was extended by including museum specimens with reliable identification and locality information for skull shape and pelage color analysis.

RESULTS: Between-group analyses of principal components revealed significant heterogeneity in skull shape, pelage color variation and loud calls across all seven populations. Furthermore, post-hoc statistical tests between pairs of populations revealed considerable discordance among different data sets for different dyads. Despite a high degree of incomplete lineage sorting among nuclear loci, significant exclusive ancestry was found for all populations, except for E. cinereiceps, based on one mitochondrial and three nuclear genetic loci.

CONCLUSIONS: Using several independent lines of evidence, our results confirm the species status of the members of the BLC under the general lineage concept of species. More generally, the present analyses demonstrate the importance and value of integrating different kinds of data in delimiting recently evolved radiations.}, } @article {pmid24159899, year = {2014}, author = {Gladyshev, VN}, title = {The free radical theory of aging is dead. Long live the damage theory!.}, journal = {Antioxidants & redox signaling}, volume = {20}, number = {4}, pages = {727-731}, pmid = {24159899}, issn = {1557-7716}, mesh = {*Aging ; Animals ; Humans ; Life Expectancy ; Oxidation-Reduction ; Oxidative Stress ; Reactive Oxygen Species/*metabolism ; }, abstract = {The free radical theory of aging posits that aging is caused by accumulation of damage inflicted by reactive oxygen species (ROS). Although this concept has been very useful in defining the contribution of oxidative damage to the aging process, an increasing number of studies contradict it. The idea that oxidative damage represents only one of many causes of aging also has limitations, as it does not explain causal relationships and inevitability of damage accumulation. Here, it is discussed that infidelity, heterogeneity, and imperfectness of each and every biological process may be responsible for the inevitable accumulation of by-products and other damage forms. Although ROS are prototypical by-products, their contribution to aging is governed by the metabolic organization of the cell, its protective systems, and genotype. These factors are controlled by natural selection and, like dietary and genetic interventions that extend lifespan, change the composition of cumulative damage and the rates of accumulation of its various forms. Oxidative damage, like other specific damage types viewed in isolation or in combination, does not represent the cause of aging. Instead, biological imperfectness, which leads to inevitable accumulation of damage in the form of mildly deleterious molecular species, may help define the true root of aging. Free radical and other specialized damage theories served their purpose in the understanding of the aging process, but in the current form they limit further progress in this area.}, } @article {pmid24134732, year = {2014}, author = {Thornhill, DJ and Lewis, AM and Wham, DC and LaJeunesse, TC}, title = {Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts.}, journal = {Evolution; international journal of organic evolution}, volume = {68}, number = {2}, pages = {352-367}, doi = {10.1111/evo.12270}, pmid = {24134732}, issn = {1558-5646}, mesh = {Adaptation, Physiological/*genetics ; *Coral Reefs ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Dinoflagellida/*genetics/physiology ; *Genetic Speciation ; Host Specificity ; Microsatellite Repeats ; *Symbiosis ; }, abstract = {Bursts in species diversification are well documented among animals and plants, yet few studies have assessed recent adaptive radiations of eukaryotic microbes. Consequently, we examined the radiation of the most ecologically dominant group of endosymbiotic dinoflagellates found in reef-building corals, Symbiodinium Clade C, using nuclear ribosomal (ITS2), chloroplast (psbA(ncr)), and multilocus microsatellite genotyping. Through a hierarchical analysis of high-resolution genetic data, we assessed whether ecologically distinct Symbiodinium, differentiated by seemingly equivocal rDNA sequence differences, are independent species lineages. We also considered the role of host specificity in Symbiodinium speciation and the correspondence between endosymbiont diversification and Caribbean paleo-history. According to phylogenetic, biological, and ecological species concepts, Symbiodinium Clade C comprises many distinct species. Although regional factors contributed to population-genetic structuring of these lineages, Symbiodinium diversification was mainly driven by host specialization. By combining patterns of the endosymbiont's host specificity, water depth distribution, and phylogeography with paleo-historical signals of climate change, we inferred that present-day species diversity on Atlantic coral reefs stemmed mostly from a post-Miocene adaptive radiation. Host-generalist progenitors spread, specialized, and diversified during the ensuing epochs of prolonged global cooling and change in reef-faunal assemblages. Our evolutionary reconstruction thus suggests that Symbiodinium undergoes "boom and bust" phases in diversification and extinction during major climate shifts.}, } @article {pmid24112308, year = {2013}, author = {Cicconardi, F and Fanciulli, PP and Emerson, BC}, title = {Collembola, the biological species concept and the underestimation of global species richness.}, journal = {Molecular ecology}, volume = {22}, number = {21}, pages = {5382-5396}, doi = {10.1111/mec.12472}, pmid = {24112308}, issn = {1365-294X}, mesh = {Animals ; Arthropods/*classification/genetics ; Bayes Theorem ; *Biodiversity ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; Genetic Variation ; Likelihood Functions ; Linkage Disequilibrium ; Molecular Sequence Data ; Panama ; *Phylogeny ; Sequence Analysis, DNA ; Sympatry ; }, abstract = {Despite its ancient origin, global distribution and abundance in nearly all habitats, the class Collembola is comprised of only 8000 described species and is estimated to number no more than 50,000. Many morphologically defined species have broad geographical ranges that span continents, and recent molecular work has revealed high genetic diversity within species. However, the evolutionary significance of this genetic diversity is unknown. In this study, we sample five morphological species of the globally distributed genus Lepidocyrtus from 14 Panamanian sampling sites to characterize genetic diversity and test morphospecies against the biological species concept. Mitochondrial and nuclear DNA sequence data were analysed and a total of 58 molecular lineages revealed. Deep lineage diversification was recovered, with 30 molecular lineages estimated to have established more than 10 million years ago, and the origin almost all contemporary lineages preceding the onset of the Pleistocene (~2 Mya). Thirty-four lineages were sampled in sympatry revealing unambiguous cosegregation of mitochondrial and nuclear DNA sequence variation, consistent with biological species. Species richness within the class Collembola and the geographical structure of this diversity are substantially misrepresented components of terrestrial animal biodiversity. We speculate that global species richness of Collembola could be at least an order of magnitude greater than a previous estimate of 50,000 species.}, } @article {pmid24098732, year = {2013}, author = {Wang, L and Liao, W and Chen, C and Fan, Q}, title = {The seed plant flora of the Mount Jinggangshan region, southeastern China.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e75834}, pmid = {24098732}, issn = {1932-6203}, mesh = {*Altitude ; *Biodiversity ; China ; Climate ; Embryophyta/classification/*genetics ; Geography ; Soil/chemistry ; }, abstract = {The Mount Jinggangshan region is located between Jiangxi and Hunan provinces in southeastern China in the central section of the Luoxiao Mountains. A detailed investigation of Mount Jinggangshan region shows that the seed plant flora comprises 2,958 species in 1,003 genera and 210 families (Engler's system adjusted according to Zhengyi Wu's concept). Among them, 23 species of gymnospermae belong to 17 genera and 9 families, and 2,935 species of angiosperms are in 986 genera and 201 families. Moreover, they can also be sorted into woody plants (350 genera and 1,295 species) and herbaceous plants (653 genera and 1,663 species). The dominant families are mainly Fagaceae, Lauraceae, Theaceae, Hamamelidaceae, Magnoliaceae, Ericaceae, Styracaceae, Aquifoliaceae, Elaeocarpaceae, Aceraceae, Rosaceae, Corylaceae, Daphniphyllaceae, Symplocaceae, Euphorbiaceae, Pinaceae, Taxodiaceae, Cupressaceae and Taxaceae. Ancient and relic taxa include Ginkgo biloba, Fokieniahodginsii, Amentotaxusargotaenia, Disanthuscercidifolia subsp. longipes, Hamamelismollis, Manglietiafordiana, Magnoliaofficinalis, Tsoongiodendronodorum, Fortuneariasinensis, Cyclocaryapaliurus, Eucommiaulmoides, Sargentodoxacuneata, Bretschneiderasinensis, Camptothecaacuminata, Tapisciasinensis, etc. The flora of Mount Jinggangshan region includes 79 cosmopolitan genera and 924 non-cosmopolitan genera, which are 7.88% and 92.12% of all genera. The latter includes 452 tropical genera (48.92%) and 472 temperate genera (51.08%). The temperate elements include 44 genera endemic to China, accounting for 4.76% of all genera. Among 1,003 genera, 465 have only a single species and 401 are oligotypic genera (with 2-5 species). These genera account for 86.34% of all genera. The floristic analysis indicates that the flora of Mount Jinggangshan region is closely related to the flora of Mount Wuyishan region in southeastern China. The flora of Mount Jinggangshan region also contains many elements of central and southern China. Mount Jinggangshan region is an important north-south floristic passageway and is also a boundary between the floras of eastern, central and south China.}, } @article {pmid24061231, year = {2014}, author = {Wang, Y and Lin, HX and Chen, L and Ding, SY and Lei, ZC and Liu, DY and Cao, XY and Liang, HJ and Jiang, YB and Tian, ZQ}, title = {What molecular assembly can learn from catalytic chemistry.}, journal = {Chemical Society reviews}, volume = {43}, number = {1}, pages = {399-411}, doi = {10.1039/c3cs60212e}, pmid = {24061231}, issn = {1460-4744}, abstract = {One important objective of molecular assembly research is to create highly complex functional chemical systems capable of responding, adapting, and evolving. Compared with living systems, the synthetic systems are still rather primitive and are far from realizing those features. Nature is by far the most important source of inspiration for designing and creating such systems. In this critical review, we summarize an alternative approach, inspired by catalysis, to examine and describe some molecular assembly processes. A new term, "catassembly," is suggested to refer to the increase in the rate and control of a molecular assembly process. This term combines the words "catalysis" and "assembly," and identifiably retains the Greek root "cat-" of catalysis. The corresponding verb is "catassemble" and the noun is "catassembler", referring to the "helper" species. Catassembly in molecular assembly is a concept that is analogous to catalysis in chemical synthesis. After using several examples to illustrate the characteristics of catassembly, we discuss future methodological and theoretical developments. We also emphasize the significance of the synergy between chemical synthesis and molecular assembly, especially for hierarchical assembly systems. Because most efforts in the field of molecular assembly have been devoted to the design and synthesis of molecular building blocks, we wish to stress the apparently missing yet critical link to complex chemical systems, i.e., the design and utilization of molecular catassemblers to facilitate the formation of functional molecular assemblies from building blocks with high efficiency and selectivity. This rational control and accelerated method will promote the systems chemistry approach, and may expand the spectrum of molecular assembly from basic science to applications.}, } @article {pmid24014899, year = {2013}, author = {Groenewald, JZ and Nakashima, C and Nishikawa, J and Shin, HD and Park, JH and Jama, AN and Groenewald, M and Braun, U and Crous, PW}, title = {Species concepts in Cercospora: spotting the weeds among the roses.}, journal = {Studies in mycology}, volume = {75}, number = {1}, pages = {115-170}, pmid = {24014899}, issn = {0166-0616}, abstract = {UNLABELLED: The genus Cercospora contains numerous important plant pathogenic fungi from a diverse range of hosts. Most species of Cercospora are known only from their morphological characters in vivo. Although the genus contains more than 5 000 names, very few cultures and associated DNA sequence data are available. In this study, 360 Cercospora isolates, obtained from 161 host species, 49 host families and 39 countries, were used to compile a molecular phylogeny. Partial sequences were derived from the internal transcribed spacer regions and intervening 5.8S nrRNA, actin, calmodulin, histone H3 and translation elongation factor 1-alpha genes. The resulting phylogenetic clades were evaluated for application of existing species names and five novel species are introduced. Eleven species are epi-, lecto- or neotypified in this study. Although existing species names were available for several clades, it was not always possible to apply North American or European names to African or Asian strains and vice versa. Some species were found to be limited to a specific host genus, whereas others were isolated from a wide host range. No single locus was found to be the ideal DNA barcode gene for the genus, and species identification needs to be based on a combination of gene loci and morphological characters. Additional primers were developed to supplement those previously published for amplification of the loci used in this study.

TAXONOMIC NOVELTIES: New species - Cercospora coniogrammes Crous & R.G. Shivas, Cercospora delaireae C. Nakash., Crous, U. Braun & H.D. Shin, Cercospora euphorbiae-sieboldianae C. Nakash., Crous, U. Braun & H.D. Shin, Cercospora pileicola C. Nakash., Crous, U. Braun & H.D. Shin, Cercospora vignigena C. Nakash., Crous, U. Braun & H.D. Shin. Typifications: epitypifications - Cercospora alchemillicola U. Braun & C.F. Hill, Cercospora althaeina Sacc., Cercospora armoraciae Sacc., Cercospora corchori Sawada, Cercospora mercurialis Pass., Cercospora olivascens Sacc., Cercospora violae Sacc.; neotypifications - Cercospora fagopyri N. Nakata & S. Takim., Cercospora sojina Hara.}, } @article {pmid24003144, year = {2013}, author = {Rabosky, DL and Matute, DR}, title = {Macroevolutionary speciation rates are decoupled from the evolution of intrinsic reproductive isolation in Drosophila and birds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {38}, pages = {15354-15359}, pmid = {24003144}, issn = {1091-6490}, mesh = {Age Factors ; Animals ; *Biological Evolution ; Birds/*genetics/physiology ; Computational Biology ; Computer Simulation ; Drosophila/*genetics/physiology ; *Genetic Speciation ; Models, Genetic ; Phylogeny ; *Reproductive Isolation ; Species Specificity ; }, abstract = {The rate at which speciation occurs varies greatly among different kinds of organisms and is frequently assumed to result from species- or clade-specific factors that influence the rate at which populations acquire reproductive isolation. This premise leads to a fundamental prediction that has never been tested: Organisms that quickly evolve prezygotic or postzygotic reproductive isolation should have faster rates of speciation than organisms that slowly acquire reproductive isolation. We combined phylogenetic estimates of speciation rates from Drosophila and birds with a method for analyzing interspecific hybridization data to test whether the rate at which individual lineages evolve reproductive isolation predicts their macroevolutionary rate of species formation. We find that some lineages evolve reproductive isolation much more quickly than others, but this variation is decoupled from rates of speciation as measured on phylogenetic trees. For the clades examined here, reproductive isolation--especially intrinsic, postzygotic isolation--does not seem to be the rate-limiting control on macroevolutionary diversification dynamics. These results suggest that factors associated with intrinsic reproductive isolation may have less to do with the tremendous variation in species diversity across the evolutionary tree of life than is generally assumed.}, } @article {pmid23936311, year = {2013}, author = {Lecointre, G and Améziane, N and Boisselier, MC and Bonillo, C and Busson, F and Causse, R and Chenuil, A and Couloux, A and Coutanceau, JP and Cruaud, C and d'Acoz, Cd and De Ridder, C and Denys, G and Dettaï, A and Duhamel, G and Eléaume, M and Féral, JP and Gallut, C and Havermans, C and Held, C and Hemery, L and Lautrédou, AC and Martin, P and Ozouf-Costaz, C and Pierrat, B and Pruvost, P and Puillandre, N and Samadi, S and Saucède, T and Schubart, C and David, B}, title = {Is the species flock concept operational? The Antarctic shelf case.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e68787}, pmid = {23936311}, issn = {1932-6203}, mesh = {Animals ; Antarctic Regions ; *Biodiversity ; *Biological Evolution ; Ecology ; Ecosystem ; Fishes/*physiology ; Population Density ; }, abstract = {There has been a significant body of literature on species flock definition but not so much about practical means to appraise them. We here apply the five criteria of Eastman and McCune for detecting species flocks in four taxonomic components of the benthic fauna of the Antarctic shelf: teleost fishes, crinoids (feather stars), echinoids (sea urchins) and crustacean arthropods. Practical limitations led us to prioritize the three historical criteria (endemicity, monophyly, species richness) over the two ecological ones (ecological diversity and habitat dominance). We propose a new protocol which includes an iterative fine-tuning of the monophyly and endemicity criteria in order to discover unsuspected flocks. As a result nine « full » species flocks (fulfilling the five criteria) are briefly described. Eight other flocks fit the three historical criteria but need to be further investigated from the ecological point of view (here called "core flocks"). The approach also shows that some candidate taxonomic components are no species flocks at all. The present study contradicts the paradigm that marine species flocks are rare. The hypothesis according to which the Antarctic shelf acts as a species flocks generator is supported, and the approach indicates paths for further ecological studies and may serve as a starting point to investigate the processes leading to flock-like patterning of biodiversity.}, } @article {pmid23931113, year = {2013}, author = {Money, NP}, title = {Against the naming of fungi.}, journal = {Fungal biology}, volume = {117}, number = {7-8}, pages = {463-465}, doi = {10.1016/j.funbio.2013.05.007}, pmid = {23931113}, issn = {1878-6146}, mesh = {Classification/methods ; Fungi/*classification/genetics/growth & development/*isolation & purification ; Phylogeny ; *Terminology as Topic ; }, abstract = {The use of molecular bar-coding and consensus on nomenclatural practices has encouraged optimism about the future of fungal taxonomy and systematics. There are, however, profound deficiencies in our understanding of fungal diversity and broader problems with the taxonomic enterprise that deserve greater attention. For 250 years mycologists have tried to reconcile fungal diversity with the Linnean fantasy of a divine order throughout nature that included unambiguous species. This effort has failed and today's taxonomy rests on an unstable philosophical foundation. Rather than persisting with the present endeavour, it may be more fruitful to abandon the notion of fungal species pending further basic research. In the meantime, mycologists should consider tagging collections with digital codes and assigning these operational taxonomic units to higher taxonomic ranks whose objective reality is corroborated by strong phylogenetic evidence.}, } @article {pmid23921637, year = {2013}, author = {Roller, M and Lucić, V and Nagy, I and Perica, T and Vlahovicek, K}, title = {Environmental shaping of codon usage and functional adaptation across microbial communities.}, journal = {Nucleic acids research}, volume = {41}, number = {19}, pages = {8842-8852}, pmid = {23921637}, issn = {1362-4962}, support = {MC_U105161047/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adaptation, Biological/*genetics ; Animals ; *Codon ; Ecosystem ; Genome, Bacterial ; Humans ; *Metagenome ; Metagenomics ; Mice ; Phylogeny ; Proteomics ; }, abstract = {Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.}, } @article {pmid23912260, year = {2013}, author = {Albarracín, MV and Six, J and Houlton, BZ and Bledsoe, CS}, title = {A nitrogen fertilization field study of carbon-13 and nitrogen-15 transfers in ectomycorrhizas of Pinus sabiniana.}, journal = {Oecologia}, volume = {173}, number = {4}, pages = {1439-1450}, pmid = {23912260}, issn = {1432-1939}, mesh = {Biomass ; California ; Carbon/metabolism ; Carbon Isotopes/analysis ; Ecosystem ; *Fertilizers ; Mycorrhizae/*physiology ; Nitrogen/*metabolism ; Nitrogen Isotopes/analysis ; Pinus/*metabolism/microbiology ; Plant Roots/metabolism/microbiology ; Soil/chemistry ; Soil Microbiology ; Trees/metabolism/microbiology ; }, abstract = {Ectomycorrhizal (EM) fungi form relationships with higher plants; plants transfer C to fungi, and fungi transfer nutrients to their host. While evidence indicates that this interaction is largely mutualistic, less is known about how nutrient supply and EM associates may alter C and nutrient exchanges, especially in intact plant-soil-microbe systems in the field. In a dual-labeling experiment with N fertilization, we used C and N stable isotopes to examine in situ transfers in EM pine trees in a Pinus sabiniana woodland in northern California. We added (15)NH4SO2 and (13)CO2 to track (13)C transfer from pine needles to EM roots and (15)N transfer from soil to EM roots and pine needles. Transfers of (13)C and (15)N differed with EM morphotype and with N fertilization. The brown morphotype received the least C per unit of N transferred (5:1); in contrast red and gold morphotypes gained more C and transferred less N (17:1 and 25:1, respectively). N fertilization increased N retention by ectomycorrhizas (EMs) but did not increase N transfer from EMs to pine needles. Therefore N fertilization positively affected both nutrient and C gains by EMs, increasing net C flows and N retention in EMs. Our work on intact and native trees/EM associations thereby extends earlier conclusions based on pot studies with young plants and culturable EM fungi; our results support the concept that EM-host relationships depend on species-level differences as well as responses to soil resources such as N.}, } @article {pmid23909947, year = {2013}, author = {Dincă, V and Wiklund, C and Lukhtanov, VA and Kodandaramaiah, U and Norén, K and Dapporto, L and Wahlberg, N and Vila, R and Friberg, M}, title = {Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex.}, journal = {Journal of evolutionary biology}, volume = {26}, number = {10}, pages = {2095-2106}, pmid = {23909947}, issn = {1420-9101}, mesh = {Animals ; Butterflies/*genetics/physiology ; DNA/chemistry ; DNA, Mitochondrial/chemistry ; Gene Flow ; Genetic Markers ; *Genetic Variation ; Geography ; Phylogeny ; *Reproductive Isolation ; Sequence Analysis, DNA ; Sexual Behavior, Animal ; }, abstract = {Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.}, } @article {pmid23889003, year = {2013}, author = {Mieszkowska, N and Milligan, G and Burrows, MT and Freckleton, R and Spencer, M}, title = {Dynamic species distribution models from categorical survey data.}, journal = {The Journal of animal ecology}, volume = {82}, number = {6}, pages = {1215-1226}, doi = {10.1111/1365-2656.12100}, pmid = {23889003}, issn = {1365-2656}, mesh = {*Animal Distribution ; Animals ; *Environment ; France ; *Models, Biological ; Population Density ; Seasons ; Snails/*physiology ; Temperature ; United Kingdom ; Water Movements ; }, abstract = {1. Species distribution models are static models for the distribution of a species, based on Hutchinson's niche concept. They make probabilistic predictions about the distribution of a species, but do not have a temporal interpretation. In contrast, density-structured models based on categorical abundance data make it possible to incorporate population dynamics into species distribution modelling. 2. Using dynamic species distribution models, temporal aspects of a species' distribution can be investigated, including the predictability of future abundance categories and the expected persistence times of local populations, and how these may respond to environmental or anthropogenic drivers. 3. We built density-structured models for two intertidal marine invertebrates, the Lusitanian trochid gastropods Phorcus lineatus and Gibbula umbilicalis, based on 9 years of field data from around the United Kingdom. Abundances were recorded on a categorical scale, and stochastic models for year-to-year changes in abundance category were constructed with winter mean sea surface temperature (SST) and wave fetch (a measure of the exposure of a shore) as explanatory variables. 4. Both species were more likely to be present at sites with high SST, but differed in their responses to wave fetch. Phorcus lineatus had more predictable future abundance and longer expected persistence times than G. umbilicalis. This is consistent with the longer lifespan of P. lineatus. 5. Where data from multiple time points are available, dynamic species distribution models of the kind described here have many applications in population and conservation biology. These include allowing for changes over time when combining historical and contemporary data, and predicting how climate change might alter future abundance conditional on current distributions.}, } @article {pmid23887892, year = {2013}, author = {Prévot, V and Jordaens, K and Van Houtte, N and Sonet, G and Janssens, K and Castilho, R and Backeljau, T}, title = {Taxonomic and population genetic re-interpretation of two color morphs of the decollate snail, Rumina decollata (Mollusca, Pulmonata) in southern France.}, journal = {Genetica}, volume = {141}, number = {7-9}, pages = {281-292}, pmid = {23887892}, issn = {1573-6857}, mesh = {Alleles ; Animals ; *Gene Frequency ; Genetic Loci ; Homozygote ; Inbreeding ; Isoenzymes/genetics ; Microsatellite Repeats ; Pigmentation/*genetics ; Polymorphism, Genetic ; Population/genetics ; Snails/anatomy & histology/classification/*genetics ; }, abstract = {The hermaphroditic terrestrial snail Rumina decollata has a mixed breeding system with a high prevalence of self-fertilization. In the Montpellier area (France), the species is represented by a dark and a light color morph. Based on allozyme data, both morphs have been reported as single, homozygous multilocus genotypes (MLG), differing at 13 out of 26 loci, but still showing occasional hybridization. Recent DNA sequence data suggest that each morph is a different phylogenetic species. In order to further evaluate this new taxonomic interpretation, the present contribution explores to what extent populations or color morphs indeed consist of single or few MLG. As such it is shown that both morphs are not single, homozygous MLG, but instead reveal a considerable amount of allelic variation and substantial numbers of heterozygous microsatellite genotypes. This suggests that outcrossing may be more prevalent than previously reported. Nevertheless, both morphs maintain a diagnostic multimarker differentiation in the presence of outcrossing in sympatric conditions, implying that they may be interpreted as species under the biological species concept. Finally, our data challenge the idea that simultaneous hermaphrodites should be either strict selfers or strict outcrossers.}, } @article {pmid23884092, year = {2013}, author = {Rossberg, AG and Rogers, T and McKane, AJ}, title = {Are there species smaller than 1 mm?.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1767}, pages = {20131248}, pmid = {23884092}, issn = {1471-2954}, mesh = {*Biodiversity ; Body Size ; Competitive Behavior ; *Genetic Variation ; Humans ; Models, Biological ; Mutation ; *Phylogeny ; Reproduction ; }, abstract = {The rapid advance in genetic sequencing technologies has provided an unprecedented amount of data on the biodiversity of meiofauna. It was hoped that these data would allow the identification and counting of species, distinguished as tight clusters of similar genomes. Surprisingly, this appears not to be the case. Here, we begin a theoretical discussion of this phenomenon, drawing on an individual-based ecological model to inform our arguments. The determining factor in the emergence (or not) of distinguishable genetic clusters in the model is the product of population size with mutation rate-a measure of the adaptability of the population as a whole. This result suggests that indeed one should not expect to observe clearly distinguishable species groupings in data gathered from ultrasequencing of meiofauna.}, } @article {pmid23880535, year = {2013}, author = {Arntzen, JW and Recuero, E and Canestrelli, D and Martínez-Solano, I}, title = {How complex is the Bufo bufo species group?.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {3}, pages = {1203-1208}, doi = {10.1016/j.ympev.2013.07.012}, pmid = {23880535}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Bufonidae/*classification/genetics ; Europe ; *Evolution, Molecular ; Genetic Speciation ; Genetics, Population ; *Hybridization, Genetic ; Isoenzymes/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Sympatry ; }, abstract = {Species delineation remains one of the most challenging tasks in the study of biodiversity, mostly owing to the application of different species concepts, which results in contrasting taxonomic arrangements. This has important practical consequences, since species are basic units in fields like ecology and conservation biology. We here review molecular genetic evidence relevant to the systematics of toads in the Bufo bufo species group (Anura, Bufonidae). Two studies recently published in this journal (Recuero et al., MPE 62: 71-86 and García-Porta et al., MPE 63: 113-130) addressed this issue but reached opposing conclusions on the taxonomy of the group (four versus two species). In particular, allozyme data in the latter paper were interpreted as evidence for hybridization across species (between B. bufo-B. spinosus and B. bufo-B. verrucosissimus). We tested claims for hybridization through re-analysis of allozyme data for individuals instead of populations, to be able to distinguish between sympatry with and without admixture, and found no evidence of hybridization across taxa. We propose alternative explanations for the observed patterns that García-Porta et al. (2012) failed to consider. In the absence of unequivocal evidence for hybridization and introgression, we reject the proposal to downgrade Bufo spinosus and Bufo verrucosissimus to the subspecies level.}, } @article {pmid23869749, year = {2014}, author = {Sangster, G}, title = {The application of species criteria in avian taxonomy and its implications for the debate over species concepts.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {89}, number = {1}, pages = {199-214}, doi = {10.1111/brv.12051}, pmid = {23869749}, issn = {1469-185X}, mesh = {Animals ; Birds/*classification/*genetics ; Classification/*methods ; *Genetic Speciation ; Phylogeny ; Species Specificity ; Time Factors ; }, abstract = {The debate over species concepts has produced a huge body of literature on how species can, may or should be delimited. By contrast, very few studies have documented how species taxa are delimited in practice. The aims of the present study were to (i) quantify the use of species criteria in taxonomy, (ii) discuss its implications for the debate over species concepts and (iii) assess recent claims about the impact of different species concepts on taxonomic stability and the 'nature' of species. The application of six species criteria was examined in taxonomic studies of birds published between 1950 and 2009. Three types of taxonomic studies were included: descriptions of new species (N = 329), proposals to change the taxonomic rank of species and subspecies (N = 808) and the taxonomic recommendations of the American Ornithologists' Union Committee on Classification and Nomenclature (N = 176). In all three datasets, diagnosability was the most frequently applied criterion, followed by reproductive isolation and degree of difference. This result is inconsistent with the popular notion that the Biological Species Concept is the dominant species concept in avian taxonomy. Since the 1950s, avian species-level taxonomy has become increasingly pluralistic and eclectic. This suggests that taxonomists consider different criteria as complementary rather than as rival approaches to species delimitation. Application of diagnosability more frequently led to the elevation of subspecies to species rank than application of reproductive isolation, although the difference was small. Hypotheses based on diagnosability and reproductive isolation were equally likely to be accepted in a mainstream checklist. These findings contradict recent claims that application of the Phylogenetic Species Concept causes instability and that broader application of the Biological Species Concept can stabilise taxonomy. The criteria diagnosability and monophyly, which are commonly associated with Phylogenetic Species Concepts, were used throughout the study period. Finally, no support was found for the idea that Phylogenetic Species Concepts have caused a change in the 'nature' of species taxa. This study demonstrates that there is a discrepancy between widely held perceptions of how species are delimited and the way species are actually delimited by taxonomists. Theoretically oriented debates over species concepts thus may benefit from empirical data on taxonomic practice.}, } @article {pmid23829102, year = {2013}, author = {Ericsson, AC and Crim, MJ and Franklin, CL}, title = {A brief history of animal modeling.}, journal = {Missouri medicine}, volume = {110}, number = {3}, pages = {201-205}, pmid = {23829102}, issn = {0026-6620}, support = {T32 OD011126/OD/NIH HHS/United States ; }, mesh = {Animals ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; Humans ; *Models, Animal ; Translational Research, Biomedical/*history ; }, abstract = {Comparative medicine is founded on the concept that other animal species share physiological, behavioral, or other characteristics with humans. Over 2,400 years ago it was recognized that by studying animals, we could learn much about ourselves. This technique has now developed to the point that animal models are employed in virtually all fields of biomedical research including, but not limited to, basic biology, immunology and infectious disease, oncology, and behavior.}, } @article {pmid23826120, year = {2013}, author = {Wolf, M and Chen, S and Song, J and Ankenbrand, M and Müller, T}, title = {Compensatory base changes in ITS2 secondary structures correlate with the biological species concept despite intragenomic variability in ITS2 sequences--a proof of concept.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e66726}, pmid = {23826120}, issn = {1932-6203}, mesh = {Animals ; DNA, Ribosomal Spacer/*genetics ; Phylogeny ; }, abstract = {Compensatory base changes (CBCs) in internal transcribed spacer 2 (ITS2) rDNA secondary structures correlate with Ernst Mayr's biological species concept. This hypothesis also referred to as the CBC species concept recently was subjected to large-scale testing, indicating two distinct probabilities. (1) If there is a CBC then there are two different species with a probability of ∼0.93. (2) If there is no CBC then there is the same species with a probability of ∼0.76. In ITS2 research, however, the main problem is the multicopy nature of ITS2 sequences. Most recently, 454 pyrosequencing data have been used to characterize more than 5000 intragenomic variations of ITS2 regions from 178 plant species, demonstrating that mutation of ITS2 is frequent, with a mean of 35 variants per species, respectively per individual organism. In this study, using those 454 data, the CBC criterion is reconsidered in the light of intragenomic variability, a proof of concept, a necessary criterion, expecting no intragenomic CBCs in variant ITS2 copies. In accordance with the CBC species concept, we could demonstrate that the probability that there is no intragenomic CBC is ∼0.99.}, } @article {pmid23818990, year = {2013}, author = {Lagache, L and Leger, JB and Daudin, JJ and Petit, RJ and Vacher, C}, title = {Putting the biological species concept to the test: using mating networks to delimit species.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e68267}, pmid = {23818990}, issn = {1932-6203}, mesh = {Computer Simulation ; Ecosystem ; Fertility/genetics/physiology ; *Genetic Speciation ; Genotype ; *Hybridization, Genetic ; Models, Genetic ; Pollination/genetics/physiology ; Quercus/classification/*genetics/*physiology ; Reproduction/genetics/physiology ; Species Specificity ; }, abstract = {Although interfertility is the key criterion upon which Mayr's biological species concept is based, it has never been applied directly to delimit species under natural conditions. Our study fills this gap. We used the interfertility criterion to delimit two closely related oak species in a forest stand by analyzing the network of natural mating events between individuals. The results reveal two groups of interfertile individuals connected by only few mating events. These two groups were largely congruent with those determined using other criteria (morphological similarity, genotypic similarity and individual relatedness). Our study, therefore, shows that the analysis of mating networks is an effective method to delimit species based on the interfertility criterion, provided that adequate network data can be assembled. Our study also shows that although species boundaries are highly congruent across methods of species delimitation, they are not exactly the same. Most of the differences stem from assignment of individuals to an intermediate category. The discrepancies between methods may reflect a biological reality. Indeed, the interfertility criterion is an environment-dependant criterion as species abundances typically affect rates of hybridization under natural conditions. Thus, the methods of species delimitation based on the interfertility criterion are expected to give results slightly different from those based on environment-independent criteria (such as the genotypic similarity criteria). However, whatever the criterion chosen, the challenge we face when delimiting species is to summarize continuous but non-uniform variations in biological diversity. The grade of membership model that we use in this study appears as an appropriate tool.}, } @article {pmid23785530, year = {2013}, author = {El Baidouri, F and Diancourt, L and Berry, V and Chevenet, F and Pratlong, F and Marty, P and Ravel, C}, title = {Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us.}, journal = {PLoS neglected tropical diseases}, volume = {7}, number = {6}, pages = {e2255}, pmid = {23785530}, issn = {1935-2735}, mesh = {Africa ; Asia ; Europe ; *Evolution, Molecular ; *Genetic Variation ; Leishmania/*classification/*genetics/isolation & purification ; Multilocus Sequence Typing ; *Phylogeography ; }, abstract = {Leishmaniasis is a complex parasitic disease from a taxonomic, clinical and epidemiological point of view. The role of genetic exchanges has been questioned for over twenty years and their recent experimental demonstration along with the identification of interspecific hybrids in natura has revived this debate. After arguing that genetic exchanges were exceptional and did not contribute to Leishmania evolution, it is currently proposed that interspecific exchanges could be a major driving force for rapid adaptation to new reservoirs and vectors, expansion into new parasitic cycles and adaptation to new life conditions. To assess the existence of gene flows between species during evolution we used MLSA-based (MultiLocus Sequence Analysis) approach to analyze 222 Leishmania strains from Africa and Eurasia to accurately represent the genetic diversity of this genus. We observed a remarkable congruence of the phylogenetic signal and identified seven genetic clusters that include mainly independent lineages which are accumulating divergences without any sign of recent interspecific recombination. From a taxonomic point of view, the strong genetic structuration of the different species does not question the current classification, except for species that cause visceral forms of leishmaniasis (L. donovani, L. infantum and L. archibaldi). Although these taxa cause specific clinical forms of the disease and are maintained through different parasitic cycles, they are not clearly distinct and form a continuum, in line with the concept of species complex already suggested for this group thirty years ago. These results should have practical consequences concerning the molecular identification of parasites and the subsequent therapeutic management of the disease.}, } @article {pmid23771888, year = {2013}, author = {Satler, JD and Carstens, BC and Hedin, M}, title = {Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus).}, journal = {Systematic biology}, volume = {62}, number = {6}, pages = {805-823}, doi = {10.1093/sysbio/syt041}, pmid = {23771888}, issn = {1076-836X}, mesh = {Animals ; California ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Microtubule Proteins/genetics ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; Reproducibility of Results ; Species Specificity ; Spiders/anatomy & histology/*classification/*genetics ; }, abstract = {Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.}, } @article {pmid23770573, year = {2013}, author = {Caisová, L and Marin, B and Melkonian, M}, title = {A consensus secondary structure of ITS2 in the chlorophyta identified by phylogenetic reconstruction.}, journal = {Protist}, volume = {164}, number = {4}, pages = {482-496}, doi = {10.1016/j.protis.2013.04.005}, pmid = {23770573}, issn = {1618-0941}, mesh = {Base Sequence ; Chlorophyta/chemistry/*classification/*genetics ; *Consensus Sequence ; DNA, Plant/*chemistry/genetics ; DNA, Ribosomal Spacer/*chemistry/genetics ; Evolution, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; }, abstract = {The definition of species plays a pivotal role in biology. It has been proposed that Compensatory Base Changes (CBCs) in the fast-evolving Internal Transcribed Spacer 2 (ITS2) correlate with speciation and thus can be used to distinguish species. The applicability of CBC - based species concepts using ITS2, however, rests on the homology of the investigated ITS2 positions. We studied the ITS2 molecule of 147 strains of Chlorophyceae (Chlorophyta, Viridiplantae) including 26 new sequences in the order Chaetophorales, and compared their secondary structures to ITS2 in the sister class Ulvophyceae, represented by the order Ulvales. Using a phylogenetic/comparative approach, it was possible to identify 1) the first consensus structure model of the ITS2 molecule that can be applied to two classes of green algae [Ulvophyceae (Ulvales), Chlorophyceae] and 2) landmarks (the spacer regions separating the ITS2 Helices) for more robust prediction of the secondary structures in green algae. Moreover, we found that CBCs in homologous positions in these 147 strains (representing 115 validly described species) are either completely absent or mostly associated with internal branches representing higher order taxonomic levels (genera, families, orders). As reported for the Ulvales, CBCs are not diagnostic at the species level in the dataset used.}, } @article {pmid23762854, year = {2013}, author = {Perše, M}, title = {Oxidative stress in the pathogenesis of colorectal cancer: cause or consequence?.}, journal = {BioMed research international}, volume = {2013}, number = {}, pages = {725710}, pmid = {23762854}, issn = {2314-6141}, mesh = {Animals ; Colon/metabolism/pathology ; Colorectal Neoplasms/*etiology/*pathology ; Cytoprotection ; Free Radicals/metabolism ; Humans ; *Oxidative Stress ; }, abstract = {There is a growing support for the concept that reactive oxygen species, which are known to be implicated in a range of diseases, may be important progenitors in carcinogenesis, including colorectal cancer (CRC). CRC is one of the most common cancers worldwide, with the highest incidence rates in western countries. Sporadic human CRC may be attributable to various environmental and lifestyle factors, such as dietary habits, obesity, and physical inactivity. In the last decades, association between oxidative stress and CRC has been intensively studied. Recently, numerous genetic and lifestyle factors that can affect an individual's ability to respond to oxidative stress have been identified. The aim of this paper is to review evidence linking oxidative stress to CRC and to provide essential background information for accurate interpretation of future research on oxidative stress and CRC risk. Brief introduction of different endogenous and exogenous factors that may influence oxidative status and modulate the ability of gut epithelial cells to cope with damaging metabolic challenges is also provided.}, } @article {pmid23755277, year = {2013}, author = {Zinetti, F and Dapporto, L and Vovlas, A and Chelazzi, G and Bonelli, S and Balletto, E and Ciofi, C}, title = {When the rule becomes the exception. no evidence of gene flow between two Zerynthia cryptic butterflies suggests the emergence of a new model group.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65746}, pmid = {23755277}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Butterflies/classification/*genetics ; DNA, Mitochondrial/genetics ; Gene Flow/*genetics ; Genetic Speciation ; Phylogeny ; }, abstract = {There is increasing evidence that most parapatric cryptic/sister taxa are reproductively compatible across their areas of contact. Consequently, the biological species concept, which assumes absence of interbreeding, is becoming a not so effective criterion in evolutionary ecology. Nevertheless, the few parapatric sister taxa showing complete reproductive barriers represent interesting models to study speciation processes and the evolution of reproductive isolation. In this study, we examined contact populations in northwestern Italy of two butterfly species, Zerynthia polyxena and Z. cassandra, characterized by different genitalic morphotypes. We studied levels of divergence among 21 populations distributed from Sicily to France using three genetic markers (the mitochondrial COI and ND1 genes and the nuclear wingless gene) and genitalic geometric morphometrics. Moreover, we performed species distribution modelling to estimate different climatic requirements of Z. polyxena and Z. cassandra. We projected climatic data into glacial maximum scenarios in order to verify if and to which extent glacial cycles could have contributed to speciation processes. Genetic and morphometric analyses identified two main groups. All specimens showed a concordant pattern of diversification, including those individuals sampled in the contact area. Haplotype distribution and climatic models showed that during glacial maxima both species experienced a strong range contraction and presumably remained separated into different microrefugia in southern France, in the Italian Peninsula and on the islands of Elba and Sicily. Long term separation was probably favoured by reduced dispersal ability and high phylopatry, while genitalic diversification probably favoured interbreeding avoidance. Conversely, the aposematic wing pattern remained almost identical. We compared our results with those obtained in other species and concluded that Z. polyxena and Z. cassandra represent a valuable model in the study of speciation.}, } @article {pmid23710621, year = {2013}, author = {Mann, DG and Vanormelingen, P}, title = {An inordinate fondness? The number, distributions, and origins of diatom species.}, journal = {The Journal of eukaryotic microbiology}, volume = {60}, number = {4}, pages = {414-420}, doi = {10.1111/jeu.12047}, pmid = {23710621}, issn = {1550-7408}, mesh = {Biodiversity ; Diatoms/classification/*genetics ; }, abstract = {The number of extant species of diatoms is estimated here to be at least 30,000 and probably ca. 100,000, by extrapolation from an eclectic sample of genera and species complexes. Available data, although few, indicate that the pseudocryptic species being discovered in many genera are not functionally equivalent. Molecular sequence data show that some diatom species are ubiquitously dispersed. A good case can be made that at least some diatom species and even a few genera are endemics, but many such claims are still weak. The combination of very large species numbers and relatively rapid dispersal in diatoms is inconsistent with some versions of the "ubiquity hypothesis" of protist biogeography, and appears paradoxical. However, population genetic data indicate geographical structure in all the (few) marine and freshwater species that have been examined in detail, sometimes over distances of a few tens of kilometres. The mode of speciation may often be parapatric, in the context of a constantly shifting mosaic of temporarily isolated (meta) populations, but if our "intermediate dispersal hypothesis" is true (that long-distance dispersal is rare, but not extremely rare), allopatric speciation could also be maximized.}, } @article {pmid23691086, year = {2013}, author = {Barker, JM and Charlier, TD and Ball, GF and Balthazart, J}, title = {A new method for in vitro detection of bromodeoxyuridine in serum: a proof of concept in a songbird species, the canary.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e63692}, pmid = {23691086}, issn = {1932-6203}, support = {R01 NS035467/NS/NINDS NIH HHS/United States ; R01-NS035467/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Blood Chemical Analysis/*methods ; Bromodeoxyuridine/*blood ; Calibration ; Canaries/*blood ; Female ; Male ; Mice ; Staining and Labeling ; }, abstract = {Systemic injection of a thymidine analogue such as bromodeoxyuridine (BrdU) in vertebrates is commonly used to detect and study cell production during development, adulthood, and pathology, particularly in studies of adult neurogenesis. Although researchers are applying this technique to multiple species in various physiological conditions, the rate of BrdU clearance from the serum remains unknown in most cases. Changes in this clearance rate as a function of the species, sex or endocrine condition could however profoundly affect the interpretation of the results. We describe a rapid, sensitive, but simple bioassay for post-injection detection and quantification of BrdU in serum. This procedure was shown to be suitable for determining the length of time a thymidine analogue remains in the bloodstream of one avian species and seems applicable to any vertebrate provided sufficiently large blood samples can be collected. This technique was used to demonstrate that, in canaries, BrdU injected at a dose of 100 mg/kg is no longer available for incorporation into DNA between 30 and 60 min post-injection, a delay shorter than anticipated based on the available literature. Preliminary data suggest a similar fast clearance in Japanese quail and mice.}, } @article {pmid23688802, year = {2013}, author = {Pigliucci, M}, title = {What are we to make of the concept of race? Thoughts of a philosopher-scientist.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {44}, number = {3}, pages = {272-277}, doi = {10.1016/j.shpsc.2013.04.008}, pmid = {23688802}, issn = {1879-2499}, mesh = {*Anthropometry ; Biological Evolution ; Humans ; *Intelligence ; Racial Groups/*genetics ; }, abstract = {Discussions about the biological bases (or lack thereof) of the concept of race in the human species seem to be never ending. One of the latest rounds is represented by a paper by Neven Sesardic, which attempts to build a strong scientific case for the existence of human races, based on genetic, morphometric and behavioral characteristics, as well as on a thorough critique of opposing positions. In this paper I show that Sesardic's critique falls far short of the goal, and that his positive case is exceedingly thin. I do this through a combination of analysis of the actual scientific findings invoked by Sesardic and of some philosophical unpacking of his conceptual analysis, drawing on a dual professional background as an evolutionary biologist and a philosopher of science.}, } @article {pmid23687647, year = {2013}, author = {Ogunyankin, MO and Longo, ML}, title = {Compositional sorting dynamics in coexisting lipid bilayer phases with variations in underlying e-beam formed curvature pattern.}, journal = {The Analyst}, volume = {138}, number = {13}, pages = {3719-3727}, pmid = {23687647}, issn = {1364-5528}, support = {R01 AI074022/AI/NIAID NIH HHS/United States ; AI074022/AI/NIAID NIH HHS/United States ; }, mesh = {Biomechanical Phenomena ; Cell Membrane/chemistry ; Hot Temperature ; Lipid Bilayers/*chemistry ; Nanotechnology/*methods ; Polymethyl Methacrylate/chemistry ; Silicon Dioxide/chemistry ; }, abstract = {Nanometer-scale curvature patterns of an underlying substrate are imposed on lipid multibilayers with each pattern imparting distinctly different sorting dynamics to a metastable pixelation pattern of coexisting liquid ordered (Lo)-liquid disordered (Ld) lipid phases. Therefore, this work provides pathways toward mechanical energy-based separations for analysis of biomembrane-associate species. The central design concept of the patterned sections of the silica substrate is a square lattice pattern of 100 nm projected radius poly(methyl methacrylate) (PMMA) hemispherical features formed by electron beam lithography which pixelates the coexisting phases in order to balance membrane bending and line energy. In one variation, we surround this pattern with three PMMA walls/fences 100 nm in height which substantially slows the loss of the high line energy pixelated Lo phase by altering the balance of two competing mechanism (Ostwald ripening vs. vesiculation). In another walled variation, we form a gradient of the spacing of the 100 nm features which forces partitioning of the Lo phase toward the end of the gradient with the most open (400 nm spacing) lattice pattern where a single vesicle could grow from the Lo phase. We show that two other variations distinctly impact the dynamics, demonstrating locally slowed loss of the high line energy pixelated Lo phase and spontaneous switching of the pixel location on the unit cell, respectively. Moreover, we show that the pixelation patterns can be regenerated and sharpened by a heating and cooling cycle. We argue that localized variations in the underlying curvature pattern have rather complex consequences because of the coupling and/or competition of dynamic processes to optimize mechanical energy such as lipid diffusion, vesiculation and growth, and phase/compositional partitioning.}, } @article {pmid23672341, year = {2013}, author = {Caron, DA}, title = {Towards a molecular taxonomy for protists: benefits, risks, and applications in plankton ecology.}, journal = {The Journal of eukaryotic microbiology}, volume = {60}, number = {4}, pages = {407-413}, doi = {10.1111/jeu.12044}, pmid = {23672341}, issn = {1550-7408}, mesh = {Ecology ; Eukaryota/classification/*genetics ; Genetic Variation/genetics ; Phylogeny ; Plankton/classification/*genetics ; }, abstract = {The increasing use of genetic information for the development of methods to study the diversity, distributions, and activities of protists in nature has spawned a new generation of powerful tools. For ecologists, one lure of these approaches lies in the potential for DNA sequences to provide the only immediately obvious means of normalizing the diverse criteria that presently exist for identifying and counting protists. A single, molecular taxonomy would allow studies of diversity across a broad range of species, as well as the detection and quantification of particular species of interest within complex, natural assemblages; goals that are not feasible using traditional methods. However, these advantages are not without their potential pitfalls and problems. Conflicts involving the species concept, disagreements over the true (physiological/ecological) meaning of genetic diversity, and a perceived threat by some that sequence information will displace knowledge regarding the morphologies, functions and physiologies of protistan taxa, have created debate and doubt regarding the efficacy and appropriateness of some genetic approaches. These concerns need continued discussion and eventual resolution as we move toward the irresistible attraction, and potentially enormous benefits, of the application of genetic approaches to protistan ecology.}, } @article {pmid23667454, year = {2013}, author = {Keith, DA and Rodríguez, JP and Rodríguez-Clark, KM and Nicholson, E and Aapala, K and Alonso, A and Asmussen, M and Bachman, S and Basset, A and Barrow, EG and Benson, JS and Bishop, MJ and Bonifacio, R and Brooks, TM and Burgman, MA and Comer, P and Comín, FA and Essl, F and Faber-Langendoen, D and Fairweather, PG and Holdaway, RJ and Jennings, M and Kingsford, RT and Lester, RE and Mac Nally, R and McCarthy, MA and Moat, J and Oliveira-Miranda, MA and Pisanu, P and Poulin, B and Regan, TJ and Riecken, U and Spalding, MD and Zambrano-Martínez, S}, title = {Scientific foundations for an IUCN Red List of ecosystems.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e62111}, pmid = {23667454}, issn = {1932-6203}, mesh = {*Biodiversity ; Conservation of Natural Resources/*methods ; *Ecosystem ; *Endangered Species ; *Models, Theoretical ; Risk Assessment/*methods ; }, abstract = {An understanding of risks to biodiversity is needed for planning action to slow current rates of decline and secure ecosystem services for future human use. Although the IUCN Red List criteria provide an effective assessment protocol for species, a standard global assessment of risks to higher levels of biodiversity is currently limited. In 2008, IUCN initiated development of risk assessment criteria to support a global Red List of ecosystems. We present a new conceptual model for ecosystem risk assessment founded on a synthesis of relevant ecological theories. To support the model, we review key elements of ecosystem definition and introduce the concept of ecosystem collapse, an analogue of species extinction. The model identifies four distributional and functional symptoms of ecosystem risk as a basis for assessment criteria: A) rates of decline in ecosystem distribution; B) restricted distributions with continuing declines or threats; C) rates of environmental (abiotic) degradation; and D) rates of disruption to biotic processes. A fifth criterion, E) quantitative estimates of the risk of ecosystem collapse, enables integrated assessment of multiple processes and provides a conceptual anchor for the other criteria. We present the theoretical rationale for the construction and interpretation of each criterion. The assessment protocol and threat categories mirror those of the IUCN Red List of species. A trial of the protocol on terrestrial, subterranean, freshwater and marine ecosystems from around the world shows that its concepts are workable and its outcomes are robust, that required data are available, and that results are consistent with assessments carried out by local experts and authorities. The new protocol provides a consistent, practical and theoretically grounded framework for establishing a systematic Red List of the world's ecosystems. This will complement the Red List of species and strengthen global capacity to report on and monitor the status of biodiversity.}, } @article {pmid23659190, year = {2013}, author = {Taylor, BN and Beidler, KV and Cooper, ER and Strand, AE and Pritchard, SG}, title = {Sampling volume in root studies: the pitfalls of under-sampling exposed using accumulation curves.}, journal = {Ecology letters}, volume = {16}, number = {7}, pages = {862-869}, doi = {10.1111/ele.12119}, pmid = {23659190}, issn = {1461-0248}, mesh = {*Plant Roots ; *Soil ; }, abstract = {Root systems are important for global models of below-ground carbon and nutrient cycling. Notoriously difficult sampling methods and the fractal distribution of root diameters in the soil make data being used in these models especially susceptible to error resulting from under-sampling. We applied the concept of species accumulation curves to root data to quantify the extent of under-sampling inherent to minirhizotron and soil coring sampling for both root uptake and carbon content studies. Based on differences in sample size alone, minirhizotron sampling missed approximately one third of the root diameters observed by soil core sampling. Sample volumes needed to encounter 90% of root diameters averaged 2481 cm(3) for uptake studies and 5878 cm(3) for root carbon content studies. These results show that small sample volumes encounter a non-representative sample of the overall root pool, and provide future guidelines for determining optimal sample volumes in root studies.}, } @article {pmid23658765, year = {2013}, author = {Denoël, M and Perez, A and Cornet, Y and Ficetola, GF}, title = {Similar local and landscape processes affect both a common and a rare newt species.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e62727}, pmid = {23658765}, issn = {1932-6203}, mesh = {Animals ; *Conservation of Natural Resources ; Ecosystem ; Endangered Species/legislation & jurisprudence/*trends ; Europe ; Female ; Male ; Ponds ; Salamandridae/*physiology ; Species Specificity ; }, abstract = {Although rare species are often the focus of conservation measures, more common species may experience similar decline and suffer from the same threatening processes. We tested this hypothesis by examining, through an information-theoretic approach, the importance of ecological processes at multiple scales in the great crested newt Triturus cristatus, regionally endangered and protected in Europe, and the more common smooth newt, Lissotriton vulgaris. Both species were similarly affected by the same processes, i.e. suitability of aquatic and terrestrial components of their habitat at different scales, connectivity among breeding sites, and the presence of introduced fish. T. cristatus depended more on water depth and aquatic vegetation than L. vulgaris. The results show that environmental pressures threaten both common and rare species, and therefore the more widespread species should not be neglected in conservation programs. Because environmental trends are leading to a deterioration of aquatic and terrestrial habitat features required by newt populations, populations of the common species may follow the fate of the rarest species. This could have substantial conservation implications because of the numerical importance of common species in ecosystems and because commonness could be a transient state moving towards rarity. On the other hand, in agreement with the umbrella species concept, targeting conservation efforts on the most demanding species would also protect part of the populations of the most common species.}, } @article {pmid23648118, year = {2013}, author = {Škaloud, P and Rindi, F}, title = {Ecological differentiation of cryptic species within an asexual protist morphospecies: a case study of filamentous green alga Klebsormidium (Streptophyta).}, journal = {The Journal of eukaryotic microbiology}, volume = {60}, number = {4}, pages = {350-362}, doi = {10.1111/jeu.12040}, pmid = {23648118}, issn = {1550-7408}, mesh = {DNA, Ribosomal/genetics ; *Ecology ; Genetic Variation/genetics ; Phylogeny ; Streptophyta/classification/*genetics ; }, abstract = {Taxa of microbial eukaryotes defined on morphological basis display a large degree of genetic diversity, implying the existence of numerous cryptic species. However, it has been postulated that genetic diversity merely mirrors accumulation of neutral mutations. As a case taxon to study cryptic diversity in protists, we used a widely distributed filamentous genus, Klebsormidium, specifically the lineage E (K. flaccidum/K. nitens complex) containing a number of morphologically similar strains. Fourteen clades were recognized in the phylogenetic analysis based on a concatenated ITS rDNA + rbcL data set of more than 70 strains. The results of inferred character evolution indicated the existence of phylogenetic signal in at least two phenotypic characters (production of hydro-repellent filaments and morphology of zoosporangia). Moreover, the lineages recovered exhibited strong ecological preferences to one of the three habitat types: natural subaerial substrata, artificial subaerial substrata, and aquatic habitats. We interpret these results as evidence of existence of a high number of cryptic species within the single morphospecies. We consider that the permanent existence of genetically and ecologically well-defined cryptic species is enabled by the mechanism of selective sweep.}, } @article {pmid23616422, year = {2013}, author = {Oliveri, AF and Elliott, EW and Carnes, ME and Hutchison, JE and Johnson, DW}, title = {Elucidating inorganic nanoscale species in solution: complementary and corroborative approaches.}, journal = {Chemphyschem : a European journal of chemical physics and physical chemistry}, volume = {14}, number = {12}, pages = {2655-2661}, doi = {10.1002/cphc.201300188}, pmid = {23616422}, issn = {1439-7641}, abstract = {The challenge of defining a length on the nanoscale is non-trivial. For a well-defined inorganic nanoscale species, a size measurement can describe a number of different dimensions (core, shell, solvation sphere). Often size is reported out of context or even inadvertently misrepresented. Since many of the techniques used to measure size depend on significant and sometimes destructive sample preparation, an additional challenge is defining "what size means" for a nanoscale species in solution. In this Concept, the distinction is made between complementary techniques that can be used together to unveil more information about the material in question, and corroborative techniques, which are used to make multiple measurements of the same property. Additionally, corroborative techniques can be used to measure the same property in and out-of solution so as to reveal details about solution behaviour. We highlight various approaches to this characterization challenge in the context of three case studies that demonstrate the use of both complementary and corroborative techniques to elucidate the various functional dimensions of different types of inorganic nanoscale species in solution.}, } @article {pmid23600520, year = {2014}, author = {Cai, J and Li, S and Zhang, H and Zhang, S and Tyree, MT}, title = {Recalcitrant vulnerability curves: methods of analysis and the concept of fibre bridges for enhanced cavitation resistance.}, journal = {Plant, cell & environment}, volume = {37}, number = {1}, pages = {35-44}, doi = {10.1111/pce.12120}, pmid = {23600520}, issn = {1365-3040}, mesh = {Hippophae/anatomy & histology/*physiology ; Models, Theoretical ; Plant Shoots/anatomy & histology/physiology ; Plant Stems/anatomy & histology/physiology ; Plant Transpiration/*physiology ; Trees ; Water/*physiology ; Wood/anatomy & histology/physiology ; Xylem/anatomy & histology/physiology ; }, abstract = {Vulnerability curves (VCs) generally can be fitted to the Weibull equation; however, a growing number of VCs appear to be recalcitrant, that is, deviate from a Weibull but seem to fit dual Weibull curves. We hypothesize that dual Weibull curves in Hippophae rhamnoides L. are due to different vessel diameter classes, inter-vessel hydraulic connections or vessels versus fibre tracheids. We used dye staining techniques, hydraulic measurements and quantitative anatomy measurements to test these hypotheses. The fibres contribute 1.3% of the total stem conductivity, which eliminates the hypothesis that fibre tracheids account for the second Weibull curve. Nevertheless, the staining pattern of vessels and fibre tracheids suggested that fibres might function as a hydraulic bridge between adjacent vessels. We also argue that fibre bridges are safer than vessel-to-vessel pits and put forward the concept as a new paradigm. Hence, we tentatively propose that the first Weibull curve may be accounted by vessels connected to each other directly by pit fields, while the second Weibull curve is associated with vessels that are connected almost exclusively by fibre bridges. Further research is needed to test the concept of fibre bridge safety in species that have recalcitrant or normal Weibull curves.}, } @article {pmid23593012, year = {2013}, author = {Ellegaard, KM and Klasson, L and Näslund, K and Bourtzis, K and Andersson, SG}, title = {Comparative genomics of Wolbachia and the bacterial species concept.}, journal = {PLoS genetics}, volume = {9}, number = {4}, pages = {e1003381}, pmid = {23593012}, issn = {1553-7404}, mesh = {Animals ; *Drosophila/genetics/microbiology ; *Genome, Bacterial ; Genomics ; New Caledonia ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Seychelles ; Species Specificity ; *Symbiosis/genetics/physiology ; *Wolbachia/genetics/physiology ; }, abstract = {The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally transmitted genes.}, } @article {pmid23584965, year = {2013}, author = {Makhalanyane, TP and Valverde, A and Lacap, DC and Pointing, SB and Tuffin, MI and Cowan, DA}, title = {Evidence of species recruitment and development of hot desert hypolithic communities.}, journal = {Environmental microbiology reports}, volume = {5}, number = {2}, pages = {219-224}, doi = {10.1111/1758-2229.12003}, pmid = {23584965}, issn = {1758-2229}, mesh = {Bacteria/classification/genetics/growth & development/*isolation & purification ; Biodiversity ; Desert Climate ; Ecosystem ; Hot Temperature ; *Soil Microbiology ; }, abstract = {Hypoliths, photosynthetic microbial assemblages found underneath translucent rocks, are widely distributed within the western region of the Namib Desert and other similar environments. Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to assess the bacterial community structure of hypoliths and surrounding soil (below and adjacent to the hypolithic rock) at a fine scale (10 m radius). Multivariate analysis of T-RFs showed that hypolithic and soil communities were structurally distinct. T-RFLP-derived operational taxonomic units were linked to 16S rRNA gene clone libraries. Applying the ecological concept of 'indicator species', six and nine indicator lineages were identified for hypoliths and soil, respectively. Hypolithic communities were dominated by cyanobacteria affiliated to Pleurocapsales, whereas actinobacteria were prevalent in the soil. These results are consistent with the concept of species sorting and suggest that the bottom of the quartz rocks provides conditions suitable for the development of discrete and demonstrably different microbial assemblages. However, we found strong evidence for neutral assembly processes, as almost 90% of the taxa present in the hypoliths were also detected in the soil. These results suggest that hypolithons do not develop independently from microbial communities found in the surrounding soil, but selectively recruit from local populations.}, } @article {pmid23571758, year = {2013}, author = {Koeppel, AF and Wu, M}, title = {Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units.}, journal = {Nucleic acids research}, volume = {41}, number = {10}, pages = {5175-5188}, pmid = {23571758}, issn = {1362-4962}, mesh = {Algorithms ; Bacteria/*classification/genetics ; *Ecotype ; *Phylogeny ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The lack of a consensus bacterial species concept greatly hampers our ability to understand and organize bacterial diversity. Operational taxonomic units (OTUs), which are clustered on the basis of DNA sequence identity alone, are the most commonly used microbial diversity unit. Although it is understood that OTUs can be phylogenetically incoherent, the degree and the extent of the phylogenetic inconsistency have not been explicitly studied. Here, we tested the phylogenetic signal of OTUs in a broad range of bacterial genera from various phyla. Strikingly, we found that very few OTUs were monophyletic, and many showed evidence of multiple independent origins. Using previously established bacterial habitats as benchmarks, we showed that OTUs frequently spanned multiple ecological habitats. We demonstrated that ecological heterogeneity within OTUs is caused by their phylogenetic inconsistency, and not merely due to 'lumping' of taxa resulting from using relaxed identity cut-offs. We argue that ecotypes, as described by the Stable Ecotype Model, are phylogenetically and ecologically more consistent than OTUs and therefore could serve as an alternative unit for bacterial diversity studies. In addition, we introduce QuickES, a new wrapper program for the Ecotype Simulation algorithm, which is capable of demarcating ecotypes in data sets with tens of thousands of sequences.}, } @article {pmid23569289, year = {2013}, author = {Kamilar, JM and Cooper, N}, title = {Phylogenetic signal in primate behaviour, ecology and life history.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1618}, pages = {20120341}, pmid = {23569289}, issn = {1471-2970}, mesh = {Animals ; *Behavior, Animal ; Biological Evolution ; Body Weight ; Brain/anatomy & histology ; Climate ; *Ecosystem ; Genetic Drift ; Organ Size ; *Phylogeny ; Primates/anatomy & histology/*classification ; Selection, Genetic ; Social Environment ; }, abstract = {Examining biological diversity in an explicitly evolutionary context has been the subject of research for several decades, yet relatively recent advances in analytical techniques and the increasing availability of species-level phylogenies, have enabled scientists to ask new questions. One such approach is to quantify phylogenetic signal to determine how trait variation is correlated with the phylogenetic relatedness of species. When phylogenetic signal is high, closely related species exhibit similar traits, and this biological similarity decreases as the evolutionary distance between species increases. Here, we first review the concept of phylogenetic signal and suggest how to measure and interpret phylogenetic signal in species traits. Second, we quantified phylogenetic signal in primates for 31 variables, including body mass, brain size, life-history, sexual selection, social organization, diet, activity budget, ranging patterns and climatic variables. We found that phylogenetic signal varies extensively across and even within trait categories. The highest values are exhibited by brain size and body mass, moderate values are found in the degree of territoriality and canine size dimorphism, while low values are displayed by most of the remaining variables. Our results have important implications for the evolution of behaviour and ecology in primates and other vertebrates.}, } @article {pmid23555034, year = {2013}, author = {Chapman, BB and Hegg, A and Ljungberg, P}, title = {Sex and the syndrome: individual and population consistency in behaviour in rock pool prawn Palaemon elegans.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59437}, pmid = {23555034}, issn = {1932-6203}, mesh = {Animals ; *Behavior, Animal ; Exploratory Behavior ; Female ; Male ; *Palaemonidae ; Personality ; Sex Factors ; Sexual Behavior, Animal ; Time Factors ; }, abstract = {Animal personality has been widely documented across a range of species. The concept of personality is composed of individual behavioural consistency across time and between situations, and also behavioural trait correlations known as behavioural syndromes. Whilst many studies have now investigated the stability of individual personality traits, few have analysed the stability over time of entire behavioural syndromes. Here we present data from a behavioural study of rock pool prawns. We show that prawns are temporally consistent in a range of behaviours, including activity, exploration and boldness, and also that a behavioural syndrome is evident in this population. We find correlations between many behavioural traits (activity, boldness, shoaling and exploration). In addition, behavioural syndrome structure was consistent over time. Finally, few studies have explicitly studied the role of sex differences in personality traits, behavioural consistency and syndrome structure. We report behavioural differences between male and female prawns but no differences in patterns of consistency. Our study adds to the growing literature on animal personality, and provides evidence showing that syndromes themselves can exhibit temporal consistency.}, } @article {pmid23550922, year = {2013}, author = {Bohm, DA and Stachel, CS and Gowik, P}, title = {Validation of a method for the determination of aminoglycosides in different matrices and species based on an in-house concept.}, journal = {Food additives & contaminants. Part A, Chemistry, analysis, control, exposure & risk assessment}, volume = {30}, number = {6}, pages = {1037-1043}, doi = {10.1080/19440049.2013.775709}, pmid = {23550922}, issn = {1944-0057}, mesh = {Aminoglycosides/*analysis ; Chromatography, Liquid ; Solid Phase Extraction ; Tandem Mass Spectrometry/methods ; }, abstract = {A simple, rapid, and sensitive method for the determination and confirmation of the aminoglycosides streptomycin, dihydrostreptomycin, spectinomycin, apramycin, kanamycin, paromomycin, gentamicin and neomycin in cow's milk as well as in bovine and porcine muscle and kidney was developed. Validation was performed on the basis of an in-house concept with different factor-level combinations in accordance with Commission Decision 2002/657/EC. After extraction with trichloroacetic acid solution, clean-up was performed by way of SPE. LC-MS/MS analysis was carried out by means of an HILIC column for the separation of the analytes, and by using MS/MS in positive ESI mode to measure the transitions of the substances in MRM mode. For quantification, matrix calibration curves in the linear range around the MRLs as well as the internal standard tobramycin were used. The calculated validation parameters like CCα, CCβ, recovery (94-103%), relative repeatability RSDr (3.6-9.7%), and relative within-laboratory reproducibility RSDwR (4.6-10.0%) fulfilled the requirements of Commission Decision 2002/657/EC.}, } @article {pmid23549436, year = {2013}, author = {Ze, X and Le Mougen, F and Duncan, SH and Louis, P and Flint, HJ}, title = {Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates.}, journal = {Gut microbes}, volume = {4}, number = {3}, pages = {236-240}, pmid = {23549436}, issn = {1949-0984}, mesh = {Colon/*microbiology ; Humans ; Hydrolysis ; Ruminococcus/*metabolism ; Starch/*metabolism ; }, abstract = {The microbial communities found in the mammalian large intestine and rumen efficiently degrade many recalcitrant substrates that are resistant to the host's digestive enzymes. These communities are known from molecular profiling to be highly diverse at the species and strain level, but it may be that only certain specialized organisms ("keystone species") have the ability to initiate degradation of such substrates, thus releasing energy on which the rest of the community depends. We have recently reported that Ruminococcus bromii has a superior ability to degrade certain forms of particulate resistant starch (RS) when compared with other highly abundant species of amylolytic bacteria found in the human colon and have presented evidence that this bacterium provides an example of a keystone species within the microbial community with respect to RS fermentation. The concept of keystone species can be equally relevant to other activities, e.g., those involved in stabilizing the community.}, } @article {pmid23542405, year = {2013}, author = {Bhatty, M and Laverde Gomez, JA and Christie, PJ}, title = {The expanding bacterial type IV secretion lexicon.}, journal = {Research in microbiology}, volume = {164}, number = {6}, pages = {620-639}, pmid = {23542405}, issn = {1769-7123}, support = {R01 GM048746/GM/NIGMS NIH HHS/United States ; R21 AI105454/AI/NIAID NIH HHS/United States ; R01GM48746/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/chemistry/classification/genetics/*metabolism ; Bacterial Infections/microbiology ; Bacterial Proteins/chemistry/genetics/*metabolism ; *Bacterial Secretion Systems ; Humans ; Phylogeny ; Protein Transport ; }, abstract = {The bacterial type IV secretion systems (T4SSs) comprise a biologically diverse group of translocation systems functioning to deliver DNA or protein substrates from donor to target cells generally by a mechanism dependent on establishment of direct cell-to-cell contact. Members of one T4SS subfamily, the conjugation systems, mediate the widespread and rapid dissemination of antibiotic resistance and virulence traits among bacterial pathogens. Members of a second subfamily, the effector translocators, are used by often medically-important pathogens to deliver effector proteins to eukaryotic target cells during the course of infection. Here we summarize our current understanding of the structural and functional diversity of T4SSs and of the evolutionary processes shaping this diversity. We compare mechanistic and architectural features of T4SSs from Gram-negative and -positive species. Finally, we introduce the concept of the 'minimized' T4SSs; these are systems composed of a conserved set of 5-6 subunits that are distributed among many Gram-positive and some Gram-negative species.}, } @article {pmid23507430, year = {2013}, author = {Sistrom, M and Donnellan, SC and Hutchinson, MN}, title = {Delimiting species in recent radiations with low levels of morphological divergence: a case study in Australian Gehyra geckos.}, journal = {Molecular phylogenetics and evolution}, volume = {68}, number = {1}, pages = {135-143}, doi = {10.1016/j.ympev.2013.03.007}, pmid = {23507430}, issn = {1095-9513}, mesh = {Animals ; Australia ; Bayes Theorem ; Desert Climate ; Genetic Speciation ; Genetic Variation ; Histones/*classification/genetics ; Lizards/*classification/genetics ; NADH Dehydrogenase/*classification/genetics ; Phylogeny ; Phylogeography ; Population Density ; Receptors, Prolactin/*classification/genetics ; Reproductive Isolation ; Sequence Analysis, DNA ; }, abstract = {Recent conceptual and methodological advances have increased the ability to apply multifaceted approaches to species delimitation, which is particularly useful in delimiting recently diversified species where single lines of evidence lead to incorrect species delimitation or assignment of individuals to species (e.g. cryptic, morphological species and paraphyletic, hybridizing species). Species of the Australian Gehyra gecko radiation have historically proven difficult to delimit due the group's uniform, almost continent-wide geographic distribution and conservative morphology, contrasting high chromosomal and genetic diversity. Using an integrated approach to species delimitation taking advantage of morphological, geographic distributional and multi-locus genetic data, we investigate the diversity within three Gehyra species from the Australian arid zone. Our results show that these species represent eight distinct phylogenetic lineages, which display different patterns of morphological distinction and reproductive isolation. Using a recently developed Bayesian species delimitation method, we also find different levels of support for putative species dependent on priors for population size and timing of diversification assumed. Our results show that the current taxonomy does not adequately account for the diversity of the group. Discrepancies between lines of evidence indicate that diversification of the group is recent and ongoing, thus posing challenges for both species concepts and delimitation.}, } @article {pmid23501341, year = {2013}, author = {van Goethem, TM and Azevedo, LB and van Zelm, R and Hayes, F and Ashmore, MR and Huijbregts, MA}, title = {Plant species sensitivity distributions for ozone exposure.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {178}, number = {}, pages = {1-6}, doi = {10.1016/j.envpol.2013.02.023}, pmid = {23501341}, issn = {1873-6424}, mesh = {Air Pollutants/*toxicity ; Environmental Monitoring ; Ozone/*toxicity ; Plants/*drug effects ; Risk Assessment ; Species Specificity ; *Stress, Physiological ; }, abstract = {This study derived Species Sensitivity Distributions (SSD), representing a cumulative stressor-response distribution based on single-species sensitivity data, for ozone exposure on natural vegetation. SSDs were constructed for three species groups, i.e. trees, annual grassland and perennial grassland species, using species-specific exposure-response data. The SSDs were applied in two ways. First, critical levels were calculated for each species group and compared to current critical levels for ozone exposure. Second, spatially explicit estimates of the potentially affected fraction of plant species in Northwestern Europe were calculated, based on ambient ozone concentrations. We found that the SSD-based critical levels were lower than for the current critical levels for ozone exposure, with conventional critical levels for ozone relating to 8-20% affected plant species. Our study shows that the SSD concept can be successfully applied to both derive critical ozone levels and estimate the potentially affected species fraction of plant communities along specific ozone gradients.}, } @article {pmid23458501, year = {2013}, author = {Shoemaker, KT and Breisch, AR and Jaycox, JW and Gibbs, JP}, title = {Reexamining the minimum viable population concept for long-lived species.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {27}, number = {3}, pages = {542-551}, doi = {10.1111/cobi.12028}, pmid = {23458501}, issn = {1523-1739}, mesh = {Age Factors ; Animals ; Bayes Theorem ; *Conservation of Natural Resources ; Endangered Species ; Longevity ; Models, Theoretical ; Population Density ; Population Dynamics ; Species Specificity ; Time Factors ; Turtles/*physiology ; }, abstract = {For decades conservation biologists have proposed general rules of thumb for minimum viable population size (MVP); typically, they range from hundreds to thousands of individuals. These rules have shifted conservation resources away from small and fragmented populations. We examined whether iteroparous, long-lived species might constitute an exception to general MVP guidelines. On the basis of results from a 10-year capture-recapture study in eastern New York (U.S.A.), we developed a comprehensive demographic model for the globally threatened bog turtle (Glyptemys muhlenbergii), which is designated as endangered by the IUCN in 2011. We assessed population viability across a wide range of initial abundances and carrying capacities. Not accounting for inbreeding, our results suggest that bog turtle colonies with as few as 15 breeding females have >90% probability of persisting for >100 years, provided vital rates and environmental variance remain at currently estimated levels. On the basis of our results, we suggest that MVP thresholds may be 1-2 orders of magnitude too high for many long-lived organisms. Consequently, protection of small and fragmented populations may constitute a viable conservation option for such species, especially in a regional or metapopulation context.}, } @article {pmid23440172, year = {2013}, author = {Abbo, S and Lev-Yadun, S and Heun, M and Gopher, A}, title = {On the 'lost' crops of the neolithic Near East.}, journal = {Journal of experimental botany}, volume = {64}, number = {4}, pages = {815-822}, pmid = {23440172}, issn = {1460-2431}, mesh = {Adaptation, Physiological ; Agriculture/history/methods ; Archaeology/methods ; Crops, Agricultural/history/*physiology ; Ecosystem ; Geography ; History, Ancient ; Lens Plant/*physiology ; Middle East ; Poaceae/*physiology ; Seeds/physiology ; }, abstract = {The claim that the 'classic' eight 'founder crop' package (einkorn wheat, emmer wheat, barley, lentil, pea, chickpea, bitter vetch, and flax) underlying the emergence of agriculture in the Near East is a relic of a larger number of domesticated species is addressed. The 'lost' crops concept relies on the idea that additional taxa were at certain points in time and in certain locations genuine crops, which were later abandoned. The issue is highly relevant to the debate concerning mono- versus polyphyletic domestication, because if there were numerous 'false starts' that were subsequently lost, this implies that plant domestication occurred over a protracted time period, and across a wide geographic range. Different criteria were used for declaring those taxa as 'lost' crops, including, but not limited to (i) identification in archaeobotanical assemblages of grains from species which are not known as crops at present; (ii) identification of such grains in what is interpreted to have been Neolithic storage facilities; and (iii) recent botanical observations on populations of crop wild relatives in disturbed habitats. The evidence for four presumed 'lost' crops (wild oat, rambling vetch, rye, and wild black lentil) and the broad bean is evaluated, and discussed in light of data on Croatian and Israeli wild pea, and Moroccan wild lentil in disturbed habitats. Based on present knowledge, the broad bean might emerge as a founder crop (without an identified wild progenitor). The same may hold true for rye, which was never lost since its adoption in the Pre-Pottery Neolithic B period in Anatolia. In the remaining three cases, there are alternative, more likely, explanations for the archaeological finds or the recent botanical observations rather than 'lost' domestication episodes.}, } @article {pmid23434841, year = {2013}, author = {Pan, X}, title = {Fundamental equations for species-area theory.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {1334}, pmid = {23434841}, issn = {2045-2322}, abstract = {Species-area theory is an important concept in ecology. However, debates still surround the species-area relationship (SAR) or endemics-area relationship (EAR) and their relations to expected extinction rates. In this paper, I introduce the concept of overlap-area relationship (OAR) to link SAR and EAR. Two fundamental equations are derived from the relationship between the area and species number in a limited whole area A: 1) the sum of species number in area a and species number, here defined as endemics, in area A - a is the total species number in area A; 2) the number of species common to both areas a and A - a (overlapping species) equals the species number in area a minus the endemics number in area a. Thus, we should carefully consider the total area on which EAR depends, when estimating extinction rate based on SAR.}, } @article {pmid23432962, year = {2013}, author = {Meier-Kolthoff, JP and Auch, AF and Klenk, HP and Göker, M}, title = {Genome sequence-based species delimitation with confidence intervals and improved distance functions.}, journal = {BMC bioinformatics}, volume = {14}, number = {}, pages = {60}, pmid = {23432962}, issn = {1471-2105}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Confidence Intervals ; DNA/chemistry ; Genomics/*methods ; Models, Statistical ; Nucleic Acid Hybridization/methods ; *Phylogeny ; Regression Analysis ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes. Its application as an in-silico replacement for DDH was recently introduced. The main challenge in the implementation of such an application is to produce digital DDH values that must mimic the wet-lab DDH values as close as possible to ensure consistency in the Prokaryotic species concept.

RESULTS: Correlation and regression analyses were used to determine the best-performing methods and the most influential parameters. GBDP was further enriched with a set of new features such as confidence intervals for intergenomic distances obtained via resampling or via the statistical models for DDH prediction and an additional family of distance functions. As in previous analyses, GBDP obtained the highest agreement with wet-lab DDH among all tested methods, but improved models led to a further increase in the accuracy of DDH prediction. Confidence intervals yielded stable results when inferred from the statistical models, whereas those obtained via resampling showed marked differences between the underlying distance functions.

CONCLUSIONS: Despite the high accuracy of GBDP-based DDH prediction, inferences from limited empirical data are always associated with a certain degree of uncertainty. It is thus crucial to enrich in-silico DDH replacements with confidence-interval estimation, enabling the user to statistically evaluate the outcomes. Such methodological advancements, easily accessible through the web service at http://ggdc.dsmz.de, are crucial steps towards a consistent and truly genome sequence-based classification of microorganisms.}, } @article {pmid23406508, year = {2013}, author = {Lass-Flörl, C and Roilides, E and Löffler, J and Wilflingseder, D and Romani, L}, title = {Minireview: host defence in invasive aspergillosis.}, journal = {Mycoses}, volume = {56}, number = {4}, pages = {403-413}, doi = {10.1111/myc.12052}, pmid = {23406508}, issn = {1439-0507}, mesh = {*Adaptive Immunity ; Aspergillus/*immunology ; Humans ; *Immunity, Innate ; Invasive Pulmonary Aspergillosis/*immunology ; Th1 Cells/immunology ; Th2 Cells/immunology ; }, abstract = {Aspergillus is a saprophytic fungus, which mainly becomes pathogenic in immunosuppressed hosts. A failure of host defences results in a diverse set of illnesses, ranging from chronic colonisation, aspergilloma, invasive disease and hypersensitivity. A key concept in immune responses to Aspergillus species is that host susceptibility determines the morphological form, antigenic structure and physical location of the fungus. Traditionally, innate immunity has been considered as a first line of defence and activates adaptive immune mechanisms by the provision of specific signals; innate and adaptive immune responses are intimately linked. The T-helper cell (TH 1) response is associated with increased production of inflammatory cytokines IFN-γ, IL-2 and IL-12 and stimulation of antifungal effector cells. Alternatively, TH 2-type responses are associated with suppression of antifungal effector cell activity, decreased production of IFN-γ and increased concentrations of IL-4 and IL-10, which promote humoral responses to Aspergillus. The host's defensive capacity is defined by the sum of resistance and tolerance. Resistance displays the ability to limit fungal burden and elimination of the pathogen, and tolerance means the ability to limit host damage caused by immune response.}, } @article {pmid23402662, year = {2013}, author = {Rybalka, N and Wolf, M and Andersen, RA and Friedl, T}, title = {Congruence of chloroplast- and nuclear-encoded DNA sequence variations used to assess species boundaries in the soil microalga Heterococcus (Stramenopiles, Xanthophyceae).}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {39}, pmid = {23402662}, issn = {1471-2148}, mesh = {Antarctic Regions ; Cell Nucleus/genetics ; DNA, Algal/genetics ; DNA, Chloroplast/*genetics ; DNA, Ribosomal Spacer/genetics ; *Evolution, Molecular ; Genetic Markers ; Likelihood Functions ; Nucleic Acid Conformation ; *Phylogeny ; Sequence Analysis, DNA ; Soil ; Stramenopiles/classification/*genetics ; }, abstract = {BACKGROUND: Heterococcus is a microalgal genus of Xanthophyceae (Stramenopiles) that is common and widespread in soils, especially from cold regions. Species are characterized by extensively branched filaments produced when grown on agarized culture medium. Despite the large number of species described exclusively using light microscopic morphology, the assessment of species diversity is hampered by extensive morphological plasticity.

RESULTS: Two independent types of molecular data, the chloroplast-encoded psbA/rbcL spacer complemented by rbcL gene and the internal transcribed spacer 2 of the nuclear rDNA cistron (ITS2), congruently recovered a robust phylogenetic structure. With ITS2 considerable sequence and secondary structure divergence existed among the eight species, but a combined sequence and secondary structure phylogenetic analysis confined to helix II of ITS2 corroborated relationships as inferred from the rbcL gene phylogeny. Intra-genomic divergence of ITS2 sequences was revealed in many strains. The 'monophyletic species concept', appropriate for microalgae without known sexual reproduction, revealed eight different species. Species boundaries established using the molecular-based monophyletic species concept were more conservative than the traditional morphological species concept. Within a species, almost identical chloroplast marker sequences (genotypes) were repeatedly recovered from strains of different origins. At least two species had widespread geographical distributions; however, within a given species, genotypes recovered from Antarctic strains were distinct from those in temperate habitats. Furthermore, the sequence diversity may correspond to adaptation to different types of habitats or climates.

CONCLUSIONS: We established a method and a reference data base for the unambiguous identification of species of the common soil microalgal genus Heterococcus which uses DNA sequence variation in markers from plastid and nuclear genomes. The molecular data were more reliable and more conservative than morphological data.}, } @article {pmid23396203, year = {2013}, author = {Tarcz, S and Przyboś, E and Surmacz, M}, title = {An assessment of haplotype variation in ribosomal and mitochondrial DNA fragments suggests incomplete lineage sorting in some species of the Paramecium aurelia complex (Ciliophora, Protozoa).}, journal = {Molecular phylogenetics and evolution}, volume = {67}, number = {1}, pages = {255-265}, doi = {10.1016/j.ympev.2013.01.016}, pmid = {23396203}, issn = {1095-9513}, mesh = {DNA, Mitochondrial/*genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal Spacer/*genetics ; Evolution, Molecular ; *Haplotypes ; Models, Genetic ; Paramecium aurelia/*classification/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The Paramecium aurelia complex (Ciliophora, Protozoa) Sonneborn (1975) is composed of 15 sibling species, which are morphologically indistinguishable but sexually isolated. Therefore, the P. aurelia complex seems to be an ideal model for testing hypotheses about recent speciation events. Here we present two-locus (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA) analyses using over 120 strains collected from around the world and representing all currently known species of the complex. According to our findings, the studied species show different levels of haplotype variability. Some of them appear on the obtained trees as polyphyletic (e.g., P. dodecaurelia), while others as monophyletic (e.g., P. quadecaurelia), clusters. The revealed discrepancies, which are manifested by different mating behavior and haplotypes not characteristic of particular species, may be explained by incomplete lineage sorting. Furthermore, the phenomena of hybridization and introgression are considered as another explanation for our results. Despite the above discrepancies, "polyphyletic taxa" should be considered true biological species based on the results of genetic crosses. Using a combination of both strain crosses (the biological species concept) and molecular methods (the phylogenetic species concept) seems to be the appropriate way of delimiting species in closely related eukaryotic microorganisms such as the P. aurelia complex.}, } @article {pmid23396155, year = {2013}, author = {Cavender, JC and Vadell, EM and Landolt, JC and Winsett, KE and Stephenson, SL and Rollins, AW and Romeralo, M}, title = {New small dictyostelids from seasonal rainforests of Central America.}, journal = {Mycologia}, volume = {105}, number = {3}, pages = {610-635}, doi = {10.3852/11-332}, pmid = {23396155}, issn = {0027-5514}, mesh = {Belize ; Central America ; DNA, Ribosomal/genetics ; Dictyosteliida/*classification/genetics/ultrastructure ; Ecosystem ; Guatemala ; Phylogeny ; Seasons ; Sequence Analysis, DNA/methods ; Soil ; Soil Microbiology ; Trees/*microbiology ; }, abstract = {Ten small dictyostelids isolated from samples collected from the surface humus layer of seasonal rainforests of Belize and Guatemala were studied morphologically, and nine were found to represent distinct species, all with an average height of < 2 mm (0.5-3.5 mm). Although their fruiting bodies (sorocarps) closely resemble one another, the nine species differ in their patterns of aggregation, stream pattern, branching development, formation of microcysts, spore shape, presence or absence of spore granules and their distribution, as well as in the shapes and behavior of their sorogens and myxamoebae. These stable morphological features were sufficient to recognize nine new species of small dictyostelids, one with two varieties. SSU rDNA sequences were generated for all these new isolates, and phylogenetic analyses of these sequences show these new isolates belong to Dictyostelid group 3. As a result of this and other recent studies, the concept of what constitutes a species in the dictyostelids has become much more restricted and well defined, in as much as some of the morphological and behavioral patterns now being observed were overlooked in the past. The extent, flow direction and conformation of streaming within the group varies from simple aggregation mounds with no streams to short streams, to somewhat longer streams and finally to well developed streams. Each of these is characterized by a particular set of distinguishing features.}, } @article {pmid23391385, year = {2013}, author = {White, T}, title = {Paleoanthropology: five's a crowd in our family tree.}, journal = {Current biology : CB}, volume = {23}, number = {3}, pages = {R112-5}, doi = {10.1016/j.cub.2012.12.001}, pmid = {23391385}, issn = {1879-0445}, mesh = {Animals ; Biodiversity ; *Fossils ; Hominidae/anatomy & histology/*classification ; Jaw/anatomy & histology ; Kenya ; *Sympatry ; }, abstract = {Two new fossil jawbones from Kenya are claimed to confirm a diversity of early Homo species. However, archaic species concepts and an inadequate fossil record continue to obscure the origins of our genus.}, } @article {pmid23390100, year = {2013}, author = {Villalobos, F and Rangel, TF and Diniz-Filho, JA}, title = {Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1756}, pages = {20122570}, pmid = {23390100}, issn = {1471-2954}, mesh = {Animals ; Biodiversity ; *Chiroptera ; Ecosystem ; Genetic Speciation ; Models, Statistical ; *Phylogeny ; Phylogeography ; }, abstract = {Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is largely focused on local scales. Here, we propose a conceptual framework to link macroecology and community phylogenetics by exploring the evolutionary context of large-scale species coexistence, introducing the phylogenetic field concept. This is defined as the phylogenetic structure of species co-occurrence within a focal species' geographical range. We developed concepts and methods for analysing phylogenetic fields and applied them to study coexistence patterns of the bat family Phyllostomidae. Our analyses showed that phyllostomid bats coexist mostly with closely related species, revealing a north-south gradient from overdispersed to clustered phylogenetic fields. Patterns at different phylogenetic levels (i.e. all species versus close relatives only) presented the same gradient. Results support the tropical niche conservatism hypothesis, potentially mediated by higher speciation rates in the region of origin coupled with shared environmental preferences among species. The phylogenetic field approach enables species-based community phylogenetics, instead of those that are site-based, allowing the description of historical processes at more appropriate macroecological and biogeographic scales.}, } @article {pmid23386959, year = {2012}, author = {Okasha, S}, title = {Emergence, hierarchy and top-down causation in evolutionary biology.}, journal = {Interface focus}, volume = {2}, number = {1}, pages = {49-54}, pmid = {23386959}, issn = {2042-8901}, abstract = {The concept of emergence and the related notion of 'downward causation' have arisen in numerous branches of science, and have also been extensively discussed in philosophy. Here, I examine emergence and downward causation in relation to evolutionary biology. I focus on the old, but ongoing discussion in evolutionary biology over the 'levels of selection' question: which level(s) of the biological hierarchy natural selection acts at, e.g. the gene, individual, group or species level? The concept of emergence has arisen in the levels-of-selection literature as a putative way of distinguishing between 'true' selection at a higher level from cases where selection acts solely at the lower level but has effects that percolate up the biological hierarchy, generating the appearance of higher level selection. At first blush, this problem seems to share a common structure with debates about emergence in other areas, but closer examination shows that it turns on issues that are sui generis to biology.}, } @article {pmid23380193, year = {2013}, author = {Samuels, J}, title = {Taxonomic notes on several wild relatives of Solanum melongena L. (Solanaceae): comments on.}, journal = {Molecular phylogenetics and evolution}, volume = {67}, number = {1}, pages = {297-299}, doi = {10.1016/j.ympev.2013.01.012}, pmid = {23380193}, issn = {1095-9513}, mesh = {*Phylogeny ; Solanum melongena/*genetics ; }, abstract = {In the recent paper by Meyer et al. (2012) some of the taxonomic assumptions relating to the closest wild relatives of Solanum melongena L., the brinjal eggplant, are unsupported. This group is well-known for its taxonomic difficulties, therefore a consistent approach to the identification, nomenclature and species concepts of experimental plant material is essential to the fullest interpretation of the results of a genomic study such as theirs. Effectively, Meyer et al., treat several of the brinjal wild relatives in their study as being conspecific. Neither their nrITS nor AFLP analysis gives confirmation of this. On this basis, the correct name for the taxon known as S. melongena group F is S. cumingii Dunal. This species is distinct from S. incanum L., which is found only as far eastwards as northern India. S. incanum and S. insanum sensu Lester and Hasan are distinct taxa. Meyer et al. hypothesise that there were two separate domestication events for brinjal; re-examination of their data suggests that there was a single domestication event, that took place in India.}, } @article {pmid23378811, year = {2012}, author = {Bond, JE}, title = {Phylogenetic treatment and taxonomic revision of the trapdoor spider genus Aptostichus Simon (Araneae, Mygalomorphae, Euctenizidae).}, journal = {ZooKeys}, volume = {}, number = {252}, pages = {1-209}, pmid = {23378811}, issn = {1313-2989}, abstract = {This systematic study documents the taxonomy, diversity, and distribution of 40 species of the predominately Californian trapdoor spider genus Aptostichus Simon, 1891. Thirty-three of these species are newly described: Aptostichus dantrippi, Aptostichus cabrillo, Aptostichus pennjillettei, Aptostichus asmodaeus, Aptostichus nateevansi, Aptostichus chiricahua, Aptostichus icenoglei, Aptostichus isabella, Aptostichus muiri, Aptostichus barackobamai, Aptostichus sinnombre, Aptostichus hedinorum, Aptostichus aguacaliente, Aptostichus chemehuevi, Aptostichus sarlacc, Aptostichus derhamgiulianii, Aptostichus anzaborrego, Aptostichus serrano, Aptostichus mikeradtkei, Aptostichus edwardabbeyi, Aptostichus killerdana, Aptostichus cahuilla, Aptostichus satleri, Aptostichus elisabethae, Aptostichus fornax, Aptostichus lucerne, Aptostichus fisheri, Aptostichus bonoi, Aptostichus cajalco, Aptostichus sierra, Aptostichus huntington, Aptostichus dorothealangeae, and Aptostichus chavezi. Most of these species are restricted to the California Floristic Province, a known biodiversity hotspot. Of the 40 recognized species, over half are considered to be imperiled or vulnerable and two have likely gone extinct over the past half-century; the conservation status of only 11 species is considered to be secure. Using 73 quantitative and qualitative morphological characters I propose a preliminary phylogeny for the genus that recognizes four major lineages: the Atomarius, Simus, Hesperus, and Sierra species groups. Additionally, the phylogenetic analysis indicates that adaptations favoring the invasion of the arid desert habitats of southern California have evolved multiple times across the group. The existence of both desert and non - desert species in three of the four species groups makes this genus an ideal candidate for the study of the evolutionary ecology of desert arthropods. A set of molecular characters based on the contiguous mitochondrial DNA genes 16S-tRNA valine-12S is used in an independent analysis to assist in placement of specimens into species. The taxonomy section explicitly identifies the concept employed in species delimitation. Niche based distribution models are constructed to predict the ranges of species for which an adequate number of sampling sites were known.}, } @article {pmid23376234, year = {2013}, author = {Jabaut, J and Ather, JL and Taracanova, A and Poynter, ME and Ckless, K}, title = {Mitochondria-targeted drugs enhance Nlrp3 inflammasome-dependent IL-1β secretion in association with alterations in cellular redox and energy status.}, journal = {Free radical biology & medicine}, volume = {60}, number = {}, pages = {233-245}, pmid = {23376234}, issn = {1873-4596}, support = {P20 GM103496/GM/NIGMS NIH HHS/United States ; R01 HL107291/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone/administration & dosage ; Carrier Proteins/genetics/*metabolism ; Energy Metabolism/drug effects ; Inflammasomes/drug effects/genetics/*metabolism ; Interleukin-1beta/genetics/*metabolism ; Macrophages, Peritoneal/cytology/drug effects ; Mice ; Mitochondria/drug effects/*metabolism/pathology ; NLR Family, Pyrin Domain-Containing 3 Protein ; Oxidation-Reduction/drug effects ; Primary Cell Culture ; Reactive Oxygen Species/metabolism ; Serum Amyloid A Protein/pharmacology ; }, abstract = {The Nlrp3 inflammasome is activated in response to an array of environmental and endogenous molecules leading to caspase-1-dependent IL-1β processing and secretion by myeloid cells. Several identified Nlrp3 inflammasome activators also trigger reactive oxygen species (ROS) production. However, the initial concept that NADPH oxidases are the primary source of ROS production during inflammasome activation is becoming less accepted. Therefore, the importance of mitochondria-derived ROS has been recently explored. In this study, we explore the impact of mitochondria dysfunction and ROS production on Nlrp3 inflammasome stimulation and IL-1β secretion induced by serum amyloid A (SAA) in primary mouse peritoneal macrophages. To induce mitochondrial dysfunction, we utilized antimycin A, which blocks electron flow at complex III, and carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP), a mitochondrial oxidative phosphorylation uncoupler. We also utilized a superoxide dismutase mimetic, MnTBAP, which targets the mitochondria, as well as the broad-spectrum antioxidants DPI (diphenyleneiodonium chloride) and ebselen. Our findings demonstrate that SAA alone induces mitochondrial ROS in a time-dependent manner. We observed that MnTBAP and ebselen blocked IL-1β secretion caused by SAA only when added before stimulation, and DPI augmented IL-1β secretion. Surprisingly, these effects were not directly related to intracellular or mitochondrial ROS levels. We also found that mitochondria-targeted drugs increased IL-1β secretion regardless of their impact on mitochondrial function and ROS levels, suggesting that mitochondrial ROS-dependent and -independent mechanisms play a role in the Nlrp3 inflammasome/IL-1β secretion axis in SAA-stimulated cells. Finally, we found that FCCP significantly sustained the association of the Nlrp3 inflammasome complex, which could explain the most robust effect among the drugs tested in enhancing IL-1β secretion in SAA-treated cells. Overall, our data suggest that the Nlrp3 inflammasome/IL-1β secretion axis is a very highly regulated inflammatory pathway that is susceptible not only to changes in mitochondrial or intracellular ROS, but also to changes in overall mitochondrial function.}, } @article {pmid23349141, year = {2013}, author = {Peshev, D and Vergauwen, R and Moglia, A and Hideg, E and Van den Ende, W}, title = {Towards understanding vacuolar antioxidant mechanisms: a role for fructans?.}, journal = {Journal of experimental botany}, volume = {64}, number = {4}, pages = {1025-1038}, pmid = {23349141}, issn = {1460-2431}, mesh = {Antioxidants/*chemistry ; Chicory/chemistry ; Cytosol/chemistry ; Disaccharides/chemistry ; Fructans/*chemistry ; Hydrogen Peroxide/chemistry ; Hydroxyl Radical/*chemistry ; Intracellular Membranes/chemistry ; Iron/chemistry ; Molecular Structure ; Oxidative Stress ; Phenols/chemistry ; Plant Extracts/chemistry ; Plant Leaves/chemistry ; Sucrose/chemistry ; Superoxides/chemistry ; Vacuoles/*chemistry ; }, abstract = {Recent in vitro, in vivo, and theoretical experiments strongly suggest that sugar-(like) molecules counteract oxidative stress by acting as genuine reactive oxygen species (ROS) scavengers. A concept was proposed to include the vacuole as a part of the cellular antioxidant network. According to this view, sugars and sugar-like vacuolar compounds work in concert with vacuolar phenolic compounds and the 'classic' cytosolic antioxidant mechanisms. Among the biologically relevant ROS (H(2)O(2), O(2)·(-), and ·OH), hydroxyl radicals are the most reactive and dangerous species since there are no enzymatic systems known to neutralize them in any living beings. Therefore, it is important to study in more detail the radical reactions between ·OH and different biomolecules, including sugars. Here, Fenton reactions were used to compare the ·OH-scavenging capacities of a range of natural vacuolar compounds to establish relationships between antioxidant capacity and chemical structure and to unravel the mechanisms of ·OH-carbohydrate reactions. The in vitro work on the ·OH-scavenging capacity of sugars and phenolic compounds revealed a correlation between structure and ·OH-scavenging capacity. The number and position of the C=C type of linkages in phenolic compounds greatly influence antioxidant properties. Importantly, the splitting of disaccharides and oligosaccharides emerged as a predominant outcome of the ·OH-carbohydrate interaction. Moreover, non-enzymatic synthesis of new fructan oligosaccharides was found starting from 1-kestotriose. Based on these and previous findings, a working model is proposed describing the putative radical reactions involving fructans and secondary metabolites at the inner side of the tonoplast and in the vacuolar lumen.}, } @article {pmid23341927, year = {2013}, author = {Stech, M and Veldman, S and Larraín, J and Muñoz, J and Quandt, D and Hassel, K and Kruijer, H}, title = {Molecular species delimitation in the Racomitrium canescens complex (Grimmiaceae) and implications for DNA barcoding of species complexes in mosses.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e53134}, pmid = {23341927}, issn = {1932-6203}, mesh = {Base Sequence ; Bryophyta/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Plant/genetics ; Genetic Variation ; Species Specificity ; }, abstract = {In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses.}, } @article {pmid23336673, year = {2013}, author = {Cray, JA and Bell, AN and Bhaganna, P and Mswaka, AY and Timson, DJ and Hallsworth, JE}, title = {The biology of habitat dominance; can microbes behave as weeds?.}, journal = {Microbial biotechnology}, volume = {6}, number = {5}, pages = {453-492}, pmid = {23336673}, issn = {1751-7915}, support = {BB/F003471/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biota ; Environmental Microbiology ; *Microbial Interactions ; Selection, Genetic ; }, abstract = {Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard-wired to behave in a vigorous and ecologically aggressive manner. These 'microbial weeds' are able to dominate the communities that develop in fertile but uncolonized--or at least partially vacant--habitats via traits enabling them to out-grow competitors; robust tolerances to habitat-relevant stress parameters and highly efficient energy-generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat-specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp., Salinibacter ruber and Haloquadratum walsbyi. Some microbes, such as Escherichia coli, Mycobacterium smegmatis and Pseudoxylaria spp., exhibit characteristics of both weed and non-weed species. We propose that the concept of nonweeds represents a 'dustbin' group that includes species such as Synodropsis spp., Polypaecilum pisce, Metschnikowia orientalis, Salmonella spp., and Caulobacter crescentus. We show that microbial weeds are conceptually distinct from plant weeds, microbial copiotrophs, r-strategists, and other ecophysiological groups of microorganism. Microbial weed species are unlikely to emerge from stationary-phase or other types of closed communities; it is open habitats that select for weed phenotypes. Specific characteristics that are common to diverse types of open habitat are identified, and implications of weed biology and open-habitat ecology are discussed in the context of further studies needed in the fields of environmental and applied microbiology.}, } @article {pmid23336076, year = {2013}, author = {Rübben, A and Nordhoff, O}, title = {A systems approach defining constraints of the genome architecture on lineage selection and evolvability during somatic cancer evolution.}, journal = {Biology open}, volume = {2}, number = {1}, pages = {49-62}, pmid = {23336076}, issn = {2046-6390}, abstract = {Most clinically distinguishable malignant tumors are characterized by specific mutations, specific patterns of chromosomal rearrangements and a predominant mechanism of genetic instability but it remains unsolved whether modifications of cancer genomes can be explained solely by mutations and selection through the cancer microenvironment.It has been suggested that internal dynamics of genomic modifications as opposed to the external evolutionary forces have a significant and complex impact on Darwinian species evolution. A similar situation can be expected for somatic cancer evolution as molecular key mechanisms encountered in species evolution also constitute prevalent mutation mechanisms in human cancers. This assumption is developed into a systems approach of carcinogenesis which focuses on possible inner constraints of the genome architecture on lineage selection during somatic cancer evolution. The proposed systems approach can be considered an analogy to the concept of evolvability in species evolution.The principal hypothesis is that permissive or restrictive effects of the genome architecture on lineage selection during somatic cancer evolution exist and have a measurable impact. The systems approach postulates three classes of lineage selection effects of the genome architecture on somatic cancer evolution: i) effects mediated by changes of fitness of cells of cancer lineage, ii) effects mediated by changes of mutation probabilities and iii) effects mediated by changes of gene designation and physical and functional genome redundancy. Physical genome redundancy is the copy number of identical genetic sequences. Functional genome redundancy of a gene or a regulatory element is defined as the number of different genetic elements, regardless of copy number, coding for the same specific biological function within a cancer cell. Complex interactions of the genome architecture on lineage selection may be expected when modifications of the genome architecture have multiple and possibly opposed effects which manifest themselves at disparate times and progression stages.Dissection of putative mechanisms mediating constraints exerted by the genome architecture on somatic cancer evolution may provide an algorithm for understanding and predicting as well as modifying somatic cancer evolution in individual patients.}, } @article {pmid23306967, year = {2013}, author = {Koroleva, ON and Dubrovin, EV and Khodak, YA and Kuzmina, NV and Yaminsky, IV and Drutsa, VL}, title = {The model of amyloid aggregation of Escherichia coli RNA polymerase σ70 subunit based on AFM data and in vitro assays.}, journal = {Cell biochemistry and biophysics}, volume = {66}, number = {3}, pages = {623-636}, doi = {10.1007/s12013-012-9507-2}, pmid = {23306967}, issn = {1559-0283}, mesh = {Amyloid/*chemistry ; Base Sequence ; DNA/genetics/metabolism ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Escherichia coli/*enzymology ; *Microscopy, Atomic Force ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutation ; *Protein Multimerization ; Protein Structure, Secondary ; Protein Subunits/*chemistry ; Sigma Factor/*chemistry/genetics/metabolism ; Transcription, Genetic ; }, abstract = {To propose a model for recently described amyloid aggregation of E.coli RNA polymerase σ(70) subunit, we have investigated the role of its N-terminal region. For this purpose, three mutant variants of protein with deletions Δ1-73, Δ1-100 and Δ74-100 were constructed and studied in a series of in vitro assays and using atomic force microscopy (AFM). Specifically, all RNA polymerase holoenzymes, reconstituted with the use of mutant σ subunits, have shown reduced affinity for promoter-containing DNA and reduced activity in run-off transcription experiments (compared to that of WT species), thus substantiating the modern concept on the modulatory role of N-terminus in formation of open complex and transcription initiation. The ability of mutant proteins to form amyloid-like structures has been investigated using AFM, which revealed the increased propensity of mutant proteins to form rodlike aggregates with the effect being more pronounced for the mutant with the deletion Δ1-73 (10 fold increase). σ(70) subunit aggregation ability has shown complex dependence on the ionic surrounding, which we explain by Debye screening effect and the change of the internal state of the protein. Basing on the obtained data, we propose the model of amyloid fibril formation by σ(70) subunit, implying the involvement of N-terminal region according to the domain swapping mechanism.}, } @article {pmid23297024, year = {2013}, author = {Alexander, SA}, title = {Infinite graphs in systematic biology, with an application to the species problem.}, journal = {Acta biotheoretica}, volume = {61}, number = {2}, pages = {181-201}, doi = {10.1007/s10441-012-9168-y}, pmid = {23297024}, issn = {1572-8358}, mesh = {*Evolution, Molecular ; Models, Biological ; Species Specificity ; *Systems Biology ; }, abstract = {We argue that C. Darwin and more recently W. Hennig worked at times under the simplifying assumption of an eternal biosphere. So motivated, we explicitly consider the consequences which follow mathematically from this assumption, and the infinite graphs it leads to. This assumption admits certain clusters of organisms which have some ideal theoretical properties of species, shining some light onto the species problem. We prove a dualization of a law of T. A. Knight and C. Darwin, and sketch a decomposition result involving the internodons of D. Kornet, J. Metz and H. Schellinx. A further goal of this paper is to respond to B. Sturmfels' question, "Can biology lead to new theorems?"}, } @article {pmid23275547, year = {2013}, author = {Reid, AJ and Berriman, M}, title = {Genes involved in host-parasite interactions can be revealed by their correlated expression.}, journal = {Nucleic acids research}, volume = {41}, number = {3}, pages = {1508-1518}, pmid = {23275547}, issn = {1362-4962}, support = {098051//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Anopheles/genetics/metabolism ; Host-Parasite Interactions/*genetics ; Insect Vectors/genetics/metabolism ; Mice ; Plasmodium berghei/genetics/metabolism ; Protein Interaction Mapping/*methods ; *Transcriptome ; }, abstract = {Molecular interactions between a parasite and its host are key to the ability of the parasite to enter the host and persist. Our understanding of the genes and proteins involved in these interactions is limited. To better understand these processes it would be advantageous to have a range of methods to predict pairs of genes involved in such interactions. Correlated gene expression profiles can be used to identify molecular interactions within a species. Here we have extended the concept to different species, showing that genes with correlated expression are more likely to encode proteins, which directly or indirectly participate in host-parasite interaction. We go on to examine our predictions of molecular interactions between the malaria parasite and both its mammalian host and insect vector. Our approach could be applied to study any interaction between species, for example, between a host and its parasites or pathogens, but also symbiotic and commensal pairings.}, } @article {pmid23245619, year = {2012}, author = {Uehling, JK and Henkel, TW and Aime, MC and Vilgalys, R and Smith, ME}, title = {New species and distribution records for Clavulina (Cantharellales, Basidiomycota) from the Guiana Shield, with a key to the lowland neotropical taxa.}, journal = {Fungal biology}, volume = {116}, number = {12}, pages = {1263-1274}, doi = {10.1016/j.funbio.2012.09.004}, pmid = {23245619}, issn = {1878-6146}, mesh = {Basidiomycota/*classification/cytology/genetics/*isolation & purification ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genes, rRNA ; Guyana ; Molecular Sequence Data ; Phylogeny ; RNA Polymerase II/genetics ; RNA, Fungal/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Spores, Fungal/cytology ; Tropical Climate ; }, abstract = {Three new and one previously described species of Clavulina (Clavulinaceae, Cantharellales, Basidiomycota) are reported from the central Guiana Shield region from tropical rainforests dominated by ectomycorrhizal trees of the leguminous genus Dicymbe (Fabaceae subfam. Caesalpinioideae). We provide morphological, DNA sequence, habitat, and fruiting occurrence data for each species. The new species conform to a generic concept of Clavulina that includes coralloid, branched basidiomata with amphigenous hymenia, basidia with two or 2-4 incurved sterigmata and postpartal septa present or absent, and smooth, hyaline, guttulate basidiospores. Placements of the new species in Clavulina were corroborated with DNA sequence data from the internal transcribed spacer and large subunit of the nuclear ribosomal repeat, and their infrageneric relationships were examined with phylogenetic analyses based on DNA from the region coding for the second largest subunit of DNA-dependent RNA polymerase II (rpb2). To facilitate future studies of the genus in the neotropics, a key is provided for all Clavulina species described from the lowland neotropics.}, } @article {pmid23170073, year = {2012}, author = {Stimpson, ML and Weston, PH and Telford, IR and Bruhl, JJ}, title = {First instalment in resolution of the Banksia spinulosa complex (Proteaceae): B. neoanglica, a new species supported by phenetic analysis, ecology and geography.}, journal = {PhytoKeys}, volume = {}, number = {14}, pages = {57-80}, pmid = {23170073}, issn = {1314-2003}, abstract = {Taxa in the Banksia spinulosa Sm. complex (Proteaceae) have populations with sympatric, parapatric and allopatric distributions and unclear or disputed boundaries. Our hypothesis is that under biological, phenetic and diagnosable species concepts that each of the currently named taxa within the Banksia spinulosa complex is a separate species. Based on specimens collected as part of this study, and data recorded from specimens in six Australian herbaria, complemented by phenetic analysis (semi-strong multidimensional scaling and UPGMA clustering) and a detailed morphological study, we investigated both morphological variation and geographic distribution in the Banksia spinulosa complex. All specimens used for this study are held at the N.C.W. Beadle Herbarium or the National Herbarium of New South Wales. In total 23 morphological characters (11 quantitative, five binary, and seven multistate characters) were analysed phenetically for 89 specimens. Ordination and cluster analysis resulted in individuals grouping strongly allowing recognition of distinct groups consistent with their recognition as separate species. Additional morphological analysis was completed on all specimens using leaf, floral, fruit and stem morphology, providing clear cut diagnosable groups and strong support for the recognition of Banksia spinulosa var. cunninghamii and Banksia spinulosa var. neoanglica as species.}, } @article {pmid23166696, year = {2012}, author = {Springer, MS and Meredith, RW and Gatesy, J and Emerling, CA and Park, J and Rabosky, DL and Stadler, T and Steiner, C and Ryder, OA and Janečka, JE and Fisher, CA and Murphy, WJ}, title = {Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49521}, pmid = {23166696}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Phylogeny ; Phylogeography ; Primates/*classification/*genetics ; }, abstract = {Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ("Grande Coupure") at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.}, } @article {pmid23166582, year = {2012}, author = {Runge, F and Ndambi, B and Thines, M}, title = {Which morphological characteristics are most influenced by the host matrix in downy mildews? A case study in Pseudoperonospora cubensis.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e44863}, pmid = {23166582}, issn = {1932-6203}, mesh = {Cucurbitaceae/*microbiology ; Czech Republic ; *Host-Pathogen Interactions ; Oomycetes/*cytology/genetics ; *Phylogeny ; Species Specificity ; Sporangia/anatomy & histology ; }, abstract = {Before the advent of molecular phylogenetics, species concepts in the downy mildews, an economically important group of obligate biotrophic oomycete pathogens, have mostly been based upon host range and morphology. While molecular phylogenetic studies have confirmed a narrow host range for many downy mildew species, others, like Pseudoperonospora cubensis affect even different genera. Although often morphological differences were found for new, phylogenetically distinct species, uncertainty prevails regarding their host ranges, especially regarding related plants that have been reported as downy mildew hosts, but were not included in the phylogenetic studies. In these cases, the basis for deciding if the divergence in some morphological characters can be deemed sufficient for designation as separate species is uncertain, as observed morphological divergence could be due to different host matrices colonised. The broad host range of P. cubensis (ca. 60 host species) renders this pathogen an ideal model organism for the investigation of morphological variations in relation to the host matrix and to evaluate which characteristics are best indicators for conspecificity or distinctiveness. On the basis of twelve morphological characterisitcs and a set of twelve cucurbits from five different Cucurbitaceae tribes, including the two species, Cyclanthera pedata and Thladiantha dubia, hitherto not reported as hosts of P. cubensis, a significant influence of the host matrix on pathogen morphology was found. Given the high intraspecific variation of some characteristics, also their plasticity has to be taken into account. The implications for morphological species determination and the confidence limits of morphological characteristics are discussed. For species delimitations in Pseudoperonospora it is shown that the ratio of the height of the first ramification to the sporangiophore length, ratio of the longer to the shorter ultimate branchlet, and especially the length and width of sporangia, as well as, with some reservations, their ratio, are the most suitable characteristics for species delimitation.}, } @article {pmid23145316, year = {2012}, author = {Shang, J and Ma, L and Li, J and Ai, W and Yu, T and Gurzadyan, GG}, title = {The origin of fluorescence from graphene oxide.}, journal = {Scientific reports}, volume = {2}, number = {}, pages = {792}, pmid = {23145316}, issn = {2045-2322}, mesh = {*Fluorescence ; Graphite/*chemistry ; Kinetics ; Oxidation-Reduction ; Oxides/*chemistry ; Spectrometry, Fluorescence ; Spectrum Analysis, Raman ; Water/chemistry ; }, abstract = {Time-resolved fluorescence measurements of graphene oxide in water show multiexponential decay kinetics ranging from 1 ps to 2 ns. Electron-hole recombination from the bottom of the conduction band and nearby localized states to wide-range valance band is suggested as origin of the fluorescence. Excitation wavelength dependence of the fluorescence was caused by relative intensity changes of few emission species. By introducing the molecular orbital concept, the dominant fluorescence was found to originate from the electronic transitions among/between the non-oxidized carbon regions and the boundary of oxidized carbon atom regions, where all three kinds of functionalized groups C-O, C = O and O = C-OH were participating. In the visible spectral range, the ultrafast fluorescence of graphene oxide was observed for the first time.}, } @article {pmid23136460, year = {2012}, author = {Cannon, PF and Damm, U and Johnston, PR and Weir, BS}, title = {Colletotrichum - current status and future directions.}, journal = {Studies in mycology}, volume = {73}, number = {1}, pages = {181-213}, pmid = {23136460}, issn = {1872-9797}, abstract = {A review is provided of the current state of understanding of Colletotrichum systematics, focusing on species-level data and the major clades. The taxonomic placement of the genus is discussed, and the evolution of our approach to species concepts and anamorph-teleomorph relationships is described. The application of multilocus technologies to phylogenetic analysis of Colletotrichum is reviewed, and selection of potential genes/loci for barcoding purposes is discussed. Host specificity and its relation to speciation and taxonomy is briefly addressed. A short review is presented of the current status of classification of the species clusters that are currently without comprehensive multilocus analyses, emphasising the orbiculare and destructivum aggregates. The future for Colletotrichum biology will be reliant on consensus classification and robust identification tools. In support of these goals, a Subcommission on Colletotrichum has been formed under the auspices of the International Commission on Taxonomy of Fungi, which will administer a carefully curated barcode database for sequence-based identification of species within the BioloMICS web environment.}, } @article {pmid23133560, year = {2012}, author = {Sánchez-Fernández, D and Aragón, P and Bilton, DT and Lobo, JM}, title = {Assessing the congruence of thermal niche estimations derived from distribution and physiological data. A test using diving beetles.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e48163}, pmid = {23133560}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Climate ; Cold Temperature ; Coleoptera/*genetics/*physiology ; *Ecology ; Ecosystem ; Geography ; Hot Temperature ; Models, Biological ; Phylogeny ; Temperature ; }, abstract = {A basic aim of ecology is to understand the determinants of organismal distribution, the niche concept and species distribution models providing key frameworks to approach the problem. As temperature is one of the most important factors affecting species distribution, the estimation of thermal limits is crucially important for inferring range constraints. It is expectable that thermal physiology data derived from laboratory experiments and species' occurrences may express different aspects of the species' niche. However, there is no study systematically testing this prediction in a given taxonomic group while controlling by potential phylogenetic inertia. We estimate the thermal niches of twelve Palaearctic diving beetles species using physiological data derived from experimental analyses in order to examine the extent to which these coincided with those estimated from distribution models based on observed occurrences. We found that thermal niche estimates derived from both approaches lack general congruence, and these results were similar before and after controlling by phylogeny. The congruence between potential distributions obtained from the two different procedures was also explored, and we found again that the percentage of agreement were not very high (~60%). We confirm that both thermal niche estimates derived from geographical and physiological data are likely to misrepresent the true range of climatic variation that these diving beetles are able to tolerate, and so these procedures could be considered as incomplete but complementary estimations of an inaccessible reality.}, } @article {pmid23131680, year = {2012}, author = {Walker, SM and Prodöhl, PA and Hoey, EM and Fairweather, I and Hanna, RE and Brennan, G and Trudgett, A}, title = {Substantial genetic divergence between morphologically indistinguishable populations of Fasciola suggests the possibility of cryptic speciation.}, journal = {International journal for parasitology}, volume = {42}, number = {13-14}, pages = {1193-1199}, doi = {10.1016/j.ijpara.2012.10.007}, pmid = {23131680}, issn = {1879-0135}, mesh = {Africa South of the Sahara/epidemiology ; Animals ; Australia/epidemiology ; Cattle ; Cattle Diseases/epidemiology/parasitology ; DNA, Mitochondrial/genetics ; Equidae ; Europe/epidemiology ; Fasciola/*genetics ; Fascioliasis/epidemiology/parasitology/*veterinary ; *Genetic Speciation ; *Genetic Variation ; Genome ; India/epidemiology ; Molecular Sequence Data ; Phylogeny ; RNA, Helminth/genetics ; RNA, Ribosomal, 28S/genetics ; Sheep ; Sheep Diseases/epidemiology/parasitology ; }, abstract = {The liver flukes, Fasciola hepatica and Fasciola gigantica, are considered to be sister species and between them present a major threat worldwide to livestock production. In this study sequence data have been employed from informative regions of the nuclear and mitochondrial genomes of over 200 morphologically F. hepatica-like or F. gigantica-like flukes from Europe, sub-Saharan Africa and South Asia to assess genetic diversity. Evidence is presented for the existence of four well-separated clades: African gigantica-like flukes, Indian gigantica-like flukes, European hepatica-like flukes and African high-altitude hepatica-like flukes. Application of the Biological Species Concept to trematodes is problematic; however, the degree of separation between these groups was sufficient for them to be considered as distinct species using the four times rule for speciation.}, } @article {pmid23106559, year = {2012}, author = {Alam, MS and Islam, MM and Khan, MR and Hasan, M and Wanichanon, R and Sumida, M}, title = {Postmating isolation in six species of three genera (Hoplobatrachus, Euphlyctis and Fejervarya) from family Dicroglossidae (anura), with special reference to spontaneous production of allotriploids.}, journal = {Zoological science}, volume = {29}, number = {11}, pages = {743-752}, doi = {10.2108/zsj.29.743}, pmid = {23106559}, issn = {0289-0003}, mesh = {Animals ; Anura/*genetics/*physiology ; Crosses, Genetic ; Female ; Gene Expression Regulation/physiology ; Larva ; Male ; Phylogeny ; Sexual Behavior, Animal/*physiology ; Species Specificity ; *Triploidy ; }, abstract = {In light of reproductive isolation being a fundamental aspect of the biological species concept, we performed crossing experiments using six species from three genera (Hoplobatrachus, Euphlyctis and Fejervarya) of family Dicroglossidae to explore postmating isolation in dicroglossid frogs. Our results revealed gametic isolation among these genera, although the intergeneric hybrids between female E. cyanophlyctis and male H. chinensis were not viable at the tadpole stage, while the hybrids between female E. cyanophlyctis and male H. tigerinus were inviable at the hatching stage. These results showed complete hybrid inviability between the two genera. Almost all interspecific hybrids between female H. tigerinus and male H. chinensis died of underdevelopment at the tadpole stage, whereas several hybrids developed normally and survived to maturity. Chromosomal observations and mtDNA and allozyme analyses confirmed that these mature hybrids were allotriploid, with two maternal genomes and one paternal genome. The present results suggest that the allotriploids were produced spontaneously, and histological observations confirmed their sex as sterile males. We also investigated the molecular relationships between H. tigerinus, H. chinensis, and the interspecific allotriploids by mitochondrial Cytb, 12S and 16S rRNA gene analyses. The maternal inheritance mode of mitochondrial genomes was retained in the hybrids. Finally, the present results suggest that the degree of postmating isolation reflects phylogenetic relationship. In addition, we speculate that allotriploids may be produced via hybridization among cryptic species.}, } @article {pmid23095099, year = {2014}, author = {Impellizeri, JA and Ciliberto, G and Aurisicchio, L}, title = {Electro-gene-transfer as a new tool for cancer immunotherapy in animals.}, journal = {Veterinary and comparative oncology}, volume = {12}, number = {4}, pages = {310-318}, doi = {10.1111/vco.12006}, pmid = {23095099}, issn = {1476-5829}, mesh = {Animals ; Cancer Vaccines/immunology/*pharmacology ; Clinical Trials as Topic ; DNA/genetics ; Dog Diseases/genetics/*immunology/*therapy ; Dogs ; Electroporation/methods/veterinary ; Gene Transfer Techniques/*veterinary ; Immunotherapy/methods/*veterinary ; Neoplasms/genetics/immunology/therapy/*veterinary ; Telomerase ; }, abstract = {The concept of vaccines based on the direct inoculation of plasmid DNA gained initial proof-of-concept in small rodent species. Further development was hampered by the difficulty to confirm immunogenicity and efficacy in large animal species and, most importantly, in human clinical trials. These negative findings led to the search of complementary technologies which, in combination with intradermal or intramuscular plasmid DNA injection would result in more robust delivery, decreased interindividual variability, clear evidence of clinical efficacy and which would eventually lead to market approval of new vaccine products. The use of high-pressure, needleless devices as an enhancing tool for plasmid DNA delivery led to recent approval by USDA of Oncept™, a therapeutic cancer vaccine directed against tyrosinase for the therapy of melanoma in dogs. An alternative approach to improve plasmid DNA delivery is electro-gene-transfer (EGT). In this article, we briefly review the principles of DNA-EGT and the evidences for efficacy of a telomerase reverse transcriptase vaccine in a dog clinical trial, and provide perspectives for the use of this technology for broader applications in pet animals.}, } @article {pmid23062191, year = {2013}, author = {Mouquet, N and Gravel, D and Massol, F and Calcagno, V}, title = {Extending the concept of keystone species to communities and ecosystems.}, journal = {Ecology letters}, volume = {16}, number = {1}, pages = {1-8}, doi = {10.1111/ele.12014}, pmid = {23062191}, issn = {1461-0248}, mesh = {Conservation of Natural Resources ; *Ecosystem ; *Models, Biological ; Monte Carlo Method ; }, abstract = {Keystone species are defined as having disproportionate importance in their community. This concept has proved useful and is now often used in conservation ecology. Here, we introduce the concept of keystone communities (and ecosystems) within metacommunities (and metaecosystems). We define keystone and burden communities as communities with impacts disproportionately large (positive or negative respectively) relative to their weight in the metacommunity. We show how a simple metric, based on the effects of single-community removals, can characterise communities along a 'keystoneness' axis. We illustrate the usefulness of this approach with examples from two different theoretical models. We further distinguish environmental heterogeneity from species trait heterogeneity as determinants of keystoneness. We suggest that the concept of keystone communities/ecosystems will be highly beneficial, not only as a fundamental step towards understanding species interactions in a spatial context, but also as a tool for the management of disturbed landscapes.}, } @article {pmid23056404, year = {2012}, author = {Bills, GF and González-Menéndez, V and Martín, J and Platas, G and Fournier, J and Peršoh, D and Stadler, M}, title = {Hypoxylon pulicicidum sp. nov. (Ascomycota, Xylariales), a pantropical insecticide-producing endophyte.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e46687}, pmid = {23056404}, issn = {1932-6203}, mesh = {DNA, Fungal/genetics ; Endophytes/classification/genetics/*metabolism ; Indole Alkaloids/*metabolism ; Insecticides/*metabolism ; Molecular Structure ; Phylogeny ; Xylariales/classification/genetics/*metabolism ; }, abstract = {BACKGROUND: Nodulisporic acids (NAs) are indole diterpene fungal metabolites exhibiting potent systemic efficacy against blood-feeding arthropods, e.g., bedbugs, fleas and ticks, via binding to arthropod specific glutamate-gated chloride channels. Intensive medicinal chemistry efforts employing a nodulisporic acid A template have led to the development of N-tert-butyl nodulisporamide as a product candidate for a once monthly treatment of fleas and ticks on companion animals. The source of the NAs is a monophyletic lineage of asexual endophytic fungal strains that is widely distributed in the tropics, tentatively identified as a Nodulisporium species and hypothesized to be the asexual state of a Hypoxylon species.

METHODS AND RESULTS: Inferences from GenBank sequences indicated that multiple researchers have encountered similar Nodulisporium endophytes in tropical plants and in air samples. Ascomata-derived cultures from a wood-inhabiting fungus, from Martinique and closely resembling Hypoxylon investiens, belonged to the same monophyletic clade as the NAs-producing endophytes. The hypothesis that the Martinique Hypoxylon collections were the sexual state of the NAs-producing endophytes was tested by mass spectrometric analysis of NAs, multi-gene phylogenetic analysis, and phenotypic comparisons of the conidial states. We established that the Martinique Hypoxylon strains produced an ample spectrum of NAs and were conspecific with the pantropical Nodulisporium endophytes, yet were distinct from H. investiens. A new species, H. pulicicidum, is proposed to accommodate this widespread organism.

CONCLUSIONS AND SIGNIFICANCE: Knowledge of the life cycle of H. pulicicidum will facilitate an understanding of the role of insecticidal compounds produced by the fungus, the significance of its infections in living plants and how it colonizes dead wood. The case of H. pulicicidum exemplifies how life cycle studies can consolidate disparate observations of a fungal organism, whether from environmental sequences, vegetative mycelia or field specimens, resulting in holistic species concepts critical to the assessment of the dimensions of fungal diversity.}, } @article {pmid23042428, year = {2013}, author = {Bruner, E}, title = {The species concept as a cognitive tool for biological anthropology.}, journal = {American journal of primatology}, volume = {75}, number = {1}, pages = {10-15}, doi = {10.1002/ajp.22087}, pmid = {23042428}, issn = {1098-2345}, mesh = {Animals ; *Anthropology ; *Communication ; Fossils ; Hominidae/*classification ; *Phylogeny ; Primates/classification ; }, abstract = {Taxonomy is caught between the search for the "perfect" theory and an elusive biological variability. The lack of major advances in issues related to how "species" and other taxonomic categories are defined suggests that perhaps we should avoid excessively rigid formalism in this regard. The risk is a separation between elegant but useless theories and confusing applications of the taxonomic tools. Communication is one of the main functions of taxonomy, and stability one of the main parameters that taxonomy users should be sensitive to. An excess of stability may generate anachronistic consequences while continuous revisions may make the tool of taxonomy scarcely practical. The current tendency pushes toward more and more fragmentation of biologically valid taxa. While taxonomy specialists enjoy such challenges, many taxonomy users feel a bit nervous and discouraged when trying to use a tool that is constantly changing. Debates over taxonomy would seem particularly unrewarding for fields with limited samples and scarce biological diversity, such as palaeoanthropology. In this context, where the information available is rarely sufficient to supply consistent taxonomical evidence, there are frequently excessive efforts to create debate on species separations. The risk is that we maintain the debate on a purely theoretical level, or else we distrust a reliable use of taxonomy. A compromise (and recommended) choice between these two extremes would be to rely on shared and reasonable interpretations of homogeneous evolutionary units, without diving into fine-grained issues that will remain, however, unresolved. Taxonomy should be a tool, not the goal, of the evolutionary biologist. Our mind needs discrete and recognizable objects to structure our perception of reality. There is no reason to expect that nature works the same way.}, } @article {pmid23028445, year = {2012}, author = {Mahé, S and Duhamel, M and Le Calvez, T and Guillot, L and Sarbu, L and Bretaudeau, A and Collin, O and Dufresne, A and Kiers, ET and Vandenkoornhuyse, P}, title = {PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e43117}, pmid = {23028445}, issn = {1932-6203}, mesh = {Base Sequence ; *Databases, Nucleic Acid ; *Evolution, Molecular ; Fungi/classification/*genetics ; *Genetic Variation ; Internet ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation.

To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ~20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples.

CONCLUSION: PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as 'reference alignments', (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/.}, } @article {pmid23009217, year = {2013}, author = {Corcoran, A and Cotter, TG}, title = {FLT3-driven redox-modulation of Ezrin regulates leukaemic cell migration.}, journal = {Free radical research}, volume = {47}, number = {1}, pages = {20-34}, doi = {10.3109/10715762.2012.733385}, pmid = {23009217}, issn = {1029-2470}, mesh = {Cell Line ; Cell Movement/drug effects/*physiology ; Cytoskeletal Proteins/genetics/*metabolism ; HL-60 Cells ; Humans ; Leukemia, Myelomonocytic, Acute/*enzymology/genetics/metabolism/*pathology ; NADPH Oxidases/antagonists & inhibitors/metabolism ; Onium Compounds/pharmacology ; Oxidation-Reduction ; Phosphorylation ; Reactive Oxygen Species/metabolism ; Signal Transduction ; Staurosporine/analogs & derivatives/pharmacology ; Transfection ; fms-Like Tyrosine Kinase 3/antagonists & inhibitors/genetics/*metabolism ; }, abstract = {The concept of reactive oxygen species (ROS) being produced via the activation of specific oncogenes provides a basis for generating genomic instability and pro-survival signalling in tumour cells. The purpose of this study was to identify downstream targets of NADPH oxidase (Nox)-derived ROS signalling in acute myeloid leukaemia cells, by performing a proteomic analysis utilizing two-dimensional phosphotyrosine immunoblotting. The majority of the targets identified were cytoskeletal-associated proteins including Ezrin, a known regulator of the cytoskeleton, which was examined further. The study demonstrated that inhibition of Nox enzymes, using diphenyleneiodonium chloride in the acute myeloid leukaemia cell line MOLM-13, resulted in a decrease in Ezrin tyrosine phosphorylation and also triggered a shift in Ezrin sub-cellular localization as detected by immunofluorescence. The change in Ezrin localization coincided with altered cell morphology, observed using scanning electron microscopy and a decreased ability to migrate through a polycarbonate transwell membrane. Similar effects were observed upon inhibition of the oncogenic receptor tyrosine kinase FLT3 using the staurosporine derivate PKC412, implicating a role for FLT3 as an upstream regulator of Ezrin. Our results indicate that FLT3 drives production of ROS by Nox, which stimulates changes in Ezrin tyrosine phosphorylation and localization via redox regulation of Src. Furthermore, inhibition of FLT3 signalling leads to alterations in MOLM-13 cell morphology and has a significant influence on cell motility.}, } @article {pmid22973561, year = {2012}, author = {Segerman, B}, title = {The genetic integrity of bacterial species: the core genome and the accessory genome, two different stories.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {116}, pmid = {22973561}, issn = {2235-2988}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genetic Variation ; *Genome, Bacterial ; }, abstract = {Strains within a bacterial species typically have a set of conserved core genes and a variable set of accessory genes. The accessory genes often appear to move laterally between strains, thereby forming new trait combinations. Sometimes, genetic material also moves laterally between species, thereby resulting in diffuse borders between them. The growing number of genome sequences offers new possibilities to study these processes. Ten species for which abundant genomic data exists were here selected for analysis of the species border integrity. The average core genome similarities and relative core genome sizes (RCGSs) were determined for strain pairs within the species and for strain pairs crossing the species border. The variability within the species as well as the border integrity varies for different bacterial species. Some have very distinct borders while others are more or less indefinable. From the growing amount of genomic data, it becomes even clearer that the concept of bacterial species is, in many cases, far from absolute.}, } @article {pmid22970128, year = {2012}, author = {Murrell, EG and Juliano, SA}, title = {Competitive abilities in experimental microcosms are accurately predicted by a demographic index for R*.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e43458}, pmid = {22970128}, issn = {1932-6203}, support = {R01 AI044793/AI/NIAID NIH HHS/United States ; R15 AI075306/AI/NIAID NIH HHS/United States ; R15 AI075306-01/AI/NIAID NIH HHS/United States ; R01-AI44793/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Competitive Behavior/*physiology ; Culicidae/*growth & development ; *Ecosystem ; Fertility ; Linear Models ; Population Dynamics ; Species Specificity ; Wings, Animal/anatomy & histology ; }, abstract = {Resource competition theory predicts that R*, the equilibrium resource amount yielding zero growth of a consumer population, should predict species' competitive abilities for that resource. This concept has been supported for unicellular organisms, but has not been well-tested for metazoans, probably due to the difficulty of raising experimental populations to equilibrium and measuring population growth rates for species with long or complex life cycles. We developed an index (R(index)) of R* based on demography of one insect cohort, growing from egg to adult in a non-equilibrium setting, and tested whether R(index) yielded accurate predictions of competitive abilities using mosquitoes as a model system. We estimated finite rate of increase (λ') from demographic data for cohorts of three mosquito species raised with different detritus amounts, and estimated each species' R(index) using nonlinear regressions of λ' vs. initial detritus amount. All three species' R(index) differed significantly, and accurately predicted competitive hierarchy of the species determined in simultaneous pairwise competition experiments. Our R(index) could provide estimates and rigorous statistical comparisons of competitive ability for organisms for which typical chemostat methods and equilibrium population conditions are impractical.}, } @article {pmid22954650, year = {2012}, author = {Fernández-Borges, N and Chianini, F and Eraña, H and Vidal, E and Eaton, SL and Pintado, B and Finlayson, J and Dagleish, MP and Castilla, J}, title = {Naturally prion resistant mammals: a utopia?.}, journal = {Prion}, volume = {6}, number = {5}, pages = {425-429}, pmid = {22954650}, issn = {1933-690X}, mesh = {Animals ; Disease Resistance ; Mice ; PrPSc Proteins/metabolism/*pathogenicity ; Prion Diseases/*metabolism ; Protein Folding ; Rabbits ; Species Specificity ; }, abstract = {Each known abnormal prion protein (PrP (Sc)) is considered to have a specific range and therefore the ability to infect some species and not others. Consequently, some species have been assumed to be prion disease resistant as no successful natural or experimental challenge infections have been reported. This assumption suggested that, independent of the virulence of the PrP (Sc) strain, normal prion protein (PrP (C)) from these 'resistant' species could not be induced to misfold. Numerous in vitro and in vivo studies trying to corroborate the unique properties of PrP (Sc) have been undertaken. The results presented in the article "Rabbits are not resistant to prion infection" demonstrated that normal rabbit PrP (C) , which was considered to be resistant to prion disease, can be misfolded to PrP (Sc) and subsequently used to infect and transmit a standard prion disease to leporids. Using the concept of species resistance to prion disease, we will discuss the mistake of attributing species specific prion disease resistance based purely on the absence of natural cases and incomplete in vivo challenges. The BSE epidemic was partially due to an underestimation of species barriers. To repeat this error would be unacceptable, especially if present knowledge and techniques can show a theoretical risk. Now that the myth of prion disease resistance has been refuted it is time to re-evaluate, using the new powerful tools available in modern prion laboratories, whether any other species could be at risk.}, } @article {pmid22937005, year = {2012}, author = {Hawlitschek, O and Nagy, ZT and Glaw, F}, title = {Island evolution and systematic revision of Comoran snakes: why and when subspecies still make sense.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42970}, pmid = {22937005}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Haplotypes ; Islands ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Snakes/*classification/*genetics ; }, abstract = {Species delimitation and species concepts have been a matter of debate among biodiversity researchers in the last decades, resulting in integrative taxonomy approaches and the use of modern species concepts, such as the phylogenetic, evolutionary or general lineage species concepts. The discussion of subspecies status and concepts has been addressed much less extensively, with some researchers completely refraining from recognizing subspecies. However, allopatric insular populations that are particularly differentiated have traditionally been assigned subspecies status. We studied the molecular phylogeny and morphology of endemic Comoran tree snakes of the genus Lycodryas. Taking an integrative taxonomic approach, we used the concept of independent lines of evidence to discriminate between evidence for specific and subspecific status. Molecular (mtDNA) and morphological data provided sufficient evidence to support four different taxa within Comoran Lycodryas. In a revision of this group, we propose two species, each with two subspecies. We present a discussion of the strong sexual dichromatism unique to Comoran Lycodryas within the genus and related genera that may be explained by sexual selection in combination with the absence of major predators. Then, we discuss the effects of insular evolution and the "island rule" on morphological traits in Comoran Lycodryas and in Liophidium mayottensis, another snake endemic to the Comoros. The absence of larger-bodied snakes may have promoted an increase in body size and the number of dorsal scale rows in these species. Finally, we discuss the subspecies concept, its applications and its significance for integrative taxonomy and for limiting taxonomic inflation. We emphasize that taxon descriptions should be based on an integrative approach using several lines of evidence, preferably in combination with statements on the underlying species concepts or operational criteria, to increase the objectivity and comparability of descriptions.}, } @article {pmid22879889, year = {2012}, author = {Tiemann, I and Rehkämper, G}, title = {Evolutionary pets: offspring numbers reveal speciation process in domesticated chickens.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e41453}, pmid = {22879889}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; Breeding ; Chickens/*genetics ; Female ; Fertilization ; *Genetic Speciation ; Humans ; Litter Size/*genetics ; Male ; Pets/*genetics ; }, abstract = {Since Darwin, the nature of the relationship between evolution and domestication has been debated. Evolution offers different mechanisms of selection that lead to adaptation and may end in the origin of new species as defined by the biological species concept. Domestication has given rise to numerous breeds in almost every domesticated species, including chickens. At the same time, so-called artificial selection seems to exclude mechanisms of sexual selection by the animals themselves. We want to forward the question to the animal itself: With whom do you reproduce successfully? This study focused on the sexual behavior of the domestic chicken Gallus gallus f.dom., particularly the White Crested Polish breed. Experiments on mate choice and the observation of fertilization and hatching rates of mixed-breeding groups revealed breed-specific preferences. In breeding groups containing White Crested Polish and a comparative breed, more purebred chicks hatched than hybrids (number of eggs collected: 1059). Mating was possible in equal shares, but in relation to the number of eggs collected, purebred offspring (62.75% ± 7.10%, M ± SE) hatched to a greater extend compared to hybrid offspring (28.75% ± 15.32%, M ± SE). These data demonstrate that the mechanism of sexual selection is still present in domestic chicken breeds, which includes the alteration of gene frequencies typical for domestication and evolutionary speciation. Due to selection and mate choice we state that breeding in principle can generate new species. Therefore, we see domestication as an evolutionary process that integrates human interests of animal breeding with innate mate choice by the animal.}, } @article {pmid22877610, year = {2012}, author = {Stat, M and Baker, AC and Bourne, DG and Correa, AM and Forsman, Z and Huggett, MJ and Pochon, X and Skillings, D and Toonen, RJ and van Oppen, MJ and Gates, RD}, title = {Molecular delineation of species in the coral holobiont.}, journal = {Advances in marine biology}, volume = {63}, number = {}, pages = {1-65}, doi = {10.1016/B978-0-12-394282-1.00001-6}, pmid = {22877610}, issn = {0065-2881}, mesh = {Animals ; Anthozoa/*classification/genetics/*physiology ; *Biodiversity ; Climate Change ; *Coral Reefs ; *Genetic Speciation ; }, abstract = {The coral holobiont is a complex assemblage of organisms spanning a diverse taxonomic range including a cnidarian host, as well as various dinoflagellate, prokaryotic and acellular symbionts. With the accumulating information on the molecular diversity of these groups, binomial species classification and a reassessment of species boundaries for the partners in the coral holobiont is a logical extension of this work and will help enhance the capacity for comparative research among studies. To aid in this endeavour, we review the current literature on species diversity for the three best studied partners of the coral holobiont (coral, Symbiodinium, prokaryotes) and provide suggestions for future work on systematics within these taxa. We advocate for an integrative approach to the delineation of species using both molecular genetics in combination with phenetic characters. We also suggest that an a priori set of criteria be developed for each taxonomic group as no one species concept or accompanying set of guidelines is appropriate for delineating all members of the coral holobiont.}, } @article {pmid24436197, year = {2012}, author = {Groves, C}, title = {Species concept in primates.}, journal = {American journal of primatology}, volume = {74}, number = {8}, pages = {687-691}, doi = {10.1002/ajp.22035}, pmid = {24436197}, issn = {1098-2345}, mesh = {Animals ; Biological Evolution ; *Phylogeny ; Primates/*classification/genetics ; *Reproductive Isolation ; Species Specificity ; }, abstract = {The way we view the Species category in Primates, as in other animals, especially other vertebrates, has been going through a revolution over the past 20 years or so. Much is wrong with the idea that we can define species according to whether or not they are "reproductively isolated": this concept, the so-called Biological Species Concept, has never offered any guidelines in the case of allopatric populations; this has now been shown to be simply wrong. Although other ways of looking at species - the Evolutionary, Recognition, Cohesion and Genetic Species Concepts - have all provided particular insights, the only proposal to offer a repeatable, falsifiable definition of species is the Phylogenetic Species Concept. This has been criticised for increasing the number of species to be recognised, although it is not clear why this should be a problem: indeed, it tells us that the world is far richer in biodiversity than we had conceived.}, } @article {pmid22848349, year = {2012}, author = {Moreno, E}, title = {Design and construction of "synthetic species".}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e39054}, pmid = {22848349}, issn = {1932-6203}, mesh = {Animals ; *Animals, Genetically Modified ; Drosophila melanogaster ; Genetic Engineering/methods/*trends ; Synthetic Biology/methods/*trends ; }, abstract = {Synthetic biology is an area of biological research that combines science and engineering. Here, I merge the principles of synthetic biology and regulatory evolution to create a new species with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfils the criteria of a new species according to Mayr's Biological Species Concept. The population described here is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other identical transgenic animals. I therefore propose the term "synthetic species" to distinguish it from "natural species", not only because it has been created by genetic manipulation, but also because it may never be able to survive outside the laboratory environment. The use of genetic engineering to design artificial species barriers could help us understand natural speciation and may have practical applications. For instance, the transition from transgenic organisms towards synthetic species could constitute a safety mechanism to avoid the hybridization of genetically modified animals with wild type populations, preserving biodiversity.}, } @article {pmid22834317, year = {2012}, author = {Gelashvili, DB and Iudin, DI and Iakimov, VN and Solntsev, LA and Rozenberg, GS and Shurganova, GV and Okhapkin, AG and Startseva, NA and Pukhnarevich, DA and Snegireva, MS}, title = {[Multifractal analysis of the species structure of freshwater hydrobiocenoses].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {3}, pages = {327-335}, pmid = {22834317}, issn = {1026-3470}, mesh = {Algorithms ; *Biota ; Ecosystem ; *Fractals ; *Fresh Water ; *Models, Biological ; *Models, Theoretical ; }, abstract = {The principles and methods of fractal analysis of the species structure of freshwater phytoplankton, zooplankton, and macrozoobenthos communities of plain water reservoirs and urban waterbodies are discussed. The theoretical foundation and experimental verification are provided for the authors' concept of self-similar (quasi-fractal) nature of the species structure of communities. According to this concept, the adequate mathematical image of species richness accumulation with growing sampling effort is quasi-monofractals, while the generalized geometric image of the species structure of the community is a multifractal spectrum.}, } @article {pmid22834165, year = {2012}, author = {Poplavskaia, NS and Lebedev, VS and Bannikova, AA and Meshcherskiĭ, IG and Surov, AV}, title = {[Karyotypes divergence in superspecies complex Cricetulus barabensis sensu lato and their interrelationships in natural contact zones].}, journal = {Zhurnal obshchei biologii}, volume = {73}, number = {3}, pages = {183-197}, pmid = {22834165}, issn = {0044-4596}, mesh = {Animals ; Biological Evolution ; Chromosome Aberrations ; Cricetinae ; Cricetulus/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Female ; Gene Flow ; Genetics, Population ; Hybridization, Genetic/*genetics ; *Karyotype ; Karyotyping/methods ; Male ; Phylogeny ; Species Specificity ; }, abstract = {Interrelationships between three chromosomal forms of striped hamsters belonging to the superspecies complex Cricetulus barabensis sensu lato (Cricetidae, Rodentia), namely 'barabensis', 'pseudogriseus', and 'griseus', are examined from the standpoint of different biological/genetic species concepts. Craniometric data suggest that differences between the karyotypes are rather of subspecies level. Cytogenetic differences between the karyotypes are also not great and correspond to the level of chromosomal races within a single species. The analysis of mitochondrial gene for cytochrome b (cytb) indicates the level of differences between forms of about 2.3-4.1%. Such a level may correspond to intraspecific differences as well as to differences between allied species. Experiments on hybridization resulted in hybrid litters obtained in different mating combinations of karyotypes. Both hybrid males and females fertility was confirmed, too. In nature, there exist several zones where contact between karyotypes 'barabensis' and 'pseudogriseus' is possible. Within one of such zones, in Central Mongolia, two males with atypical karyotype were detected by use of chromosome analysis. With chromosomes number and form, this karyotype may correspond to the hybrid between second and subsequent generations. However, typing of gene cytb and the intron localized in Y-chromosome (DBY1) did not reveal any traces of recent or ancient hybridization. In the other zone where contact between the karyotypes is possible, in South Buryatia, 'barabensis' and 'pseudogriseus' populations are separated by the River Chika and the distance between them does not exceed 5 km. Nevertheless, no hamsters with non-standard karyotypes and no traces of gene flow are detected by karyological and molecular analyses of these populations. The results of Tajima's test, analysis of pairwise differences distribution and indices of nucleotide diversity obtained in the course of examining gene cytb full nucleotide sequence all suggest that both contact zones studied have formed long ago and the absence of gene flow cannot be explained by their forming in the recent past. Thus, the karyotypes studied appear to be evolutionary lines developing independently from each other.}, } @article {pmid22832347, year = {2012}, author = {Materna, AC and Friedman, J and Bauer, C and David, C and Chen, S and Huang, IB and Gillens, A and Clarke, SA and Polz, MF and Alm, EJ}, title = {Shape and evolution of the fundamental niche in marine Vibrio.}, journal = {The ISME journal}, volume = {6}, number = {12}, pages = {2168-2177}, pmid = {22832347}, issn = {1751-7370}, mesh = {*Biological Evolution ; Ecology/methods ; *Ecosystem ; *Models, Biological ; Phylogeny ; Salinity ; Temperature ; Vibrio/classification/growth & development/*physiology ; }, abstract = {Hutchinson's fundamental niche, defined by the physical and biological environments in which an organism can thrive in the absence of inter-species interactions, is an important theoretical concept in ecology. However, little is known about the overlap between the fundamental niche and the set of conditions species inhabit in nature, and about natural variation in fundamental niche shape and its change as species adapt to their environment. Here, we develop a custom-made dual gradient apparatus to map a cross-section of the fundamental niche for several marine bacterial species within the genus Vibrio based on their temperature and salinity tolerance, and compare tolerance limits to the environment where these species commonly occur. We interpret these niche shapes in light of a conceptual model comprising five basic niche shapes. We find that the fundamental niche encompasses a much wider set of conditions than those strains typically inhabit, especially for salinity. Moreover, though the conditions that strains typically inhabit agree well with the strains' temperature tolerance, they are negatively correlated with the strains' salinity tolerance. Such relationships can arise when the physiological response to different stressors is coupled, and we present evidence for such a coupling between temperature and salinity tolerance. Finally, comparison with well-documented ecological range in V. vulnificus suggests that biotic interactions limit the occurrence of this species at low-temperature-high-salinity conditions. Our findings highlight the complex interplay between the ecological, physiological and evolutionary determinants of niche morphology, and caution against making inferences based on a single ecological factor.}, } @article {pmid22821567, year = {2012}, author = {Namiki, T and Hachiya, T and Tanaka, H and Sakakibara, Y}, title = {MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.}, journal = {Nucleic acids research}, volume = {40}, number = {20}, pages = {e155}, pmid = {22821567}, issn = {1362-4962}, mesh = {Algorithms ; Bacteria/classification ; Gastrointestinal Tract/microbiology ; Genome, Bacterial ; Humans ; Metagenomics/*methods ; *Sequence Analysis, DNA ; Software ; }, abstract = {An important step in 'metagenomics' analysis is the assembly of multiple genomes from mixed sequence reads of multiple species in a microbial community. Most conventional pipelines use a single-genome assembler with carefully optimized parameters. A limitation of a single-genome assembler for de novo metagenome assembly is that sequences of highly abundant species are likely misidentified as repeats in a single genome, resulting in a number of small fragmented scaffolds. We extended a single-genome assembler for short reads, known as 'Velvet', to metagenome assembly, which we called 'MetaVelvet', for mixed short reads of multiple species. Our fundamental concept was to first decompose a de Bruijn graph constructed from mixed short reads into individual sub-graphs, and second, to build scaffolds based on each decomposed de Bruijn sub-graph as an isolate species genome. We made use of two features, the coverage (abundance) difference and graph connectivity, for the decomposition of the de Bruijn graph. For simulated datasets, MetaVelvet succeeded in generating significantly higher N50 scores than any single-genome assemblers. MetaVelvet also reconstructed relatively low-coverage genome sequences as scaffolds. On real datasets of human gut microbial read data, MetaVelvet produced longer scaffolds and increased the number of predicted genes.}, } @article {pmid22815589, year = {2012}, author = {Bensch, K and Braun, U and Groenewald, JZ and Crous, PW}, title = {The genus Cladosporium.}, journal = {Studies in mycology}, volume = {72}, number = {1}, pages = {1-401}, pmid = {22815589}, issn = {1872-9797}, abstract = {UNLABELLED: A monographic revision of the hyphomycete genus Cladosporium s. lat. (Cladosporiaceae, Capnodiales) is presented. It includes a detailed historic overview of Cladosporium and allied genera, with notes on their phylogeny, systematics and ecology. True species of Cladosporium s. str. (anamorphs of Davidiella), are characterised by having coronate conidiogenous loci and conidial hila, i.e., with a convex central dome surrounded by a raised periclinal rim. Recognised species are treated and illustrated with line drawings and photomicrographs (light as well as scanning electron microscopy). Species known from culture are described in vivo as well as in vitro on standardised media and under controlled conditions. Details on host range/substrates and the geographic distribution are given based on published accounts, and a re-examination of numerous herbarium specimens. Various keys are provided to support the identification of Cladosporium species in vivo and in vitro. Morphological datasets are supplemented by DNA barcodes (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-α gene sequences) diagnostic for individual species. In total 993 names assigned to Cladosporium s. lat., including Heterosporium (854 in Cladosporium and 139 in Heterosporium), are treated, of which 169 are recognized in Cladosporium s. str. The other taxa are doubtful, insufficiently known or have been excluded from Cladosporium in its current circumscription and re-allocated to other genera by the authors of this monograph or previous authors.

TAXONOMIC NOVELTIES: Cladosporium allicinum (Fr.: Fr.) Bensch, U. Braun & Crous, comb. nov., C. astroideum var. catalinense U. Braun, var. nov., Fusicladium tectonicola (Yong H. He & Z.Y. Zhang) U. Braun & Bensch, comb. nov., Septoidium uleanum (Henn.) U. Braun, comb. nov., Zasmidium adeniae (Hansf.) U. Braun, comb. nov., Zasmidium dianellae (Sawada & Katsuki) U. Braun, comb. nov., Zasmidium lythri (Westend.) U. Braun & H.D. Shin, comb. nov., Zasmidium wikstroemiae (Petch) U. Braun, comb. nov.}, } @article {pmid22802945, year = {2012}, author = {Schön, I and Pinto, RL and Halse, S and Smith, AJ and Martens, K and Birky, CW}, title = {Cryptic species in putative ancient asexual darwinulids (Crustacea, Ostracoda).}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e39844}, pmid = {22802945}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Crustacea/classification/*genetics ; DNA, Mitochondrial/chemistry ; Electron Transport Complex I/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; Phylogeny ; Reproduction, Asexual/*genetics ; }, abstract = {BACKGROUND: Fully asexually reproducing taxa lack outcrossing. Hence, the classic Biological Species Concept cannot be applied.

We used DNA sequences from the mitochondrial COI gene and the nuclear ITS2 region to check species boundaries according to the evolutionary genetic (EG) species concept in five morphospecies in the putative ancient asexual ostracod genera, Penthesilenula and Darwinula, from different continents. We applied two methods for detecting cryptic species, namely the K/θ method and the General Mixed Yule Coalescent model (GMYC). We could confirm the existence of species in all five darwinulid morphospecies and additional cryptic diversity in three morphospecies, namely in Penthesilenula brasiliensis, Darwinula stevensoni and in P. aotearoa. The number of cryptic species within one morphospecies varied between seven (P. brasiliensis), five to six (D. stevensoni) and two (P. aotearoa), respectively, depending on the method used. Cryptic species mainly followed continental distributions. We also found evidence for coexistence at the local scale for Brazilian cryptic species of P. brasiliensis and P. aotearoa. Our ITS2 data confirmed that species exist in darwinulids but detected far less EG species, namely two to three cryptic species in P. brasiliensis and no cryptic species at all in the other darwinulid morphospecies.

CONCLUSIONS/SIGNIFICANCE: Our results clearly demonstrate that both species and cryptic diversity can be recognized in putative ancient asexual ostracods using the EG species concept, and that COI data are more suitable than ITS2 for this purpose. The discovery of up to eight cryptic species within a single morphospecies will significantly increase estimates of biodiversity in this asexual ostracod group. Which factors, other than long-term geographic isolation, are important for speciation processes in these ancient asexuals remains to be investigated.}, } @article {pmid22768317, year = {2012}, author = {Mazzuoli, G and Schemann, M}, title = {Mechanosensitive enteric neurons in the myenteric plexus of the mouse intestine.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e39887}, pmid = {22768317}, issn = {1932-6203}, mesh = {Animals ; Colon/innervation/physiology ; Ileum/innervation/physiology ; Mechanoreceptors/*physiology ; Mechanotransduction, Cellular/*physiology ; Mice ; Myenteric Plexus/*physiology ; Neurons/*physiology ; }, abstract = {BACKGROUND: Within the gut the autonomous enteric nervous system (ENS) is able to sense mechanical stimuli and to trigger gut reflex behaviour. We previously proposed a novel sensory circuit in the ENS which consists of multifunctional rapidly adapting mechanosensitive enteric neurons (RAMEN) in the guinea pig. The aim of this study was to validate this concept by studying its applicability to other species or gut regions.

We deformed myenteric ganglia in the mouse small and large intestine and recorded spike discharge using voltage sensitive dye imaging. We also analysed expression of markers hitherto proposed to label mouse sensory myenteric neurons in the ileum (NF145kD) or colon (calretinin). RAMEN constituted 22% and 15% of myenteric neurons per ganglion in the ileum and colon, respectively. They encoded dynamic rather than sustained deformation. In the colon, 7% of mechanosensitive neurons fired throughout the sustained deformation, a behaviour typical for slowly adapting echanosensitive neurons (SAMEN). RAMEN and SAMEN responded directly to mechanical deformation as their response remained unchanged after synaptic blockade in low Ca(++)/high Mg(++). Activity levels of RAMEN increased with the degree of ganglion deformation. Recruitment of more RAMEN with stronger stimuli may suggest low and high threshold RAMEN. The majority of RAMEN were cholinergic but most lacked expression of NF145kD or calretinin.

CONCLUSIONS/SIGNIFICANCE: We showed for the first time that fundamental properties of mechanosensitive enteric neurons, such as firing pattern, encoding of dynamic deformation, cholinergic phenotype and their proportion, are conserved across species and regions. We conclude that RAMEN are important for mechanotransduction in the ENS. They directly encode dynamic changes in force as their firing frequency is proportional to the degree of deformation of the ganglion they reside in. The additional existence of SAMEN in the colon is likely an adaptation to colonic motor patterns which consist of phasic and tonic contractions.}, } @article {pmid22759297, year = {2012}, author = {Borregaard, MK and Gotelli, NJ and Rahbek, C}, title = {Are range-size distributions consistent with species-level heritability?.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {7}, pages = {2216-2226}, doi = {10.1111/j.1558-5646.2012.01581.x}, pmid = {22759297}, issn = {1558-5646}, mesh = {Animals ; *Biological Evolution ; Birds/classification/*physiology ; *Ecosystem ; Geography ; *Models, Biological ; Phylogeny ; Population Dynamics ; South America ; Species Specificity ; Stochastic Processes ; }, abstract = {The concept of species-level heritability is widely contested. Because it is most likely to apply to emergent, species-level traits, one of the central discussions has focused on the potential heritability of geographic range size. However, a central argument against range-size heritability has been that it is not compatible with the observed shape of present-day species range-size distributions (SRDs), a claim that has never been tested. To assess this claim, we used forward simulation of range-size evolution in clades with varying degrees of range-size heritability, and compared the output of three different models to the range-size distribution of the South American avifauna. Although there were differences among the models, a moderate-to-high degree of range-size heritability consistently leads to SRDs that were similar to empirical data. These results suggest that range-size heritability can generate realistic SRDs, and may play an important role in shaping observed patterns of range sizes.}, } @article {pmid22737234, year = {2012}, author = {El Fatimy, R and Tremblay, S and Dury, AY and Solomon, S and De Koninck, P and Schrader, JW and Khandjian, EW}, title = {Fragile X mental retardation protein interacts with the RNA-binding protein Caprin1 in neuronal RiboNucleoProtein complexes [corrected].}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e39338}, pmid = {22737234}, issn = {1932-6203}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Amino Acid Motifs ; Animals ; Antibodies, Monoclonal/chemistry ; Base Sequence ; Brain/metabolism ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism ; Cell Cycle Proteins/*metabolism ; DNA Primers/genetics ; Fragile X Mental Retardation Protein/*metabolism ; HeLa Cells ; Humans ; Immunoprecipitation ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Microtubule-Associated Proteins/metabolism ; Molecular Sequence Data ; NIH 3T3 Cells ; Neurons/*metabolism ; Polyribosomes/metabolism ; Protein Binding ; Protein Biosynthesis ; RNA-Binding Proteins/*metabolism ; Ribonucleoproteins/*chemistry ; }, abstract = {Fragile X syndrome is caused by the absence of the Fragile X Mental Retardation Protein (FMRP), an RNA-binding protein. FMRP is associated with messenger RiboNucleoParticles (mRNPs) present in polyribosomes and its absence in neurons leads to alteration in synaptic plasticity as a result of translation regulation defects. The molecular mechanisms by which FMRP plays a role in translation regulation remain elusive. Using immunoprecipitation approaches with monoclonal Ab7G1-1 and a new generation of chicken antibodies, we identified Caprin1 as a novel FMRP-cellular partner. In vivo and in vitro evidence show that Caprin1 interacts with FMRP at the level of the translation machinery as well as in trafficking neuronal granules. As an RNA-binding protein, Caprin1 has in common with FMRP at least two RNA targets that have been identified as CaMKIIα and Map1b mRNAs. In view of the new concept that FMRP species bind to RNA regardless of known structural motifs, we propose that protein interactors might modulate FMRP functions.}, } @article {pmid22727018, year = {2012}, author = {Willis, SC and Macrander, J and Farias, IP and Ortí, G}, title = {Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus cichla) using multi-locus data.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {96}, pmid = {22727018}, issn = {1471-2148}, mesh = {Animals ; Cell Nucleus/*genetics ; Cichlids/anatomy & histology/classification/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Evolution, Molecular ; Female ; Fish Proteins/genetics ; Genetic Variation ; Geography ; Haplotypes ; *Hybridization, Genetic ; Male ; Microsatellite Repeats/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; South America ; Species Specificity ; }, abstract = {BACKGROUND: Introgression likely plays a significant role in evolution, but understanding the extent and consequences of this process requires a clear identification of species boundaries in each focal group. The delimitation of species, however, is a contentious endeavor. This is true not only because of the inadequacy of current tools to identify species lineages, but also because of the inherent ambiguity between natural populations and species paradigms. The result has been a debate about the supremacy of various species concepts and criteria. Here, we utilized multiple separate sources of molecular data, mtDNA, nuclear sequences, and microsatellites, to delimit species under a polytypic species concept (PTSC) and estimate the frequency and genomic extent of introgression in a Neotropical genus of cichlid fishes (Cichla). We compared our inferences of species boundaries and introgression under this paradigm to those when species are identified under a diagnostic species concept (DSC).

RESULTS: We find that, based on extensive molecular data and an inclusive species concept, 8 separate biological entities should be recognized rather than the 15 described species of Cichla. Under the PTSC, fewer individuals are expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but a similar number of the species exhibit introgression from at least one other species (75% vs. 60%). Under either species concept, the phylogenetic breadth of introgression in this group is notable, with both sister species and species from different major mtDNA clades exhibiting introgression.

CONCLUSIONS: Introgression was observed to be a widespread phenomenon for delimited species in this group. While several instances of introgressive hybridization were observed in anthropogenically altered habitats, most were found in undisturbed natural habitats, suggesting that introgression is a natural but ephemeral part of the evolution of many tropical species. Nevertheless, even transient introgression may facilitate an increase in genetic diversity or transfer of adaptive mutations that have important consequences in the evolution of tropical biodiversity.}, } @article {pmid22713467, year = {2012}, author = {Muehlfelder, M and Arias-Loza, PA and Fritzemeier, KH and Pelzer, T}, title = {Both estrogen receptor subtypes, ERα and ERβ, prevent aldosterone-induced oxidative stress in VSMC via increased NADPH bioavailability.}, journal = {Biochemical and biophysical research communications}, volume = {423}, number = {4}, pages = {850-856}, doi = {10.1016/j.bbrc.2012.06.053}, pmid = {22713467}, issn = {1090-2104}, mesh = {Aldosterone/pharmacology/*physiology ; Animals ; Biological Availability ; Cells, Cultured ; Estrogen Receptor alpha/agonists/antagonists & inhibitors/*physiology ; Estrogen Receptor beta/agonists/antagonists & inhibitors/*physiology ; Female ; Glucosephosphate Dehydrogenase/metabolism ; Muscle, Smooth, Vascular/metabolism/*physiology ; Myocytes, Smooth Muscle/metabolism/*physiology ; NADP/*metabolism ; *Oxidative Stress ; Phosphoproteins/metabolism ; Rats ; Rats, Inbred WKY ; Reactive Oxygen Species/metabolism ; }, abstract = {Activation of vascular mineralocorticoid (MR) or estrogen receptors (ER) exerts opposing effects on vascular remodeling. As we have previously shown, activation of either estrogen receptor subtype, ERα or ERβ, is fully sufficient to attenuate vascular remodeling in aldosterone salt-treated rats. To further elucidate the underlying mechanism(s) we tested the hypothesis that ER and MR activation might differentially modulate vascular reactive oxygen species (ROS) generation. In support of this concept, aldosterone increased ROS generation in vascular smooth muscle cells as determined by quantitative dihydroethidium fluorescence microscopy. Co-treatment with the selective ERα agonist 16α-LE2, the selective ERβ agonist 8β-VE2 or the non-selective ER agonist 17β-estradiol (E2) significantly reduced aldosterone-induced ROS generation. The pure ER antagonist ICI 182,780 completely blocked these salutary effects of E2, 16α-LE2 and 8β-VE2. Activation of ERα or ERβ fully blocked the reduction of intracellular nicotinamide adenine dinucleotide phosphate (NADPH) levels observed in aldosterone treated vascular smooth muscle cells. Intracellular NADPH levels were closely associated with expression and activity of the NADPH generating enzyme glucose-6-phosphate dehydrogenase. In conclusion, estrogens attenuate the detrimental vascular effects of excessive MR activation at least in part by preventing the depletion of intracellular NADPH levels.}, } @article {pmid22682185, year = {2012}, author = {Vera-Cabrera, L and Salinas-Carmona, MC and Waksman, N and Messeguer-Pérez, J and Ocampo-Candiani, J and Welsh, O}, title = {Host defenses in subcutaneous mycoses.}, journal = {Clinics in dermatology}, volume = {30}, number = {4}, pages = {382-388}, doi = {10.1016/j.clindermatol.2011.09.008}, pmid = {22682185}, issn = {1879-1131}, mesh = {Antifungal Agents/*therapeutic use ; Chromoblastomycosis/drug therapy/etiology ; Communicable Diseases/*drug therapy/etiology ; Humans ; Immunologic Factors/*therapeutic use ; Mycetoma/drug therapy/etiology ; Mycoses/*drug therapy/etiology/immunology ; Rural Health ; Sporotrichosis/drug therapy/etiology ; Subcutaneous Tissue/immunology/*microbiology ; }, abstract = {Subcutaneous mycoses include diverse clinical syndromes, characterized by invasion of the skin and subcutaneous tissue by saprobic fungi. Individuals living in rural areas constantly suffer lesions or trauma; however, only a few of them develop disease. In this contribution, we describe recent advances in the understanding of the virulence of these organisms, focusing on the most prevalent infections, sporotrichosis, chromoblastomycosis, and mycetoma. Although these infectious diseases are considered neglected tropical diseases, modern molecular techniques have been able to identify the etiologic agents and observe variations in the former monolithic concept of the species, which was based mostly on morphologic characteristics. The complete genetic characterization of the causative agents, along with that of their host, will help in the understanding of the factors on which the development of these infections depends.}, } @article {pmid22674415, year = {2012}, author = {Noor-Mohammadi, S and Pourmir, A and Johannes, TW}, title = {Method to assemble and integrate biochemical pathways into the chloroplast genome of Chlamydomonas reinhardtii.}, journal = {Biotechnology and bioengineering}, volume = {109}, number = {11}, pages = {2896-2903}, doi = {10.1002/bit.24569}, pmid = {22674415}, issn = {1097-0290}, mesh = {Acid Phosphatase/analysis/genetics ; Carboxylic Ester Hydrolases/analysis/genetics ; Chlamydomonas reinhardtii/*genetics/*metabolism ; Gene Expression Profiling ; Genes, Reporter ; *Genome, Chloroplast ; Green Fluorescent Proteins/analysis/genetics ; Metabolic Engineering/*methods ; Metabolic Networks and Pathways/*genetics ; RNA, Messenger/analysis/genetics ; Saccharomyces cerevisiae/genetics ; }, abstract = {Recombinant protein expression in the chloroplasts of green algae has recently become more routine; however, the heterologous expression of multiple proteins or complete biosynthetic pathways remains a significant challenge. Here, we show that a modified DNA Assembler approach can be used to rapidly assemble multiple-gene biosynthetic pathways in yeast and then integrate these assembled pathways at a site-specific location in the chloroplast genome of the microalgal species Chlamydomonas reinhardtii. As a proof of concept, this method was used to successfully integrate and functionally express up to three reporter proteins (AphA6, AadA, and GFP) in the chloroplast of C. reinhardtii. An analysis of the relative gene expression of the engineered strains showed significant differences in the mRNA expression levels of the reporter genes and thus highlights the importance of proper promoter/untranslated region selection when constructing a target pathway. This new method represents a useful genetic tool in the construction and integration of complex biochemical pathways into the chloroplast genome of microalgae and should aid current efforts to engineer algae for biofuels production and other desirable natural products.}, } @article {pmid22666447, year = {2012}, author = {Webb, JM and Jacobus, LM and Funk, DH and Zhou, X and Kondratieff, B and Geraci, CJ and DeWalt, RE and Baird, DJ and Richard, B and Phillips, I and Hebert, PD}, title = {A DNA barcode library for North American Ephemeroptera: progress and prospects.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e38063}, pmid = {22666447}, issn = {1932-6203}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Female ; Insecta/*classification/growth & development ; Life Cycle Stages ; Male ; North America ; Species Specificity ; }, abstract = {DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 nominal and 90 provisional species of mayflies (Insecta: Ephemeroptera) from Canada, Mexico, and the United States. No species shared barcode sequences and all can be identified with barcodes with the possible exception of some Caenis. Minimum interspecific distances ranged from 0.3-24.7% (mean: 12.5%), while the average intraspecific divergence was 1.97%. The latter value was inflated by the presence of very high divergences in some taxa. In fact, nearly 20% of the species included two or three haplotype clusters showing greater than 5.0% sequence divergence and some values are as high as 26.7%. Many of the species with high divergences are polyphyletic and likely represent species complexes. Indeed, many of these polyphyletic species have numerous synonyms and individuals in some barcode clusters show morphological attributes characteristic of the synonymized species. In light of our findings, it is imperative that type or topotype specimens be sequenced to correctly associate barcode clusters with morphological species concepts and to determine the status of currently synonymized species.}, } @article {pmid22639145, year = {2012}, author = {Peterson, SW}, title = {Aspergillus and Penicillium identification using DNA sequences: barcode or MLST?.}, journal = {Applied microbiology and biotechnology}, volume = {95}, number = {2}, pages = {339-344}, doi = {10.1007/s00253-012-4165-2}, pmid = {22639145}, issn = {1432-0614}, mesh = {Aspergillus/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Fungal/*chemistry/genetics ; Multilocus Sequence Typing/*methods ; Penicillium/*classification/*genetics ; }, abstract = {Current methods in DNA technology can detect single nucleotide polymorphisms with measurable accuracy using several different approaches appropriate for different uses. If there are even single nucleotide differences that are invariant markers of the species, we can accomplish identification through rapid DNA-based tests. The question of whether we can reliably detect and identify species of Aspergillus and Penicillium turns mainly upon the completeness of our alpha taxonomy, our species concepts, and how well the available DNA data coincide with the taxonomic diversity in the family Trichocomaceae. No single gene is yet known that is invariant within species and variable between species as would be optimal for the barcode approach. Data are published that would make an MLST approach to isolate identification possible in the most well-studied clades of Aspergillus and Penicillium.}, } @article {pmid22605529, year = {2012}, author = {Rosenberger, AL}, title = {New world monkey nightmares: science, art, use, and abuse (?) in platyrrhine taxonomic nomenclature.}, journal = {American journal of primatology}, volume = {74}, number = {8}, pages = {692-695}, doi = {10.1002/ajp.22037}, pmid = {22605529}, issn = {1098-2345}, mesh = {Animals ; Biological Evolution ; Classification/methods ; *Phylogeny ; Platyrrhini/*classification ; Terminology as Topic ; }, abstract = {The taxonomy and nomenclature of New World monkeys is becoming precariously unstable and impractical, plagued by revisions aimed at conforming to approaches that reject the Biological Species Concept for narrowly construed reasons and resulting in a hyperinflated taxonomy at species (often) and genus (sometimes) levels. This undermines a major goal of classification at the most basic taxonomic levels to ease communication and facilitate research. Since it is difficult to justify extensive changes in terminology without a deeply justified theoretical purpose or without showing what scientific benefits these alterations can bring, working primatologists need not accept this doctrinaire trend. Knowing as little as we do about what a species actually is, does not justify contorting the value of a species nomenclature so that it reflects nothing more than coat color, a node, or endpoint of a dendrogram.}, } @article {pmid22575840, year = {2012}, author = {Mendelson, TC and Shaw, KL}, title = {The (mis)concept of species recognition.}, journal = {Trends in ecology & evolution}, volume = {27}, number = {8}, pages = {421-427}, doi = {10.1016/j.tree.2012.04.001}, pmid = {22575840}, issn = {1872-8383}, mesh = {Animals ; *Biological Evolution ; Female ; Genetic Speciation ; Male ; *Mating Preference, Animal ; Models, Biological ; Phenotype ; Reproductive Isolation ; }, abstract = {To many, the concept of 'species recognition' is integral to the origin and maintenance of species. However, the heuristic value of species recognition is hampered by its reliance on the problematic concept of species. In this paper, we first discuss assumptions associated with prevailing use of the term, including the typological implications of the concept, the false dichotomy of compatibility and mate quality, and the commonly held model of species recognition in which animals determine taxonomic status before mate status. Subsequently, we propose research directions aimed to improve our understanding of the role of courtship behavior in speciation. We propose two complementary research approaches, one addressing the processes that drive the evolution of mate recognition systems and the other addressing the phenotypic architecture of behavioral isolation. Our approach emphasizes the fitness consequences and multidimensional nature of mate choice.}, } @article {pmid22574681, year = {2012}, author = {Kahlke, T and Goesmann, A and Hjerde, E and Willassen, NP and Haugen, P}, title = {Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {179}, pmid = {22574681}, issn = {1471-2164}, mesh = {Adaptation, Biological/*genetics ; Cluster Analysis ; Databases, Genetic ; Gene Transfer, Horizontal ; *Genome, Bacterial ; Multigene Family ; Phylogeny ; Software ; Species Specificity ; Vibrionaceae/classification/*genetics ; }, abstract = {BACKGROUND: The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups.

RESULTS: The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin.

CONCLUSION: The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.}, } @article {pmid22559068, year = {2012}, author = {Genin, S and Denny, TP}, title = {Pathogenomics of the Ralstonia solanacearum species complex.}, journal = {Annual review of phytopathology}, volume = {50}, number = {}, pages = {67-89}, doi = {10.1146/annurev-phyto-081211-173000}, pmid = {22559068}, issn = {1545-2107}, mesh = {Biological Evolution ; Gene Regulatory Networks/*genetics ; Genes, Bacterial/genetics ; Genetic Speciation ; *Genetic Variation ; Genome, Bacterial/*genetics ; *Genomics ; Host Specificity/genetics ; Phylogeny ; Plant Diseases/*microbiology ; Ralstonia solanacearum/genetics/*pathogenicity ; Sequence Analysis, DNA ; Virulence/genetics ; }, abstract = {Ralstonia solanacearum is a major phytopathogen that attacks many crops and other plants over a broad geographical range. The extensive genetic diversity of strains responsible for the various bacterial wilt diseases has in recent years led to the concept of an R. solanacearum species complex. Genome sequencing of more than 10 strains representative of the main phylogenetic groups has broadened our knowledge of the evolution and speciation of this pathogen and led to the identification of novel virulence-associated functions. Comparative genomic analyses are now opening the way for refined functional studies. The many molecular determinants involved in pathogenicity and host-range specificity are described, and we also summarize current understanding of their roles in pathogenesis and how their expression is tightly controlled by an intricate virulence regulatory network.}, } @article {pmid22524202, year = {2012}, author = {Anwari, K and Webb, CT and Poggio, S and Perry, AJ and Belousoff, M and Celik, N and Ramm, G and Lovering, A and Sockett, RE and Smit, J and Jacobs-Wagner, C and Lithgow, T}, title = {The evolution of new lipoprotein subunits of the bacterial outer membrane BAM complex.}, journal = {Molecular microbiology}, volume = {84}, number = {5}, pages = {832-844}, pmid = {22524202}, issn = {1365-2958}, support = {R01 GM076698/GM/NIGMS NIH HHS/United States ; R01 GM065835-09/GM/NIGMS NIH HHS/United States ; GM065835/GM/NIGMS NIH HHS/United States ; R01 GM065835/GM/NIGMS NIH HHS/United States ; R01 GM076698-04/GM/NIGMS NIH HHS/United States ; GM076698/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Outer Membrane Proteins/*genetics ; DNA, Bacterial/genetics ; *Evolution, Molecular ; Genotype ; Lipoproteins/*genetics ; Protein Subunits/genetics ; Proteobacteria/*genetics ; }, abstract = {The β-barrel assembly machine (BAM) complex is an essential feature of all bacteria with an outer membrane. The core subunit of the BAM complex is BamA and, in Escherichia coli, four lipoprotein subunits: BamB, BamC, BamD and BamE, also function in the BAM complex. Hidden Markov model analysis was used to comprehensively assess the distribution of subunits of the BAM lipoproteins across all subclasses of proteobacteria. A patchwork distribution was detected which is readily reconciled with the evolution of the α-, β-, γ-, δ- and ε-proteobacteria. Our findings lead to a proposal that the ancestral BAM complex was composed of two subunits: BamA and BamD, and that BamB, BamC and BamE evolved later in a distinct sequence of events. Furthermore, in some lineages novel lipoproteins have evolved instead of the lipoproteins found in E. coli. As an example of this concept, we show that no known species of α-proteobacteria has a homologue of BamC. However, purification of the BAM complex from the model α-proteobacterium Caulobacter crescentus identified a novel subunit we refer to as BamF, which has a conserved sequence motif related to sequences found in BamC. BamF and BamD can be eluted from the BAM complex under similar conditions, mirroring the BamC:D module seen in the BAM complex of γ-proteobacteria such as E. coli.}, } @article {pmid22479332, year = {2012}, author = {Dementhon, K and El-Kirat-Chatel, S and Noël, T}, title = {Development of an in vitro model for the multi-parametric quantification of the cellular interactions between Candida yeasts and phagocytes.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e32621}, pmid = {22479332}, issn = {1932-6203}, mesh = {Animals ; Candida/classification/*immunology/physiology ; Candida albicans/immunology/physiology ; Cell Line ; Cell Survival/immunology ; Cells, Cultured ; Flow Cytometry ; Fluorometry ; Host-Pathogen Interactions/immunology ; Humans ; Kinetics ; Macrophages/*immunology/metabolism/microbiology ; Microbial Viability/immunology ; Microscopy, Fluorescence ; Microscopy, Video ; Models, Immunological ; Neutrophils/*immunology/metabolism/microbiology ; Phagocytosis/*immunology ; Species Specificity ; Time Factors ; }, abstract = {We developed a new in vitro model for a multi-parameter characterization of the time course interaction of Candida fungal cells with J774 murine macrophages and human neutrophils, based on the use of combined microscopy, fluorometry, flow cytometry and viability assays. Using fluorochromes specific to phagocytes and yeasts, we could accurately quantify various parameters simultaneously in a single infection experiment: at the individual cell level, we measured the association of phagocytes to fungal cells and phagocyte survival, and monitored in parallel the overall phagocytosis process by measuring the part of ingested fungal cells among the total fungal biomass that changed over time. Candida albicans, C. glabrata, and C. lusitaniae were used as a proof of concept: they exhibited species-specific differences in their association rate with phagocytes. The fungal biomass uptaken by the phagocytes differed significantly according to the Candida species. The measure of the survival of fungal and immune cells during the interaction showed that C. albicans was the more aggressive yeast in vitro, destroying the vast majority of the phagocytes within five hours. All three species of Candida were able to survive and to escape macrophage phagocytosis either by the intraphagocytic yeast-to-hyphae transition (C. albicans) and the fungal cell multiplication until phagocytes burst (C. glabrata, C. lusitaniae), or by the avoidance of phagocytosis (C. lusitaniae). We demonstrated that our model was sensitive enough to quantify small variations of the parameters of the interaction. The method has been conceived to be amenable to the high-throughput screening of mutants in order to unravel the molecular mechanisms involved in the interaction between yeasts and host phagocytes.}, } @article {pmid22466926, year = {2012}, author = {Powers, SK and Smuder, AJ and Judge, AR}, title = {Oxidative stress and disuse muscle atrophy: cause or consequence?.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {15}, number = {3}, pages = {240-245}, pmid = {22466926}, issn = {1473-6519}, support = {R01 HL072789/HL/NHLBI NIH HHS/United States ; R01 HL-062361/HL/NHLBI NIH HHS/United States ; R03AR056418/AR/NIAMS NIH HHS/United States ; R01 HL062361/HL/NHLBI NIH HHS/United States ; P30 AG028740/AG/NIA NIH HHS/United States ; R03 AR056418/AR/NIAMS NIH HHS/United States ; HL-087839/HL/NHLBI NIH HHS/United States ; R01 HL087839/HL/NHLBI NIH HHS/United States ; R01 HL-072789/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Muscle Proteins/metabolism ; Muscle, Skeletal/metabolism/pathology ; Muscular Atrophy/etiology/metabolism/*pathology ; Muscular Disorders, Atrophic/complications/metabolism/*pathology ; *Oxidative Stress ; Proteolysis ; Reactive Oxygen Species/*metabolism ; Signal Transduction ; }, abstract = {PURPOSE OF REVIEW: This review will discuss the evidence both for and against the concept that reactive oxygen species (ROS) play an important role in the regulation of inactivity-induced skeletal muscle atrophy.

RECENT FINDINGS: It is well established that prolonged skeletal muscle inactivity causes muscle fiber atrophy and a decrease in muscle force production. This disuse-induced muscle atrophy is the consequence of a loss in muscle protein resulting from increased protein degradation and decreased protein synthesis. Recent studies suggest that oxidative stress can influence cell-signaling pathways that regulate both muscle protein breakdown and synthesis during prolonged periods of disuse. Specifically, it is feasible that increased ROS production in muscle fibers can promote increased proteolysis and also depress protein synthesis during periods of skeletal muscle inactivity.

SUMMARY: Although it is established that oxidants can participate in the regulation of protein turnover in cells, there remains debate as to whether oxidative stress is required for disuse skeletal muscle atrophy. Nonetheless, based on emerging evidence we conclude that increased ROS production in skeletal muscles significantly contributes to inactivity-induced muscle atrophy.}, } @article {pmid22462721, year = {2012}, author = {Kraus, RH and Kerstens, HH and van Hooft, P and Megens, HJ and Elmberg, J and Tsvey, A and Sartakov, D and Soloviev, SA and Crooijmans, RP and Groenen, MA and Ydenberg, RC and Prins, HH}, title = {Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {45}, pmid = {22462721}, issn = {1471-2148}, mesh = {Animals ; Ducks/*genetics ; Female ; Gene Frequency ; Gene Transfer, Horizontal ; *Genetic Speciation ; Genotyping Techniques ; Linkage Disequilibrium ; Male ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct.

RESULTS: We show that the degree of shared single nucleotide polymorphisms (SNPs) between five species of dabbling ducks (genus Anas) is an order of magnitude higher than that previously reported between any pair of eukaryotic species with comparable evolutionary distances. We demonstrate that hybridisation has led to sustained exchange of genetic material between duck species on an evolutionary time scale without disintegrating species boundaries. Even though behavioural, genetic and ecological factors uphold species boundaries in ducks, we detect opposing forces allowing for viable interspecific hybrids, with long-term evolutionary implications. Based on the superspecies concept we here introduce the novel term "supra-population" to explain the persistence of SNPs identical by descent within the studied ducks despite their history as distinct species dating back millions of years.

CONCLUSIONS: By reviewing evidence from speciation theory, palaeogeography and palaeontology we propose a fundamentally new model of speciation to accommodate our genetic findings in dabbling ducks. This model, we argue, may also shed light on longstanding unresolved general speciation and hybridisation patterns in higher organisms, e.g. in other bird groups with unusually high hybridisation rates. Observed parallels to horizontal gene transfer in bacteria facilitate the understanding of why ducks have been such an evolutionarily successful group of animals. There is large evolutionary potential in the ability to exchange genes among species and the resulting dramatic increase of effective population size to counter selective constraints.}, } @article {pmid22457972, year = {2012}, author = {Anderson, DM and Cembella, AD and Hallegraeff, GM}, title = {Progress in understanding harmful algal blooms: paradigm shifts and new technologies for research, monitoring, and management.}, journal = {Annual review of marine science}, volume = {4}, number = {}, pages = {143-176}, pmid = {22457972}, issn = {1941-1405}, support = {P50 ES012742/ES/NIEHS NIH HHS/United States ; 1-P50-ES012742/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Climate Change ; Environmental Monitoring/*methods ; *Harmful Algal Bloom ; Humans ; Oceans and Seas ; *Research Design ; }, abstract = {The public health, tourism, fisheries, and ecosystem impacts from harmful algal blooms (HABs) have all increased over the past few decades. This has led to heightened scientific and regulatory attention, and the development of many new technologies and approaches for research and management. This, in turn, is leading to significant paradigm shifts with regard to, e.g., our interpretation of the phytoplankton species concept (strain variation), the dogma of their apparent cosmopolitanism, the role of bacteria and zooplankton grazing in HABs, and our approaches to investigating the ecological and genetic basis for the production of toxins and allelochemicals. Increasingly, eutrophication and climate change are viewed and managed as multifactorial environmental stressors that will further challenge managers of coastal resources and those responsible for protecting human health. Here we review HAB science with an eye toward new concepts and approaches, emphasizing, where possible, the unexpected yet promising new directions that research has taken in this diverse field.}, } @article {pmid22447105, year = {2012}, author = {Verheyen, L and Merckx, R and Smolders, E}, title = {A resin-buffered nutrient solution for controlling metal speciation in the algal bottle assay.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {114-115}, number = {}, pages = {200-205}, doi = {10.1016/j.aquatox.2012.02.021}, pmid = {22447105}, issn = {1879-1514}, mesh = {Biological Assay/methods ; Buffers ; Cadmium/*metabolism ; Chlorides/*pharmacology ; Chlorophyta/*metabolism ; Culture Media/chemistry ; Metals/*chemistry ; Resins, Synthetic/*chemistry ; Time Factors ; }, abstract = {Metal speciation in solution is uncontrolled during algal growth in the traditional algal bottle assay. A resin-buffered nutrient solution was developed to overcome this problem and this was applied to test the effect of chloride (Cl[-]) on cadmium (Cd) uptake. Standard nutrient solution was enriched with 40 mM of either NaNO3 or NaCl, and was prepared to contain equal Cd[2+] but varying dissolved Cd due to the presence of CdCl(n)(2-n) complexes. Both solutions were subsequently used in an algal assay in 100 mL beakers that contained only the solution (designated "-R") or contained the solution together with a cation exchange sulfonate resin (2 g L[-1], designated "+R") as a deposit on the bottom of the beaker. Pseudokirchneriella subcapitata was grown for 72 h (1.4 × 10[5]-1.4 × 10[6] cells mL[-1]) in stagnant solution and shaken three times a day. Growth was unaffected by the presence of the resin (p>0.05). The Cd concentrations in solution of the -R devices decreased with 50-58% of initial values due to Cd uptake. No such changes were found in the +R devices or in abiotic controls. Cd uptake was unaffected by either NaNO3 or NaCl treatment in the +R device, confirming that Cd[2+] is the preferred Cd species in line with the general concept of metal bioavailability. In contrast, Cd uptake in the -R devices was two-fold larger in the NaCl treatment than in the NaNO3 treatment (p<0.001), suggesting that CdCl(n)(2-n) complexes are bioavailable in this traditional set-up. However this bioavailability is partially, but not completely, an apparent one, because of the considerable depletion of solution [109]Cd in this set-up. Resin-buffered solutions are advocated in the algal bottle assay to control trace metal supply and to better identify the role of metal complexes on bioavailability.}, } @article {pmid22430372, year = {2012}, author = {Miller, TE and terHorst, CP}, title = {Testing successional hypotheses of stability, heterogeneity, and diversity in pitcher-plant inquiline communities.}, journal = {Oecologia}, volume = {170}, number = {1}, pages = {243-251}, pmid = {22430372}, issn = {1432-1939}, mesh = {Aquatic Organisms ; Bacteria/growth & development ; *Biodiversity ; *Ecosystem ; Food Chain ; Plant Leaves ; Population Dynamics ; *Sarraceniaceae ; Time Factors ; }, abstract = {Succession is a foundation concept in ecology that describes changes in species composition through time, yet many successional patterns have not been thoroughly investigated. We highlight three hypotheses about succession that are often not clearly stated or tested: (1) individual communities become more stable over time, (2) replicate communities become more similar over time, and (3) diversity peaks at mid-succession. Testing general patterns of succession requires estimates of variation in trajectories within and among replicate communities. We followed replicate aquatic communities found within leaves of purple pitcher plants (Sarracenia purpurea) to test these three hypotheses. We found that stability of individual communities initially decreased, but then increased in older communities. Predation was highest in younger leaves but then declined, while competition was likely strongest in older leaves, as resources declined through time. Higher levels of predation and competition corresponded with periods of higher stability. As predicted, heterogeneity among communities decreased with age, suggesting that communities became more similar over time. Changes in diversity depended on trophic level. The diversity of bacteria slightly declined over time, but the diversity of consumers of bacteria increased linearly and strongly throughout succession. We suggest that studies need to focus on the variety of environmental drivers of succession, which are likely to vary through time and across habitats.}, } @article {pmid22422764, year = {2012}, author = {Simon, UK and Trajanoski, S and Kroneis, T and Sedlmayr, P and Guelly, C and Guttenberger, H}, title = {Accession-specific haplotypes of the internal transcribed spacer region in Arabidopsis thaliana--a means for barcoding populations.}, journal = {Molecular biology and evolution}, volume = {29}, number = {9}, pages = {2231-2239}, doi = {10.1093/molbev/mss093}, pmid = {22422764}, issn = {1537-1719}, mesh = {Arabidopsis/classification/*genetics ; Base Sequence ; *DNA Barcoding, Taxonomic ; *DNA, Ribosomal Spacer ; *Haplotypes ; INDEL Mutation ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {Eukaryote genomes contain multiple copies of nuclear ribosomal DNA (nrDNA) harboring both highly conserved and variable regions. This has made nrDNA the most popular genetic marker for phylogenetic studies and the region of choice for barcoding projects. Furthermore, many scientists believe that all copies of nrDNA within one nucleus are practically identical due to concerted evolution. Here, we investigate the model plant species Arabidopsis thaliana for intragenomic variation of the internal transcribed spacer (ITS) region of nrDNA. Based on a modified deep sequencing approach, we provide a comprehensive list of ITS polymorphisms present in the two most widely used accessions of A. thaliana-Col-0 and Ler. Interestingly, we found that some polymorphisms are shared between these genetically very distinct accessions. On the other hand, the high number of accession-specific polymorphisms shows that each accession can be clearly and easily characterized by its specific ITS polymorphism patterns and haplotypes. Network analysis based on the detected haplotypes demonstrates that the study of ITS polymorphism patterns and haplotypes is an extremely powerful tool for population genetics. Using the methods proposed here, it will now be possible to extend the traditionally species-bound barcoding concept to populations.}, } @article {pmid22377402, year = {2012}, author = {Nagai, T and Horio, T and Yokoyama, A and Kamiya, T and Takano, H and Makino, T}, title = {Ecological risk assessment of on-site soil washing with iron(III) chloride in cadmium-contaminated paddy field.}, journal = {Ecotoxicology and environmental safety}, volume = {80}, number = {}, pages = {84-90}, doi = {10.1016/j.ecoenv.2012.02.011}, pmid = {22377402}, issn = {1090-2414}, mesh = {Agriculture ; Animals ; Aquatic Organisms ; Cadmium/*analysis/chemistry/toxicity ; Chlorides/*chemistry ; Environmental Restoration and Remediation/*methods ; Ferric Compounds/*chemistry ; Japan ; Oryza ; Risk Assessment ; Soil/*chemistry ; Soil Pollutants/*analysis/chemistry/toxicity ; }, abstract = {On-site soil washing with iron(III) chloride reduces Cd levels in soil, and thus the human health risks caused by Cd in food. However, it may threaten aquatic organisms when soil washing effluent is discharged to open aquatic systems. Therefore, we conducted trial-scale on-site soil washing and ecological risk assessment in Nagano and Niigata prefectures, Japan. The ecological effect of effluent water was investigated by two methods. The first was bioassay using standard aquatic test organisms. Twice-diluted effluent water from the Nagano site and the original effluent water from the Niigata site had no significant effects on green algae, water flea, caddisfly, and fish. The safe dilution rates were estimated as 20 times and 10 times for the Nagano and Niigata sites, respectively, considering an assessment factor of 10. The second method was probabilistic effect analysis using chemical analysis and the species sensitivity distribution concept. The mixture effects of CaCl(2), Al, Zn, and Mn were considered by applying a response additive model. The safe dilution rates, assessed for a potentially affected fraction of species of 5%, were 7.1 times and 23.6 times for the Nagano and Niigata sites, respectively. The actual dilution rates of effluent water by river water at the Nagano and Niigata sites were 2200-67,000 times and 1300-110,000 times, respectively. These are much larger than the safe dilution rates derived from the two approaches. Consequently, the ecological risk to aquatic organisms of soil washing is evaluated as being below the concern level.}, } @article {pmid22373076, year = {2012}, author = {Pereira-da-Conceicoa, LL and Price, BW and Barber-James, HM and Barker, NP and de Moor, FC and Villet, MH}, title = {Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in southern Africa.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {26}, pmid = {22373076}, issn = {1471-2148}, mesh = {Animals ; Cell Nucleus/genetics ; *Genetic Variation ; Insecta/*classification/cytology/*genetics ; Mitochondria/genetics ; Phylogeny ; South Africa ; }, abstract = {BACKGROUND: Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9-10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa.

RESULTS: Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1α] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1α gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1α gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4-11.5 mya).

CONCLUSIONS: The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams found within eastern South Africa, Malawi and Zambia. The results of this study suggest that B. harrisoni as it is currently recognised is not a single species with a wide geographic range and pH-tolerance, but may comprise up to five species under the phylogenetic species concept, each with limited pH-tolerances, and that the B. harrisoni species group is thus in need of taxonomic review.}, } @article {pmid22372767, year = {2012}, author = {Camadro, EL and Erazzú, LE and Maune, JF and Bedogni, MC}, title = {A genetic approach to the species problem in wild potato.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {14}, number = {4}, pages = {543-554}, doi = {10.1111/j.1438-8677.2012.00563.x}, pmid = {22372767}, issn = {1438-8677}, mesh = {Alleles ; Breeding ; *Genetic Speciation ; Hybridization, Genetic ; *Phylogeny ; Reproduction ; Self-Incompatibility in Flowering Plants ; Solanum tuberosum/*classification/*genetics/physiology ; }, abstract = {Wild potatoes are native to the Americas, where they present very wide geographical and ecological distribution. Most are diploid, obligate out-crossers due to a multiallelic gametophytic self-incompatibility (S) locus that prevents self-fertilisation and crossing between individuals carrying identical S-alleles. They have two alternative modes of reproduction: sexual (by seeds) and asexual (by stolons and tubers), which provide, respectively, for genetic flexibility in changing environments and high fitness of adapted genotypes under stable conditions. Since the early twentieth century, their taxonomic classification has been mostly based on morphological phenotypes (Taxonomic Species Concept). More recently, attempts have been made to establish phylogenetic relationships, applying molecular tools in samples of populations (accessions) with a previously assigned specific category. However, neither the reproductive biology and breeding relations among spontaneous populations nor the morphological and genetic variability expected in obligate allogamous populations are considered when the taxonomic species concept is applied. In nature, wild potato populations are isolated through external and internal hybridisation barriers; the latter, which are genetically determined, can be either pre-zygotic (pollen-pistil incompatibility) or post-zygotic (abortion of embryo, endosperm or both tissues, sterility, and hybrid weakness and breakdown in segregating generations). The internal barriers, however, can be incomplete, providing opportunities for hybridisation and introgression within and between populations and ploidy levels in areas of overlap. The widespread occurrence of spontaneous hybrids in nature was recognised in the mid-twentieth century. Using genetic approaches, results have been obtained that provide strong support to the assertion that populations are at different stages of genetic divergence and are not at the end of the evolutionary process, as presupposed by the Taxonomic Species Concept. Furthermore, since wild potatoes have uniparental and biparental overlapping generations, the Biological Species Concept - developed for sexually reproducing biparental organisms - cannot be applied to them. In this paper, morphological, genetic, molecular and taxonomic studies in wild potato are reviewed, considering the genetic consequences of their reproductive biology, in an attempt to shed light on the species problem, because of its relevance in germplasm conservation and breeding.}, } @article {pmid22363207, year = {2012}, author = {Cadillo-Quiroz, H and Didelot, X and Held, NL and Herrera, A and Darling, A and Reno, ML and Krause, DJ and Whitaker, RJ}, title = {Patterns of gene flow define species of thermophilic Archaea.}, journal = {PLoS biology}, volume = {10}, number = {2}, pages = {e1001265}, pmid = {22363207}, issn = {1545-7885}, mesh = {Base Sequence ; *Ecosystem ; Gene Flow/*genetics ; *Genetic Speciation ; Genetics, Population ; High-Throughput Nucleotide Sequencing/methods ; Homologous Recombination/genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phenotype ; *Phylogeny ; Russia ; Species Specificity ; Sulfolobus/classification/*genetics ; }, abstract = {Despite a growing appreciation of their vast diversity in nature, mechanisms of speciation are poorly understood in Bacteria and Archaea. Here we use high-throughput genome sequencing to identify ongoing speciation in the thermoacidophilic Archaeon Sulfolobus islandicus. Patterns of homologous gene flow among genomes of 12 strains from a single hot spring in Kamchatka, Russia, demonstrate higher levels of gene flow within than between two persistent, coexisting groups, demonstrating that these microorganisms fit the biological species concept. Furthermore, rates of gene flow between two species are decreasing over time in a manner consistent with incipient speciation. Unlike other microorganisms investigated, we do not observe a relationship between genetic divergence and frequency of recombination along a chromosome, or other physical mechanisms that would reduce gene flow between lineages. Each species has its own genetic island encoding unique physiological functions and a unique growth phenotype that may be indicative of ecological specialization. Genetic differentiation between these coexisting groups occurs in large genomic "continents," indicating the topology of genomic divergence during speciation is not uniform and is not associated with a single locus under strong diversifying selection. These data support a model where species do not require physical barriers to gene flow but are maintained by ecological differentiation.}, } @article {pmid22353848, year = {2012}, author = {Bacon, CD and McKenna, MJ and Simmons, MP and Wagner, WL}, title = {Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia).}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {23}, pmid = {22353848}, issn = {1471-2148}, mesh = {Arecaceae/classification/*genetics ; Cell Nucleus/genetics ; DNA, Plant/genetics ; Gene Flow ; Genes, Plant ; *Genetic Speciation ; Hawaii ; Microsatellite Repeats ; *Phylogeny ; Plastids/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Robust species delimitations are fundamental for conservation, evolutionary, and systematic studies, but they can be difficult to estimate, particularly in rapid and recent radiations. The consensus that species concepts aim to identify evolutionarily distinct lineages is clear, but the criteria used to distinguish evolutionary lineages differ based on the perceived importance of the various characteristics of evolving populations. We examined three different species-delimitation criteria (monophyly, absence of genetic intermediates, and diagnosability) to determine whether currently recognized species of Hawaiian Pritchardia are distinct lineages.

RESULTS: Data from plastid and nuclear genes, microsatellite loci, and morphological characters resulted in various levels of lineage subdivision that were likely caused by differing evolutionary rates between data sources. Additionally, taxonomic entities may be confounded because of the effects of incomplete lineage sorting and/or gene flow. A coalescent species tree was largely congruent with the simultaneous analysis, consistent with the idea that incomplete lineage sorting did not mislead our results. Furthermore, gene flow among populations of sympatric lineages likely explains the admixture and lack of resolution between those groups.

CONCLUSIONS: Delimiting Hawaiian Pritchardia species remains difficult but the ability to understand the influence of the evolutionary processes of incomplete lineage sorting and hybridization allow for mechanisms driving species diversity to be inferred. These processes likely extend to speciation in other Hawaiian angiosperm groups and the biota in general and must be explicitly accounted for in species delimitation.}, } @article {pmid22334449, year = {2012}, author = {Lambertini, C and Mendelssohn, IA and Gustafsson, MH and Olesen, B and Riis, T and Sorrell, BK and Brix, H}, title = {Tracing the origin of Gulf Coast Phragmites (Poaceae): a story of long-distance dispersal and hybridization.}, journal = {American journal of botany}, volume = {99}, number = {3}, pages = {538-551}, doi = {10.3732/ajb.1100396}, pmid = {22334449}, issn = {1537-2197}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Biological Evolution ; Demography ; Genetic Markers ; Genetic Variation ; Hybridization, Genetic/*genetics ; Poaceae/*genetics/*physiology ; Species Specificity ; }, abstract = {PREMISE OF THE STUDY: Long-distance dispersal can affect speciation processes in two opposing ways. Dispersal can promote geographic isolation or it can bring together geographically distant and distantly related genotypes, thus counteracting local differentiation. We used the Gulf Coast of North America (GC), a "hot spot" of reed diversity and evolutionary dynamics, as a model system to study the diversification processes within the invasive, cosmopolitan, polyploid grass Phragmites.

METHODS: Genetic diversity was studied using collections representing all species of the genus and from all continents (except Antarctica). A range of molecular markers, including chloroplast and nuclear sequences, microsatellites, and AFLPs, was analyzed to detect DNA variation from the population to the species level and to infer phylogenetic relationships across continents.

KEY RESULTS: An interspecific hybrid, Phragmites mauritianus × P. australis, and four P. australis cp-DNA haplotypes from Africa, Europe, and North America have been dispersed to the GC and interbreed with each other.

CONCLUSIONS: Long-distance dispersal and weak breeding barriers appear to be recurring phenomena, not only in the GC, but worldwide. We present data strongly suggesting that interspecific hybridization and introgression among different Phragmites species take place and appear to have contributed significantly to the diversification processes within the genus. Hence, the application of traditional species concepts within Phragmites might be inappropriate.}, } @article {pmid22322873, year = {2012}, author = {Ito, M and Sato, I and Koitabashi, M and Yoshida, S and Imai, M and Tsushima, S}, title = {A novel actinomycete derived from wheat heads degrades deoxynivalenol in the grain of wheat and barley affected by Fusarium head blight.}, journal = {Applied microbiology and biotechnology}, volume = {96}, number = {4}, pages = {1059-1070}, doi = {10.1007/s00253-012-3922-6}, pmid = {22322873}, issn = {1432-0614}, mesh = {Actinomycetales/classification/genetics/isolation & purification/*metabolism ; Fusarium/*physiology ; Hordeum/*microbiology ; Molecular Sequence Data ; Mycotoxins/*metabolism ; Phylogeny ; Plant Diseases/*microbiology ; Seeds/microbiology ; Trichothecenes/*metabolism ; Triticum/*microbiology ; }, abstract = {Deoxynivalenol (DON) is a hazardous and globally prevalent mycotoxin in cereals. It commonly accumulates in the grain of wheat, barley and other small grain cereals affected by Fusarium head blight (caused by several Fusarium species). The concept of reducing DON in naturally contaminated grain of wheat or barley using a DON-degrading bacterium is promising but has not been accomplished. In this study, we isolated a novel DON-utilising actinomycete, Marmoricola sp. strain MIM116, from wheat heads through a novel isolation procedure including an in situ plant enrichment step. Strain MIM116 had background degradation activity, and the activity was enhanced twofold by the consumption of DON. Among Tween 20, Triton X-100 and Tween 80, we selected Tween 80 as a spreading agent of strain MIM116 because it promoted DON degradation and the growth of strain MIM116 in the presence of DON. The inoculation of MIM116 cell suspension plus 0.01% Tween 80 into 1,000 harvested kernels of wheat and barley resulted in a DON decrease from approximately 3 mg kg(-1) to less than 1 mg kg(-1) of dry kernels, even when cells had only basal levels of DON-degrading activity. To the best of our knowledge, this is the first report that describes (1) the isolation of a DON-degrading bacterium from wheat heads, (2) the effects of surfactants on the biodegradation of DON and (3) the decrease of DON levels in naturally contaminated wheat and barley grain using a DON-degrading bacterium.}, } @article {pmid22309706, year = {2012}, author = {Leclère, L and Jager, M and Barreau, C and Chang, P and Le Guyader, H and Manuel, M and Houliston, E}, title = {Maternally localized germ plasm mRNAs and germ cell/stem cell formation in the cnidarian Clytia.}, journal = {Developmental biology}, volume = {364}, number = {2}, pages = {236-248}, doi = {10.1016/j.ydbio.2012.01.018}, pmid = {22309706}, issn = {1095-564X}, mesh = {Animals ; Base Sequence ; Embryo, Nonmammalian/metabolism ; Embryonic Development ; Female ; Germ Cells/*metabolism ; Hydrozoa/genetics/*metabolism ; Male ; Molecular Sequence Data ; RNA, Messenger, Stored/*metabolism ; Stem Cells/metabolism ; }, abstract = {The separation of the germ line from the soma is a classic concept in animal biology, and depending on species is thought to involve fate determination either by maternally localized germ plasm ("preformation" or "maternal inheritance") or by inductive signaling (classically termed "epigenesis" or "zygotic induction"). The latter mechanism is generally considered to operate in non-bilaterian organisms such as cnidarians and sponges, in which germ cell fate is determined at adult stages from multipotent stem cells. We have found in the hydrozoan cnidarian Clytia hemisphaerica that the multipotent "interstitial" cells (i-cells) in larvae and adult medusae, from which germ cells derive, express a set of conserved germ cell markers: Vasa, Nanos1, Piwi and PL10. In situ hybridization analyses unexpectedly revealed maternal mRNAs for all these genes highly concentrated in a germ plasm-like region at the egg animal pole and inherited by the i-cell lineage, strongly suggesting i-cell fate determination by inheritance of animal-localized factors. On the other hand, experimental tests showed that i-cells can form by epigenetic mechanisms in Clytia, since larvae derived from both animal and vegetal blastomeres separated during cleavage stages developed equivalent i-cell populations. Thus Clytia embryos appear to have maternal germ plasm inherited by i-cells but also the potential to form these cells by zygotic induction. Reassessment of available data indicates that maternally localized germ plasm molecular components were plausibly present in the common cnidarian/bilaterian ancestor, but that their role may not have been strictly deterministic.}, } @article {pmid22299709, year = {2012}, author = {Espinosa, A and Paz-Y-Miño-C, G}, title = {Discrimination, crypticity, and incipient taxa in entamoeba.}, journal = {The Journal of eukaryotic microbiology}, volume = {59}, number = {2}, pages = {105-110}, pmid = {22299709}, issn = {1550-7408}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; P20 RR016457/RR/NCRR NIH HHS/United States ; P20 RR016457-11/RR/NCRR NIH HHS/United States ; P20RR16457-11/RR/NCRR NIH HHS/United States ; }, mesh = {Entamoeba/*classification/genetics/*isolation & purification/physiology ; Evolution, Molecular ; Phylogeny ; }, abstract = {Persistent difficulties in resolving clear lineages in diverging populations of prokaryotes or unicellular eukaryotes (protistan polyphyletic groups) are challenging the classical species concept. Although multiple integrated approaches would render holistic taxonomies, most phylogenetic studies are still based on single-gene or morphological traits. Such methodologies conceal natural lineages, which are considered "cryptic." The concept of species is considered artificial and inadequate to define natural populations. Social organisms display differential behaviors toward kin than to nonrelated individuals. In "social" microbes, kin discrimination has been used to help resolve crypticity. Aggregative behavior could be explored in a nonsocial protist to define phylogenetic varieties that are considered "cryptic." Two Entamoeba invadens strains, IP-1 and VK-1:NS are considered close populations of the same "species." This study demonstrates that IP-1 and VK-1:NS trophozoites aggregate only with alike members and discriminate members of different strains based on behavioral and chemical signals. Combined morphological, behavioral/chemical, and ecological studies could improve Archamoebae phylogenies and define cryptic varieties. Evolutionary processes in which selection acted continuously and cumulatively on ancestors of Entamoeba populations gave rise to chemical and behavioral signals that allowed individuals to discriminate nonpopulation members and, gradually, to the emergence of new lineages; alternative views that claim a "Designer" or "Creator" as responsible for protistan diversity are unfounded.}, } @article {pmid22289771, year = {2012}, author = {Abreu, LM and Costa, SS and Pfenning, LH and Takahashi, JA and Larsen, TO and Andersen, B}, title = {Chemical and molecular characterization of Phomopsis and Cytospora-like endophytes from different host plants in Brazil.}, journal = {Fungal biology}, volume = {116}, number = {2}, pages = {249-260}, doi = {10.1016/j.funbio.2011.11.008}, pmid = {22289771}, issn = {1878-6146}, mesh = {Ascomycota/*chemistry/classification/*genetics/isolation & purification ; Brazil ; Chromatography, High Pressure Liquid ; Chromatography, Liquid ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Endophytes/*chemistry/classification/*genetics/isolation & purification ; Genotype ; Mass Spectrometry ; *Metabolome ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Plants/*microbiology ; Sequence Analysis, DNA ; Spectrophotometry ; }, abstract = {Phomopsis and related taxa comprise important endophytic and plant pathogenic species, and are known for the production of a diverse array of secondary metabolites. Species concepts within this group based on morphological characters and assumed host specificity do not reflect phylogenetic affinities. Additional phenotypic characters, such as profiles of secondary metabolites, are needed for practical species recognition. We investigated 36 strains of Phomopsis spp. and Cytospora-like fungi, obtained as endophytes of different host plants in Brazil, using metabolite profiling based on HPLC-UV/liquid chromatography -mass spectrometry (LC-MS) combined with cluster analysis of the results. Strains were also subjected to phylogenetic analyses based on internal transcribed spacer (ITS) rDNA. Six chemotypes were identified. Chemotypes 1-5 contained Phomopsis strains, while Cytospora-like strains formed the chemotype 6. Strains of chemotype 1 typically produced alternariols, altenusin, altenuene, cytosporones, and dothiorelones. Alternariol and seven unknown compounds were consistently produced by strains of chemotype 2. Members of chemotypes 3-5 produced poor metabolite profiles containing few chemical markers. Cytospora-like endophytes (chemotype 6) produced a characteristic set of metabolites including cytosporones and dothiorelones. Bayesian and Maximum Parsimony (MP) trees classified strains of each chemotype into single phylogenetic lineages or closely related groups. Strains of chemotypes 1 and 2 formed a monophyletic group along with Diaporthe neotheicola. The remaining Phomopsis strains formed monophyletic (chemotype 4) or polyphyletic (chemotypes 3 and 5) lineages inside a large and well supported clade. Cytospora-like strains formed a monophyletic lineage located at an intermediary position between Diaporthe/Phomopsis and Valsa/Cytospora clades. The combined results show that the production of secondary metabolites by Phomopsis and related Diaporthales may be species-specific, giving support to the use of metabolite profiling and chemical classification for phenotypic recognition and delimitation of species.}, } @article {pmid22259304, year = {2011}, author = {Kerr, PH}, title = {Six new species of Acomoptera from North America (Diptera, Mycetophilidae).}, journal = {ZooKeys}, volume = {}, number = {137}, pages = {41-76}, doi = {10.3897/zookeys.137.1764}, pmid = {22259304}, issn = {1313-2970}, abstract = {Six new species are described, raising the number of North American Acomoptera species to seven and the genus total to ten, and nearly doubling the number of species within the putative clade containing Acomoptera, Drepanocercus, and Paratinia. These novel species forms have implications for the concept of Acomoptera that in turn, may impact our understanding of its generic relationships and the evolution and composition of Gnoristinae and Sciophilinae. The new species, Acomoptera crispa, Acomoptera digitata, Acomoptera echinosa, Acomoptera forculata, Acomoptera nelsoni,and Acomoptera vockerothi, are compared with the type species of the genus, Acomoptera plexipus (Garrett), whose diagnostic features are imaged and illustrated for the first time. The European species, Acomoptera difficilis (Dziedzicki) is also illustrated and compared. Acomoptera spinistyla (Søli) comb. n. is transferred from Drepanocercus. A key to species is provided. Future work will seek to incorporate this knowledge into a systematic phylogenetic study of relationships between these species and their sister taxa.}, } @article {pmid22247548, year = {2012}, author = {Mannervik, B}, title = {Five decades with glutathione and the GSTome.}, journal = {The Journal of biological chemistry}, volume = {287}, number = {9}, pages = {6072-6083}, pmid = {22247548}, issn = {1083-351X}, mesh = {Animals ; Biochemistry/*history ; Energy Metabolism/physiology ; Faculty, Medical/*history ; Glutathione/*history/metabolism ; Glutathione Transferase/*history/metabolism ; History, 20th Century ; History, 21st Century ; Humans ; Lactoylglutathione Lyase/*history/metabolism ; Sweden ; }, abstract = {Uncle Folke inspired me to become a biochemist by demonstrating electrophoresis experiments on butterfly hemolymph in his kitchen. Glutathione became the subject for my undergraduate project in 1964 and has remained a focal point in my research owing to its multifarious roles in the cell. Since the 1960s, the multiple forms of glutathione transferase (GST), the GSTome, were isolated and characterized, some of which were discovered in our laboratory. Products of oxidative processes were found to be natural GST substrates. Examples of toxic compounds against which particular GSTs provide protection include 4-hydroxynonenal and ortho-quinones, with possible links to the etiology of Alzheimer and Parkinson diseases and other degenerative conditions. The role of thioltransferase and glutathione reductase in the cellular reduction of disulfides and other oxidized forms of thiols was clarified. Glyoxalase I catalyzes still another glutathione-dependent detoxication reaction. The unusual steady-state kinetics of this zinc-containing enzyme initiated model discrimination by regression analysis. Functional properties of the enzymes have been altered by stochastic mutations based on DNA shuffling and rationally tailored by structure-based redesign. We found it useful to represent promiscuous enzymes by vectors or points in multidimensional substrate-activity space and visualize them by multivariate analysis. Adopting the concept "molecular quasi-species," we describe clusters of functionally related enzyme variants that may emerge in natural as well as directed evolution.}, } @article {pmid22244071, year = {2012}, author = {Nixon, AJ and Watts, AE and Schnabel, LV}, title = {Cell- and gene-based approaches to tendon regeneration.}, journal = {Journal of shoulder and elbow surgery}, volume = {21}, number = {2}, pages = {278-294}, doi = {10.1016/j.jse.2011.11.015}, pmid = {22244071}, issn = {1532-6500}, mesh = {Animals ; Forecasting ; Genetic Therapy/*methods/trends ; Humans ; Mesenchymal Stem Cell Transplantation/*methods/trends ; Recovery of Function ; Regeneration/*physiology ; Rotator Cuff Injuries ; Tendon Injuries/*therapy ; Tendons/physiology ; Tensile Strength ; Treatment Outcome ; Wound Healing/physiology ; }, abstract = {Repair of rotator cuff tears in experimental models has been significantly improved by the use of enhanced biologic approaches, including platelet-rich plasma, bone marrow aspirate, growth factor supplements, and cell- and gene-modified cell therapy. Despite added complexity, cell-based therapies form an important part of enhanced repair, and combinations of carrier vehicles, growth factors, and implanted cells provide the best opportunity for robust repair. Bone marrow-derived mesenchymal stem cells provide a stimulus for repair in flexor tendons, but application in rotator cuff repair has not shown universally positive results. The use of scaffolds such as platelet-rich plasma, fibrin, and synthetic vehicles and the use of gene priming for stem cell differentiation and local anabolic and anti-inflammatory impact have both provided essential components for enhanced tendon and tendon-to-bone repair in rotator cuff disruption. Application of these research techniques in human rotator cuff injury has generally been limited to autologous platelet-rich plasma, bone marrow concentrate, or bone marrow aspirates combined with scaffold materials. Cultured mesenchymal progenitor therapy and gene-enhanced function have not yet reached clinical trials in humans. Research in several animal species indicates that the concept of gene-primed stem cells, particularly embryonic stem cells, combined with effective culture conditions, transduction with long-term integrating vectors carrying anabolic growth factors, and development of cells conditioned by use of RNA interference gene therapy to resist matrix metalloproteinase degradation, may constitute potential advances in rotator cuff repair. This review summarizes cell- and gene-enhanced cell research for tendon repair and provides future directions for rotator cuff repair using biologic composites.}, } @article {pmid24260650, year = {2012}, author = {Ferreira-Neto, M and Artoni, RF and Vicari, MR and Moreira-Filho, O and Camacho, JP and Bakkali, M and de Oliveira, C and Foresti, F}, title = {Three sympatric karyomorphs in the fish Astyanax fasciatus (Teleostei, Characidae) do not seem to hybridize in natural populations.}, journal = {Comparative cytogenetics}, volume = {6}, number = {1}, pages = {29-40}, pmid = {24260650}, issn = {1993-0771}, abstract = {Ninety individuals of the characid fish Astyanax fasciatus (Cuvier, 1819) were collected at Água da Madalena stream (Botucatu, São Paulo, Brazil) and analyzed for diploid chromosome number 2n and karyotype composition as well as for the chromosomal location of the 5S and 18S ribosomal DNA (rDNA). Whereas no chromosome differences were associated with sex, three different karyomorphs with diploid chromosome numbers 2n=46, 2n=48 and 2n=50 were found. No intermediate 2n numbers were discovered. The 2n=50 karyomorph showed some differences in 18S rDNA location compared to the two other karyomorphs. Finally, all specimens with the 2n=46 karyomorph showed the presence of a partly heterochromatic macro supernumerary chromosome, which was absent in all individuals with the two other karyomorphs. All these results suggest that indviduals of the three different karyomorphs are not likely to hybridize in the examined populations. Our findings strongly suggest the presence of three separate species (sensu biological species concept) easily diagnosed on the basis of differences in the diploid chromosome numbers and other chromosomal markers.}, } @article {pmid22183677, year = {2012}, author = {Rintoul, TL and Eggertson, QA and Lévesque, CA}, title = {Multigene phylogenetic analyses to delimit new species in fungal plant pathogens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {835}, number = {}, pages = {549-569}, doi = {10.1007/978-1-61779-501-5_34}, pmid = {22183677}, issn = {1940-6029}, mesh = {DNA, Fungal/genetics/isolation & purification ; Fungi/*genetics ; Multigene Family ; *Phylogeny ; Plants/*microbiology ; Sequence Analysis, DNA/methods ; Species Specificity ; }, abstract = {Supporting the identification of unknown strains or specimens by sequencing a genetic marker commonly used for phylogenetics or DNA barcoding is now standard practice for mycologists and plant pathologists. Does one have a new species when a strain differs by a few base pairs when compared to reference sequences from taxonomically well-characterized species that do not differ morphologically from this new strain? If variation at the intra- and interspecific levels for the locus used for identification is already understood for all the closely related species, it is possible to make a reliable prediction of a new species status, but ultimately this question can only be properly addressed by determining the presence or absence of gene flow among a group of strains of the putative new species and strains of previously delimited species. The Phylogenetic Species Concept (PSC) and its assessment using multigene phylogeny and Genealogical Concordance Phylogenetic Species Recognition (GCPSR) are the basis for this chapter. The theoretical framework and a variety of tools to apply these concepts are explained, to assist in the assessment of whether a species is distinct or new when confronted with some sequence divergence from reference data.}, } @article {pmid22174334, year = {2012}, author = {Moran, EV and Willis, J and Clark, JS}, title = {Genetic evidence for hybridization in red oaks (Quercus sect. Lobatae, Fagaceae).}, journal = {American journal of botany}, volume = {99}, number = {1}, pages = {92-100}, doi = {10.3732/ajb.1100023}, pmid = {22174334}, issn = {1537-2197}, mesh = {Amplified Fragment Length Polymorphism Analysis ; *Gene Flow ; *Genetic Structures ; Genetics, Population ; Genome, Plant/genetics ; Genotype ; *Hybridization, Genetic ; North Carolina ; Phenotype ; Plant Leaves/anatomy & histology/genetics ; Quercus/anatomy & histology/*genetics ; Seedlings/anatomy & histology/genetics ; Species Specificity ; Trees ; }, abstract = {PREMISE OF THE STUDY: Hybridization is pervasive in many plant taxa, with consequences for species taxonomy, local adaptation, and management. Oaks (Quercus spp.) are thought to hybridize readily yet retain distinct traits, drawing into question the biological species concept for such taxa, but the true extent of gene flow is controversial. Genetic data are beginning to shed new light on this issue, but red oaks (section Lobatae), an important component of North American forests, have largely been neglected. Moreover, gene flow estimates may be sensitive to the choice of life stage, marker type, or genetic structure statistic.

METHODS: We coupled genetic structure data with parentage analyses for two mixed-species stands in North Carolina. Genetic structure analyses of adults (including F(ST), R(ST), G'(ST), and structure) reflect long-term patterns of gene flow, while the percentage of seedlings with parents of two different species reflect current levels of gene flow.

KEY RESULTS: Genetic structure analyses revealed low differentiation in microsatellite allele frequencies between co-occurring species, suggesting past gene flow. However, methods differed in their sensitivity to differentiation, indicating a need for caution when drawing conclusions from a single method. Parentage analyses identified >20% of seedlings as potential hybrids. The species examined exhibit distinct morphologies, suggesting selection against intermediate phenotypes.

CONCLUSIONS: Our results suggest that hybridization between co-occurring red oaks occurs, but that selection may limit introgression, especially at functional loci. However, by providing a source of genetic variation, hybridization could influence the response of oaks and other hybridizing taxa to environmental change.}, } @article {pmid22171189, year = {2011}, author = {Martínez-Azorín, M and Crespo, MB and Dold, AP and Barker, NP}, title = {The identity of Albuca caudata Jacq. (Hyacinthaceae) and a description of a new related species: A. bakeri.}, journal = {PhytoKeys}, volume = {}, number = {5}, pages = {5-19}, pmid = {22171189}, issn = {1314-2003}, abstract = {The name Albuca caudata Jacq. has been widely misunderstood or even ignored since its description in 1791. After studying herbarium specimens and living populations in South Africa, plants fitting Jacquin´s concept of that species are found to be widely distributed in the Eastern Cape, mainly in the Albany centre of Endemism. Furthermore, some divergent specimens matching Baker´s concept of Albuca caudata are described as a new related species: Albuca bakeri. Data on typification, morphology, ecology, and distribution are reported for both taxa. Affinities and divergences with other close allies are also discussed.}, } @article {pmid22155360, year = {2012}, author = {Heinrichs, J and Bombosch, A and Feldberg, K and Kreier, HP and Hentschel, J and Eckstein, J and Long, D and Zhu, RL and Schäfer-Verwimp, A and Schmidt, AR and Shaw, B and Shaw, AJ and Váňa, J}, title = {A phylogeny of the northern temperate leafy liverwort genus Scapania (Scapaniaceae, Jungermanniales).}, journal = {Molecular phylogenetics and evolution}, volume = {62}, number = {3}, pages = {973-985}, doi = {10.1016/j.ympev.2011.11.029}, pmid = {22155360}, issn = {1095-9513}, mesh = {DNA, Plant ; Hepatophyta/*classification/*genetics ; Multilocus Sequence Typing ; *Phylogeny ; }, abstract = {Scapania is a northern temperate genus with a few disjunctions in the south. Despite receiving considerable attention, the supraspecific classification of this genus remains unsatisfactorily solved. We use three molecular markers (nrITS, cpDNA trnL-F region, atpB-rbcL spacer) and 175 accessions belonging to 50 species (plus eight outgroup taxa) to estimate the phylogeny and to test current classification systems. Our data support the classification of Scapania into six rather than three subgenera, rearrangements within numerous sections, and inclusion of Macrodiplophyllum microdontum. Scapania species with a plicate perianth form three early diverging lineages; the most speciose subgenus, Scapania s.str., represents a derived clade. Most morphological species concepts are supported by the molecular topologies but classification of sect. Curtae requires further study. Southern lineages are nested in northern hemispheric clades. Palearctic-Nearctic distribution ranges are supported for several species.}, } @article {pmid22143443, year = {2012}, author = {Tsutsumi, S and Ushitani, T and Tomonaga, M and Fujita, K}, title = {Infant monkeys' concept of animacy: the role of eyes and fluffiness.}, journal = {Primates; journal of primatology}, volume = {53}, number = {2}, pages = {113-119}, pmid = {22143443}, issn = {1610-7365}, mesh = {Aging ; Animals ; Attention ; *Concept Formation ; *Discrimination, Psychological ; Female ; *Fixation, Ocular ; Macaca/*physiology ; Male ; *Pattern Recognition, Visual ; }, abstract = {Both human and nonhuman primates have been suggested to possess some essential knowledge about animate entities, but it remains unclear whether the concept of animacy is shared across species, which properties are used as an "animacy marker," and whether such ability is present at birth. We investigated infant Japanese monkeys' looking responses towards novel objects varying in both physical appearance and self-propelled motion, with the aim of depicting the role of eyes and fluffiness in the early recognition of animacy. Presented with an inanimate natural stone, three-month-old monkeys showed longer looking times at the stone's self-propelled motion than at its baseline still posture. This effect became significantly smaller when artificial fur was attached to the stone, while adding artificial eyes did not elicit a departing pattern in their looking behavior. In contrast, one-month-old monkeys showed no systematic differences in their looking behavior. This suggests that the concept of animacy in terms of self-propelledness may develop between one and three months of age, with sensitivity to texture emerging by three months. Development of biological knowledge is discussed in relation to social knowledge from both ontogenetic and phylogenetic perspectives.}, } @article {pmid22124951, year = {2012}, author = {Poletika, NN and Teply, M and Dominguez, LG and Cramer, SP and Schocken, MJ and Habig, C and Kern, M and Ochoa-Acuña, H and Mitchell, GC}, title = {A spatially and temporally explicit risk assessment for salmon from a prey base exposed to agricultural insecticides.}, journal = {Integrated environmental assessment and management}, volume = {8}, number = {2}, pages = {285-300}, doi = {10.1002/ieam.1273}, pmid = {22124951}, issn = {1551-3793}, mesh = {Acetylcholinesterase/metabolism ; Animals ; Carbamates/toxicity ; *Environmental Exposure ; Environmental Monitoring/*methods ; Fresh Water/chemistry ; Insecticides/*toxicity ; Invertebrates/*drug effects ; Models, Biological ; Oncorhynchus mykiss/growth & development/*metabolism ; Oregon ; Organophosphorus Compounds/toxicity ; Risk Assessment ; Species Specificity ; Uncertainty ; Water Pollutants, Chemical/*toxicity ; }, abstract = {This risk assessment applied a framework for determining probable co-occurrence of juvenile spring Chinook salmon (Oncorhynchus tshawytscha) with agricultural pesticides in the Willamette Basin, Oregon (Teply et al. this issue) to characterize risk to the threatened population. The assessment accounted for spatial and temporal distribution of 6 acetylcholinesterase-inhibiting insecticides in salmonid habitat within the basin and their relative contributions to mixture toxicity estimated from chemical monitoring data. The 6 insecticides were chlorpyrifos, diazinon, malathion, carbaryl, carbofuran, and methomyl. Seasonal distributions of the juvenile salmon prey base across the basin were determined and compared to co-occurrence with the insecticide mixture to determine the probability of prey reduction and reduced production of juvenile fish. Probability of effect on freshwater aquatic invertebrates was based on acute toxicity species sensitivity distributions (normalized to the most potent compound, chlorpyrifos) using a novel approach to apply the toxicological concept of concentration addition to species sensitivity distributions with differing slopes. The chlorpyrifos distribution was then used to determine relative sensitivity among various species tested within the important taxa making up the prey base. A prey base index was devised, incorporating diet composition and prey availability, to evaluate the indirect effects of the insecticide mixture on juvenile salmon production occurring as a result of a reduction in the prey base. Our analysis targeted fish use of backwater and off-channel habitat units, because they generally coincide with agricultural lands in lowlands and represent shallow habitat with limited water exchange. The percentage of agricultural land use within 300 m of critical habitat stream reaches was used to scale chemical measurement data from a site with high agricultural land use across the full extent of the basin to provide estimates of chemical exposure in each reach. Seasonal impacts were evaluated from mean monthly concentrations. Stressor impact on 5 key taxa was evaluated at each time step and for each reach, and the outcome was compared to a conservation threshold assigned to the prey base index. Only 13% of juveniles reared in backwater, off-channel habitat within 300 m of agricultural land. Percent reduction of carrying capacity as a consequence of reduced prey was estimated to be 5% over the entire brood year. This can be considered lost capacity that is probably compensated elsewhere via increased occupancy (emigration to other habitat units within the reach), which is not accounted for in the model.}, } @article {pmid22123327, year = {2011}, author = {Kawasaki, M}, title = {Verification of a taxonomy of dermatophytes based on mating results and phylogenetic analyses.}, journal = {Medical mycology journal}, volume = {52}, number = {4}, pages = {291-295}, doi = {10.3314/mmj.52.291}, pmid = {22123327}, issn = {1882-0476}, mesh = {Animals ; Humans ; *Phylogeny ; Trichophyton/*classification/physiology ; }, abstract = {A newly proposed taxonomy of Trichophyton mentagrophytes and related species was introduced and verified with the grounds for the new classification, phylogenetic analysis, and Templeton's cohesive species concept. So-called asexual species were shown to retain sexual ability and different host preferences were shown not to be comparable to different ecological niches. We showed that genealogical concordance phylogenetic species recognition (GCPSR) can be applied to so-called asexual Trichophyton species. The results of GCPSR analysis and mating experiments demonstrated that Arthroderma simii, A. vanbreuseghemii, T. mentagrophytes var. interdigitale, and T. tonsurans may be considered as single phylogenetic species, and that A. benhamiae, T. concentricum, T. verrucosum, and T. mentagrophytes var. erinacei may also be considered as single phylogenetic species. In addition, the conspecificity of three Arthroderma species may also be demonstrated in future. In conclusion, we should not hastily revise the nomenclature based on the phylogenetic tree from only one gene, because different genes can yield different phylogenetic trees. Therefore, we recommend retaining the previous taxonomy until an acceptable taxonomy is proposed.}, } @article {pmid22113699, year = {2012}, author = {Tang, L and Liu, SL}, title = {The 3Cs provide a novel concept of bacterial species: messages from the genome as illustrated by Salmonella.}, journal = {Antonie van Leeuwenhoek}, volume = {101}, number = {1}, pages = {67-72}, doi = {10.1007/s10482-011-9680-0}, pmid = {22113699}, issn = {1572-9699}, mesh = {Classification/*methods ; *Genome, Bacterial ; *Phylogeny ; Salmonella/*classification/*genetics ; }, abstract = {A key issue troubling bacterial taxonomy and systematics is the lack of a biological species definition. Criteria to be used for defining bacterial species on genetic and biological bases should be able to reveal clear-cut boundaries among clusters of bacteria. To date, DNA-DNA re-association assays and ribosomal RNA sequence comparison have been useful in determining relative evolutionary distances among bacteria but the data are continuous and thus cannot define bacterial clusters as taxonomic units to be called species. Using Salmonella as models, we have looked for definite genetic and biologic uniqueness of clusters of bacteria. Based on our findings that each Salmonella lineage has a unique genome structure shared by strains of the same lineage but not overlapping with strains of other Salmonella lineages, we conclude that this is a result of genetic isolation following divergence of the bacteria. We propose that there should be genetic boundaries between different species of bacteria at the genomic level, which awaits further genomic information for validation.}, } @article {pmid22099653, year = {2011}, author = {Superville, PJ and Louis, Y and Billon, G and Prygiel, J and Omanović, D and Pižeta, I}, title = {An adaptable automatic trace metal monitoring system for on line measuring in natural waters.}, journal = {Talanta}, volume = {87}, number = {}, pages = {85-92}, doi = {10.1016/j.talanta.2011.09.045}, pmid = {22099653}, issn = {1873-3573}, mesh = {Calibration ; Electrochemical Techniques/*instrumentation ; Environmental Monitoring/*instrumentation ; Equipment Design ; France ; Fresh Water/*analysis ; Metals/*analysis ; Rivers/chemistry ; Water Pollutants, Chemical/*analysis ; }, abstract = {An adaptable automatic trace metal monitoring system (ATMS) was assembled and embedded in a mobile monitoring station belonging to the French Water Agency Artois-Picardie (AEAP) and deployed in the field to measure the concentration of trace metals (electroactive and acid leachable fractions) in natural waters by anodic stripping voltammetry with a hanging mercury drop electrode. Cathodic stripping voltammetry procedures were included to estimate the concentration of dissolved oxygen and reduced sulphur species. The concept of the measuring system enables easy adaptation of methods and procedures to analytes of concern and gives the opportunity to undertake in real-time a routine analysis of the dynamic behaviour of trace metals in river, pond and seawater. The system was tested in two aquatic bodies: in a pond where eutrophication processes occur recurrently and in the Deûle River, where sediments are highly contaminated by several metals such as Pb and Zn and frequently resuspended because of the river traffic. Preliminary field studies demonstrated that trace metal concentrations can evolve quickly as a function of time, depending on the turbidity and luminescence, i.e. day-night cycles. The obtained results were compared with an Environmental Quality Standard (EQS), the Criteria Maximum Concentration (CMC) and the Criterion Continuous Concentration (CCC). The whole system is also prepared for the task of "early warning".}, } @article {pmid22086912, year = {2012}, author = {Kautmanová, I and Adamcík, S and Lizon, P and Jancovicová, S}, title = {Revision of taxonomic concept and systematic position of some Clavariaceae species.}, journal = {Mycologia}, volume = {104}, number = {2}, pages = {521-539}, doi = {10.3852/11-121}, pmid = {22086912}, issn = {0027-5514}, mesh = {Agaricales/*classification/genetics/ultrastructure ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Europe ; Molecular Sequence Data ; *Phylogeny ; RNA, Fungal/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; Spores, Fungal/ultrastructure ; }, abstract = {A taxonomic and nomenclatural revision of some representatives of Clavariaceae is presented based on extensive collecting in central and western Europe. Five species originally described from Europe are identified, redescribed and delimited: Clavaria fragilis, Ramariopsis crocea, R. corniculata, R. helvola and R. pulchella. Lectotypes, epitypes or neotypes are designated for all these species. Descriptions are based on macro- and micromorphological characters and supplemented with DNA analyses of the nrLSU regions from 20 specimens. The molecular phylogenetic analyses reconstructed a phylogram showing relationships among the discussed species as well as some closely related taxa. The taxonomic value of the ratio of length and width of spores (Q-value) is discussed.}, } @article {pmid22073788, year = {2011}, author = {Carson, HS and Cook, GS and López-Duarte, PC and Levin, LA}, title = {Evaluating the importance of demographic connectivity in a marine metapopulation.}, journal = {Ecology}, volume = {92}, number = {10}, pages = {1972-1984}, doi = {10.1890/11-0488.1}, pmid = {22073788}, issn = {0012-9658}, mesh = {Animals ; Demography ; *Ecosystem ; Environmental Monitoring ; Larva/physiology ; Models, Biological ; Mytilus/*physiology ; Oceans and Seas ; Population Dynamics ; }, abstract = {Recently researchers have gone to great lengths to measure marine metapopulation connectivity via tagging, genetic, and trace-elemental fingerprinting studies. These empirical estimates of larval dispersal are key to assessing the significance of metapopulation connectivity within a demographic context, but the life-history data required to do this are rarely available. To evaluate the demographic consequences of connectivity we constructed seasonal, size-structured metapopulation matrix models for two species of mytilid mussel in San Diego County, California, USA. The self-recruitment and larval exchange terms were produced from a time series of realized connectivities derived from trace-elemental fingerprinting of larval shells during spring and fall from 2003 to 2008. Both species exhibited a strong seasonal pattern of southward movement of recruits in spring and northward movement in fall. Growth and mortality terms were estimated using mark-recapture data from representative sites for each species and subpopulation, and literature estimates of juvenile mortality. Fecundity terms were estimated using county-wide settlement data from 2006-2008; these data reveal peak reproduction and recruitment in fall for Mytilus californianus, and spring for M. galloprovincialis. Elasticity and life-stage simulation analyses were employed to identify the season- and subpopulation-specific vital rates and connectivity terms to which the metapopulation growth rate (lambda) was most sensitive. For both species, metapopulation growth was most sensitive to proportional changes in adult fecundity, survival and growth of juvenile stages, and population connectivity, in order of importance, but relatively insensitive to adult growth or survival. The metapopulation concept was deemed appropriate for both Mytilus species as exchange between the subpopulations was necessary for subpopulation persistence. However, highest metapopulation growth occurred in years when a greater proportion of recruits was retained within the predominant source subpopulation. Despite differences in habitat and planktonic duration, both species exhibited similar overall metapopulation dynamics with respect to key life stages and processes. However, different peak reproductive periods in an environment of seasonal current reversals led to different regional (subpopulation) contributions to metapopulation maintenance; this result emphasizes the importance of connectivity analysis for spatial management of coastal resources.}, } @article {pmid22004596, year = {2011}, author = {Jones, AC and White, RJ and Orme, ER}, title = {Identifying and relating biological concepts in the Catalogue of Life.}, journal = {Journal of biomedical semantics}, volume = {2}, number = {1}, pages = {7}, pmid = {22004596}, issn = {2041-1480}, abstract = {BACKGROUND: In this paper we describe our experience of adding globally unique identifiers to the Species 2000 and ITIS Catalogue of Life, an on-line index of organisms which is intended, ultimately, to cover all the world's known species. The scientific species names held in the Catalogue are names that already play an extensive role as terms in the organisation of information about living organisms in bioinformatics and other domains, but the effectiveness of their use is hindered by variation in individuals' opinions and understanding of these terms; indeed, in some cases more than one name will have been used to refer to the same organism. This means that it is desirable to be able to give unique labels to each of these differing concepts within the catalogue and to be able to determine which concepts are being used in other systems, in order that they can be associated with the concepts in the catalogue. Not only is this needed, but it is also necessary to know the relationships between alternative concepts that scientists might have employed, as these determine what can be inferred when data associated with related concepts is being processed. A further complication is that the catalogue itself is evolving as scientific opinion changes due to an increasing understanding of life.

RESULTS: We describe how we are using Life Science Identifiers (LSIDs) as globally unique identifiers in the Catalogue of Life, explaining how the mapping to species concepts is performed, how concepts are associated with specific editions of the catalogue, and how the Taxon Concept Schema has been adopted in order to express information about concepts and their relationships. We explore the implications of using globally unique identifiers in order to refer to abstract concepts such as species, which incorporate at least a measure of subjectivity in their definition, in contrast with the more traditional use of such identifiers to refer to more tangible entities, events, documents, observations, etc.

CONCLUSIONS: A major reason for adopting identifiers such as LSIDs is to facilitate data integration. We have demonstrated the incorporation of LSIDs into the Catalogue of Life, in a manner consistent with the biodiversity informatics community's conventions for LSID use. The Catalogue of Life is therefore available as a taxonomy of organisms for use within various disciplines, including biomedical research, by software written with an awareness of these conventions.}, } @article {pmid21968217, year = {2011}, author = {Shah, AD and Kim, JH and Huang, CH}, title = {Tertiary amines enhance reactions of organic contaminants with aqueous chlorine.}, journal = {Water research}, volume = {45}, number = {18}, pages = {6087-6096}, doi = {10.1016/j.watres.2011.09.010}, pmid = {21968217}, issn = {1879-2448}, mesh = {Amines/*chemistry ; Chlorine/*chemistry ; Fluoroquinolones/chemistry ; Kinetics ; Methylamines/chemistry ; Organic Chemicals/*chemistry ; Salicylic Acid/chemistry ; Sulfonic Acids/chemistry ; Trimethoprim/chemistry ; Water/*chemistry ; Water Pollutants, Chemical/*chemistry ; }, abstract = {Through various anthropogenic inputs, tertiary amines can readily contaminate wastewater and drinking water sources and can form chlorammonium species (R(3)N(+)-Cl) during aqueous chlorine disinfection. This study investigated the less understood concept that these chlorammonium species can potentially enhance organic contaminant loss and increase disinfection byproduct formation to a greater extent than aqueous chlorine. Tertiary amines' effectiveness was highly dependent on amine structure as trimethylamine (TMA) and 4-morpholineethanesulfonic acid (MES) enhanced organic contaminant loss, while others (nitrilotriacetic acid (NTA) and creatinine (CRE)) were ineffective. MES addition up to 25 μM led to increased organic contaminant chlorination by up to three orders of magnitude while observing pseudo-first order kinetic behavior and a linear amine dose response. TMA addition up to 0.5 μM accelerated organic contaminant chlorination by almost two orders of magnitude, but occasionally deviated from pseudo-first order kinetics with incomplete organic contaminant degradation and a non-linear amine dose response - a result linked to TMA's rapid auto-decomposition over time. Byproduct formation was identical with and without amine addition, and thus the chlorination mechanisms are likely similar to aqueous chlorine. Results from this study improve the mechanistic understanding behind tertiary amine-enhanced chlorination.}, } @article {pmid21948330, year = {2011}, author = {Blair, ME and Sterling, EJ and Hurley, MM}, title = {Taxonomy and conservation of Vietnam's primates: a review.}, journal = {American journal of primatology}, volume = {73}, number = {11}, pages = {1093-1106}, doi = {10.1002/ajp.20986}, pmid = {21948330}, issn = {1098-2345}, mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources ; Geography ; Primates/*classification ; Vietnam ; }, abstract = {Vietnam has the highest number of primate taxa overall (24-27) and the highest number of globally threatened primate taxa (minimum 20) in Mainland Southeast Asia. Conservation management of these species depends in part on resolving taxonomic uncertainties, which remain numerous among the Asian primates. Recent research on genetic, morphological, and acoustic diversity in Vietnam's primates has clarified some of these uncertainties, although a number of significant classification issues still remain. Herein, we summarize and compare the major current taxonomic classifications of Vietnam's primates, discuss recent advances in the context of these taxonomies, and suggest key areas for additional research to best inform conservation efforts in a region crucial to global primate diversity. Among the most important next steps for the conservation of Vietnam's primates is a new consensus list of Asian primates that resolves current differences between major taxonomies, incorporates recent research advances, and recognizes units of diversity at scales below the species-level, whether termed populations, morphs, or subspecies. Priority should be placed on recognizing distinct populations, regardless of the species concept in use, in order to foster the evolutionary processes necessary for primate populations to cope with inevitable environmental changes. The long-term conservation of Vietnam's primates depends not only on an accepted and accurate taxonomy but also on funding for on-the-ground conservation activities, including training, and the continued dedication and leadership of Vietnamese researchers and managers.}, } @article {pmid21938639, year = {2011}, author = {Jurasinski, G and Koch, M}, title = {Commentary: do we have a consistent terminology for species diversity? We are on the way.}, journal = {Oecologia}, volume = {167}, number = {4}, pages = {893-902; discussion 903-11}, pmid = {21938639}, issn = {1432-1939}, mesh = {Animals ; *Biodiversity ; *Terminology as Topic ; }, abstract = {A consistent terminology for species diversity is subject of an ongoing debate. Recently Tuomisto (Oecologia 164:853-860, 2010) stated that a consistent terminology for diversity already exists. The paper comments on recent papers by ourselves (Jurasinski et al. Oecologia 159:15-26, 2009) and by Moreno and Rodriguez (Oecologia 163:279-282, 2010). Both started from Whittaker's diversity concept to discuss the ambiguities of the terminology and propose a new, more consistent terminology that is based on the different approaches to diversity analysis. In contrast, Tuomisto adheres to a strict school of thinking and derives a diversity framework in the sense of Whittaker (alpha, beta, gamma) from the conceptual definition of diversity itself. A third group of papers discusses appropriate methods for the analysis of the variation in species composition. Here, we support the idea that alpha, beta and gamma diversity should be used in a strict sense that is based only on the conceptual definition of diversity. We accordingly extend and modify our terminological concept for species diversity. All approaches to the analysis and quantification of species composition and diversity can be assigned to three abstraction levels (species composition, variation in species composition,and variation in variation in species composition) and two scale levels (sample scale, aggregation scale). All methods that investigate the variation in species composition across scale levels evaluate beta relation with beta diversity being just one form of beta relation, which is calculated by dividing gamma diversity of order q by the appropriate alpha diversity of the same order. In contrast, differentiation refers to a pairwise calculation of resemblance in species composition. It is restricted to sample scale and is therefore most often only an intermediate step of analysis. Many ecological questions can be addressed either by direct analysis of the variation in species composition using raw data approaches or by further analysis of differentiation datasets on aggregation scale with or without respect to an external gradient.}, } @article {pmid21935372, year = {2011}, author = {Charlton-Robb, K and Gershwin, LA and Thompson, R and Austin, J and Owen, K and McKechnie, S}, title = {A new dolphin species, the Burrunan Dolphin Tursiops australis sp. nov., endemic to southern Australian coastal waters.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24047}, pmid = {21935372}, issn = {1932-6203}, mesh = {Animals ; Bottle-Nosed Dolphin/classification/physiology ; Classification ; Cluster Analysis ; Cytochromes b/metabolism ; DNA, Mitochondrial/metabolism ; Dolphins/*classification/*physiology ; Genetic Variation ; Haplotypes ; Microsatellite Repeats ; Phylogeny ; Sequence Analysis, DNA ; South Australia ; }, abstract = {Small coastal dolphins endemic to south-eastern Australia have variously been assigned to described species Tursiops truncatus, T. aduncus or T. maugeanus; however the specific affinities of these animals is controversial and have recently been questioned. Historically 'the southern Australian Tursiops' was identified as unique and was formally named Tursiops maugeanus but was later synonymised with T. truncatus. Morphologically, these coastal dolphins share some characters with both aforementioned recognised Tursiops species, but they also possess unique characters not found in either. Recent mtDNA and microsatellite genetic evidence indicates deep evolutionary divergence between this dolphin and the two currently recognised Tursiops species. However, in accordance with the recommendations of the Workshop on Cetacean Systematics, and the Unified Species Concept the use of molecular evidence alone is inadequate for describing new species. Here we describe the macro-morphological, colouration and cranial characters of these animals, assess the available and new genetic data, and conclude that multiple lines of evidence clearly indicate a new species of dolphin. We demonstrate that the syntype material of T. maugeanus comprises two different species, one of which is the historical 'southern form of Tursiops' most similar to T. truncatus, and the other is representative of the new species and requires formal classification. These dolphins are here described as Tursiops australis sp. nov., with the common name of 'Burrunan Dolphin' following Australian aboriginal narrative. The recognition of T. australis sp. nov. is particularly significant given the endemism of this new species to a small geographic region of southern and south-eastern Australia, where only two small resident populations in close proximity to a major urban and agricultural centre are known, giving them a high conservation value and making them susceptible to numerous anthropogenic threats.}, } @article {pmid21933414, year = {2011}, author = {Caisová, L and Marin, B and Melkonian, M}, title = {A close-up view on ITS2 evolution and speciation - a case study in the Ulvophyceae (Chlorophyta, Viridiplantae).}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {262}, pmid = {21933414}, issn = {1471-2148}, mesh = {Base Pairing/genetics ; Base Sequence ; Bayes Theorem ; Chlorophyta/*genetics ; Cluster Analysis ; DNA Primers/genetics ; DNA, Ribosomal Spacer/*genetics ; *Evolution, Molecular ; *Genetic Speciation ; Likelihood Functions ; Models, Genetic ; *Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The second Internal Transcriber Spacer (ITS2) is a fast evolving part of the nuclear-encoded rRNA operon located between the 5.8S and 28S rRNA genes. Based on crossing experiments it has been proposed that even a single Compensatory Base Change (CBC) in helices 2 and 3 of the ITS2 indicates sexual incompatibility and thus separates biological species. Taxa without any CBC in these ITS2 regions were designated as a 'CBC clade'. However, in depth comparative analyses of ITS2 secondary structures, ITS2 phylogeny, the origin of CBCs, and their relationship to biological species have rarely been performed. To gain 'close-up' insights into ITS2 evolution, (1) 86 sequences of ITS2 including secondary structures have been investigated in the green algal order Ulvales (Chlorophyta, Viridiplantae), (2) after recording all existing substitutions, CBCs and hemi-CBCs (hCBCs) were mapped upon the ITS2 phylogeny, rather than merely comparing ITS2 characters among pairs of taxa, and (3) the relation between CBCs, hCBCs, CBC clades, and the taxonomic level of organisms was investigated in detail.

RESULTS: High sequence and length conservation allowed the generation of an ITS2 consensus secondary structure, and introduction of a novel numbering system of ITS2 nucleotides and base pairs. Alignments and analyses were based on this structural information, leading to the following results: (1) in the Ulvales, the presence of a CBC is not linked to any particular taxonomic level, (2) most CBC 'clades' sensu Coleman are paraphyletic, and should rather be termed CBC grades. (3) the phenetic approach of pairwise comparison of sequences can be misleading, and thus, CBCs/hCBCs must be investigated in their evolutionary context, including homoplasy events (4) CBCs and hCBCs in ITS2 helices evolved independently, and we found no evidence for a CBC that originated via a two-fold hCBC substitution.

CONCLUSIONS: Our case study revealed several discrepancies between ITS2 evolution in the Ulvales and generally accepted assumptions underlying ITS2 evolution as e.g. the CBC clade concept. Therefore, we developed a suite of methods providing a critical 'close-up' view into ITS2 evolution by directly tracing the evolutionary history of individual positions, and we caution against a non-critical use of the ITS2 CBC clade concept for species delimitation.}, } @article {pmid21918109, year = {2011}, author = {Moore, JM and Székely, T and Büki, J and Devoogd, TJ}, title = {Motor pathway convergence predicts syllable repertoire size in oscine birds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {39}, pages = {16440-16445}, pmid = {21918109}, issn = {1091-6490}, mesh = {*Animal Communication ; Animals ; Phylogeny ; Songbirds/classification/*physiology ; }, abstract = {Behavioral specializations are frequently associated with expansions of the brain regions controlling them. This principle of proper mass spans sensory, motor, and cognitive abilities and has been observed in a wide variety of vertebrate species. Yet, it is unknown if this concept extrapolates to entire neural pathways or how selection on a behavioral capacity might otherwise shape circuit structure. We investigate these questions by comparing the songs and neuroanatomy of 49 species from 17 families of songbirds, which vary immensely in the number of unique song components they produce and possess a conserved neural network dedicated to this behavior. We find that syllable repertoire size is strongly related to the degree of song motor pathway convergence. Repertoire size is more accurately predicted by the number of neurons in higher motor areas relative to that in their downstream targets than by the overall number of neurons in the song motor pathway. Additionally, the convergence values along serial premotor and primary motor projections account for distinct portions of the behavioral variation. These findings suggest that selection on song has independently shaped different components of this hierarchical pathway, and they elucidate how changes in pathway structure could have underlain elaborations of this learned motor behavior.}, } @article {pmid21912592, year = {2011}, author = {Neusser, TP and Jörger, KM and Schrödl, M}, title = {Cryptic species in tropic sands--interactive 3D anatomy, molecular phylogeny and evolution of meiofaunal Pseudunelidae (Gastropoda, Acochlidia).}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e23313}, pmid = {21912592}, issn = {1932-6203}, mesh = {Animals ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Female ; Gastropoda/*anatomy & histology/*genetics ; Genes, Mitochondrial/genetics ; Genetic Markers/genetics ; Genetic Variation ; Male ; *Models, Anatomic ; Pacific Islands ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *Silicon Dioxide ; *Tropical Climate ; User-Computer Interface ; }, abstract = {BACKGROUND: Towards realistic estimations of the diversity of marine animals, tiny meiofaunal species usually are underrepresented. Since the biological species concept is hardly applicable on exotic and elusive animals, it is even more important to apply a morphospecies concept on the best level of information possible, using accurate and efficient methodology such as 3D modelling from histological sections. Molecular approaches such as sequence analyses may reveal further, cryptic species. This is the first case study on meiofaunal gastropods to test diversity estimations from traditional taxonomy against results from modern microanatomical methodology and molecular systematics.

RESULTS: The examined meiofaunal Pseudunela specimens from several Indo-Pacific islands cannot be distinguished by external features. Their 3D microanatomy shows differences in the organ systems and allows for taxonomic separation in some cases. Additional molecular analyses based on partial mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA markers revealed considerable genetic structure that is largely congruent with anatomical or geographical patterns. Two new species (Pseudunela viatoris and P. marteli spp. nov.) are formally described integrating morphological and genetic analyses. Phylogenetic analysis using partial 16S rRNA, COI and the nuclear 18S rRNA markers shows a clade of Pseudunelidae species as the sister group to limnic Acochlidiidae. Within Pseudunela, two subtypes of complex excretory systems occur. A complex kidney already evolved in the ancestor of Hedylopsacea. Several habitat shifts occurred during hedylopsacean evolution.

CONCLUSIONS: Cryptic species occur in tropical meiofaunal Pseudunela gastropods, and likely in other meiofaunal groups with poor dispersal abilities, boosting current diversity estimations. Only a combined 3D microanatomical and molecular approach revealed actual species diversity within Pseudunela reliably. Such integrative methods are recommended for all taxonomic approaches and biodiversity surveys on soft-bodied and small-sized invertebrates. With increasing taxon sampling and details studied, the evolution of acochlidian panpulmonates is even more complex than expected.}, } @article {pmid21908269, year = {2011}, author = {Hamir, AN and Kehrli, ME and Kunkle, RA and Greenlee, JJ and Nicholson, EM and Richt, JA and Miller, JM and Cutlip, RC}, title = {Experimental interspecies transmission studies of the transmissible spongiform encephalopathies to cattle: comparison to bovine spongiform encephalopathy in cattle.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {23}, number = {3}, pages = {407-420}, doi = {10.1177/1040638711403404}, pmid = {21908269}, issn = {1943-4936}, mesh = {Animals ; Cattle ; Cattle Diseases/transmission ; Creutzfeldt-Jakob Syndrome/transmission/veterinary ; Deer ; Disease Susceptibility/veterinary ; Encephalopathy, Bovine Spongiform/*transmission ; Goat Diseases/transmission ; Goats ; Humans ; Prion Diseases/*transmission ; Prions/pathogenicity ; Scrapie/transmission ; Sheep ; Sheep Diseases/transmission ; Wasting Disease, Chronic/transmission ; }, abstract = {Prion diseases or transmissible spongiform encephalopathies (TSEs) of animals include scrapie of sheep and goats; transmissible mink encephalopathy (TME); chronic wasting disease (CWD) of deer, elk and moose; and bovine spongiform encephalopathy (BSE) of cattle. The emergence of BSE and its spread to human beings in the form of variant Creutzfeldt-Jakob disease (vCJD) resulted in interest in susceptibility of cattle to CWD, TME and scrapie. Experimental cross-species transmission of TSE agents provides valuable information for potential host ranges of known TSEs. Some interspecies transmission studies have been conducted by inoculating disease-causing prions intracerebrally (IC) rather than orally; the latter is generally effective in intraspecies transmission studies and is considered a natural route by which animals acquire TSEs. The "species barrier" concept for TSEs resulted from unsuccessful interspecies oral transmission attempts. Oral inoculation of prions mimics the natural disease pathogenesis route whereas IC inoculation is rather artificial; however, it is very efficient since it requires smaller dosage of inoculum, and typically results in higher attack rates and reduces incubation time compared to oral transmission. A species resistant to a TSE by IC inoculation would have negligible potential for successful oral transmission. To date, results indicate that cattle are susceptible to IC inoculation of scrapie, TME, and CWD but it is only when inoculated with TME do they develop spongiform lesions or clinical disease similar to BSE. Importantly, cattle are resistant to oral transmission of scrapie or CWD; susceptibility of cattle to oral transmission of TME is not yet determined.}, } @article {pmid21900313, year = {2012}, author = {Ezard, TH and Pearson, PN and Aze, T and Purvis, A}, title = {The meaning of birth and death (in macroevolutionary birth-death models).}, journal = {Biology letters}, volume = {8}, number = {1}, pages = {139-142}, pmid = {21900313}, issn = {1744-957X}, mesh = {*Biological Evolution ; Classification/*methods ; Computer Simulation ; *Extinction, Biological ; Foraminifera/*cytology ; *Genetic Speciation ; *Models, Biological ; Species Specificity ; }, abstract = {Birth-death models are central to much macroevolutionary theory. The fundamental parameters of these models concern durations. Different species concepts realize different species durations because they represent different ideas of what birth (speciation) and death (extinction) mean. Here, we use Cenozoic macroperforate planktonic foraminifera as a case study to ask: what are the dynamical consequences of changing the definition of birth and death? We show strong evidence for biotic constraints on diversification using evolutionary species, but less with morphospecies. Discussing reasons for this discrepancy, we emphasize that clarity of species concept leads to clarity of meaning when interpreting macroevolutionary birth-death models.}, } @article {pmid21897436, year = {2012}, author = {Gourbière, S and Dorn, P and Tripet, F and Dumonteil, E}, title = {Genetics and evolution of triatomines: from phylogeny to vector control.}, journal = {Heredity}, volume = {108}, number = {3}, pages = {190-202}, pmid = {21897436}, issn = {1365-2540}, support = {R15 AI079672/AI/NIAID NIH HHS/United States ; 1R15 A1079672-01A1//PHS HHS/United States ; }, mesh = {Animals ; Chagas Disease/parasitology/transmission ; *Evolution, Molecular ; Genetics, Population ; Host-Parasite Interactions ; Host-Pathogen Interactions ; Humans ; Insect Vectors/classification/*genetics/microbiology ; Pest Control, Biological ; Phylogeny ; Phylogeography ; Triatominae/classification/*genetics/microbiology ; }, abstract = {Triatomines are hemipteran bugs acting as vectors of the protozoan parasite Trypanosoma cruzi. This parasite causes Chagas disease, one of the major parasitic diseases in the Americas. Studies of triatomine genetics and evolution have been particularly useful in the design of rational vector control strategies, and are reviewed here. The phylogeography of several triatomine species is now slowly emerging, and the struggle to reconcile the phenotypic, phylogenetic, ecological and epidemiological species concepts makes for a very dynamic field. Population genetic studies using different markers indicate a wide range of population structures, depending on the triatomine species, ranging from highly fragmented to mobile, interbreeding populations. Triatomines transmit T. cruzi in the context of complex interactions between the insect vectors, their bacterial symbionts and the parasites; however, an integrated view of the significance of these interactions in triatomine biology, evolution and in disease transmission is still lacking. The development of novel genetic markers, together with the ongoing sequencing of the Rhodnius prolixus genome and more integrative studies, will provide key tools to expanding our understanding of these important insect vectors and allow the design of improved vector control strategies.}, } @article {pmid21872668, year = {2011}, author = {Salicini, I and Ibáñez, C and Juste, J}, title = {Multilocus phylogeny and species delimitation within the Natterer's bat species complex in the Western Palearctic.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {3}, pages = {888-898}, doi = {10.1016/j.ympev.2011.08.010}, pmid = {21872668}, issn = {1095-9513}, mesh = {Alleles ; Animals ; Arctic Regions ; Bayes Theorem ; Cell Nucleus/genetics ; Chiroptera/*genetics ; Cluster Analysis ; Genetic Loci/*genetics ; Genetic Markers ; Geography ; Introns/genetics ; Mediterranean Region ; Mitochondria/genetics ; *Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Software ; Species Specificity ; }, abstract = {Delimiting species is a crucial issue for many biological disciplines and is of primary importance for designing effective conservation plans. Traditional taxonomy based on morphological characters can be misled by the presence of phenotypic plesiomorphism or adaptative convergence. The use of multiple locus genetic data appears thus as a powerful tool for recognizing species boundaries. In this study, we used six nuclear introns and two mitochondrial markers to conduct a phylogenetic study of the Myotis nattereri species complex in the Western Palearctic. We combined tree-based and non-tree-based analyses, and also used concatenated phylogenetic methods of the separated nuclear and mitochondrial dataset as well as a recent coalescence-based multilocus approach. The strong concordance between the results of the analyses conducted confirms that M. nattereri is a paraphyletic group that is composed of four well-differentiated lineages in the study area. In the framework of the unified species concept, these four clades can be confidently considered as four valid species. This recognition of new cryptic species in the Western Mediterranean region shows that the biodiversity of this well-studied area is still not fully understood.}, } @article {pmid21829662, year = {2011}, author = {Fiore-Donno, AM and Novozhilov, YK and Meyer, M and Schnittler, M}, title = {Genetic structure of two protist species (Myxogastria, Amoebozoa) suggests asexual reproduction in sexual Amoebae.}, journal = {PloS one}, volume = {6}, number = {8}, pages = {e22872}, pmid = {21829662}, issn = {1932-6203}, mesh = {Amoeba/classification/*genetics/physiology ; Animals ; Base Sequence ; DNA Primers ; Phylogeny ; *Reproduction, Asexual ; }, abstract = {Plasmodial slime molds (Myxogastria or Myxomycetes) are common and widespread unicellular organisms that are commonly assumed to have a sexual life cycle culminating with the formation of often macroscopic fruiting bodies that efficiently disseminate spores. However, laboratory studies based on mating compatibility revealed the coexistence of asexual as well as sexual strains. To test this hypothesis in natural populations, we investigated the genetic variability of two species of the genus Lamproderma. Detailed ecological relevés were carried out in 2007 and 2009 in several deep ravines in the Elbsandsteingebirge (Saxony, south-eastern Germany). Morphological characters of 93 specimens of Lamproderma were recorded and genetic analyses, based on the small subunit ribosomal gene, the internal transcribed spacer 1 and partial elongation factor 1α sequences were carried out for 52 specimens. Genetic analyses showed the existence of two major clades, each composed of several discrete lineages. Most of these lineages were composed of several identical sequences (SSU, ITS 1 and EF-1α) which is explained best by an asexual mode of reproduction. Detrended Correspondence Analysis of morphological characters revealed two morphospecies that corresponded to the two major clades, except for one genotype (Lc6), thus challenging the morphospecies concept. Genetic patterns were not related to the geographical distribution: specimens belonging to the same genotype were found in distinct ravines, suggesting effective long-distance dispersal via spores, except for the Lc6 genotype which was found only in one ravine. Implications for the morphological and biological species concept are discussed.}, } @article {pmid21819939, year = {2011}, author = {Casaregola, S and Weiss, S and Morel, G}, title = {New perspectives in hemiascomycetous yeast taxonomy.}, journal = {Comptes rendus biologies}, volume = {334}, number = {8-9}, pages = {590-598}, doi = {10.1016/j.crvi.2011.05.006}, pmid = {21819939}, issn = {1768-3238}, mesh = {Ascomycota/*classification ; Biological Evolution ; Classification/*methods ; DNA, Fungal/genetics ; Genes, Fungal ; Genomics/trends ; Multigene Family/genetics ; Nucleic Acid Hybridization ; Yeasts/*classification ; }, abstract = {DNA sequencing has revolutionized yeast taxonomy. Although initially rDNA sequences proved to be universal and convenient for assigning phylogenetic relationships, it was eventually supplanted by multigene analysis, which provided more discriminating and robust results. This led to a new classification of the major yeast clades, which is still used as a reference today. More recently, the availability of a large number of complete genome sequences has given a new perspective on the molecular taxonomy of yeasts by providing a high number of genes to compare. It also highlighted an unexpected aspect of yeast genome evolution: the existence of interspecific hybrids outside of the industrial Saccharomyces clade. Together with the loss of heterozygosity in interspecific hybrids and a reduced sexuality leading to clonal propagation, this observation obliges us to reexamine the present concept of species. In parallel, the ongoing challenge is to find a universal molecular marker, to improve fast authentication and, if possible, phylogeny of yeasts. The future of yeast taxonomy will involve the sequencing of more genomes, thorough analysis of populations to obtain a good representation of the biodiversity and integration of these data into dedicated databases.}, } @article {pmid21814545, year = {2011}, author = {Clare, EL}, title = {Cryptic species? Patterns of maternal and paternal gene flow in eight neotropical bats.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e21460}, pmid = {21814545}, issn = {1932-6203}, mesh = {Animals ; Chiroptera/classification/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Fathers ; Female ; *Gene Flow ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Male ; Mitochondria/genetics ; Mothers ; Phylogeny ; Reproductive Isolation ; Species Specificity ; }, abstract = {Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7(th) intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of the genetic species concept but demonstrate that estimates of mitochondrial diversity alone do not accurately represent gene flow in these species and that contact/hybrid zones must be explored to evaluate reproductive isolation.}, } @article {pmid21795751, year = {2011}, author = {Lassalle, F and Campillo, T and Vial, L and Baude, J and Costechareyre, D and Chapulliot, D and Shams, M and Abrouk, D and Lavire, C and Oger-Desfeux, C and Hommais, F and Guéguen, L and Daubin, V and Muller, D and Nesme, X}, title = {Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {762-781}, pmid = {21795751}, issn = {1759-6653}, mesh = {Adaptation, Biological ; Agrobacterium tumefaciens/classification/*genetics/physiology ; Bacterial Proteins/genetics ; *Ecology ; *Evolution, Molecular ; Genetic Speciation ; Genome, Bacterial ; *Genomics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome-one on the circular chromosome and six on the linear chromosome-suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species.}, } @article {pmid21790783, year = {2011}, author = {Murphy, DD and Weiland, PS and Cummins, KW}, title = {A critical assessment of the use of surrogate species in conservation planning in the Sacramento-San Joaquin Delta, California (U.S.A.).}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {25}, number = {5}, pages = {873-878}, doi = {10.1111/j.1523-1739.2011.01711.x}, pmid = {21790783}, issn = {1523-1739}, mesh = {Animals ; California ; Conservation of Natural Resources/*methods ; *Endangered Species ; *Models, Biological ; Salmon/*growth & development ; Species Specificity ; }, abstract = {Conservation biology has provided wildlife managers with a wealth of concepts and tools for use in conservation planning; among them is the surrogate species concept. Over the past 20 years, a growing body of empirical literature has demonstrated the limited effectiveness of surrogates as management tools, unless it is first established that the target species and surrogate will respond similarly to a given set of environmental conditions. Wildlife managers and policy makers have adopted the surrogate species concept, reflecting the limited information available on most species at risk of extirpation or extinction and constraints on resources available to support conservation efforts. We examined the use of surrogate species, in the form of cross-taxon response-indicator species (that is, one species from which data are used to guide management planning for another, distinct species) in the Sacramento-San Joaquin Delta, California (U.S.A.). In that system there has been increasing reliance on surrogates in conservation planning for species listed under federal or state endangered species acts, although the agencies applying the surrogate species concept did not first validate that the surrogate and target species respond similarly to relevant environmental conditions. During the same period, conservation biologists demonstrated that the surrogate concept is generally unsupported by ecological theory and empirical evidence. Recently developed validation procedures may allow for the productive use of surrogates in conservation planning, but, used without validation, the surrogate species concept is not a reliable planning tool.}, } @article {pmid21774948, year = {2011}, author = {Schubert, H and Feuerpfeil, P and Marquardt, R and Telesh, I and Skarlato, S}, title = {Macroalgal diversity along the Baltic Sea salinity gradient challenges Remane's species-minimum concept.}, journal = {Marine pollution bulletin}, volume = {62}, number = {9}, pages = {1948-1956}, doi = {10.1016/j.marpolbul.2011.06.033}, pmid = {21774948}, issn = {1879-3363}, mesh = {*Biodiversity ; Chlorophyta/classification/growth & development ; Finland ; Germany ; Phaeophyta/classification/growth & development ; Rhodophyta/classification/growth & development ; *Salinity ; Seawater/*chemistry ; Seaweed/*classification/growth & development ; Sodium Chloride/*analysis ; Sweden ; }, abstract = {Remane's species-minimum concept, which states that the lowest number of taxa occurs at the horohalinicum (5-8psu), was tested by investigating macroalgal diversity on hard substrates along the natural salinity gradient in the Baltic Sea. Field data on species occurrence and abundance were collected by SCUBA diving along 10 transects of the Finnish, Swedish and German coasts, covering a salinity range from 3.9 to 27psu. Macroalgal species numbers declined steadily with salinity, decreasing until 7.2psu was reached, but in the horohalinicum, a marked reduction of species number and a change in diversity were indicated by the Shannon index and evenness values. The non-linear decrease in macroalgal diversity at 5-8psu and the lack of increase in species numbers at salinities below 5psu imply a restricted applicability of Remane's species-minimum concept to macroalgae.}, } @article {pmid21731083, year = {2011}, author = {Day, MD and Beck, D and Foster, JA}, title = {Microbial Communities as Experimental Units.}, journal = {Bioscience}, volume = {61}, number = {5}, pages = {398-406}, pmid = {21731083}, issn = {0006-3568}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR016448-01/RR/NCRR NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; P20 RR016454-06/RR/NCRR NIH HHS/United States ; }, abstract = {Artificial ecosystem selection is an experimental technique that treats microbial communities as though they were discrete units by applying selection on community-level properties. Highly diverse microbial communities associated with humans and other organisms can have significant impacts on the health of the host. It is difficult to find correlations between microbial community composition and community-associated diseases, in part because it may be impossible to define a universal and robust species concept for microbes. Microbial communities are composed of potentially thousands of unique populations that evolved in intimate contact, so it is appropriate in many situations to view the community as the unit of analysis. This perspective is supported by recent discoveries using metagenomics and pangenomics. Artificial ecosystem selection experiments can be costly, but they bring the logical rigor of biological model systems to the emerging field of microbial community analysis.}, } @article {pmid21722292, year = {2011}, author = {Baumgartner, K and Coetzee, MP and Hoffmeister, D}, title = {Secrets of the subterranean pathosystem of Armillaria.}, journal = {Molecular plant pathology}, volume = {12}, number = {6}, pages = {515-534}, pmid = {21722292}, issn = {1364-3703}, mesh = {Armillaria/classification/*pathogenicity/*physiology ; Geography ; Host Specificity ; *Host-Pathogen Interactions ; Plant Diseases/*microbiology/prevention & control/statistics & numerical data ; Plant Roots/microbiology ; }, abstract = {UNLABELLED: Armillaria root disease affects fruit and nut crops, timber trees and ornamentals in boreal, temperate and tropical regions of the world. The causal pathogens are members of the genus Armillaria (Basidiomycota, Physalacriaceae). This review summarizes the state of knowledge and highlights recent advances in Armillaria research.

TAXONOMY: Armillaria includes more than 40 morphological species. However, the identification and delineation of species on the basis of morphological characters are problematic, resulting in many species being undetected. Implementation of the biological species' concept and DNA sequence comparisons in the contemporary taxonomy of Armillaria have led to the discovery of a number of new species that are not linked to described morphological species.

HOST RANGE: Armillaria exhibits a range of symbioses with both plants and fungi. As plant pathogens, Armillaria species have broad host ranges, infecting mostly woody species. Armillaria can also colonize orchids Galeola and Gastrodia but, in this case, the fungus is the host and the plant is the parasite. Similar to its contrasting relationships with plants, Armillaria acts as either host or parasite in its interactions with other fungi. Disease control: Recent research on post-infection controls has revealed promising alternatives to the former pre-plant eradication attempts with soil fumigants, which are now being regulated more heavily or banned outright because of their negative effects on the environment. New study tools for genetic manipulation of the pathogen and characterization of the molecular basis of the host response will greatly advance the development of resistant rootstocks in a new stage of research. The depth of the research, regardless of whether traditional or genomic approaches are used, will depend on a clear understanding of where the different propagules of Armillaria attack a root system, which of the pathogen's diverse biolymer-degrading enzymes and secondary metabolites facilitate infection, and how the course of infection differs between resistant and susceptible hosts.}, } @article {pmid21709412, year = {2011}, author = {Brown, JD and Carone, DM and Flynn, BL and Finn, CE and Mlynarski, EE and O'Neill, RJ}, title = {Centromere conversion and retention in somatic cell hybrids.}, journal = {Cytogenetic and genome research}, volume = {134}, number = {3}, pages = {182-190}, doi = {10.1159/000328830}, pmid = {21709412}, issn = {1424-859X}, mesh = {Animals ; Blotting, Southern ; *Centromere ; Cricetinae ; Cricetulus ; DNA Probes ; *Hybrid Cells ; Immunohistochemistry ; In Situ Hybridization, Fluorescence ; Marsupialia ; Mice ; }, abstract = {The generation of somatic cell hybridization-derived cell lines between highly divergent species affords the opportunity to examine the concept of 'genome dominance' in the context of genetic and epigenetic changes. While whole-scale genome dominance has been well documented in natural hybrids among closely related species, an examination of centromere position and sequence retention in 2 marsupial-eutherian hybrids has revealed a mechanism for 'centromere dominance' as a driving force in the generation of stable somatic cell hybrids following an initial period of genomic instability. While one somatic cell hybrid cell line appeared to retain marsupial centromere sequences which remained competent to recruit the centromere-specific histone variant CENP-A in a Chinese hamster background, fusion events between marsupial and mouse-derived chromosomes in another hybrid line led to a centromere sequence conversion from one species to the other. We postulate that the necessity to maintain an epigenetically defined centromere following genome hybridization may be responsible for retention of specific chromosomes and may result in rapid sequence turnover to facilitate the recruitment of CENP-A containing histones.}, } @article {pmid21707318, year = {2011}, author = {Pereira, LH and Pazian, MF and Hanner, R and Foresti, F and Oliveira, C}, title = {DNA barcoding reveals hidden diversity in the Neotropical freshwater fish Piabina argentea (Characiformes: Characidae) from the Upper Paraná Basin of Brazil.}, journal = {Mitochondrial DNA}, volume = {22 Suppl 1}, number = {}, pages = {87-96}, doi = {10.3109/19401736.2011.588213}, pmid = {21707318}, issn = {1940-1744}, mesh = {Animals ; Biodiversity ; Brazil ; Characidae/*classification/*genetics ; Cytochromes b/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/analysis/genetics ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; Fresh Water ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Tropical Climate ; }, abstract = {BACKGROUND AND AIMS: We analyzed a small and wide geographically distributed Neotropical freshwater fish, the Piabina argentea from the Upper Paraná Basin, to check the hypothesis that this species is composed of more than one biological unit, since it has a limited dispersion, through the DNA barcode technique.

MATERIALS AND METHODS: Partial mitochondrial COI and CytB gene sequences were obtained for 58 specimens drawn from 13 localities.

RESULTS: Phylogenetic analysis revealed six major clusters of P. argentea. Kimura-two-parameter (K2P) genetic divergences among these six P. argentea clusters ranged from 2 to 5.6% and from 2.3 to 5.4% for COI and CytB genes, respectively, and these values were on average approximately nine times greater than intra-cluster K2P divergences. The fixation index (F(ST)) among clusters showed very high values and the haplotype network analysis displayed seven unconnected units.

CONCLUSION: These results reinforce the hypothesis that the widely distributed P. argentea species concept as currently conceived actually represents more than one species (possibly six). These results demonstrate the efficacy of DNA barcoding for the discovery of hidden diversity in Neotropical freshwater fishes, and we conclude that barcoding is a useful tool for alpha taxonomy.}, } @article {pmid21642343, year = {2011}, author = {Lendemer, JC}, title = {A taxonomic revision of the North American species of Lepraria s.l. that produce divaricatic acid, with notes on the type species of the genus L. incana.}, journal = {Mycologia}, volume = {103}, number = {6}, pages = {1216-1229}, doi = {10.3852/11-032}, pmid = {21642343}, issn = {0027-5514}, mesh = {Lichens/*classification/genetics/metabolism ; North America ; Phylogeny ; }, abstract = {The divaricatic acid-producing populations of Lepraria in North America north of Mexico are revised with traditional morphological characters, chemistry, ecology, biogeography, and ITS1, 5.8S, and ITS2 sequence data. Three taxa are accepted: L. cryophila, L. hodkinsoniana sp. nov. and L. pacifica sp. nov. Both Lepraria crassissima and L. incana are excluded from the study area. Noncryptic, semicryptic and fully cryptic species concepts in Lepraria are discussed with emphasis on the practical integration of molecular characters into taxonomic frameworks based on non-molecular characters.}, } @article {pmid21632049, year = {2011}, author = {Lenz, M and da Gama, BA and Gerner, NV and Gobin, J and Gröner, F and Harry, A and Jenkins, SR and Kraufvelin, P and Mummelthei, C and Sareyka, J and Xavier, EA and Wahl, M}, title = {Non-native marine invertebrates are more tolerant towards environmental stress than taxonomically related native species: results from a globally replicated study.}, journal = {Environmental research}, volume = {111}, number = {7}, pages = {943-952}, doi = {10.1016/j.envres.2011.05.001}, pmid = {21632049}, issn = {1096-0953}, mesh = {Acclimatization ; Animals ; Bivalvia/classification/*physiology ; Crustacea/classification/*physiology ; Ecosystem ; *Introduced Species ; Oxygen Consumption ; Population Dynamics ; Salinity ; *Stress, Physiological ; Temperature ; Urochordata/classification/*physiology ; }, abstract = {To predict the risk associated with future introductions, ecologists seek to identify traits that determine the invasiveness of species. Among numerous designated characteristics, tolerance towards environmental stress is one of the most favored. However, there is little empirical support for the assumption that non-native species generally cope better with temporarily unfavorable conditions than native species. To test this concept, we ran five pairwise comparisons between native and non-native marine invertebrates at temperate, subtropical, and tropical sites. We included (natives named first) six bivalves: Brachidontes exustus and Perna viridis, P. perna and Isognomon bicolor, Saccostrea glomerata and Crassostrea gigas, two ascidians: Diplosoma listerianum and Didemnum vexillum as well as two crustaceans: Gammarus zaddachi and G. tigrinus. We simulated acute fluctuations in salinity, oxygen concentration, and temperature, while we measured respiration and survival rates. Under stressful conditions, non-native species consistently showed less pronounced deviations from their normal respiratory performance than their native counterparts. We suggest that this indicates that they have a wider tolerance range. Furthermore, they also revealed higher survival rates under stress. Thus, stress tolerance seems to be a property of successful invaders and could therefore be a useful criterion for screening profiles and risk assessment protocols.}, } @article {pmid21620328, year = {2011}, author = {Kartavtsev, YP}, title = {Sequence divergence at mitochondrial genes in animals: applicability of DNA data in genetics of speciation and molecular phylogenetics.}, journal = {Marine genomics}, volume = {4}, number = {2}, pages = {71-81}, doi = {10.1016/j.margen.2011.02.002}, pmid = {21620328}, issn = {1876-7478}, mesh = {Animals ; Base Sequence/*genetics ; Classification/*methods ; Cytochromes b/genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genes, Mitochondrial/*genetics ; *Genetic Speciation ; *Genetic Variation ; Models, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {Nucleotide diversity estimates for the genes Cyt-b (cytochrome b) and Co-1 (cytochrome oxidase 1) are analyzed. Genetic divergence of populations (1) and taxa of different rank, such as subspecies, semispecies or/and sibling species (2), species within a genus (3), species from different genera within a family (4), and species from separate families within an order (5) have been compared using a database of p-distances and similar measures. Empirical data for 20,731 vertebrate and invertebrate animal species reveal various and increasing levels of genetic divergence of the sequences of the two genes, Cyt-b and Co-1, in the five groups compared. Mean unweighted scores of p-distances (%) for five groups are: Cyt-b (1) 1.38±0.30, (2) 5.10±0.91, (3) 10.31±0.93, (4) 17.86±1.36, (5) 26.36±3.88 and Co-1 (1) 0.89±0.16, (2) 3.78±1.18, (3) 11.06±0.53, (4) 16.60±0.69, (5) 20.57±0.40. These estimates testify to the applicability of p-distance for most intraspecies and interspecies comparisons of genetic divergence up to the order level for the two genes compared. The results of the analysis of the nucleotide divergence within species and higher taxa of animals suggest that a phyletic evolution in animals is likely to prevail at the molecular level, and speciation mainly corresponds to the geographic or divergence mode (type D1). The prevalence of the D1 speciation mode does not mean that other modes are absent. At least seven possible modes of speciation are considered. The approach suggested that allows recognize the speciation modes formally with the operational genetic criteria. Such approach may help to solve a key problem of the biological species concept, i.e. the lack of ability to monitor in most cases the reproductive isolation barriers between species.}, } @article {pmid21616907, year = {2010}, author = {Valcárcel, V and Vargas, P}, title = {Quantitative morphology and species delimitation under the general lineage concept: Optimization for Hedera (Araliaceae).}, journal = {American journal of botany}, volume = {97}, number = {9}, pages = {1555-1573}, doi = {10.3732/ajb.1000115}, pmid = {21616907}, issn = {0002-9122}, abstract = {PREMISE OF THE STUDY: The use of continuous morphological characters in taxonomy is traditionally contingent on the existence of discrete diagnostic characters. When plant species are the result of recent divergence and gene flow and/or hybridization occur, the use of continuous morphological characters may help in species identification and delimitation. Between nine and 15 species have been recognized in the last treatments of Hedera. The recent divergence of the species and the involvement of allopolyploidization as the main force in this process may have greatly impeded the establishment of clear limits and contributed to multiple taxonomic proposals. •

METHODS: A multivariate statistical decision-making procedure was applied to 56 quantitative morphological characters and 602 specimens to identify and delimit Hedera species under the general lineage concept. Species' exclusive genetic ancestry was evaluated with the genealogical sorting index from the Bayesian inference trees of 30 Hedera ITS sequences. •

KEY RESULTS: The decision-making procedure allowed recognizing 12 species and two groups (stellate and scale-like trichome groups) in Hedera and provided statistical support for making decisions about long-standing taxonomic controversies. Common ancestry was detected for the populations of three species even in the absence of the species monophyly. •

CONCLUSIONS: Quantitative variation supports discrete variation and provides statistical support for the taxa recognized in some recent proposals of Hedera. The need of explicit analysis of quantitative data are claimed to reduce taxonomic subjectivity and ease decision-making when qualitative data fail.}, } @article {pmid21613059, year = {2011}, author = {Pettengill, JB and Neel, MC}, title = {A sequential approach using genetic and morphological analyses to test species status: the case of United States federally endangered Agalinis acuta (Orobanchaceae).}, journal = {American journal of botany}, volume = {98}, number = {5}, pages = {859-871}, doi = {10.3732/ajb.1000267}, pmid = {21613059}, issn = {1537-2197}, mesh = {Biological Evolution ; *Conservation of Natural Resources ; DNA, Chloroplast/*analysis ; Endangered Species ; Microsatellite Repeats ; Orobanchaceae/anatomy & histology/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; United States ; }, abstract = {PREMISE OF THE STUDY: Given that inaccurate taxonomy can have negative consequences for species of conservation concern and result in erroneous conclusions regarding macroecological patterns, efficient methods for resolving taxonomic uncertainty are essential. The primary objective of this study was to assess the evolutionary distinctiveness of the federally endangered plant species Agalinis acuta (Orobanchaceae) to ensure it represents a distinct taxon warranting protection under the United States Endangered Species Act.

METHODS: We describe and implement a sequential approach that begins with the most restrictive criteria of genealogical exclusivity within which we first conducted a phylogenetic analysis based on six chloroplast DNA loci assayed from multiple representatives of five putative species. Because of the possibility that incomplete lineage sorting is responsible for the lack of genealogical exclusivity among A. acuta individuals, we then conducted intensive population level analyses based on 21 microsatellite loci and 61 morphological traits.

KEY RESULTS: The distinctiveness of A. acuta from Agalinis decemloba and Agalinis tenella was not supported under the genealogical species concept. The results from the analyses of microsatellite loci and morphological characters evaluated under alternative species concepts also did not support the distinctiveness of A. acuta from A. decemloba .

CONCLUSIONS: Through this successive approach, we found insufficient evidence to support the evolutionary distinctiveness of the listed taxon A. acuta . We recommend that it be synonymized under A. decemloba and also conclude that the taxon that would now include A. acuta is deserving of protection under the Endangered Species Act.}, } @article {pmid21612415, year = {2011}, author = {Whittington, ID and Deveney, MR}, title = {New Benedenia species (Monogenea: Capsalidae) from Diagramma labiosum (Perciformes: Haemulidae) on the Great Barrier Reef, Australia, with oncomiracidial descriptions and a report of egg attachment to the host.}, journal = {The Journal of parasitology}, volume = {97}, number = {6}, pages = {1026-1034}, doi = {10.1645/GE-2812.1}, pmid = {21612415}, issn = {1937-2345}, mesh = {Animals ; Fish Diseases/*parasitology ; Gills/*parasitology ; Ovum/physiology ; Perciformes/*parasitology ; Platyhelminths/anatomy & histology/*classification/physiology ; Queensland ; Seawater ; Trematode Infections/parasitology/*veterinary ; }, abstract = {The slate sweetlips, Diagramma labiosum Macleay, 1883 (Perciformes: Haemulidae), off Heron Island, Great Barrier Reef, Queensland, Australia, hosts 2 new species of Benedenia Diesing, 1858 (Monogenea: Monopisthocotylea: Capsalidae). Benedenia beverleyburtonae n. sp. infects proximal regions of the primary gill lamellae and gill arches. The adult is characterized by a dorsal vaginal pore anterior to the common genital pore and a voluminous, highly coiled vas deferens. This species also has fine muscle fibrils concentrically arranged in the haptor. Its ciliated oncomiracidium differs little from larvae of other Benedenia species, with the exception of at least 4 gland cells containing a granular secretion on each side of the body at the level of the excretory bladders, with fine ducts opening anterior to the eyes. Benedenia disciliata n. sp. infects gill arches and gill rakers, and the adult is characterized by its small total length, anterior hamuli with a small proximal notch, posterior hamuli with a broad, triangular shape proximally, a conspicuous internal fertilization chamber, and asymmetrical eggs. None of the 5 specimens collected had testes, but their definite absence is undetermined. Their absence and the fact that the vas deferens was discernable only distally in the specimens of B. disciliata examined may represent atrophying of the male organs. Benedenia disciliata is unique among Benedenia species because eggs are attached to the host's gill arches by tight wrapping of the appendages around spines on the gill rakers and the larva is not ciliated. Among Capsalidae species, these features are shared only with species of Dioncus Goto, 1899. Recent molecular evidence has indicated Benedenia is polyphyletic, but with no clear morphological characters available to divide the genus, the 2 new species fit the current concept for the genus more closely than other capsalid genera. Proposal and description of these taxa and accounts of their oncomiracidia and other aspects of their biology indicate potentially useful characters for division of the genus in the future.}, } @article {pmid21593870, year = {2011}, author = {He, F and Hubbell, SP}, title = {Species-area relationships always overestimate extinction rates from habitat loss.}, journal = {Nature}, volume = {473}, number = {7347}, pages = {368-371}, pmid = {21593870}, issn = {1476-4687}, mesh = {Animals ; Biodiversity ; *Ecosystem ; *Extinction, Biological ; Models, Biological ; *Models, Statistical ; Passeriformes/classification ; Population Density ; Trees/growth & development ; United States ; }, abstract = {Extinction from habitat loss is the signature conservation problem of the twenty-first century. Despite its importance, estimating extinction rates is still highly uncertain because no proven direct methods or reliable data exist for verifying extinctions. The most widely used indirect method is to estimate extinction rates by reversing the species-area accumulation curve, extrapolating backwards to smaller areas to calculate expected species loss. Estimates of extinction rates based on this method are almost always much higher than those actually observed. This discrepancy gave rise to the concept of an 'extinction debt', referring to species 'committed to extinction' owing to habitat loss and reduced population size but not yet extinct during a non-equilibrium period. Here we show that the extinction debt as currently defined is largely a sampling artefact due to an unrecognized difference between the underlying sampling problems when constructing a species-area relationship (SAR) and when extrapolating species extinction from habitat loss. The key mathematical result is that the area required to remove the last individual of a species (extinction) is larger, almost always much larger, than the sample area needed to encounter the first individual of a species, irrespective of species distribution and spatial scale. We illustrate these results with data from a global network of large, mapped forest plots and ranges of passerine bird species in the continental USA; and we show that overestimation can be greater than 160%. Although we conclude that extinctions caused by habitat loss require greater loss of habitat than previously thought, our results must not lead to complacency about extinction due to habitat loss, which is a real and growing threat.}, } @article {pmid21560681, year = {2011}, author = {Grace, JB and Harrison, S and Damschen, EI}, title = {Local richness along gradients in the Siskiyou herb flora: R. H. Whittaker revisited.}, journal = {Ecology}, volume = {92}, number = {1}, pages = {108-120}, doi = {10.1890/09-2137.1}, pmid = {21560681}, issn = {0012-9658}, mesh = {*Altitude ; *Ecosystem ; Oregon ; Plants/*classification ; *Soil ; *Trees ; }, abstract = {In his classic study in the Siskiyou Mountains (Oregon, USA), one of the most botanically rich forested regions in North America, R. H. Whittaker (1960) foreshadowed many modern ideas on the multivariate control of local species richness along environmental gradients related to productivity. Using a structural equation model to analyze his data, which were never previously statistically analyzed, we demonstrate that Whittaker was remarkably accurate in concluding that local herb richness in these late-seral forests is explained to a large extent by three major abiotic gradients (soils, topography, and elevation), and in turn, by the effects of these gradients on tree densities and the numbers of individual herbs. However, while Whittaker also clearly appreciated the significance of large-scale evolutionary and biogeographic influences on community composition, he did not fully articulate the more recent concept that variation in the species richness of local communities could be explained in part by variation in the sizes of regional species pools. Our model of his data is among the first to use estimates of regional species pool size to explain variation in local community richness along productivity-related gradients. We find that regional pool size, combined with a modest number of other interacting abiotic and biotic factors, explains most of the variation in local herb richness in the Siskiyou biodiversity hotspot.}, } @article {pmid21559328, year = {2011}, author = {Korcsmáros, T and Szalay, MS and Rovó, P and Palotai, R and Fazekas, D and Lenti, K and Farkas, IJ and Csermely, P and Vellai, T}, title = {Signalogs: orthology-based identification of novel signaling pathway components in three metazoans.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e19240}, pmid = {21559328}, issn = {1932-6203}, mesh = {Algorithms ; Animals ; Caenorhabditis elegans ; Computational Biology/methods ; Databases, Genetic ; Drosophila melanogaster ; Gene Expression Regulation ; Genetics ; Humans ; Phenotype ; RNA Interference ; Receptors, Notch/metabolism ; *Signal Transduction ; Species Specificity ; }, abstract = {BACKGROUND: Uncovering novel components of signal transduction pathways and their interactions within species is a central task in current biological research. Orthology alignment and functional genomics approaches allow the effective identification of signaling proteins by cross-species data integration. Recently, functional annotation of orthologs was transferred across organisms to predict novel roles for proteins. Despite the wide use of these methods, annotation of complete signaling pathways has not yet been transferred systematically between species.

PRINCIPAL FINDINGS: Here we introduce the concept of 'signalog' to describe potential novel signaling function of a protein on the basis of the known signaling role(s) of its ortholog(s). To identify signalogs on genomic scale, we systematically transferred signaling pathway annotations among three animal species, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and humans. Using orthology data from InParanoid and signaling pathway information from the SignaLink database, we predict 88 worm, 92 fly, and 73 human novel signaling components. Furthermore, we developed an on-line tool and an interactive orthology network viewer to allow users to predict and visualize components of orthologous pathways. We verified the novelty of the predicted signalogs by literature search and comparison to known pathway annotations. In C. elegans, 6 out of the predicted novel Notch pathway members were validated experimentally. Our approach predicts signaling roles for 19 human orthodisease proteins and 5 known drug targets, and suggests 14 novel drug target candidates.

CONCLUSIONS: Orthology-based pathway membership prediction between species enables the identification of novel signaling pathway components that we referred to as signalogs. Signalogs can be used to build a comprehensive signaling network in a given species. Such networks may increase the biomedical utilization of C. elegans and D. melanogaster. In humans, signalogs may identify novel drug targets and new signaling mechanisms for approved drugs.}, } @article {pmid21558500, year = {2011}, author = {Buyck, B and Cruaud, C and Couloux, A and Hofstetter, V}, title = {Cantharellus texensis sp. nov. from Texas, a southern lookalike of C. cinnabarinus revealed by tef-1 sequence data.}, journal = {Mycologia}, volume = {103}, number = {5}, pages = {1037-1046}, doi = {10.3852/10-261}, pmid = {21558500}, issn = {0027-5514}, mesh = {Base Sequence ; Basidiomycota/*classification/cytology/*genetics ; DNA, Fungal/analysis ; Fungal Proteins/*genetics ; *Genes, Fungal ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Spores, Fungal/classification ; Texas ; Transcriptional Elongation Factors/*genetics ; United States ; }, abstract = {This contribution to the genus Cantharellus in North America deals with the smaller, reddish pink species from the Gulf of Mexico states and eastern United States. C. texensis sp. nov. is presented as a new southern lookalike of C. cinnabarinus. The morphological species concepts are supported by newly generated molecular sequence data from the protein coding gene tef1. Similarities to C. persicinus, a third pinkish taxon, are discussed. The very different microscopic features for the three taxa are illustrated in detail. C. cinnabarinus is neotypified. C. minor forma intensissima is considered to be possibly unrelated not only to the discussed taxa in this paper but also to typical C. minor.}, } @article {pmid21558210, year = {2010}, author = {Daly, M and Gusmão, LC and Reft, AJ and Rodríguez, E}, title = {Phylogenetic signal in mitochondrial and nuclear markers in sea anemones (Cnidaria, Actiniaria).}, journal = {Integrative and comparative biology}, volume = {50}, number = {3}, pages = {371-388}, doi = {10.1093/icb/icq081}, pmid = {21558210}, issn = {1557-7023}, mesh = {Animals ; Biomarkers ; Cell Nucleus/*genetics ; DNA/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Genetic Variation ; *Phylogeny ; Sea Anemones/*genetics ; Sequence Analysis, DNA ; Signal Transduction/*genetics ; }, abstract = {The mitochondrial genome of basal animals is generally more slowly evolving than that of bilaterians. This difference in rate complicates the study of relationships among members of these lineages and the discovery of cryptic species or the testing of morphological species concepts within them. We explore the properties of mitochondrial and nuclear ribosomal genes in the cnidarian order Actiniaria, using both an ordinal- and familial-scale sample of taxa. Although the markers do not show significant incongruence, they differ in their phylogenetic informativeness and the kinds of relationships they resolve. Among the markers studied here, the fragments of 12S rDNA and 18S rDNA most effectively recover well-supported nodes; those of 16S rDNA and 28S rDNA are less effective. The general patterns we observed are similar to those in other hexacorallians, although Actiniaria alone show saturation of transitions for ordinal-scale analyses.}, } @article {pmid21550608, year = {2011}, author = {Riede, T and York, A and Furst, S and Müller, R and Seelecke, S}, title = {Elasticity and stress relaxation of a very small vocal fold.}, journal = {Journal of biomechanics}, volume = {44}, number = {10}, pages = {1936-1940}, pmid = {21550608}, issn = {1873-2380}, support = {R01 DC008612-05/DC/NIDCD NIH HHS/United States ; R01 DC008612/DC/NIDCD NIH HHS/United States ; R01 DC008612-01A1/DC/NIDCD NIH HHS/United States ; R01 DC008612-04/DC/NIDCD NIH HHS/United States ; R01 DC008612-06/DC/NIDCD NIH HHS/United States ; R01DC008612/DC/NIDCD NIH HHS/United States ; R01 DC008612-02/DC/NIDCD NIH HHS/United States ; R01 DC008612-03/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Biomechanical Phenomena ; Elasticity ; Larynx/pathology ; Male ; Models, Statistical ; Phonation/physiology ; Rats ; Rats, Sprague-Dawley ; Reproducibility of Results ; Stress, Mechanical ; Tensile Strength ; Vocal Cords/*physiology ; }, abstract = {Across mammals many vocal sounds are produced by airflow induced vocal fold oscillation. We tested the hypothesis that stress-strain and stress-relaxation behavior of rat vocal folds can be used to predict the fundamental frequency range of the species' vocal repertoire. In a first approximation vocal fold oscillation has been modeled by the string model but it is not known whether this concept equally applies to large and small species. The shorter the vocal fold, the more the ideal string law may underestimate normal mode frequencies. To accommodate the very small size of the tissue specimen, a custom-built miniaturized tensile test apparatus was developed. Tissue properties of 6 male rat vocal folds were measured. Rat vocal folds demonstrated the typical linear stress-strain behavior in the low strain region and an exponential stress response at strains larger than about 40%. Approximating the rat's vocal fold oscillation with the string model suggests that fundamental frequencies up to about 6 kHz can be produced, which agrees with frequencies reported for audible rat vocalization. Individual differences and time-dependent changes in the tissue properties parallel findings in other species, and are interpreted as universal features of the laryngeal sound source.}, } @article {pmid21530920, year = {2011}, author = {Porter, TM and Martin, W and James, TY and Longcore, JE and Gleason, FH and Adler, PH and Letcher, PM and Vilgalys, R}, title = {Molecular phylogeny of the Blastocladiomycota (Fungi) based on nuclear ribosomal DNA.}, journal = {Fungal biology}, volume = {115}, number = {4-5}, pages = {381-392}, doi = {10.1016/j.funbio.2011.02.004}, pmid = {21530920}, issn = {1878-6146}, mesh = {Animals ; Blastocladiomycota/classification/*genetics ; Cell Nucleus/genetics ; DNA, Fungal/genetics ; DNA, Ribosomal/*genetics ; Evolution, Molecular ; Insecta/microbiology ; Larva/microbiology ; *Phylogeny ; }, abstract = {The Blastocladiomycota is a recently described phylum of ecologically diverse zoosporic fungi whose species have not been thoroughly sampled and placed within a molecular phylogeny. In this study, we investigated the phylogeny of the Blastocladiomycota based on ribosomal DNA sequences from strains identified by traditional morphological and ultrastructural characters. Our results support the monophyly of the Coelomomycetaceae and Physodermataceae but the Blastocladiaceae and Catenariaceae are paraphyletic or polyphyletic. The data support two clades within Allomyces with strains identified as Allomyces arbusculus in both clades, suggesting that species concepts in Allomyces are in need of revision. A clade of Catenaria species isolated from midge larvae group separately from other Catenaria species, suggesting that this genus may need revision. In the Physodermataceae, Urophlyctis species cluster with a clade of Physoderma species. The algal parasite Paraphysoderma sedebokerensis nom. prov. clusters sister to other taxa in the Physodermataceae. Catenomyces persicinus, which has been classified in the Catenariaceae, groups with the Chytridiomycota rather than Blastocladiomycota. The rDNA operon seems to be suitable for classification within the Blastocladiomycota and distinguishes among genera; however, this region alone is not suitable to determine the position of the Blastocladiomycota among other basal fungal phyla with statistical support. A focused effort to find and isolate, or directly amplify DNA from additional taxa will be necessary to evaluate diversity in this phylum. We provide this rDNA phylogeny as a preliminary framework to guide further taxon and gene sampling and to facilitate future ecological, morphological, and systematic studies.}, } @article {pmid21526989, year = {2011}, author = {Ryu, T and Mavromatis, CH and Bayer, T and Voolstra, CR and Ravasi, T}, title = {Unexpected complexity of the reef-building coral Acropora millepora transcription factor network.}, journal = {BMC systems biology}, volume = {5}, number = {}, pages = {58}, pmid = {21526989}, issn = {1752-0509}, mesh = {Animals ; Anthozoa/*genetics/growth & development ; Biological Evolution ; DNA Footprinting/methods ; *Gene Expression Profiling ; Genomics ; Models, Biological ; Oceans and Seas ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Transcription Factors/*genetics ; }, abstract = {BACKGROUND: Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental changes especially at the molecular level. This is mostly because of the paucity of genome-wide studies on corals and the application of systems approaches that incorporate the latter. Like in any other organism, the response of corals to stress is tightly controlled by the coordinated interplay of many transcription factors.

RESULTS: Here, we develop and apply a new system-wide approach in order to infer combinatorial transcription factor networks of the reef-building coral Acropora millepora. By integrating sequencing-derived transcriptome measurements, a network of physically interacting transcription factors, and phylogenetic network footprinting we were able to infer such a network. Analysis of the network across a phylogenetically broad sample of five species, including human, reveals that despite the apparent simplicity of corals, their transcription factors repertoire and interaction networks seem to be largely conserved. In addition, we were able to identify interactions among transcription factors that appear to be species-specific lending strength to the novel concept of "Taxonomically Restricted Interactions".

CONCLUSIONS: This study provides the first look at transcription factor networks in corals. We identified a transcription factor repertoire encoded by the coral genome and found consistencies of the domain architectures of transcription factors and conserved regulatory subnetworks across eumetazoan species, providing insight into how regulatory networks have evolved.}, } @article {pmid21523190, year = {2011}, author = {Gräfenhan, T and Schroers, HJ and Nirenberg, HI and Seifert, KA}, title = {An overview of the taxonomy, phylogeny, and typification of nectriaceous fungi in Cosmospora, Acremonium, Fusarium, Stilbella, and Volutella.}, journal = {Studies in mycology}, volume = {68}, number = {}, pages = {79-113}, pmid = {21523190}, issn = {1872-9797}, abstract = {A comprehensive phylogenetic reassessment of the ascomycete genus Cosmospora (Hypocreales, Nectriaceae) is undertaken using fresh isolates and historical strains, sequences of two protein encoding genes, the second largest subunit of RNA polymerase II (rpb2), and a new phylogenetic marker, the larger subunit of ATP citrate lyase (acl1). The result is an extensive revision of taxonomic concepts, typification, and nomenclatural details of many anamorph- and teleomorph-typified genera of the Nectriaceae, most notably Cosmospora and Fusarium. The combined phylogenetic analysis shows that the present concept of Fusarium is not monophyletic and that the genus divides into two large groups, one basal in the family, the other terminal, separated by a large group of species classified in genera such as Calonectria, Neonectria, and Volutella. All accepted genera received high statistical support in the phylogenetic analyses. Preliminary polythetic morphological descriptions are presented for each genus, providing details of perithecia, micro- and/or macro-conidial synanamorphs, cultural characters, and ecological traits. Eight species are included in our restricted concept of Cosmospora, two of which have previously documented teleomorphs and all of which have Acremonium-like microconidial anamorphs. A key is provided to the three anamorphic species recognised in Atractium, which is removed from synonymy with Fusarium and epitypified for two macroconidial synnematous species and one sporodochial species associated with waterlogged wood. Dialonectria is recognised as distinct from Cosmospora and two species with teleomorph, macroconidia and microconidia are accepted, including the new species D. ullevolea. Seven species, one with a known teleomorph, are classified in Fusicolla, formerly considered a synonym of Fusarium including members of the F. aquaeductuum and F. merismoides species complex, with several former varieties raised to species rank. Originally a section of Nectria, Macroconia is raised to generic rank for five species, all producing a teleomorph and macroconidial anamorph. A new species of the Verticillium-like anamorphic genus Mariannaea is described as M. samuelsii. Microcera is recognised as distinct from Fusarium and a key is included for four macroconidial species, that are usually parasites of scale insects, two of them with teleomorphs. The four accepted species of Stylonectria each produce a teleomorph and micro- and macroconidial synanamorphs. The Volutella species sampled fall into three clades. Pseudonectria is accepted for a perithecial and sporodochial species that occurs on Buxus. Volutella s. str. also includes perithecial and/or sporodochial species and is revised to include a synnematous species formerly included in Stilbella. The third Volutella-like clade remains unnamed. All fungi in this paper are named using a single name system that gives priority to the oldest generic names and species epithets, irrespective of whether they are originally based on anamorph or teleomorph structures. The rationale behind this is discussed.}, } @article {pmid21518061, year = {2011}, author = {Triponez, Y and Buerki, S and Borer, M and Naisbit, RE and Rahier, M and Alvarez, N}, title = {Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe.}, journal = {Molecular ecology}, volume = {20}, number = {11}, pages = {2442-2463}, doi = {10.1111/j.1365-294X.2011.05096.x}, pmid = {21518061}, issn = {1365-294X}, mesh = {Animals ; Base Sequence ; Coleoptera/*anatomy & histology/*genetics ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Europe ; Genetic Variation ; *Ice Cover ; Molecular Sequence Data ; *Phylogeny ; *Phylogeography ; Plant Leaves/*parasitology ; Polymorphism, Genetic ; Time Factors ; }, abstract = {Pleistocene glacial and interglacial periods have moulded the evolutionary history of European cold-adapted organisms. The role of the different mountain massifs has, however, not been accurately investigated in the case of high-altitude insect species. Here, we focus on three closely related species of non-flying leaf beetles of the genus Oreina (Coleoptera, Chrysomelidae), which are often found in sympatry within the mountain ranges of Europe. After showing that the species concept as currently applied does not match barcoding results, we show, based on more than 700 sequences from one nuclear and three mitochondrial genes, the role of biogeography in shaping the phylogenetic hypothesis. Dating the phylogeny using an insect molecular clock, we show that the earliest lineages diverged more than 1 Mya and that the main shift in diversification rate occurred between 0.36 and 0.18 Mya. By using a probabilistic approach on the parsimony-based dispersal/vicariance framework (MP-DIVA) as well as a direct likelihood method of state change optimization, we show that the Alps acted as a cross-roads with multiple events of dispersal to and reinvasion from neighbouring mountains. However, the relative importance of vicariance vs. dispersal events on the process of rapid diversification remains difficult to evaluate because of a bias towards overestimation of vicariance in the DIVA algorithm. Parallels are drawn with recent studies of cold-adapted species, although our study reveals novel patterns in diversity and genetic links between European mountains, and highlights the importance of neglected regions, such as the Jura and the Balkanic range.}, } @article {pmid21505762, year = {2011}, author = {Hall, MS and Katz, LA}, title = {On the nature of species: insights from Paramecium and other ciliates.}, journal = {Genetica}, volume = {139}, number = {5}, pages = {677-684}, pmid = {21505762}, issn = {1573-6857}, support = {R15 GM081865/GM/NIGMS NIH HHS/United States ; R15 GM081865-01/GM/NIGMS NIH HHS/United States ; 1R15GM081865-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Epigenomics ; *Genetic Speciation ; Isoenzymes/genetics ; Paramecium/*genetics ; *Phylogeny ; }, abstract = {The multiple species concepts currently in use by the scientific community (e.g. Morphological, Biological, Phylogenetic) are united in that they all aim to capture the process of divergence between populations. For example, the Biological Species Concept defines a species as a natural group of organisms that is reproductively isolated from other such groups. Here we synthesize nearly a century of research on the ciliate genus Paramecium that highlights the shortcomings of our prevailing notions on the nature of species. In this lineage, there is discordance between morphology, mating behavior, and genetics, features assumed to be correlated, at least after sufficient time has passed, under all species concepts. Intriguingly, epigenetic phenomena are well documented in ciliates where they influence features such as germline/soma differentiation and mating type determination. Consequently, we hypothesize that divergence within ciliate populations is due to a dynamic interaction between genetic and epigenetic factors. The growing list of examples of epigenetic phenomena that potentially impact speciation (i.e. by influencing the dynamics of sex chromosomes, fate of hybrids, zygotic drive and genomic conflicts) suggests that interactions between genetics and epigenetics may also drive divergence in other eukaryotic lineages.}, } @article {pmid21482777, year = {2011}, author = {Avise, JC and Liu, JX}, title = {Multiple mating and its relationship to brood size in pregnant fishes versus pregnant mammals and other viviparous vertebrates.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {17}, pages = {7091-7095}, pmid = {21482777}, issn = {1091-6490}, mesh = {Animals ; Clutch Size ; Female ; Fishes ; Male ; Mammals/*physiology ; Mating Preference, Animal/*physiology ; *Models, Biological ; Pregnancy/*physiology ; Viviparity, Nonmammalian/*physiology ; }, abstract = {We summarize the literature on rates of multiple paternity and sire numbers per clutch in viviparous fishes vs. mammals, two vertebrate groups in which pregnancy is common but entails very different numbers of embryos (for species surveyed, piscine broods averaged >10-fold larger than mammalian litters). As deduced from genetic parentage analyses, multiple mating by the pregnant sex proved to be common in assayed species but averaged significantly higher in fish than mammals. However, within either of these groups we found no significant correlations between brood size and genetically deduced incidence of multiple mating by females. Overall, these findings offer little support for the hypothesis that clutch size in pregnant species predicts the outcome of selection for multiple mating by brooders. Instead, whatever factors promote multiple mating by members of the gestating sex seem to do so in surprisingly similar ways in live-bearing vertebrates otherwise as different as fish and mammals. Similar conclusions emerged when we extended the survey to viviparous amphibians and reptiles. One notion consistent with these empirical observations is that although several fitness benefits probably accrue from multiple mating, logistical constraints on mate-encounter rates routinely truncate multiple mating far below levels that otherwise could be accommodated, especially in species with larger broods. We develop this concept into a "logistical constraint hypothesis" that may help to explain these mating outcomes in viviparous vertebrates. Under the logistical constraint hypothesis, propensities for multiple mating in each species register a balance between near-universal fitness benefits from multiple mating and species-idiosyncratic logistical limits on polygamy.}, } @article {pmid21482632, year = {2011}, author = {Rehner, SA and Minnis, AM and Sung, GH and Luangsa-ard, JJ and Devotto, L and Humber, RA}, title = {Phylogeny and systematics of the anamorphic, entomopathogenic genus Beauveria.}, journal = {Mycologia}, volume = {103}, number = {5}, pages = {1055-1073}, doi = {10.3852/10-302}, pmid = {21482632}, issn = {0027-5514}, mesh = {Animals ; Arthropods/*microbiology ; Base Sequence ; Beauveria/*classification/*genetics/pathogenicity ; DNA, Fungal/analysis/*genetics ; DNA, Ribosomal Spacer/genetics ; Eukaryotic Initiation Factors ; Genetic Variation ; Pest Control, Biological ; Phylogeny ; Polymerase Chain Reaction ; RNA Polymerase II/genetics ; Sequence Analysis, DNA ; }, abstract = {Beauveria is a cosmopolitan anamorphic genus of arthropod pathogens that includes the agronomically important species, B. bassiana and B. brongniartii, which are used as mycoinsecticides for the biological control of pest insects. Recent phylogenetic evidence demonstrates that Beauveria is monophyletic within the Cordycipitaceae (Hypocreales), and both B. bassiana and B. brongniartii have been linked developmentally and phylogenetically to Cordyceps species. Despite recent interest in the genetic diversity and molecular ecology of Beauveria, particularly as it relates to their role as pathogens of insects in natural and agricultural environments, the genus has not received critical taxonomic review for several decades. A multilocus phylogeny of Beauveria based on partial sequences of RPB1, RPB2, TEF and the nuclear intergenic region, Bloc, is presented and used to assess diversity within the genus and to evaluate species concepts and their taxonomic status. B. bassiana and B. brongniartii, both which represent species complexes and which heretofore have lacked type specimens, are redescribed and types are proposed. In addition six new species are described including B. varroae and B. kipukae, which form a biphyletic, morphologically cryptic sister lineage to B. bassiana, B. pseudobassiana, which also is morphologically similar to but phylogenetically distant from B. bassiana, B. asiatica and B. australis, which are sister lineages to B. brongniartii, and B. sungii, an Asian species that is linked to an undetermined species of Cordyceps. The combination B. amorpha is validly published and an epitype is designated.}, } @article {pmid21471294, year = {2011}, author = {Rajchenberg, M}, title = {Nuclear behavior of the mycelium and the phylogeny of Polypores (Basidiomycota).}, journal = {Mycologia}, volume = {103}, number = {4}, pages = {677-702}, doi = {10.3852/10-310}, pmid = {21471294}, issn = {0027-5514}, mesh = {Cell Nucleus/genetics/*physiology ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Genes, Mating Type, Fungal ; Mycelium/genetics/physiology ; Phylogeny ; Polyporales/classification/genetics/*physiology ; }, abstract = {This is a review of the available knowledge on nuclear behavior of the mycelium within polypore genera (Agaricomycetes, Basidiomycota). Information on 68 genera showed that nuclear behavior is a distinct and consistent feature at genus level and can be coupled with phylogenetic differentiation. The sole exception was found in Polyporus, where different species with normal, heterocytic and astatocoenocytic nuclear behaviors were found. Of the 68 genera treated 41 (60.3%) displayed a normal nuclear behavior, nine (13.2%) were heterocytic, nine (13.2%) were astatocoenocytic and another eight (11.8%) were holocoenocytic. In 95% of the genera a unique compatibility system was found, with the exceptions of Antrodia, which includes both homothallic and bipolar species all associated with a normal nuclear behavior, and Spongipellis, in which bipolar and tetrapolar species are found, all displaying an astatocoenocytic nuclear behavior. Normal and heterocytic nuclear behaviors were associated mostly with tetrapolarity, astatocoenocity was associated mostly with bipolarity, and holocoenocity was associated with either bipolarity or purported homothallism. The combination of nuclear behavior with mating system and brown or white rot capability appeared as a strong feature characterizing and distinguishing the genera of polypores, each combination being valuable to differentiate between apparently related genera, as is supported by phylogenetic studies. Several examples are presented to support this idea, as well as the cases of species that are problematic to this concept. Poroid genera of Hymenochaetaceae were treated apart because of the lack of knowledge regarding their nuclear behavior. In addition new information on the sexuality and/or nuclear behavior of 15 polyporoid taxa is given.}, } @article {pmid21463293, year = {2011}, author = {Hausdorf, B}, title = {Progress toward a general species concept.}, journal = {Evolution; international journal of organic evolution}, volume = {65}, number = {4}, pages = {923-931}, doi = {10.1111/j.1558-5646.2011.01231.x}, pmid = {21463293}, issn = {1558-5646}, mesh = {*Biological Evolution ; Classification/*methods ; Genetic Fitness ; *Genetic Speciation ; *Hybridization, Genetic ; Phylogeny ; Species Specificity ; *Terminology as Topic ; }, abstract = {New insights in the speciation process and the nature of "species" that accumulated in the past decade demand adjustments of the species concept. The standing of some of the most broadly accepted or most innovative species concepts in the light of the growing evidence that reproductive barriers are semipermeable to gene flow, that species can differentiate despite ongoing interbreeding, that a single species can originate polyphyletically by parallel evolution, and that uniparental organisms are organised in units that resemble species of biparental organisms is discussed. As a synthesis of ideas in existing concepts and the new insights, a generalization of the genic concept is proposed that defines species as groups of individuals that are reciprocally characterized by features that would have negative fitness effects in other groups and that cannot be regularly exchanged between groups upon contact. The benefits of this differential fitness species concept are that it classifies groups that keep differentiated and keep on differentiating despite interbreeding as species, that it is not restricted to specific mutations or mechanisms causing speciation, and that it can be applied to the whole spectrum of organisms from uni- to biparentals.}, } @article {pmid21460564, year = {2011}, author = {Pintor, LM and Brown, JS and Vincent, TL}, title = {Evolutionary game theory as a framework for studying biological invasions.}, journal = {The American naturalist}, volume = {177}, number = {4}, pages = {410-423}, doi = {10.1086/658149}, pmid = {21460564}, issn = {1537-5323}, mesh = {*Biological Evolution ; Ecosystem ; *Game Theory ; *Introduced Species ; *Models, Biological ; Population Dynamics ; Species Specificity ; }, abstract = {Although biological invasions pose serious threats to biodiversity, they also provide the opportunity to better understand interactions between the ecological and evolutionary processes structuring populations and communities. However, ecoevolutionary frameworks for studying species invasions are lacking. We propose using game theory and the concept of an evolutionarily stable strategy (ESS) as a conceptual framework for integrating the ecological and evolutionary dynamics of invasions. We suggest that the pathways by which a recipient community may have no ESS provide mechanistic hypotheses for how such communities may be vulnerable to invasion and how invaders can exploit these vulnerabilities. We distinguish among these pathways by formalizing the evolutionary contexts of the invader relative to the recipient community. We model both the ecological and the adaptive dynamics of the interacting species. We show how the ESS concept provides new mechanistic hypotheses for when invasions result in long- or short-term increases in biodiversity, species replacement, and subsequent evolutionary changes.}, } @article {pmid21442403, year = {2011}, author = {Shaw, KL and Mullen, SP}, title = {Genes versus phenotypes in the study of speciation.}, journal = {Genetica}, volume = {139}, number = {5}, pages = {649-661}, pmid = {21442403}, issn = {1573-6857}, mesh = {*Genetic Speciation ; Genetic Variation ; *Phenotype ; Selection, Genetic ; Species Specificity ; }, abstract = {Despite persistent debate on the nature of species, the widespread adoption of Mayr's biological species concept has led to a heavy emphasis on the importance of reproductive isolation to the speciation process. Equating the origin of species with the evolution of reproductive isolation has become common practice in the study of speciation, coincident with an increasing focus on elucidating the specific genetic changes (i.e.-speciation genes) underlying intrinsic reproductive barriers between species. In contrast, some have recognized that reproductive isolation is usually a signature effect rather than a primary cause of speciation. Here we describe a research paradigm that shifts emphasis from effects to causes in order to resolve this apparent contradiction and galvanize the study of speciation. We identify major elements necessary for a balanced and comprehensive investigation of the origin of species and place the study of so-called "speciation genes" into its appropriate context. We emphasize the importance of characterizing diverging phenotypes, identifying relevant evolutionary forces acting on those phenotypes and their role in the causal origins of reduced gene flow between incipient species, and the nature of the genetic and phenotypic boundaries that results from such processes. This approach has the potential to unify the field of speciation research, by allowing us to make better "historical" predictions about the fate of diverging populations regardless of taxon.}, } @article {pmid21424771, year = {2011}, author = {Spijker, J and Mol, G and Posthuma, L}, title = {Regional ecotoxicological hazards associated with anthropogenic enrichment of heavy metals.}, journal = {Environmental geochemistry and health}, volume = {33}, number = {4}, pages = {409-426}, pmid = {21424771}, issn = {1573-2983}, mesh = {Ecotoxicology/*methods ; Environmental Monitoring/*methods ; Environmental Pollution/analysis/prevention & control ; Epidemiological Monitoring ; Hazardous Substances/*analysis/toxicity ; Humans ; Metals, Heavy/*analysis/toxicity ; Netherlands/epidemiology ; Risk Assessment/methods ; Soil Pollutants/*analysis/toxicity ; }, abstract = {Regional geochemical data of heavy metals are commonly used for environmental risk assessment and management. Often these data are based on so-called total concentrations, whereas the exposure to the mobile or reactive fraction of these elements finally determines whether the exposed ecosystem is at risk and to which extent. The objective of our research was to develop a wider applicable method for quantitative hazard assessment of soil metal contamination attributable to the activity of man, based on and illustrated with data from the Netherlands. Since chemical availability (0.43 M HNO3 extractable concentrations) of Cd, Cu, Pb and Zn appeared strongly related to the estimated anthropogenic enrichment, we used these concentrations to assess the hazard of human-induced enrichment of these metals. We expressed the enrichment hazard using the toxic pressure concept, which estimates the fraction of biological species (varying between 0 and 1) potentially affected due to the level of exposure to single metals or their local mixtures. This is done using logistic (enrichment) concentration/response models parameterized with ecotoxicological effect data from toxicity tests and mixture models. Hazards varied from very low toxic pressures (lower than 0.01) to (most often) toxic pressure less than 0.05, whereby the latter relates to the so-called 95%-protection criterion used in some soil protection legislations. In rare cases, the toxic pressure exceeded the value of 0.05, to an upper limit of 0.054 for Cd. The rank order of metal enrichment hazards suggests that Cd enrichment induces the largest hazard increase. There are limited (rank order) differences in enrichment hazards between soil types. Comparing the judgement of soils based on soil screening levels and based on toxic pressure of anthropogenic Cd, Cu, Pb and Zn enrichments, the soil screening values appear to more conservative. This exemplifies the use of soil screening values as a method to note regulatory concern, but not always indicating an actual hazard or risk. When screening values are exceeded, refined hazard insights can be obtained, as illustrated in this paper. This provides a more refined insight in the ecotoxic implications of human-induced metal enrichments in soils, as refined basis for risk management decisions.}, } @article {pmid21417732, year = {2011}, author = {Myler, HA and Given, A and Kolz, K and Mora, JR and Hristopoulos, G}, title = {Biotherapeutic bioanalysis: a multi-indication case study review.}, journal = {Bioanalysis}, volume = {3}, number = {6}, pages = {623-643}, doi = {10.4155/bio.11.33}, pmid = {21417732}, issn = {1757-6199}, mesh = {Animals ; Antibodies, Monoclonal/*analysis ; Biological Products/*analysis ; Chemistry Techniques, Analytical/*methods ; Humans ; Pharmaceutical Preparations/*analysis ; Recombinant Proteins/analysis ; }, abstract = {A thorough understanding of the structure and biology of a biotherapeutic is crucial to defining a suitable strategy for pharmacokinetic characterization in proof-of-concept disease models, toxicology species as well as the healthy and disease indication patient populations. This manuscript summarizes parameters that impact bioanalytical strategy for over 50 biotherapeutics indicated for the treatment of oncology, rheumatoid arthritis, allergy, multiple sclerosis, hematology, metabolism and infectious disease. We have addressed numerous therapeutic modalities including chimeric, humanized and fully human monoclonal antibodies, replacement proteins, peptides and fusion proteins, including polyethylene glycol and Fc fusions, as well as antibody-drug conjugates. With the rapid evolution of biotherapeutics over the last 20 years and the contraction of the pharmaceutical and biotechnology labor force, efficient workflow management becomes a crucial bioanalytical component. Thus, we have also addressed new technologies that have demonstrated either increased throughput or enhanced characterization, including Meso Scale Discovery, Gyrolab and affinity MS.}, } @article {pmid21401590, year = {2011}, author = {Stouffer, DB and Rezende, EL and Amaral, LA}, title = {The role of body mass in diet contiguity and food-web structure.}, journal = {The Journal of animal ecology}, volume = {80}, number = {3}, pages = {632-639}, pmid = {21401590}, issn = {1365-2656}, support = {/HHMI_/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Biological Evolution ; *Body Size ; *Diet ; Ecosystem ; Environment ; *Food Chain ; *Models, Biological ; Phylogeny ; }, abstract = {1. The idea that species occupy distinct niches is a fundamental concept in ecology. Classically, the niche was described as an n-dimensional hypervolume where each dimension represents a biotic or abiotic characteristic. More recently, it has been hypothesised that a single dimension may be sufficient to explain the system-level organization of trophic interactions observed between species in a community. 2. Here, we test the hypothesis that species body mass is that single dimension. Specifically, we determine how the intervality of food webs ordered by body size compares to that of randomly ordered food webs. We also extend this analysis beyond the community level to the effect of body mass in explaining the diets of individual species. 3. We conclude that body mass significantly explains the ordering of species and the contiguity of diets in empirical communities. 4. At the species-specific level, we find that the degree to which body mass is a significant explanatory variable depends strongly on the phylogenetic history, suggesting that other evolutionarily conserved traits partly account for species' roles in the food web. 5. Our investigation of the role of body mass in food webs thus helps us to better understand the important features of community food-web structure and the evolutionary forces that have led us to the communities we observe.}, } @article {pmid21392337, year = {2010}, author = {Barberousse, A and Samadi, S}, title = {Species from Darwin onward.}, journal = {Integrative zoology}, volume = {5}, number = {3}, pages = {187-197}, doi = {10.1111/j.1749-4877.2010.00204.x}, pmid = {21392337}, issn = {1749-4877}, mesh = {Classification ; *Genetic Speciation ; History, 19th Century ; *Selection, Genetic ; Species Specificity ; }, abstract = {Controversy regarding the species problem has been going on for many decades and no consensus has ever been reached about what a "species" really is and how best to define the concept. De Queiroz (1998) introduced a distinction between two aspects of this problem: on the one hand, the definition proper, and on the other, the criteria allowing biologists to recognize species in practice. This distinction is a first step on the way toward a solution of the problem. In the present paper, we show that de Queiroz's distinction is made possible by the radical theoretical change introduced by Darwin. We emphasize that the species problem did not appear in the 20th century, but long before, and that Darwin addresses it indirectly in the Origin of Species. It might seem paradoxical to refer to Darwin's views about species, because they are usually considered as unclear. However, we propose that an analysis of these views in the context of Darwin's own theory of evolution might reveal how a definition of the concept of species is made possible by being anchored to the very theory of evolution. To this aim, we present a plausible reconstruction of Darwin's implicit conception of species and show how this conception fits with the debates on species that took place in the 18th and 19th centuries. We then turn to today's biology and show what changes Darwin's implicit conception of species has brought about relative to the species concept and species delimitation.}, } @article {pmid21389269, year = {2011}, author = {Kempel, A and Schädler, M and Chrobock, T and Fischer, M and van Kleunen, M}, title = {Tradeoffs associated with constitutive and induced plant resistance against herbivory.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {14}, pages = {5685-5689}, pmid = {21389269}, issn = {1091-6490}, mesh = {Adaptation, Biological/*genetics ; *Biological Evolution ; *Phylogeny ; Plant Development ; Plants/*genetics ; Regression Analysis ; Species Specificity ; }, abstract = {Several prominent hypotheses have been posed to explain the immense variability among plant species in defense against herbivores. A major concept in the evolutionary ecology of plant defenses is that tradeoffs of defense strategies are likely to generate and maintain species diversity. In particular, tradeoffs between constitutive and induced resistance and tradeoffs relating these strategies to growth and competitive ability have been predicted. We performed three independent experiments on 58 plant species from 15 different plant families to address these hypotheses in a phylogenetic framework. Because evolutionary tradeoffs may be altered by human-imposed artificial selection, we used 18 wild plant species and 40 cultivated garden-plant species. Across all 58 plant species, we demonstrate a tradeoff between constitutive and induced resistance, which was robust to accounting for phylogenetic history of the species. Moreover, the tradeoff was driven by wild species and was not evident for cultivated species. In addition, we demonstrate that more competitive species-but not fast growing ones-had lower constitutive but higher induced resistance. Thus, our multispecies experiments indicate that the competition-defense tradeoff holds for constitutive resistance and is complemented by a positive relationship of competitive ability with induced resistance. We conclude that the studied genetically determined tradeoffs are indeed likely to play an important role in shaping the high diversity observed among plant species in resistance against herbivores and in life history traits.}, } @article {pmid21385165, year = {2011}, author = {Li, J and Ban, J and Santiago, LS}, title = {Nonparametric tests for homogeneity of species assemblages: a data depth approach.}, journal = {Biometrics}, volume = {67}, number = {4}, pages = {1481-1488}, doi = {10.1111/j.1541-0420.2011.01573.x}, pmid = {21385165}, issn = {1541-0420}, mesh = {*Biodiversity ; Biometry/*methods ; Computer Simulation ; *Data Interpretation, Statistical ; Ecology/*statistics & numerical data ; *Ecosystem ; *Models, Statistical ; Population Dynamics ; Trees/*classification ; }, abstract = {Testing homogeneity of species assemblages has important applications in ecology. Due to the unique structure of abundance data often collected in ecological studies, most classical statistical tests cannot be applied directly. In this article, we propose two novel nonparametric tests for comparing species assemblages based on the concept of data depth. They can be considered as a natural generalization of the Kolmogorov-Smirnov and the Cramér-von Mises tests (KS and CM) in this species assemblage comparison context. Our simulation studies show that the proposed test is more powerful than other existing methods under various settings. A real example is used to demonstrate how the proposed method is applied to compare species assemblages using plant community data from a highly diverse tropical forest at Barro Colorado Island, Panama.}, } @article {pmid21366771, year = {2011}, author = {Ready, PD}, title = {Should sand fly taxonomy predict vectorial and ecological traits?.}, journal = {Journal of vector ecology : journal of the Society for Vector Ecology}, volume = {36 Suppl 1}, number = {}, pages = {S17-22}, doi = {10.1111/j.1948-7134.2011.00108.x}, pmid = {21366771}, issn = {1948-7134}, mesh = {Animals ; Ecology ; Insect Vectors/*classification/growth & development/parasitology ; Leishmaniasis/transmission ; Psychodidae/*classification/growth & development/parasitology ; }, abstract = {I review species concepts, the taxonomy of phlebotomine sand flies, and some transmission cycles of leishmaniasis in order to illustrate the difficulties of classifying these vectors in a way that will be ideal both for medical parasitologists and sand fly specialists. Choices will have to be made between different classifications, either maintaining a practical one containing few vectorial genera (mostly Phlebotomus for the Old World and Lutzomyia for the Neotropics) or changing the generic names of many vectors so that the classification represents an evolutionary hypothesis. However, sand flies also transmit arboviruses and members of other sand fly genera bite humans, and so vectorial status alone might not provide the criteria for recognizing only a few genera. Vectorial roles are often determined by species-level co-evolution of susceptibility to Leishmania species, with selection being initiated and maintained by ecological contacts. There is only imperfect co-cladogenesis of genus-level groups or subgeneric complexes of sand flies and Leishmania species. Natural hybridization between sand fly species has been recorded in several species complexes, and this highlights the need to focus on gene flow and the distribution of phenotypes of biomedical importance, not on taxa.}, } @article {pmid21361929, year = {2011}, author = {Farias, AA and Jaksic, FM}, title = {Low functional richness and redundancy of a predator assemblage in native forest fragments of Chiloe island, Chile.}, journal = {The Journal of animal ecology}, volume = {80}, number = {4}, pages = {809-817}, doi = {10.1111/j.1365-2656.2011.01824.x}, pmid = {21361929}, issn = {1365-2656}, mesh = {Animals ; *Biota ; *Carnivora ; Chile ; Conservation of Natural Resources ; *Ecosystem ; Food Chain ; *Raptors ; Trees ; }, abstract = {1. Changes in land use and habitat fragmentation are major drivers of global change, and studying their effects on biodiversity constitutes a major research programme. However, biodiversity is a multifaceted concept, with a functional component linking species richness to ecosystem function. Currently, the interaction between functional and taxonomic components of biodiversity under realistic scenarios of habitat degradation is poorly understood. 2. The expected functional richness (FR)-species richness relationship (FRSR) is positive, and attenuated for functional redundancy in species-rich assemblages. Further, environmental filters are expected to flatten that association by sorting species with similar traits. Thus, analysing FRSR can inform about the response of biodiversity to environmental gradients and habitat fragmentation, and its expected functional consequences. 3. Top predators affect ecosystem functioning through prey consumption and are particularly vulnerable to changes in land use and habitat fragmentation, being good indicators of ecosystem health and suitable models for assessing the effects of habitat fragmentation on their FR. 4. Thus, this study analyses the functional redundancy of a vertebrate predator assemblage at temperate forest fragments in a rural landscape of Chiloe island (Chile), testing the existence of environmental filters by contrasting an empirically derived FRSR against those predicted from null models, and testing the association between biodiversity components and the structure of forest fragments. 5. Overall, contrasts against null models indicate that regional factors determine low levels of FR and redundancy for the vertebrate predator assemblage studied, while recorded linear FRSR indicates proportional responses of the two biodiversity components to the structure of forest fragments. Further, most species were positively associated with either fragment size or shape complexity, which are highly correlated. This, and the absence of ecological filters at the single-fragment scale, rendered taxonomically and functionally richer predator assemblages at large complex-shaped fragments. 6. These results predict strong effects of deforestation on both components of biodiversity, potentially affecting the functioning of remnants of native temperate forest ecosystems. Thus, the present study assesses general responses of functional and taxonomic components of biodiversity to a specific human-driven process.}, } @article {pmid21338699, year = {2011}, author = {Pons, J and Fujisawa, T and Claridge, EM and Savill, RA and Barraclough, TG and Vogler, AP}, title = {Deep mtDNA subdivision within Linnean species in an endemic radiation of tiger beetles from New Zealand (genus Neocicindela).}, journal = {Molecular phylogenetics and evolution}, volume = {59}, number = {2}, pages = {251-262}, doi = {10.1016/j.ympev.2011.02.013}, pmid = {21338699}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Coleoptera/classification/*genetics ; DNA, Mitochondrial/genetics ; *Demography ; *Genetic Variation ; Haplotypes ; Models, Genetic ; Molecular Sequence Data ; New Zealand ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The invertebrate fauna of New Zealand is of great interest as a geologically tractable model for the study of species diversification, but direct comparisons with closely related lineages elsewhere are lacking. Integrating population-level analyses with studies of taxonomy and clade diversification, we performed mtDNA analysis on Neocicindela (Cicindelidae, tiger beetles) for a broad sample of populations from 11 of 12 known species and 161 specimens (three loci, 1883 nucleotides), revealing 123 distinct haplotypes. Phylogenetic reconstruction recovered two main lineages, each composed of 5-6 Linnean species whose origin was dated to 6.66 and 7.26 Mya, while the Neocicindela stem group was placed at 10.82 ± 0.48 Mya. Species delimitation implementing a character-based (diagnostic) species concept recognized 19 species-level groups that were in general agreement with Linnean species but split some of these into mostly allopatric subgroups. Tree-based methods of species delimitation using a mixed Yule-coalescence model were inconclusive, and recognized 32-51 entities (including singletons), splitting existing species into up to 8 partially sympatric groups. These findings were different from patterns in the Australian sister genus Rivacindela, where character-based and tree-based methods were previously shown to produce highly congruent groupings. In Neocicindela, the pattern of mtDNA variation was characterized by high intra-population and intra-species haplotype divergence, the coexistence of divergent haplotypes in sympatry, and a poor correlation of genetic and geographic distance. These observations combined suggest a scenario of phylogeographic divergence and secondary contact driven by orogenetic and climatic changes of the Pleistocene/Pliocene. The complex evolutionary history of most species of Neocicindela due to the relative instability of the New Zealand biota resulted in populations of mixed ancestry but not in a general loss of genetic variation.}, } @article {pmid21336930, year = {2011}, author = {Voigt, K and Kirk, PM}, title = {Recent developments in the taxonomic affiliation and phylogenetic positioning of fungi: impact in applied microbiology and environmental biotechnology.}, journal = {Applied microbiology and biotechnology}, volume = {90}, number = {1}, pages = {41-57}, doi = {10.1007/s00253-011-3143-4}, pmid = {21336930}, issn = {1432-0614}, mesh = {Biotechnology ; Environment ; Fungi/*classification/genetics/*isolation & purification/metabolism ; *Phylogeny ; }, abstract = {The goal of modern taxonomy is to understand the relationships of living organisms in terms of evolutionary descent. Thereby, the relationships between living organisms are understood in terms of nested clades--every time a speciation event takes place, two new clades are produced. Life comprises three domains of living organisms, these are the Bacteria, the Archaea and the Eukaryota. Within the eukaryotic domain, the fungi form a monophyletic group of the eukaryotic crown group and are thus high up in the evolutionary hierarchy of life. Fungus-like organisms possess certain morphological features of fungi, such as the hyphal organization of the Oomycota or the spores and reproductive structures inside a fructification of plasmodiophorids (Plasmodiophoromycota) and slime moulds (Mycetozoa). The first group are algae which secondarily lost their plastids during evolution and contain cellulose in their cell walls. Both osmotrophic phyla, the Oomycota and the Plasmidiophoromycota belong to the Chromista and Rhizaria, respectively, whereas the last group, the cellular and plasmodial slime moulds (Mycetozoa) are phagotrophic amoeboid protists belonging to the Amoebozoa. These fungus-like organisms are not considered further in this review. The Fungi sensu stricto comprise a heterogenous, often inconspicuous group of microorganisms which (1) are primarily heterotrophic with an (2) osmotrophic style of nutrition containing (3) chitin and its derivatives in the cell wall. This review discusses species concepts and current strategies in fungal taxonomy, phylogenetic affiliations of miscellaneous fungus-like groups like the microsporidia, perspectives of fungal nomenclature, and their impact on natural product research.}, } @article {pmid21315308, year = {2011}, author = {Choi, YJ and Thines, M and Runge, F and Hong, SB and Telle, S and Shin, HD}, title = {Evidence for high degrees of specialisation, evolutionary diversity, and morphological distinctiveness in the genus Bremia.}, journal = {Fungal biology}, volume = {115}, number = {2}, pages = {102-111}, doi = {10.1016/j.funbio.2010.10.010}, pmid = {21315308}, issn = {1878-6146}, mesh = {Asteraceae/microbiology ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; *Genetic Variation ; Molecular Sequence Data ; Oomycetes/*classification/genetics/*growth & development/isolation & purification ; Phylogeny ; Plant Diseases/microbiology ; }, abstract = {Bremia lactucae is one of the most important pathogens in lettuce production. Recent molecular studies revealed considerable genetic variation in this species complex. However, only few accessions from the same host have been examined for most species and no study investigating the morphological distinctiveness of phylogenetic lineages of Bremia has so far been reported. Thus it is believed that morphological species delimitation in Bremia is not feasible. In the present study, multiple accessions of neglected species, which had been described decades ago, but have not been widely accepted, were investigated, considering both multi-gene phylogenies and morphological characters. All previously described species from host genera other than Lactuca investigated, Bremia microspora, Bremia ovata, Bremia saussureae, and Bremia sonchicola, could be confirmed as distinct, host-specific entities. Also, morphological characteristics of their conidiophores and conidia allowed delimitation of these species. Therefore, not only the wide species concept to merge all Bremia species on the Asteraceae under B. lactucae is inappropriate but also their delimitation on the basis of morphological characters seems feasible. In addition, it has been shown that Bremia elliptica is phylogenetically distinct from the other species infecting the genus Lactuca, B. lactucae. It is therefore concluded that B. lactucae is most likely limited to Lactuca sativa and closely-related species, and that most species of Bremia are highly host specific. This finding might stimulate the search for durable resistance genes in genera closely related to the genus Lactuca and in divergent species of the genus itself.}, } @article {pmid21311589, year = {2011}, author = {Stielow, B and Bratek, Z and Orczán, AK and Rudnoy, S and Hensel, G and Hoffmann, P and Klenk, HP and Göker, M}, title = {Species delimitation in taxonomically difficult fungi: the case of Hymenogaster.}, journal = {PloS one}, volume = {6}, number = {1}, pages = {e15614}, pmid = {21311589}, issn = {1932-6203}, mesh = {Base Sequence ; Basidiomycota/*classification/genetics ; Classification ; Cluster Analysis ; DNA, Ribosomal/genetics ; Europe ; Genetic Speciation ; Phylogeny ; Sequence Alignment ; }, abstract = {BACKGROUND: False truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions.

METHODOLOGY: In this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software.

CONCLUSIONS: Among distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season). In particular, taxa described in the 19(th) century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-)automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general.}, } @article {pmid21304686, year = {2010}, author = {Auch, AF and Klenk, HP and Göker, M}, title = {Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs.}, journal = {Standards in genomic sciences}, volume = {2}, number = {1}, pages = {142-148}, pmid = {21304686}, issn = {1944-3277}, abstract = {DNA-DNA hybridization (DDH) is a widely applied wet-lab technique to obtain an estimate of the overall similarity between the genomes of two organisms. To base the species concept for prokaryotes ultimately on DDH was chosen by microbiologists as a pragmatic approach for deciding about the recognition of novel species, but also allowed a relatively high degree of standardization compared to other areas of taxonomy. However, DDH is tedious and error-prone and first and foremost cannot be used to incrementally establish a comparative database. Recent studies have shown that in-silico methods for the comparison of genome sequences can be used to replace DDH. Considering the ongoing rapid technological progress of sequencing methods, genome-based prokaryote taxonomy is coming into reach. However, calculating distances between genomes is dependent on multiple choices for software and program settings. We here provide an overview over the modifications that can be applied to distance methods based in high-scoring segment pairs (HSPs) or maximally unique matches (MUMs) and that need to be documented. General recommendations on determining HSPs using BLAST or other algorithms are also provided. As a reference implementation, we introduce the GGDC web server (http://ggdc.gbdp.org).}, } @article {pmid21304684, year = {2010}, author = {Auch, AF and von Jan, M and Klenk, HP and Göker, M}, title = {Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison.}, journal = {Standards in genomic sciences}, volume = {2}, number = {1}, pages = {117-134}, pmid = {21304684}, issn = {1944-3277}, abstract = {The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.}, } @article {pmid21303503, year = {2011}, author = {Heethoff, M and Laumann, M and Weigmann, G and Raspotnig, G}, title = {Integrative taxonomy: Combining morphological, molecular and chemical data for species delineation in the parthenogenetic Trhypochthonius tectorum complex (Acari, Oribatida, Trhypochthoniidae).}, journal = {Frontiers in zoology}, volume = {8}, number = {1}, pages = {2}, pmid = {21303503}, issn = {1742-9994}, support = {P 18486/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {BACKGROUND: There is a long-standing controversial about how parthenogenetic species can be defined in absence of a generally accepted species concept for this reproductive mode. An integrative approach was suggested, combining molecular and morphological data to identify distinct monophyletic entities. Using this approach, speciation of parthenogenetic lineages was recently demonstrated for groups of bdelloid rotifers and oribatid mites. Trhypochthonius tectorum, an oribatid mite from the entirely parthenogenetic desmonomatan family Trhypochthoniidae, is traditionally treated as a single species in Central Europe. However, two new morphological lineages were recently proposed for some Austrian populations of T. tectorum, and were described as novel subspecies (T. silvestris europaeus) or form (T. japonicus forma occidentalis). We used the morphological and morphometrical data which led to this separation, and added mitochondrial and nuclear DNA sequences and the chemical composition of complex exocrine oil gland secretions to test this taxonomical hypothesis. This is the first attempt to combine these three types of data for integrative taxonomical investigations of oribatid mites.

RESULTS: We show that the previous European species T. tectorum represents a species complex consisting of three distinct lineages in Austria (T.tectorum, T. silvestris europaeus and T. japonicus forma occidentalis), each clearly separated by morphology, oil gland secretion profiles and mitochondrial cox1 sequences. This diversification happened in the last ten million years. In contrast to these results, no variation among the lineages was found in the nuclear 18S rDNA.

CONCLUSIONS: Our approach combined morphological, molecular and chemical data to investigate diversity and species delineation in a parthenogenetic oribatid mite species complex. To date, hypotheses of a general oribatid mite phylogeny are manifold, and mostly based on single-method approaches. Probably, the integrative approach proposed here can be used to uncover further hidden biodiversity of glandulate Oribatida and help to build up more stable phylogenetic hypotheses in the future.}, } @article {pmid21291366, year = {2011}, author = {Gutierrez-Merino, C and Lopez-Sanchez, C and Lagoa, R and Samhan-Arias, AK and Bueno, C and Garcia-Martinez, V}, title = {Neuroprotective actions of flavonoids.}, journal = {Current medicinal chemistry}, volume = {18}, number = {8}, pages = {1195-1212}, doi = {10.2174/092986711795029735}, pmid = {21291366}, issn = {1875-533X}, mesh = {Animals ; Antioxidants/adverse effects/chemistry/*pharmacology ; Flavonoids/adverse effects/chemistry/*pharmacology ; Humans ; Molecular Structure ; Nerve Degeneration/*prevention & control ; Neuroprotective Agents/adverse effects/chemistry/*pharmacology ; Oxidative Stress/drug effects ; Reactive Oxygen Species/metabolism ; }, abstract = {The experimental evidences accumulated during last years point out a relevant role of oxidative stress in neurodegeneration. As anti-cellular oxidative stress agents flavonoids can act either as direct chemical antioxidants, the classic view of flavonoids as antioxidants, or as modulators of enzymes and metabolic and signaling pathways leading to an overshot of reactive oxygen species (ROS) formation, a more recently emerging concept. Flavonoids, a large family of natural antioxidants, undergo a significant hepatic metabolism leading to flavonoid-derived metabolites that are also bioactive as antioxidant agents. The development of more efficient flavonoid's based anti-oxidative stress therapies should also take into account their bioavailability in the brain using alternate administration protocols, and also that the major ROS triggering the cellular oxidative stress are not the same for all neurodegenerative insults and diseases. On these grounds, we have reviewed the reports on neuroprotection by different classes of flavonoids on cellular cultures and model animals. In addition, as they are now becoming valuable pharmacological drugs, due to their low toxicity, the reported adverse effects of flavonoids in model experimental animals and humans are briefly discussed.}, } @article {pmid21288462, year = {2010}, author = {Hüsken, A and Prescher, S and Schiemann, J}, title = {Evaluating biological containment strategies for pollen-mediated gene flow.}, journal = {Environmental biosafety research}, volume = {9}, number = {2}, pages = {67-73}, doi = {10.1051/ebr/2010009}, pmid = {21288462}, issn = {1635-7922}, mesh = {Containment of Biohazards/*methods ; Crops, Agricultural/*genetics ; *Gene Flow ; Genetic Engineering/methods ; Plant Infertility ; *Plants, Genetically Modified ; Pollen/*genetics ; Recombination, Genetic ; Transgenes ; }, abstract = {Several biological containment methods have been developed to reduce pollen dispersal; many of them only have a proof of concept in a model plant species. This review focuses on biological containment measures which were tested for their long-term efficiency at the greenhouse or field scale level, i.e. plastid transformation, transgene excission, cleistogamy and cytoplasmic male sterility (CMS). Pollen-mediated gene transfer in transplastomic tobacco could occur at very low frequencies if the predominant mode of inheritance is maternal. Transgene excision from tobacco pollen can be made highly efficient by coexpression of two recombinases. For cleistogamous oilseed rape it was shown that some flowers were partially open depending on genotypes, environment and recording dates. Reports on the stability of CMS in maize and sunflower indicated that there is a high variability for different genotypes under different environmental conditions and over successive years. But for both crop types some stable lines could be selected. These data demonstrate that the biological containment methods discussed are very promising for reducing gene flow but that no single containment strategy provides 100% reduction. However, the necessary efficiency of biological containment methods depends on the level of containment required. The containment level may need to be higher for safety purposes (e.g. production of special plant-made pharmaceuticals), while much lower containment levels may already be sufficient to reach coexistence goals. It is concluded that where pollen-mediated gene flow must be prevented altogether, combinations of complementary containment systems will be required.}, } @article {pmid21273465, year = {2011}, author = {Gibbons, A}, title = {Anthropology. The species problem.}, journal = {Science (New York, N.Y.)}, volume = {331}, number = {6016}, pages = {394}, doi = {10.1126/science.331.6016.394}, pmid = {21273465}, issn = {1095-9203}, mesh = {Animals ; *Genetic Speciation ; Genetic Variation ; Hominidae/*classification/*genetics/physiology ; Humans ; Hybridization, Genetic ; }, } @article {pmid21267648, year = {2011}, author = {Rico, A and Waichman, AV and Geber-Corrêa, R and van den Brink, PJ}, title = {Effects of malathion and carbendazim on Amazonian freshwater organisms: comparison of tropical and temperate species sensitivity distributions.}, journal = {Ecotoxicology (London, England)}, volume = {20}, number = {4}, pages = {625-634}, pmid = {21267648}, issn = {1573-3017}, mesh = {Animals ; Aquatic Organisms/*drug effects ; Benzimidazoles/*toxicity ; Carbamates/*toxicity ; Dose-Response Relationship, Drug ; Ecosystem ; Fishes ; Fungicides, Industrial/*toxicity ; Insecticides/*toxicity ; Invertebrates/drug effects ; Malathion/*toxicity ; Risk Assessment ; Rivers/chemistry ; Toxicity Tests, Acute ; Water Pollutants, Chemical/toxicity ; }, abstract = {The risk assessment of pesticides for freshwater ecosystems in the Amazon has relied on the use of toxicity data and water quality criteria derived for temperate regions due to a lack of ecotoxicological studies performed with indigenous species. This leaves an unknown margin of uncertainty for the protection of Amazonian ecosystems, as differences in environmental conditions and species sensitivity are not taken into account. To address this issue, the acute toxic effects of malathion (an organophosphorus insecticide) and carbendazim (a benzimidazole fungicide) were assessed on five fish and five freshwater invertebrates endemic to the Amazonian region. Subsequently, the intrinsic sensitivity of Amazonian and temperate freshwater species was compared using the species sensitivity distribution (SSD) concept. Amazonian species sensitivity to malathion was found to be similar to that of their temperate counterparts, with LC50 values ranging between 111 and 1507 μg/l for fish species and 2.1-426 μg/l for arthropod species. However, Amazonian fish appeared to be slightly less sensitive for carbendazim than temperate fish with LC50 values ranging between 1648 and 4238 μg/l, and Amazonian invertebrates were found to be significantly more resistant than their temperate counterparts, with LC50 values higher than 16000 μg/l. The results of this study suggest that for these compounds, the use of water quality criteria derived with laboratory toxicity data for temperate species will result in a sufficient protection level for Amazonian freshwater organisms. Recommendations for further research include the validation of threshold concentrations derived with temperate standard test species and with the SSD model with semi-field experiments considering larger assemblages of indigenous species under local environmental conditions.}, } @article {pmid21262795, year = {2011}, author = {Ricklefs, RE}, title = {Applying a regional community concept to forest birds of eastern North America.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {6}, pages = {2300-2305}, pmid = {21262795}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Birds/*physiology ; *Ecosystem ; *Models, Biological ; North America ; *Trees ; }, abstract = {The regional community concept embraces the idea that species interactions across large areas shape both the geographic/ecological distributions and the local abundances of populations. Within this framework, I analyzed the distribution and abundance of 79 species of land birds across 142 ca. 10-ha census plots from standardized breeding bird censuses in deciduous and mixed forests of eastern North America. To characterize the regional ecological space, plots were ordinated on the basis of species abundances. Within the regional community defined by these synthetic axes, the distribution and abundance of individual species did not appear to be shaped by competition or to reflect the adaptations of individuals: (i) local abundance and population extent across the ordination axes were unrelated, (ii) pairwise correlation coefficients of species abundances were centered on 0, (iii) average species distribution and abundance were independent of the number of close relatives, and (iv) distribution and abundance exhibited no evolutionary (phylogenetic) conservatism. To explain these seemingly random patterns, I speculate that species are approximately evenly matched competitors over much of the region and that their distributions and relative abundances are determined by the labile coevolutionary outcomes of interactions with specialized pathogens. Thus, despite the appearance that random processes determine patterns in the distribution and abundance of populations in the regional community, it is plausible that species-specific deterministic interactions are responsible. Although competition is a dominant force in ecological communities, variation in the distribution and abundance of individual species might instead reflect the outcome of interactions with specialized antagonists, including pathogens.}, } @article {pmid21253629, year = {2011}, author = {Zirngast, M and Pump, E and Leitgeb, A and Albering, JH and Slugovc, C}, title = {Pyridine as trigger for chloride isomerisation in chelated ruthenium benzylidene complexes: implications for olefin metathesis.}, journal = {Chemical communications (Cambridge, England)}, volume = {47}, number = {8}, pages = {2261-2263}, doi = {10.1039/c0cc04897f}, pmid = {21253629}, issn = {1364-548X}, abstract = {The cationic pyridine adduct of a ruthenium complex bearing a chelating benzylidene and an N-heterocyclic carbene was identified as an intermediate during the activation of cis dichloro species and a novel triggering concept for olefin metathesis catalysts based on cationic species was disclosed.}, } @article {pmid21218996, year = {2011}, author = {Ramaswamy, R and Sbalzarini, IF}, title = {A partial-propensity formulation of the stochastic simulation algorithm for chemical reaction networks with delays.}, journal = {The Journal of chemical physics}, volume = {134}, number = {1}, pages = {014106}, doi = {10.1063/1.3521496}, pmid = {21218996}, issn = {1089-7690}, mesh = {*Algorithms ; Kinetics ; *Molecular Dynamics Simulation ; }, abstract = {Several real-world systems, such as gene expression networks in biological cells, contain coupled chemical reactions with a time delay between reaction initiation and completion. The non-Markovian kinetics of such reaction networks can be exactly simulated using the delay stochastic simulation algorithm (dSSA). The computational cost of dSSA scales with the total number of reactions in the network. We reduce this cost to scale at most with the smaller number of species by using the concept of partial reaction propensities. The resulting delay partial-propensity direct method (dPDM) is an exact dSSA formulation for well-stirred systems of coupled chemical reactions with delays. We detail dPDM and present a theoretical analysis of its computational cost. Furthermore, we demonstrate the implications of the theoretical cost analysis in two prototypical benchmark applications. The dPDM formulation is shown to be particularly efficient for strongly coupled reaction networks, where the number of reactions is much larger than the number of species.}, } @article {pmid22696829, year = {2011}, author = {Nikisianis, N and Stamou, GP}, title = {Quantifying nature: ideological representations in the concept of diversity.}, journal = {History and philosophy of the life sciences}, volume = {33}, number = {3}, pages = {365-388}, pmid = {22696829}, issn = {0391-9714}, mesh = {*Biodiversity ; Conservation of Natural Resources ; Ecology/*history ; History, 20th Century ; *Philosophy ; }, abstract = {The conflicts around the scientific status of the concept of diversity are considered here as symptoms of hidden, socially originated, ideological representations inherent in the theoretical context of western ecology. Species diversity was coined in the 1940s, as a constant in the statistical models that described the distribution of individuals into different species and, therefore, as the expression of all the parameters that determine ecologically this distribution. The assumption of such a regular distribution is attributed to the influence of organicism and the correlated presuppositions of harmony and homeostasis. Nevertheless, as species diversity was the only unknown parameter in these models, it reversed the direction of the functions and established itself as the main variable under question. After the 1950s, the concept of species diversity was empowered by the strong impact of cybernetics and systems theories; in this context, diversity was considered as a self-regulating mechanism that assures overall stability. Diversity emerges as a natural and one-dimensional measure of community complexity, maturity, and stability. In the perspective of the arising ecological crisis, diversity--because of its property to compare and evaluate--arises as the nodal point of the new scientific/ideological fields of nature conservation and ecosystem management.}, } @article {pmid22696828, year = {2011}, author = {Ellis, MW}, title = {The problem with the species problem.}, journal = {History and philosophy of the life sciences}, volume = {33}, number = {3}, pages = {343-363}, pmid = {22696828}, issn = {0391-9714}, mesh = {Biological Evolution ; Biology/*history ; Classification/*methods ; *Genetic Speciation ; History, 19th Century ; History, 20th Century ; }, abstract = {When Charles Darwin convinced the scientific community that species evolve, the long-held essentialist view of each species as fixed was rejected and a clear conceptual understanding of the term was lost. For the next century, a real species problem existed that became culturally entrenched within the scientific community. Although largely solved decades ago, the species problem remains entrenched today due to a suite of factors. Most of the factors that help maintain its perceived intractability have been revealed and logically dismissed; yet this is not widely known so those factors continue to be influential. It is time to recognize this false foundation and relegate the species problem to history.}, } @article {pmid21177905, year = {2011}, author = {Ho, CC and Lau, CC and Martelli, P and Chan, SY and Tse, CW and Wu, AK and Yuen, KY and Lau, SK and Woo, PC}, title = {Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: a proof-of-concept study.}, journal = {Journal of clinical microbiology}, volume = {49}, number = {3}, pages = {814-821}, pmid = {21177905}, issn = {1098-660X}, mesh = {Animals ; Bacteriological Techniques/*methods ; Burkholderia/*classification/genetics/*isolation & purification ; Burkholderia Infections/diagnosis/microbiology ; DNA Primers/genetics ; DNA, Bacterial/chemistry/genetics ; Environmental Microbiology ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Sequence Analysis, DNA ; }, abstract = {Burkholderia pseudomallei, Burkholderia thailandensis, and the Burkholderia cepacia complex differ greatly in pathogenicity and epidemiology. Yet, they are occasionally misidentified by biochemical profiling, and even 16S rRNA gene sequencing may not offer adequate discrimination between certain species groups. Using the 23 B. pseudomallei, four B. thailandensis, and 16 B. cepacia complex genome sequences available, we identified gene targets specific to each of them (a Tat domain protein, a 70-kDa protein, and a 12-kDa protein for B. pseudomallei, B. thailandensis, and the B. cepacia complex, respectively), with an in-house developed algorithm. Using these targets, we designed a robust multiplex PCR assay useful for their identification and detection from soil and simulated sputum samples. For all 43 B. pseudomallei, seven B. thailandensis, and 20 B. cepacia complex (B. multivorans, n = 6; B. cenocepacia, n = 3; B. cepacia, n = 4; B. arboris, n = 2; B. contaminans, B. anthina, and B. pyrrocinia, n = 1 each; other unnamed members, n = 2) isolates, the assay produced specific products of predicted size without false positives or negatives. Of the 60 soil samples screened, 19 (31.6%) and 29 (48.3%) were positive for B. pseudomallei and the B. cepacia complex, respectively, and in four (6.7%) soil samples, the organisms were codetected. DNA sequencing confirmed that all PCR products originated from their targeted loci. This novel pan-genomic analysis approach in target selection is simple, computationally efficient, and potentially applicable to any species that harbors species-specific genes. A multiplex PCR assay for rapid and accurate identification and detection of B. pseudomallei, B. thailandensis, and the B. cepacia complex was developed and verified.}, } @article {pmid21161777, year = {2010}, author = {Howie, JA and Tolkamp, BJ and Bley, T and Kyriazakis, I}, title = {Short-term feeding behaviour has a similar structure in broilers, turkeys and ducks.}, journal = {British poultry science}, volume = {51}, number = {6}, pages = {714-724}, doi = {10.1080/00071668.2010.528749}, pmid = {21161777}, issn = {1466-1799}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Chickens/*physiology ; Ducks/*physiology ; *Feeding Behavior ; Female ; Male ; Species Specificity ; Time Factors ; Turkeys/*physiology ; }, abstract = {1. This study is the first to quantitatively compare the structure of feeding behaviour of broilers, ducks and turkeys as recorded by electronic feeders. It tests the hypothesis that this structure is so similar that the same models would be suitable to group the feeding behaviour of these species into meals. 2. Visits to electronic feeders were recorded from 3470 broilers, 3314 turkeys and 480 ducks. The frequency distributions of the length of short intervals between visits to feeders varied between species as a result of differences in the number of visits within a feeding bout, the frequency of re-visits to the same feeder and probably in the likelihood of birds drinking within meals. 3. The lengths of longer day-time intervals between visits to feeders were all log-normally distributed. Disaggregation of these intervals by feeding strategy (meal frequency) showed that the probability of birds starting to feed increased with time since feeding last in all species, which is consistent with the satiety concept. 4. Two methods, one based on fitting a truncated log-normal, function, the other on observed changes in the probability of birds starting to feed with time since last feeding, gave very similar meal criteria estimates. These ranged from 1050 to 1200 s in broilers, 1650 to 1725 s in ducks and 1250 to 1320 s in turkeys. 5. There were large between-species differences in the average number of daily meals, intake per meal, and feeding rate. Despite this variation, the overall structure of feeding behaviour of broilers, ducks and turkeys was so similar that the same models were suitable for application in all three species. This would allow for standardised analyses of feeding behaviour of different avian species kept in different husbandry systems.}, } @article {pmid21145608, year = {2011}, author = {Leong, SL and Pettersson, OV and Rice, T and Hocking, AD and Schnürer, J}, title = {The extreme xerophilic mould Xeromyces bisporus--growth and competition at various water activities.}, journal = {International journal of food microbiology}, volume = {145}, number = {1}, pages = {57-63}, doi = {10.1016/j.ijfoodmicro.2010.11.025}, pmid = {21145608}, issn = {1879-3460}, mesh = {Agar ; Antibiosis ; Aspergillus/growth & development ; Chrysosporium/growth & development ; Coculture Techniques ; Culture Media ; Eurotiales/*growth & development/physiology ; Fructose/metabolism ; Glucose/metabolism ; Penicillium/growth & development ; *Temperature ; Water/*physiology ; }, abstract = {Little is known about the mould, Xeromyces bisporus, unique in its strong xerophilicity and ability to grow at water activity (a(w)) 0.62, lower than for any other known organism. The linear growth rates of one fast and one slow-growing strain of X. bisporus were assessed at 20, 25, 30 and 37 °C on solid agar media containing a mixture of glucose and fructose to reduce a(w) to 0.94, 0.88, 0.84, 0.80, 0.76 and 0.66. Growth rates of xerophilic species closely related to X. bisporus, viz. Chrysosporium inops, C. xerophilum and Monascus eremophilus, were also assessed. Optimal conditions for growth of both X. bisporus strains were approx. 0.84 a(w) and 30°C, despite FRR 2347 growing two- to five-fold faster than CBS 185.75. X. bisporus FRR 2347 even grew well at 0.66 a(w) (0.48 mm/day). C. inops and C. xerophilum were more tolerant of high a(w) than X. bisporus, and could be differentiated from each other based on: the faster growth of C. xerophilum; its preference for temperatures ≥ 30 °C and a(w) ≥ 0.94 (c.f.≤ 25 °C and ~0.88 a(w) for C. inops); and its ability to grow at 0.66 a(w), which is the lowest a(w) reported to date for this species. M. eremophilus grew slowly (max. 0.4mm/day) even in its optimal conditions of ~0.88 a(w) and 25 °C. To investigate the competitive characteristics of X. bisporus at low a(w), both X. bisporus strains were grown in dual-culture with xerotolerant species Aspergillus flavus and Penicillium roqueforti, and xerophilic species A. penicillioides, C. inops, C. xerophilum and Eurotium chevalieri, on glucose-fructose agar plates at 0.94, 0.84, 0.80 and 0.76 a(w) and at 25 °C. Growth rates and types of interactions were assessed. Excretion of inhibitory substances acting over a long-range was not observed by any species; inhibitors acting over a short-range that temporarily slowed competitors' growth or produced a protective zone around the colony were occasionally observed for A. penicillioides, C. inops and C. xerophilum. Instead, rapid growth relative to the competitor was the most common means of dominance. The xerotolerant species, A. flavus and P. roqueforti were dominant over X. bisporus at 0.94 a(w). E. chevalieri was often dominant due to its rapid growth over the entire a(w) range. At a(w)<0.80, X. bisporus was competitive because it grew faster than the other species examined. This supports the concept that its ideal environmental niche is sugary foods with low a(w).}, } @article {pmid22679576, year = {2010}, author = {Crespo, A and Lumbsch, HT}, title = {Cryptic species in lichen-forming fungi.}, journal = {IMA fungus}, volume = {1}, number = {2}, pages = {167-170}, pmid = {22679576}, issn = {2210-6359}, abstract = {This contribution provides a synopsis of the presentations and discussions during the SIG session on cryptic speciation in lichen-forming fungi held during IMC9. In several cases, a re-examination of morphology against the background of molecular phylogenetic evidence revealed, sometimes subtle, morphological and/or chemical characters, supporting the distinction of particular clades at species level. However, there are also examples of cryptic species in which no morphological characters could be identified to distinguish between lineages. Several cases were presented in which distinct lineages are correlated with biogeographical patterns. When and how to name cryptic species was debated, and the use of terms such as "complex" or "aggregate" commended where the taxa formed part of a single lineage.}, } @article {pmid21114625, year = {2011}, author = {Chabé, M and Aliouat-Denis, CM and Delhaes, L and Aliouat, el M and Viscogliosi, E and Dei-Cas, E}, title = {Pneumocystis: from a doubtful unique entity to a group of highly diversified fungal species.}, journal = {FEMS yeast research}, volume = {11}, number = {1}, pages = {2-17}, doi = {10.1111/j.1567-1364.2010.00698.x}, pmid = {21114625}, issn = {1567-1364}, mesh = {Animals ; Humans ; Lung/microbiology ; Mammals ; *Phylogeny ; Pneumocystis/*classification/cytology/genetics/pathogenicity ; Pneumocystis Infections/*epidemiology/*microbiology/pathology ; }, abstract = {At the end of the 20th century the unique taxonomically enigmatic entity called Pneumocystis carinii was identified as a heterogeneous group of microscopic Fungi, constituted of multiple stenoxenic biological entities largely spread across ecosystems, closely adapted to, and coevolving in parallel with, mammal species. The discoveries and reasoning that led to the current conceptions about the taxonomy of Pneumocystis at the species level are examined here. The present review also focuses on the biological, morphological and phylogenetical features of Pneumocystis jirovecii, Pneumocystis oryctolagi, Pneumocystis murina, P. carinii and Pneumocystis wakefieldiae, the five Pneumocystis species described until now, mainly on the basis of the phylogenetic species concept. Interestingly, Pneumocystis organisms exhibit a successful adaptation enabling them to dwell and replicate in the lungs of both immunocompromised and healthy mammals, which can act as infection reservoirs. The role of healthy carriers in aerial disease transmission is nowadays recognized as a major contribution to Pneumocystis circulation, and Pneumocystis infection of nonimmunosuppressed hosts has emerged as a public health issue. More studies need to be undertaken both on the clinical consequences of the presence of Pneumocystis in healthy carriers and on the intricate Pneumocystis life cycle to better define its epidemiology, to adapt existing therapies to each clinical context and to discover new drug targets.}, } @article {pmid21108640, year = {2011}, author = {Hart, MW}, title = {The species concept as an emergent property of population biology.}, journal = {Evolution; international journal of organic evolution}, volume = {65}, number = {3}, pages = {613-616}, doi = {10.1111/j.1558-5646.2010.01202.x}, pmid = {21108640}, issn = {1558-5646}, mesh = {Biological Evolution ; *Genetic Speciation ; Genetics, Population ; }, abstract = {Resurgent interest in the genetics of population divergence and speciation coincides with recent critical evaluation of species concepts and proposals for species delimitation. An important result of these parallel trends is a slight but important conceptual shift in focus away from species diagnoses based on prior species concepts or definitions, and toward analyses of the processes acting on lineages of metapopulations that eventually lead to differences recognizable as species taxa. An advantage of this approach is that it identifies quantitative metapopulation differences in continuous variables, rather than discrete entities that do or do not conform to a prior species concept, and species taxa are recognized as an emergent property of population-level processes. The tension between species concepts and diagnosis versus emergent recognition of species taxa is at least as old as Darwin, and is unlikely to be resolved soon in favor of either view, because the products of both approaches (discrete utilitarian taxon names for species, process-based understanding of the origins of differentiated metapopulations) continue to have important applications.}, } @article {pmid21091767, year = {2011}, author = {Branton, M and Richardson, JS}, title = {Assessing the value of the umbrella-species concept for conservation planning with meta-analysis.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {25}, number = {1}, pages = {9-20}, doi = {10.1111/j.1523-1739.2010.01606.x}, pmid = {21091767}, issn = {1523-1739}, mesh = {Animals ; Biodiversity ; Birds ; Conservation of Natural Resources/*methods ; *Environmental Policy ; Mammals ; Population Dynamics ; }, abstract = {The umbrella-species concept, which suggests that conservation strategies designed for one species may benefit co-occurring species, has been promoted as a framework for conservation planning. Nevertheless, there has been considerable variation in the outcome of empirical tests of this concept that has led researchers to question its value, so we used data from 15 published studies in a meta-analysis to evaluate whether conservation of putative umbrella species also conserves co-occurring species. We tested the effectiveness of putative umbrella species categorized by taxonomic group, taxonomic similarity to co-occurring species, body size, generality of resource use, and trophic level to evaluate criteria proposed to guide the selection of umbrella species. We compared species richness and number of individuals (by species and higher taxonomic group) between sites with and without putative umbrella species to test whether more co-occurring species were present in greater abundances when the area or resource needs of umbrella species were met. Species richness and abundance of co-occurring species were consistently higher in sites where umbrella species were present than where they were not and for conservation schemes with avian than with mammalian umbrella species. There were no differences in species richness or species abundance with resource generalist or specialist umbrella species or based on taxonomic similarity of umbrella and co-occurring species. Taxonomic group abundance was higher in across-taxonomic umbrella species schemes than when umbrella species were of the same taxon as co-occurring species. Co-occurring species had similar, or higher, species richness with small-bodied umbrella species relative to larger-bodied umbrella species. The only significant difference among umbrella species categorized by trophic level was that species richness was higher with omnivorous than it was with carnivorous avian umbrella species. Our results suggest there is merit to the umbrella-species concept for conservation, but they do not support the use of the criteria we used to identify umbrella species.}, } @article {pmid21088008, year = {2011}, author = {Reeves, PA and Richards, CM}, title = {Species delimitation under the general lineage concept: an empirical example using wild North American hops (Cannabaceae: Humulus lupulus).}, journal = {Systematic biology}, volume = {60}, number = {1}, pages = {45-59}, doi = {10.1093/sysbio/syq056}, pmid = {21088008}, issn = {1076-836X}, mesh = {Amplified Fragment Length Polymorphism Analysis/*methods ; DNA, Plant/genetics ; Ecosystem ; Evolution, Molecular ; Gene Flow ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; Humulus/*classification/genetics/physiology ; Models, Genetic ; North America ; Phylogeny ; }, abstract = {There is an emerging consensus that the intent of most species concepts is to identify evolutionarily distinct lineages. However, the criteria used to identify lineages differ among concepts depending on the perceived importance of various attributes of evolving populations. We have examined five different species criteria to ask whether the three taxonomic varieties of Humulus lupulus (hops) native to North America are distinct lineages. Three criteria (monophyly, absence of genetic intermediates, and diagnosability) focus on evolutionary patterns and two (intrinsic reproductive isolation and niche specialization) consider evolutionary processes. Phylogenetic analysis of amplified fragment length polymorphism (AFLP) data under a relaxed molecular clock, a stochastic Dollo substitution model, and parsimony identified all varieties as monophyletic, thus they satisfy the monophyly criterion for species delimitation. Principal coordinate analysis and a Bayesian assignment procedure revealed deep genetic subdivisions and little admixture between varieties, indicating an absence of genetic intermediates and compliance with the genotypic cluster species criterion. Diagnostic morphological and AFLP characters were found for all varieties, thus they meet the diagnosability criterion. Natural history information suggests that reproductive isolating barriers may have evolved in var. pubescens, potentially qualifying it as a species under a criterion of intrinsic reproductive isolation. Environmental niche modeling showed that the preferred habitat of var. neomexicanus is climatically unique, suggesting niche specialization and thus compliance with an ecological species criterion. Isolation by distance coupled with imperfect sampling can lead to erroneous lineage identification using some species criteria. Compliance with complementary pattern- and process-oriented criteria provides powerful corroboration for a species hypothesis and mitigates the necessity for comprehensive sampling of the entire species range, a practical impossibility in many systems. We hypothesize that var. pubescens maintains its genetic identity, despite substantial niche overlap with var. lupuloides, via the evolution of partial reproductive isolating mechanisms. Variety neomexicanus, conversely, will likely persist as a distinct lineage, regardless of limited gene flow with vars. lupuloides and pubescens because of ecological isolation--adaptation to the unique conditions of the Rocky Mountain cordillera. Thus, we support recognition of vars. neomexicanus and pubescens as species, but delay making a recommendation for var. lupuloides until sampling of genetic variation is complete or a stable biological process can be identified to explain its observed genetic divergence.}, } @article {pmid21075209, year = {2012}, author = {Glor, RE and Laport, RG}, title = {Are subspecies of Anolis lizards that differ in dewlap color and pattern also genetically distinct? A mitochondrial analysis.}, journal = {Molecular phylogenetics and evolution}, volume = {64}, number = {2}, pages = {255-260}, doi = {10.1016/j.ympev.2010.11.004}, pmid = {21075209}, issn = {1095-9513}, mesh = {Animals ; Bahamas ; DNA, Mitochondrial/*genetics ; Dominican Republic ; Female ; Genetic Drift ; Genetic Variation ; Haplotypes ; Lizards/*classification/*genetics ; Male ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; *Pigmentation ; RNA, Transfer/genetics/metabolism ; Skin ; Species Specificity ; }, abstract = {Subspecies of Anolis lizards are often defined on the basis of geographic variation in the color and pattern of the dewlap, an extensible throat fan considered central to species recognition and sexual selection. Among the most impressive examples of this phenomenon are two species of trunk anoles found across Hispaniola and the Bahamas: Anolis distichus is divided into 16 subspecies with dewlap colors ranging from deep wine red to pale yellow while Anolis brevirostris is divided into three subspecies with dewlaps ranging from pale yellow to orange. Limited sampling of allozyme data indicates some genetic divergence among subspecies and suggests that they may deserve recognition at the species-level. Our goal here is to use more comprehensive geographic sampling of mtDNA haplotypes to test whether the five subspecies of A. distichus and three subspecies of A. brevirostris that occur in the Dominican Republic correspond with genetically distinct populations that may warrant recognition under the general lineage concept. We obtain an aligned dataset of 1462bp comprised of the genes encoding ND2 and adjacent tRNAs from 76 individuals of A. distichus from 28 localities and 12 individuals of A. brevirostris from five localities. We find that haplotypes sampled from each Dominican subspecies of A. distichus form well-supported and deeply divergent clades (>10% uncorrected sequence divergence). Strong concordance between mtDNA haplotype structure and previously diagnosed phenotypic variation in traits central to interspecific communication (i.e., the dewlap) leads us to hypothesize that each of the presently recognized Dominican subspecies of A. distichus and A. brevirostris deserves elevation to full species status under the general lineage concept.}, } @article {pmid21071229, year = {2011}, author = {Vos, M}, title = {A species concept for bacteria based on adaptive divergence.}, journal = {Trends in microbiology}, volume = {19}, number = {1}, pages = {1-7}, doi = {10.1016/j.tim.2010.10.003}, pmid = {21071229}, issn = {1878-4380}, mesh = {Bacteria/*classification/*genetics ; Biological Evolution ; Classification/*methods ; *Genetic Speciation ; Multilocus Sequence Typing ; Phylogeny ; }, abstract = {Bacterial strains are currently grouped into species based on overall genomic similarity and sharing of phenotypes deemed ecologically important. Many believe this polyphasic taxonomy is in need of revision because it lacks grounding in evolutionary theory, and boundaries between species are arbitrary. Recent taxonomy efforts using multilocus sequence typing (MLST) data are based on the identification of distinct phylogenetic clusters. However, these approaches face the problem of deciding the phylogenetic level at which clusters are representative of evolutionary or taxonomically distinct units. In this review, I propose classifying two phylogenetic clusters as separate species only when they have statistically significantly diverged as a result of adaptive evolution. More than a method for classification, the concept of adaptive divergence can be used in a 'reverse ecology' approach to identify lineages that are in the process of speciation or genes involved in initial adaptive divergence.}, } @article {pmid21061639, year = {2010}, author = {Giliarov, AM}, title = {[In search of universal patterns in community organization: the concept of neutrality paved the way to a new approach].}, journal = {Zhurnal obshchei biologii}, volume = {71}, number = {5}, pages = {386-401}, pmid = {21061639}, issn = {0044-4596}, mesh = {Animals ; *Biological Evolution ; *Biota ; }, abstract = {The recent renewal of interest in community structure was strongly stimulated by the concept of neutrality, a new view on the problem of species coexistence. In contrast to traditional approach claiming that species competing for common resources should occupy different ecological niches, the neutrality concept assumes that species can coexist if they are ecologically identical, i.e., they have similar specific (per individual) rate of population growth, probability of extinction and the rate of colonization of free space. The analysis of recent literature, full of contradictory opinions on the ideas of neutrality and niche, can be resulted in form of following questions: (1) What do we suggest when we say that "species coexist"? (2) How can we explain the usual pattern of species relative abundances in a community, the so-called "hollow curve" (the distribution of numbers of species arranged in classes of abundance)? (3) Do rare species have some advantages in comparison with abundant species? (4) Can the mechanisms implied by neutrality concept and traditional niche approach work simultaneously in the same community? Trying to answer these questions we should: (1) refuse the demand of indefinite coexistence of species although this condition was considered as necessary in classical mathematical models of competition; (2) accept that community structure depends not only on ecological processes (species dispersal, competition and others) but also on the evolutionary ones (speciation) that determine the pool of species; (3) accept that rare species have some advantages as compared with the most abundant species; (4) accept that in any real community species can coexist either occupying the different niches or approaching ecological similarity. Despite considerable progress achieved in understanding of general principles of community organization, we still don't know how to answer the question "Why are there so many kinds of animals?" that was posed by Hutchinson 50 years ago.}, } @article {pmid21060687, year = {2010}, author = {Roy, S and Tyagi, A and Shukla, V and Kumar, A and Singh, UM and Chaudhary, LB and Datt, B and Bag, SK and Singh, PK and Nair, NK and Husain, T and Tuli, R}, title = {Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species.}, journal = {PloS one}, volume = {5}, number = {10}, pages = {e13674}, pmid = {21060687}, issn = {1932-6203}, mesh = {Berberis/*genetics ; DNA, Plant/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task.

We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome--ITS, and three from plastid genome--trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation.

CONCLUSIONS/SIGNIFICANCE: We reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case.}, } @article {pmid21046338, year = {2010}, author = {Hong, SB and Kim, DH and Park, IC and Choi, YJ and Shin, HD and Samson, R}, title = {Re-identification of Aspergillus fumigatus sensu lato based on a new concept of species delimitation.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {48}, number = {5}, pages = {607-615}, pmid = {21046338}, issn = {1976-3794}, mesh = {Aspergillus fumigatus/*classification/genetics ; Cluster Analysis ; *DNA Fingerprinting ; Genotype ; Multilocus Sequence Typing ; *Mycological Typing Techniques ; Phylogeny ; Random Amplified Polymorphic DNA Technique ; }, abstract = {The species concept of Aspergillus fumigatus sensu stricto has recently been defined by polyphasic taxonomy. Based on the new concept of species delimitations, 146 worldwide strains of Aspergillus fumigatus sensu lato were re-identified. Of those 146 strains, 140 (95.8%) could be identified as A. fumigatus sensu stricto, 3 (2.1%) as A. lentulus, and the remaining 3 strains as A. viridinutans complex, Neosartorya udagawae, and N. cf. nishimurae. Of 98 clinical strains, only 1 from dolphin nostril was identified as A. lentulus and not A. fumigatus sensu stricto. Random amplification of polymorphic DNA-polymerase chain reaction (RAPD-PCR) with primers PELF and URP1F produced nearly the same band patterns among 136 strains of A. fumigatus sensu stricto while discriminated the species from its related species. We also discussed about identification of several atypical A. fumigatus strains from clinical environments.}, } @article {pmid21043779, year = {2010}, author = {Schemske, DW}, title = {Adaptation and the origin of species.}, journal = {The American naturalist}, volume = {176 Suppl 1}, number = {}, pages = {S4-S25}, doi = {10.1086/657060}, pmid = {21043779}, issn = {1537-5323}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biology/history ; *Ecosystem ; *Genetic Speciation ; History, 19th Century ; Plants/genetics ; Research/trends ; Selection, Genetic ; }, abstract = {As reflected in the title of his masterwork On the Origin of Species, Darwin proposed that adaptation is the primary mechanism of speciation. On this, Darwin was criticized for his neglect of reproductive isolation, his lack of appreciation for the role of geographic barriers, his failure to distinguish varieties from species, and his typological species concept. Two developments since Darwin, the biological species concept of Ernst Mayr and the methods of Coyne and Orr for estimating the contribution of different barriers to the total reproductive isolation, provide a framework for reconciling Darwin's view on the primacy of adaptation in speciation with later proposals that emphasize reproductive isolation. A review of the few studies that have estimated the contributions of multiple isolating barriers suggests that habitat isolation and other barriers that operate before hybrid formation are much stronger than intrinsic postzygotic isolation. In light of these data, I suggest that Darwin's focus on adaptation in the origin of species was essentially correct, a conclusion that calls for future studies that explore the links between adaptation and speciation, in particular, ecogeographic isolating barriers that result from adaptive divergence in habitat use. The recent revival in thinking about ecological factors and adaptive divergence in the origin of species echoes Darwin's much-criticized "principle of divergence" and suggests that the emerging views from today's naturalists are not so different from those espoused by Darwin some 150 years ago.}, } @article {pmid21038699, year = {2010}, author = {Tănase, AM and Vassu, T and Stoica, I}, title = {[The concept of bacterial species].}, journal = {Bacteriologia, virusologia, parazitologia, epidemiologia (Bucharest, Romania : 1990)}, volume = {55}, number = {1}, pages = {5-10}, pmid = {21038699}, issn = {1220-3696}, mesh = {Bacteria/*classification/genetics/growth & development ; Classification/methods ; *Genes, rRNA ; Genetic Speciation ; Genetic Techniques ; Phylogeny ; Prokaryotic Cells/classification ; Species Specificity ; }, abstract = {Prokaryotes are the most abundant living organisms and also most diverse from genetically and metabolically point of view, being responsible for the majority of biogeochemical processes playing the most important role in life cycle on the planet. Considering this, there is a general agreement among taxonomists, that there is a very small number of bacterial species recognized and described today, mostly because of controversial issues concerning bacterial species concept. One of the most accepted approaches, even today, is the polyphasic taxonomy because it is based on diverse information, obtained from classic taxonomy but also from molecular level. The development of new molecular techniques, especially sequencing rRNA genes conducted to an improved concept, that we intended to evaluate in this review, and even more, to reconstruction of group specific phylogenetic tree.}, } @article {pmid21037964, year = {2010}, author = {Göker, M and Grimm, GW and Auch, AF and Aurahs, R and Kučera, M}, title = {A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA.}, journal = {Evolutionary bioinformatics online}, volume = {6}, number = {}, pages = {97-112}, pmid = {21037964}, issn = {1176-9343}, abstract = {Identifying species is challenging in the case of organisms for which primarily molecular data are available. Even if morphological features are available, molecular taxonomy is often necessary to revise taxonomic concepts and to analyze environmental DNA sequences. However, clustering approaches to delineate molecular operational taxonomic units often rely on arbitrary parameter choices. Also, distance calculation is difficult for highly alignment-ambiguous sequences. Here, we applied a recently described clustering optimization method to highly divergent planktonic foraminifera SSU rDNA sequences. We determined the distance function and the clustering setting that result in the highest agreement with morphological reference data. Alignment-free distance calculation, when adapted to the use with partly non-homologous sequences caused by distinct primer pairs, outperformed multiple sequence alignment. Clustering optimization offers new perspectives for the barcoding of species diversity and for environmental sequencing. It bridges the gap between traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both genetic divergence and given species concepts.}, } @article {pmid20971197, year = {2010}, author = {Fraser, CI and Winter, DJ and Spencer, HG and Waters, JM}, title = {Multigene phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales).}, journal = {Molecular phylogenetics and evolution}, volume = {57}, number = {3}, pages = {1301-1311}, doi = {10.1016/j.ympev.2010.10.011}, pmid = {20971197}, issn = {1095-9513}, mesh = {Cell Nucleus/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Kelp/classification/*genetics ; Pacific Ocean ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Durvillaea (southern bull-kelp) is an economically and ecologically important brown algal genus that dominates many exposed, rocky coasts in the cold-temperate Southern Hemisphere. Of its five currently-recognized species, four are non-buoyant and restricted to the south-western Pacific, whereas one is both buoyant and widely distributed. Durvillaea has had an unsettled taxonomic history. Although its position within the brown algae (Phaeophyceae) has now been largely resolved through the use of molecular techniques, the taxonomic status of several Durvillaea species/morphotypes remains unresolved. Previous molecular phylogenetic studies of phaeophycean taxa have included few Durvillaea samples, and have consequently paid little or no attention to variation within this genus. The current study presents phylogenetic analyses of four genetic markers (mitchondrial: COI; chloroplast: rbcL; and nuclear: 18S and 28S) to resolve phylogenetic relationships within Durvillaea. Results support the monophyly of solid-bladed taxa D. willana, D. potatorum, and D. sp. A (an undescribed species from the Antipodes Islands), whereas the widespread, buoyant D. antarctica is paraphyletic, with solid-bladed D.chathamensis placed sister to a D. antarctica clade from northern NZ but within D. antarctica sensu lato. The phylogenetic and ecological diversity detected within D. antarctica indicate that it is a species complex of five deeply divergent clades. Under a phylogenetic species concept, Durvillaea can be interpreted as a complex of nine distinct evolutionary lineages, only one of which has an intercontinental distribution ('subantarctic'D. antarctica).}, } @article {pmid20943543, year = {2010}, author = {Fotouhifar, KB and Hedjaroude, GA and Leuchtmann, A}, title = {ITS rDNA phylogeny of Iranian strains of Cytospora and associated teleomorphs.}, journal = {Mycologia}, volume = {102}, number = {6}, pages = {1369-1382}, doi = {10.3852/10-034}, pmid = {20943543}, issn = {0027-5514}, mesh = {Ascomycota/*classification/genetics/*isolation & purification ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/*genetics ; Genetic Variation ; Iran ; Molecular Sequence Data ; *Phylogeny ; Plant Diseases/microbiology ; Trees/*microbiology ; }, abstract = {Cytospora spp. and associated teleomorphic species (Ascomycota, Diaporthales, Valsaceae) are among the most common and widespread canker- and dieback-causing fungi on trees, shrubs and herbaceous plants worldwide. From specimens collected all over Iran a total of 114 isolates were morphologically identified, representing 20 Cytospora, one Leucostoma and five Valsa species from 38 plant species. Nine of the identified taxa were new records for Iran, and many new hosts were identified. The phylogenetic relationships of the Iranian strains, along with sequences of 13 reference strains from GenBank, were inferred from ITS1-5.8S-ITS2 nuclear rDNA sequences. Parsimony analysis established five distinct major clades and 12 subclades, which represented accepted species and genera. Some of these subclades corresponded to morphologically based taxonomic concepts of single Cytospora species, while others contained more than one morphospecies. Teleomorphic states were present in six subclades, and most clustered with the corresponding anamorphs. This suggests that morphological and phylogenetic species concepts overlap and that in most cases they are meaningful for correct species identification.}, } @article {pmid20928980, year = {2010}, author = {Chacín-Bonilla, L}, title = {[Amebiasis: implications of the recognition of Entamoeba dispar and the identification of Entamoeba moshkovskii in humans].}, journal = {Investigacion clinica}, volume = {51}, number = {2}, pages = {239-256}, pmid = {20928980}, issn = {0535-5133}, mesh = {Amebicides/therapeutic use ; Developing Countries ; Entamoeba/classification/enzymology/*isolation & purification ; Entamoeba histolytica/genetics/isolation & purification/physiology ; Entamoebiasis/diagnosis/drug therapy/epidemiology/*history/parasitology ; Forecasting ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Host-Parasite Interactions ; Humans ; Isoenzymes/analysis ; Parasitology/*history/trends ; Protozoan Proteins/analysis ; Species Specificity ; Virulence ; }, abstract = {The history of Entamoeba histolytica is very confuse and shows several wrong concepts about the parasite and its relationship with the host. The poor correlation between the prevalence of asymptomatic and symptomatic amebiasis originated the proposal of three explicative hypothesis, among them was the concept of Brumpt that E. histolytica comprised two morphologically identical species, E. dysenteriae and E. dispar. The application of modern molecular techniques irrefutably proved that E. histolytica was really a complex of two species, confirming the concept of Brumpt almost 7 decades later. Recent studies have identified in humans E. moshkovskii, morphologically indistinguishable from E. histolytica and E. dispar, a great genetic diversity within each of these species, and heterogeneity in virulence among E. histolytica strains. The redescription of E. dispar, and the recovery of E. moshkovskii from humans have had a major impact in our understanding of E. histolytica and amebiasis with important clinical and epidemiologic implications. This has led to the need of a reevaluation of the infection in terms of prevalence and morbidity in the global population and to study the geographic distribution, prevalence, and transmission pattern of E. histolytica strains in order to detect those with epidemiologic relevance and predict the risk of amebic disease in a population.}, } @article {pmid20877444, year = {2010}, author = {Bensch, K and Groenewald, JZ and Dijksterhuis, J and Starink-Willemse, M and Andersen, B and Summerell, BA and Shin, HD and Dugan, FM and Schroers, HJ and Braun, U and Crous, PW}, title = {Species and ecological diversity within the Cladosporium cladosporioides complex (Davidiellaceae, Capnodiales).}, journal = {Studies in mycology}, volume = {67}, number = {}, pages = {1-94}, pmid = {20877444}, issn = {1872-9797}, abstract = {The genus Cladosporium is one of the largest genera of dematiaceous hyphomycetes, and is characterised by a coronate scar structure, conidia in acropetal chains and Davidiella teleomorphs. Based on morphology and DNA phylogeny, the species complexes of C. herbarum and C. sphaerospermum have been resolved, resulting in the elucidation of numerous new taxa. In the present study, more than 200 isolates belonging to the C. cladosporioides complex were examined and phylogenetically analysed on the basis of DNA sequences of the nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-α gene sequences. For the saprobic, widely distributed species Cladosporium cladosporioides, both a neotype and epitype are designated in order to specify a well established circumscription and concept of this species. Cladosporium tenuissimum and C. oxysporum, two saprobes abundant in the tropics, are epitypified and shown to be allied to, but distinct from C. cladosporioides. Twenty-two species are newly described on the basis of phylogenetic characters and cryptic morphological differences. The most important phenotypic characters for distinguishing species within the C. cladosporioides complex, which represents a monophyletic subclade within the genus, are shape, width, length, septation and surface ornamentation of conidia and conidiophores; length and branching patterns of conidial chains and hyphal shape, width and arrangement. Many of the treated species, e.g., C. acalyphae, C. angustisporum, C. australiense, C. basiinflatum, C. chalastosporoides, C. colocasiae, C. cucumerinum, C. exasperatum, C. exile, C. flabelliforme, C. gamsianum, and C. globisporum are currently known only from specific hosts, or have a restricted geographical distribution. A key to all species recognised within the C. cladosporioides complex is provided.}, } @article {pmid20872905, year = {2011}, author = {Struijs, J and De Zwart, D and Posthuma, L and Leuven, RS and Huijbregts, MA}, title = {Field sensitivity distribution of macroinvertebrates for phosphorus in inland waters.}, journal = {Integrated environmental assessment and management}, volume = {7}, number = {2}, pages = {280-286}, doi = {10.1002/ieam.141}, pmid = {20872905}, issn = {1551-3793}, mesh = {Animals ; Environmental Monitoring/*methods ; Fresh Water/*analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {The magnitude of ecological damage caused by elevated phosphorus concentrations (C(P)) in Dutch inland waters is expressed as the fraction of disappeared macroinvertebrate genera. We used field observations of species occurrence from 1980 to 2005 that were stored in the Limnodata Neerlandica to derive the presence of 867 aquatic macroinvertebrate genera in the water column of freshwater bodies with total phosphorus (P(tot)) concentrations ranging from 0.001 to 40 mg/L. At concentrations > 0.3 mg/L, which is considered to cause nutrient enrichment of freshwater bodies, the disappeared fraction (DF) of macroinvertebrate genera can be described as a logistic function of the C(P) : DF = 1/(1 + 4.07/C(P)[1]·[11]). The logistic function suggests that half of the macroinvertebrate genera that potentially occur in the freshwater column in the Netherlands would disappear at a C(P) = 3.5 mg/L. This field-based effect expression resembles the cumulative sensitivity distribution function for a toxic substance based on the species sensitivity distribution (SSD) concept and exposure data. Whereas an SSD for a toxic chemical is derived from laboratory sensitivity data for a small number of species, our DF is derived from field observations of many macroinvertebrate genera at numerous C(P) levels. By applying this damage function to measured phosphorus in the rivers Rhine, Meuse, and Scheldt, we found that the observed C(P) values in 1975 imply diversity losses of 15% for the Rhine and Meuse, and 20% for the Scheldt. For 2000, the calculated diversity losses are 3% (Rhine), 6% (Meuse), and 9% (Scheldt). The cumulative genera sensitivity distribution function for phosphorus from national freshwater monitoring data can be applied in various environmental screening systems, such as multistress impact assessment of surface waters, and in life cycle impact assessment of products.}, } @article {pmid20865522, year = {2010}, author = {Mahadevan, P and Seto, D}, title = {Taxonomic parsing of bacteriophages using core genes and in silico proteome-based CGUG and applications to small bacterial genomes.}, journal = {Advances in experimental medicine and biology}, volume = {680}, number = {}, pages = {379-385}, doi = {10.1007/978-1-4419-5913-3_43}, pmid = {20865522}, issn = {0065-2598}, mesh = {*Algorithms ; Bacteriophage P22/classification/genetics ; Bacteriophage T7/classification/genetics ; Bacteriophage lambda/classification/genetics ; Bacteriophages/*classification/*genetics ; Burkholderia cenocepacia/classification/genetics ; Computational Biology ; Genes, Viral ; Genome, Bacterial ; Genomics/*statistics & numerical data ; Internet ; Podoviridae/classification/genetics ; Proteome ; Proteomics/statistics & numerical data ; }, abstract = {A combined genomics and in situ proteomics approach can be used to determine and classify the relatedness of organisms. The common set of proteins shared within a group of genomes is encoded by the "core" set of genes, which is increasingly recognized as a metric for parsing viral and bacterial species. These can be described by the concept of a "pan-genome", which consists of this "core" set and a "dispensable" set, i.e., genes found in one or more but not all organisms in the grouping. "CoreGenesUniqueGenes" (CGUG) is a web-based tool that determines this core set of proteins in a set of genomes as well as parses the dispensable set of unique proteins in a pair of viral or small bacterial genomes. This proteome-based methodology is validated using bacteriophages, aiding the reevaluation of current classifications of bacteriophages. The utility of CGUG in the analysis of small bacterial genomes and the annotation of hypothetical proteins is also presented.}, } @article {pmid20863581, year = {2010}, author = {Redshaw, CH and Sutter, D and Myers, TL and Naar, J and Kubanek, J}, title = {Tracking losses of brevetoxins on exposure to phytoplankton competitors: Mechanistic insights.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {100}, number = {4}, pages = {365-372}, doi = {10.1016/j.aquatox.2010.08.015}, pmid = {20863581}, issn = {1879-1514}, mesh = {Biotransformation ; Diatoms/drug effects/metabolism ; Marine Toxins/*metabolism/toxicity ; Oxocins/*metabolism/toxicity ; Phytoplankton/drug effects/*metabolism ; Poisons/*metabolism/toxicity ; Water Pollutants, Chemical/metabolism/toxicity ; }, abstract = {The increasing frequency of devastating blooms of the harmful dinoflagellate Karenia brevis has motivated investigations into understanding bloom dynamics and the potential for mitigation. Previous findings indicate that waterborne concentrations of the most abundant brevetoxin (brevetoxin B or PbTx-2) associated with these blooms decrease in the presence of other phytoplankton species. The current study explores the mechanism of brevetoxin removal from seawater upon exposure to phytoplankton competitors. Live phytoplankton removed waterborne brevetoxins more rapidly than lysates, but phytoplankton did not need to be in a state of active metabolism. Biomolecules, probably proteins, exuded from phytoplankton appeared to be responsible for the loss of brevetoxins, either by irreversible complexation or by degradation. Selective removal of PbTx-2 and -1, but not PbTx-3, -9 or BTX-B5, by cultured phytoplankton revealed that brevetoxin removal is dependent upon the presence of an α,β-unsaturated aldehyde functionality. The mechanism of biotransformation appears to be common among phytoplankton, since members of various taxonomic groups including diatoms, dinoflagellates, and a cryptophyte each caused 75-90% decrease in PbTx-2 concentration, as did a generic protein (bovine serum albumin) added to seawater at high concentration. These findings support the concept of potentially using competitor phytoplankton species or compounds derived from phytoplankton as biocontrol agents for waterborne toxins associated with red tide.}, } @article {pmid20842352, year = {2010}, author = {Grienberger, HJ and Pillai, DR and Schlachetzki, F and Gruber, M and Dittmar, MS}, title = {Detection of free radicals by isolated perfusion of the rat brain following hemorrhagic stroke: a novel approach to cerebrovascular biomarker research.}, journal = {Experimental brain research}, volume = {206}, number = {3}, pages = {311-317}, pmid = {20842352}, issn = {1432-1106}, mesh = {Animals ; Biomarkers/blood ; Cerebral Hemorrhage/blood/*metabolism/physiopathology ; Cerebrovascular Circulation/*physiology ; Corpus Striatum/blood supply/metabolism/physiopathology ; Disease Models, Animal ; Free Radicals/*blood ; Male ; Oxidative Stress/physiology ; Perfusion/*methods ; Rats ; Rats, Wistar ; Reactive Oxygen Species/blood ; Stroke/blood/*metabolism/physiopathology ; Up-Regulation/physiology ; }, abstract = {Blood-borne biomarkers are a mainstay of diagnosis and follow-up in many diseases. For stroke, however, no reliable biomarkers have thus far been identified. To remedy this situation, we investigated the usefulness of a modified in situ isolated brain perfusion (IBP) technique for screening potential biomarker candidates. As a proof of concept, the production of reactive oxygen species (ROS) was estimated in a rat model of experimental intracerebral hemorrhage (ICH). After stereotactic infusion of whole blood into the rat striatum, we initiated IBP without intracranial manipulation or discontinuation of cerebral blood flow. To detect ROS, we employed the salicylate trapping method, which involves the hydroxylation of salicylic acid during oxidative stress into dihydroxybenzoic acid (DHBA), and quantification of the latter in venous eluate by using high-performance liquid chromatography. Venous eluate was collected separately from both injured and healthy hemispheres (n=10). Control groups consisted of sham-injured (n=4) and healthy animals (n=3). In animals subjected to ICH (n=10), 50% more 2,5-DHBA was detected in venous eluate on the injured side than in eluate on the contralateral side. Hemorrhagic hemispheres produced more 2,5-DHBA than hemispheres in sham-injured and healthy animals (72 and 110% more 2,5-DHBA, respectively). Isolated brain perfusion combined with salicylate trapping produced data indicating an elevation in the formation of ROS subsequent to ICH. Our findings suggest that isolated in situ brain perfusion is a promising approach to detecting biomarkers of cerebrovascular pathologic conditions.}, } @article {pmid20836045, year = {2010}, author = {Teusink, B and Westerhoff, HV and Bruggeman, FJ}, title = {Comparative systems biology: from bacteria to man.}, journal = {Wiley interdisciplinary reviews. Systems biology and medicine}, volume = {2}, number = {5}, pages = {518-532}, doi = {10.1002/wsbm.74}, pmid = {20836045}, issn = {1939-005X}, support = {BB/C008219/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/D019079/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/genetics/metabolism ; Computational Biology ; Drug Discovery ; Feedback, Physiological ; Genomics ; Glycolysis ; Humans ; Metabolic Networks and Pathways ; Models, Biological ; Saccharomyces cerevisiae/genetics/metabolism ; Species Specificity ; *Systems Biology/trends ; }, abstract = {Comparative analyses, as carried out by comparative genomics and bioinformatics, have proven extremely powerful to obtain insight into the identity of specific genes that underlie differences and similarities across species. The central concept developed in this chapter is that important aspects of the functional differences between organisms derive not only from the differences in genetic components (which underlies comparative genomics) but also from dynamic, molecular (physical) interactions. Approaches that aim at identifying such network-based rather than component-based homologies between species we shall call Comparative Systems Biology. It will be illustrated by a number of examples from metabolic networks from prokaryotes, via yeast, to man. The potential for species comparisons, at the genome-scale using classical approaches and at the more detailed level of dynamic molecular networks will be illustrated. In our opinion, comparative systems biology, as a marriage between bioinformatics and systems biology, will offer new insights into the nature of organisms for the benefit of medicine, biotechnology, and drug design. As dynamic modeling is becoming more mainstream in cell biology, the potential of comparative systems biology will become more evident.}, } @article {pmid20821295, year = {2010}, author = {Yang, Y and Zhou, Z}, title = {New insights into the species problem.}, journal = {Science China. Life sciences}, volume = {53}, number = {8}, pages = {964-972}, doi = {10.1007/s11427-010-4037-x}, pmid = {20821295}, issn = {1869-1889}, mesh = {Animals ; Biological Evolution ; *Species Specificity ; }, abstract = {Historical opinions of the "species problem" are briefly reviewed, and four salient stages are recognized according to origin of species concepts. We propose that species is the unit preserving superior gene assembly and is maintained by specific mechanisms. Based on characteristics of plant evolution, we assume that understanding plant species may include three stages, i.e. morphological recognition stage, multidisciplinary verification stage, and illuminating mechanisms preserving superior gene assembly.}, } @article {pmid20816683, year = {2010}, author = {Sapijanskas, J and Loreau, M}, title = {Cascading extinctions, functional complementarity, and selection in two-trophic-level model communities: a trait-based mechanistic approach.}, journal = {Journal of theoretical biology}, volume = {267}, number = {3}, pages = {375-387}, doi = {10.1016/j.jtbi.2010.08.031}, pmid = {20816683}, issn = {1095-8541}, mesh = {Algorithms ; *Biodiversity ; Biomass ; Computer Simulation ; Ecosystem ; *Extinction, Biological ; *Models, Biological ; Population Dynamics ; }, abstract = {The influence of diversity on ecosystem functioning and ecosystem services is now well established. Yet predictive mechanistic models that link species traits and community-level processes remain scarce, particularly for multitrophic systems. Here we revisit MacArthur's classical consumer resource model and develop a trait-based approach to predict the effects of consumer diversity on cascading extinctions and aggregated ecosystem processes in a two-trophic-level system. We show that functionally redundant efficient consumers generate top-down cascading extinctions. This counterintuitive result reveals the limits of the functional redundancy concept to predict the consequences of species deletion. Our model also predicts that the biodiversity-ecosystem functioning relationship is different for different ecosystem processes and depends on the range of variation of consumer traits in the regional species pool, which determines the sign of selection effects. Lastly, competition among resources and consumer generalism both weaken complementarity effects, which suggests that selection effects may prevail at higher trophic levels. Our work emphasizes the potential of trait-based approaches for transforming biodiversity and ecosystem functioning research into a more predictive science.}, } @article {pmid20813193, year = {2010}, author = {Ley, AC and Hardy, OJ}, title = {Species delimitation in the Central African herbs Haumania (Marantaceae) using georeferenced nuclear and chloroplastic DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {57}, number = {2}, pages = {859-867}, doi = {10.1016/j.ympev.2010.08.027}, pmid = {20813193}, issn = {1095-9513}, mesh = {Africa, Central ; DNA Barcoding, Taxonomic ; DNA, Chloroplast/*genetics ; DNA, Plant/*genetics ; Gene Flow/genetics ; Marantaceae/*classification/*genetics ; *Phylogeny ; Phylogeography ; Species Specificity ; }, abstract = {Species delimitation is a fundamental biological concept which is frequently discussed and altered to integrate new insights. These revealed that speciation is not a one step phenomenon but an ongoing process and morphological characters alone are not sufficient anymore to properly describe the results of this process. Here we want to assess the degree of speciation in two closely related lianescent taxa from the tropical African genus Haumania which display distinct vegetative traits despite a high similarity in reproductive traits and a partial overlap in distribution area which might facilitate gene flow. To this end, we combined phylogenetic and phylogeographic analyses using nuclear (nr) and chloroplast (cp) DNA sequences in comparison to morphological species descriptions. The nuclear dataset unambiguously supports the morphological species concept in Haumania. However, the main chloroplastic haplotypes are shared between species and, although a geographic analysis of cpDNA diversity confirms that individuals from the same taxon are more related than individuals from distinct taxa, cp-haplotypes display correlated geographic distributions between species. Hybridization is the most plausible reason for this pattern. A scenario involving speciation in geographic isolation followed by range expansion is outlined. The study highlights the gain of information on the speciation process in Haumania by adding georeferenced molecular data to the morphological characteristics. It also shows that nr and cp sequence data might provide different but complementary information, questioning the reliability of the unique use of chloroplast data for species recognition by DNA barcoding.}, } @article {pmid20809982, year = {2010}, author = {Fried, G and Petit, S and Reboud, X}, title = {A specialist-generalist classification of the arable flora and its response to changes in agricultural practices.}, journal = {BMC ecology}, volume = {10}, number = {}, pages = {20}, pmid = {20809982}, issn = {1472-6785}, mesh = {Agriculture/*methods ; *Biota ; Crops, Agricultural/growth & development ; Ecology/methods ; France ; Herbicides ; Plant Weeds/*classification ; }, abstract = {BACKGROUND: Theory in ecology points out the potential link between the degree of specialisation of organisms and their responses to disturbances and suggests that this could be a key element for understanding the assembly of communities. We evaluated this question for the arable weed flora as this group has scarcely been the focus of ecological studies so far and because weeds are restricted to habitats characterised by very high degrees of disturbance. As such, weeds offer a case study to ask how specialization relates to abundance and distribution of species in relation to the varying disturbance regimes occurring in arable crops.

RESULTS: We used data derived from an extensive national monitoring network of approximately 700 arable fields scattered across France to quantify the degree of specialisation of 152 weed species using six different ecological methods. We then explored the impact of the level of disturbance occurring in arable fields by comparing the degree of specialisation of weed communities in contrasting field situations.The classification of species as specialist or generalist was consistent between different ecological indices. When applied on a large-scale data set across France, this classification highlighted that monoculture harbour significantly more specialists than crop rotations, suggesting that crop rotation increases abundance of generalist species rather than sets of species that are each specialised to the individual crop types grown in the rotation. Applied to a diachronic dataset, the classification also shows that the proportion of specialist weed species has significantly decreased in cultivated fields over the last 30 years which suggests a biotic homogenization of agricultural landscapes.

CONCLUSIONS: This study shows that the concept of generalist/specialist species is particularly relevant to understand the effect of anthropogenic disturbances on the evolution of plant community composition and that ecological theories developed in stable environments are valid in highly disturbed environments such as agro-ecosystems. The approach developed here to classify arable weeds according to the breadth of their ecological niche is robust and applicable to a wide range of organisms. It is also sensitive to disturbance regime and we show here that recent changes in agricultural practices, i.e. increased levels of disturbance have favoured the most generalist species, hence leading to biotic homogenisation in arable landscapes.}, } @article {pmid20806003, year = {2010}, author = {Lombard, L and Crous, PW and Wingfield, BD and Wingfield, MJ}, title = {Species concepts in Calonectria (Cylindrocladium).}, journal = {Studies in mycology}, volume = {66}, number = {}, pages = {1-13}, pmid = {20806003}, issn = {1872-9797}, abstract = {Species of Calonectria and their Cylindrocladium anamorphs are important plant pathogens worldwide. At present 52 Cylindrocladium spp. and 37 Calonectria spp. are recognised based on sexual compatibility, morphology and phylogenetic inference. The polyphasic approach of integrating Biological, Morphological and Phylogenetic Species Concepts has revolutionised the taxonomy of fungi. This review aims to present an overview of published research on the genera Calonectria and Cylindrocladium as they pertain to their taxonomic history. The nomenclature as well as future research necessary for this group of fungi are also briefly discussed.}, } @article {pmid20800099, year = {2010}, author = {Yassin, A and Markow, TA and Narechania, A and O'Grady, PM and DeSalle, R}, title = {The genus Drosophila as a model for testing tree- and character-based methods of species identification using DNA barcoding.}, journal = {Molecular phylogenetics and evolution}, volume = {57}, number = {2}, pages = {509-517}, doi = {10.1016/j.ympev.2010.08.020}, pmid = {20800099}, issn = {1095-9513}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Drosophila/*classification/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {DNA barcoding has recently been proposed as a promising tool for the (1) rapid assignment of unknown samples to described species by non-expert workers and (2) a potential method of new species discovery based on degree of DNA sequence divergence. Two broad methods have been used, one based on degree of DNA sequence variation, within and between species and another requiring the recovery of species as discrete clades (monophyly) on a phylogenetic tree. An alternative method relies on the identification of a set of specific diagnostic nucleotides for a given species (characters). The genus Drosophila has long served as a model system in genetics, development, ecology and evolutionary biology. As a result of this work, species boundaries within this genus are quite well delimited, with most taxa being defined by morphological characters and also conforming to a biological species concept (e.g., partial or complete reproductive isolation has used to erect and define species). In addition, some of the species in this group have also been subjected to phylogenetic analysis, yielding cases where taxa both conform and conflict with a phylogenetic species concept. Here, we analyzed 1058 COI sequences belonging to 68 species belonging to Drosophila and its allied genus Zaprionus and with more than a single representative to assess the performance of the three DNA barcoding methods. 26% of the species could not be defined using distance methods, i.e. had a barcoding gap of ≤ 0, and 23% were not monophyletic. We focused then on four groups of closely-related species whose taxonomy is well-established on non-molecular basis (e.g., morphology, geography, reproductive isolation) and to which most of the problematic species belonged. We showed that characters performed better than other approaches in the case of paraphyletic species, but all methods failed in the case of polyphyletic species. For these polyphyletic species, other sources of evidence (e.g., morphology, geography, reproductive isolation) are more relevant than COI sequences, highlighting the limitation of DNA barcoding and the needs for integrative taxonomy approaches. In conclusion, DNA barcoding of Drosophila shows no reason to alter the 250 years old tradition of character-based taxonomy, and many reasons to shy away from the alternatives.}, } @article {pmid20711777, year = {2011}, author = {Rubach, MN and Crum, SJ and Van den Brink, PJ}, title = {Variability in the dynamics of mortality and immobility responses of freshwater arthropods exposed to chlorpyrifos.}, journal = {Archives of environmental contamination and toxicology}, volume = {60}, number = {4}, pages = {708-721}, pmid = {20711777}, issn = {1432-0703}, mesh = {Animals ; Arthropods/*drug effects/growth & development ; Chlorpyrifos/*toxicity ; Data Interpretation, Statistical ; Dose-Response Relationship, Drug ; Endpoint Determination ; Fresh Water/*chemistry ; Lethal Dose 50 ; Motor Activity/*drug effects ; Species Specificity ; *Toxicity Tests/methods/standards ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The species sensitivity distribution (SSD) concept is an important probabilistic tool for environmental risk assessment (ERA) and accounts for differences in species sensitivity to different chemicals. The SSD model assumes that the sensitivity of the species included is randomly distributed. If this assumption is violated, indicator values, such as the 50% hazardous concentration, can potentially change dramatically. Fundamental research, however, has discovered and described specific mechanisms and factors influencing toxicity and sensitivity for several model species and chemical combinations. Further knowledge on how these mechanisms and factors relate to toxicologic standard end points would be beneficial for ERA. For instance, little is known about how the processes of toxicity relate to the dynamics of standard toxicity end points and how these may vary across species. In this article, we discuss the relevance of immobilization and mortality as end points for effects of the organophosphate insecticide chlorpyrifos on 14 freshwater arthropods in the context of ERA. For this, we compared the differences in response dynamics during 96 h of exposure with the two end points across species using dose response models and SSDs. The investigated freshwater arthropods vary less in their immobility than in their mortality response. However, differences in observed immobility and mortality were surprisingly large for some species even after 96 h of exposure. As expected immobility was consistently the more sensitive end point and less variable across the tested species and may therefore be considered as the relevant end point for population of SSDs and ERA, although an immobile animal may still potentially recover. This is even more relevant because an immobile animal is unlikely to survive for long periods under field conditions. This and other such considerations relevant to the decision-making process for a particular end point are discussed.}, } @article {pmid20688752, year = {2010}, author = {Lefébure, T and Bitar, PD and Suzuki, H and Stanhope, MJ}, title = {Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {646-655}, pmid = {20688752}, issn = {1759-6653}, support = {N01AI30054/AI/NIAID NIH HHS/United States ; }, mesh = {Campylobacter coli/*genetics ; Campylobacter jejuni/*genetics ; Chromosome Mapping ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Bacterial ; }, abstract = {Defining bacterial species and understanding the relative cohesiveness of different components of their genomes remains a fundamental problem in microbiology. Bacterial species tend to be comprised of both a set of core and dispensable genes, with the sum of these two components forming the species pan-genome. The role of the core and dispensable genes in defining bacterial species and the question of whether pan-genomes are finite or infinite remain unclear. Here we demonstrate, through the analysis of 96 genome sequences derived from two closely related sympatric sister species of pathogenic bacteria (Campylobacter coli and C. jejuni), that their pan-genome is indeed finite and that there are unique and cohesive features to each of their genomes defining their genomic identity. The two species have a similar pan-genome size; however, C. coli has acquired a larger core genome and each species has evolved a number of species-specific core genes, possibly reflecting different adaptive strategies. Genome-wide assessment of the level of lateral gene transfer within and between the two sister species, as well as within the core and non-core genes, demonstrates a resistance to interspecies recombination in the core genome of the two species and therefore provides persuasive support for the core genome hypothesis for bacterial species.}, } @article {pmid20673351, year = {2010}, author = {Bittner, L and Halary, S and Payri, C and Cruaud, C and de Reviers, B and Lopez, P and Bapteste, E}, title = {Some considerations for analyzing biodiversity using integrative metagenomics and gene networks.}, journal = {Biology direct}, volume = {5}, number = {}, pages = {47}, pmid = {20673351}, issn = {1745-6150}, mesh = {Animals ; *Biodiversity ; Gene Regulatory Networks/*genetics ; Humans ; Metagenomics/*methods ; Models, Theoretical ; }, abstract = {BACKGROUND: Improving knowledge of biodiversity will benefit conservation biology, enhance bioremediation studies, and could lead to new medical treatments. However there is no standard approach to estimate and to compare the diversity of different environments, or to study its past, and possibly, future evolution.

We argue that there are two conditions for significant progress in the identification and quantification of biodiversity. First, integrative metagenomic studies - aiming at the simultaneous examination (or even better at the integration) of observations about the elements, functions and evolutionary processes captured by the massive sequencing of multiple markers - should be preferred over DNA barcoding projects and over metagenomic projects based on a single marker. Second, such metagenomic data should be studied with novel inclusive network-based approaches, designed to draw inferences both on the many units and on the many processes present in the environments.

TESTING THE HYPOTHESIS: We reached these conclusions through a comparison of the theoretical foundations of two molecular approaches seeking to assess biodiversity: metagenomics (mostly used on prokaryotes and protists) and DNA barcoding (mostly used on multicellular eukaryotes), and by pragmatic considerations of the issues caused by the 'species problem' in biodiversity studies.

Evolutionary gene networks reduce the risk of producing biodiversity estimates with limited explanatory power, biased either by unequal rates of LGT, or difficult to interpret due to (practical) problems caused by type I and type II grey zones. Moreover, these networks would easily accommodate additional (meta)transcriptomic and (meta)proteomic data.}, } @article {pmid20665095, year = {2010}, author = {Schmitt, S}, title = {Lacepède's syncretic contribution to the debates on natural history in France around 1800.}, journal = {Journal of the history of biology}, volume = {43}, number = {3}, pages = {429-457}, pmid = {20665095}, issn = {0022-5010}, mesh = {*Classification ; France ; History, 18th Century ; History, 19th Century ; Natural History/*history ; }, abstract = {Lacepède was a key figure in the French intellectual world from the Old Regime to the Restoration, sinc e he was not only a scientist, but also a musician, a writer, and a politician. His brilliant career is a good example of the progress of the social status of scientists in France around 1800. In the life sciences, he was considered the heir to Buffon and continued the latter's Histoire naturelle, but he also borrowed ideas from anti-Buffonian (e.g. Linnaean) scientists. He broached many important subjects such as the nature of man, the classification of animals, the concept of species, and the history of the Earth. All these topics led to tensions in the French sciences, but Lacepède dealt with them in a consensual, indeed even ambiguous way. For example, he held transformist views, but his concept of evolution was far less precise and daring than Lamarck's contemporaneous attempts. His somewhat confused eclecticism allowed him to be accepted by opposing camps of the French scientific community at that time and makes his case interesting for historians, since the opinions of such an opportunistic figure can illuminate the figure of the French intellectual better than more original works could do. In turn, Lacepède's important social and scientific position gave his views a significant visibility. In this sense, his contributions probably exerted an influence, in particular with regard to the emergence of transformist theories.}, } @article {pmid20662634, year = {2011}, author = {Van Der Linden, JW and Warris, A and Verweij, PE}, title = {Aspergillus species intrinsically resistant to antifungal agents.}, journal = {Medical mycology}, volume = {49 Suppl 1}, number = {}, pages = {S82-9}, doi = {10.3109/13693786.2010.499916}, pmid = {20662634}, issn = {1460-2709}, mesh = {Antifungal Agents/*pharmacology/therapeutic use ; Aspergillosis/*drug therapy/microbiology ; Aspergillus/classification/*drug effects/pathogenicity ; Drug Resistance, Fungal/drug effects ; Humans ; Microbial Sensitivity Tests/methods ; }, abstract = {Polyphasic taxonomy has had a major impact on the species concept of the genus Aspergillus. New sibling species have been described that exhibit in vitro susceptibility profiles that differ significantly from that of Aspergillus fumigatus. While acquired resistance is an emerging problem in A. fumigatus, non-A. fumigatus Aspergillus species may be intrinsically resistant to specific classes of antifungal agents. Minimum inhibitory concentrations of amphotericin B and azoles for some of the non-A. fumigatus Aspergillus species are elevated compared to A. fumigatus. Furthermore, the clinical presentation and evolution of invasive infections caused by these species may differ from that commonly observed for A. fumigatus. As the role of the newly identified Aspergillus species in causing invasive aspergillosis remains unclear, surveillance networks that incorporate sequence-based identification of clinical isolates are needed to determine the species distribution, the clinical disease and outcome of patients with invasive aspergillosis. Preclinical and clinical studies are needed to further improve the methods for in vitro susceptibility testing and to investigate the impact of elevated MICs on antifungal drug efficacy.}, } @article {pmid20643217, year = {2010}, author = {Ploch, S and Choi, YJ and Rost, C and Shin, HD and Schilling, E and Thines, M}, title = {Evolution of diversity in Albugo is driven by high host specificity and multiple speciation events on closely related Brassicaceae.}, journal = {Molecular phylogenetics and evolution}, volume = {57}, number = {2}, pages = {812-820}, doi = {10.1016/j.ympev.2010.06.026}, pmid = {20643217}, issn = {1095-9513}, mesh = {*Biodiversity ; Brassicaceae/*microbiology ; Host Specificity/genetics/*physiology ; Oomycetes/*classification/genetics/*physiology ; *Phylogeny ; }, abstract = {The Albuginaceae, responsible for white blister rust disease on various angiosperms, are obligate biotrophic oomycetes that are only distantly related to downy mildews (Peronosporaceae). Their diversity has been much underestimated during the past decades, mainly because of the paucity of morphological characters for species delimitation, which led to the application of a broad species concept. Recent phylogenetic analyses have revealed three new species within Albugo parasitic to Brassicaceae, but the overall evolution of these plant pathogens remains poorly understood. Especially the diversity of Albugo in various plant genera is almost completely unknown. Based on ITS and cox2 sequence data of 72 Albugo specimens, predominantly from herbarium archives, and focusing on the widespread genus Cardamine, a high degree of phylogenetic diversity was revealed in Albugo. In particular, the hypothesis that one host genus can be colonised by more than one white blister rust species is confirmed. In addition, it is revealed that there are hitherto overlooked lineages with close relationships to the generalist species Albugo candida. Evidence for at least three different species of Albugo infecting Cardamine is presented in this study. Based on molecular phylogenetic and morphological data three new white blister rust species are described, Albugo hohenheimia, Albugo hesleri, and Albugo leimonios infecting Cardamine hirsuta, Cardamine diphylla and Cardamine pratensis, respectively. The fact that these species each have different ecological niches, suggests that environmental factors may have played a role in the speciation process in Albugo. Our findings suggest that other larger genera of the Brassicaceae may harbour unrecognized white blister rust species and that only a small fraction of the true biodiversity of white blister rusts is known at present.}, } @article {pmid20633043, year = {2010}, author = {Hulcr, J and Cognato, AI}, title = {Repeated evolution of crop theft in fungus-farming ambrosia beetles.}, journal = {Evolution; international journal of organic evolution}, volume = {64}, number = {11}, pages = {3205-3212}, doi = {10.1111/j.1558-5646.2010.01055.x}, pmid = {20633043}, issn = {1558-5646}, mesh = {Animals ; Bayes Theorem ; Behavior, Animal ; *Biological Evolution ; Coleoptera/*genetics/*physiology ; DNA, Fungal/genetics ; Fungi/*metabolism ; Host-Parasite Interactions ; Models, Genetic ; Phylogeny ; Species Specificity ; Symbiosis ; }, abstract = {Ambrosia beetles, dominant wood degraders in the tropics, create tunnels in dead trees and employ gardens of symbiotic fungi to extract nutrients from wood. Specificity of the beetle-fungus relationship has rarely been examined, and simple vertical transmission of a specific fungal cultivar by each beetle species is often assumed in literature. We report repeated evolution of fungal crop stealing, termed mycocleptism, among ambrosia beetles. The mycocleptic species seek brood galleries of other species, and exploit their established fungal gardens by tunneling through the ambient mycelium-laden wood. Instead of carrying their own fungal sybmbionts, mycocleptae depend on adopting the fungal assemblages of their host species, as shown by an analysis of fungal DNA from beetle galleries. The evidence for widespread horizontal exchange of fungi between beetles challenges the traditional concept of ambrosia fungi as species-specific symbionts. Fungus stealing appears to be an evolutionarily successful strategy. It evolved independently in several beetle clades, two of which have radiated, and at least one case was accompanied by a loss of the beetles' fungus-transporting organs. We demonstrate this using the first robust phylogeny of one of the world's largest group of ambrosia beetles, Xyleborini.}, } @article {pmid20598770, year = {2010}, author = {Arnold, ML and Martin, NH}, title = {Hybrid fitness across time and habitats.}, journal = {Trends in ecology & evolution}, volume = {25}, number = {9}, pages = {530-536}, doi = {10.1016/j.tree.2010.06.005}, pmid = {20598770}, issn = {0169-5347}, mesh = {Adaptation, Physiological/*genetics ; Animals ; *Ecosystem ; Genetic Speciation ; *Hybridization, Genetic ; Plants/genetics ; }, abstract = {There has been considerable debate about the role of hybrids in the evolutionary process. One question has involved the relative fitness of hybrid versus non-hybrid genotypes. For some, the assumption of lower hybrid fitness continues to be integral to their concept of species and speciation. In contrast, numerous workers have suggested that hybrid genotypes might demonstrate higher relative fitness under various environmental settings. Of particular importance in deciding between these opposing hypotheses are long-term analyses coupling ecological and genetic information. Although currently rare, such analyses have provided a test of the fitness of hybrid genotypes across generations and habitats and their role in adaptation and speciation. Here we discuss examples of these analyses applied to viruses, prokaryotes, plants and Darwin's Finches.}, } @article {pmid21975257, year = {2010}, author = {Barratt, BI and Todd, JH and Burgess, EP and Malone, LA}, title = {Developing biosafety risk hypotheses for invertebrates exposed to GM plants using conceptual food webs: a case study with elevated triacylglyceride levels in ryegrass.}, journal = {Environmental biosafety research}, volume = {9}, number = {3}, pages = {163-179}, doi = {10.1051/ebr/2011107}, pmid = {21975257}, issn = {1635-7922}, mesh = {Animals ; *Food Chain ; Gastropoda/metabolism ; Lolium/*genetics/metabolism ; Moths/metabolism ; *Plants, Genetically Modified ; Risk Assessment ; Triglycerides/metabolism ; }, abstract = {Regulators are acutely aware of the need for meaningful risk assessments to support decisions on the safety of GM crops to non-target invertebrates in determining their suitability for field release. We describe a process for developing appropriate, testable risk hypotheses for invertebrates in agroecosystems that might be exposed to plants developed by GM and future novel technologies. An existing model (PRONTI) generates a ranked list of invertebrate species for biosafety testing by accessing a database of biological, ecological and food web information about species which occur in cropping environments and their potential interactions with a particular stressor (Eco Invertebase). Our objective in this contribution is to explore and further utilise these resources to assist in the process of problem formulation by identifying potentially significant effects of the stressor on the invertebrate community and the ecosystem services they provide. We propose that for high ranking species, a conceptual food web using information in Eco Invertebase is constructed, and using an accepted regulatory risk analysis framework, the likelihood of risk, and magnitude of impact for each link in the food web is evaluated. Using as filters only those risks evaluated as likely to extremely likely, and the magnitude of an effect being considered as moderate to massive, the most significant potential effects can be identified. A stepwise approach is suggested to develop a sequence of appropriate tests. The GM ryegrass plant used as the "stressor" in this study has been modified to increase triacylglyceride levels in foliage by 100% to increase the metabolisable energy content of forage for grazing animals. The high-ranking "test" species chosen to illustrate the concept are New Zealand native species Wiseana cervinata (Walker) (Lepidoptera: Hepialidae), Persectania aversa (Walker) (Lepidoptera: Noctuidae), and the self-introduced grey field slug, Deroceras reticulatum (Müller).}, } @article {pmid20583707, year = {2010}, author = {Spasojevic, MJ and Aicher, RJ and Koch, GR and Marquardt, ES and Mirotchnick, N and Troxler, TG and Collins, SL}, title = {Fire and grazing in a mesic tallgrass prairie: impacts on plant species and functional traits.}, journal = {Ecology}, volume = {91}, number = {6}, pages = {1651-1659}, doi = {10.1890/09-0431.1}, pmid = {20583707}, issn = {0012-9658}, mesh = {Animals ; Bison/*physiology ; *Ecosystem ; Feeding Behavior ; *Fires ; Kansas ; Plants/*classification ; Time Factors ; }, abstract = {Fire is a globally distributed disturbance that impacts terrestrial ecosystems and has been proposed to be a global "herbivore." Fire, like herbivory, is a top-down driver that converts organic materials into inorganic products, alters community structure, and acts as an evolutionary agent. Though grazing and fire may have some comparable effects in grasslands, they do not have similar impacts on species composition and community structure. However, the concept of fire as a global herbivore implies that fire and herbivory may have similar effects on plant functional traits. Using 22 years of data from a mesic, native tallgrass prairie with a long evolutionary history of fire and grazing, we tested if trait composition between grazed and burned grassland communities would converge, and if the degree of convergence depended on fire frequency. Additionally, we tested if eliminating fire from frequently burned grasslands would result in a state similar to unburned grasslands, and if adding fire into a previously unburned grassland would cause composition to become more similar to that of frequently burned grasslands. We found that grazing and burning once every four years showed the most convergence in traits, suggesting that these communities operate under similar deterministic assembly rules and that fire and herbivory are similar disturbances to grasslands at the trait-group level of organization. Three years after reversal of the fire treatment we found that fire reversal had different effects depending on treatment. The formerly unburned community that was then burned annually became more similar to the annually burned community in trait composition suggesting that function may be rapidly restored if fire is reintroduced. Conversely, after fire was removed from the annually burned community trait composition developed along a unique trajectory indicating hysteresis, or a time lag for structure and function to return following a change in this disturbance regime. We conclude that functional traits and species-based metrics should be considered when determining and evaluating goals for fire management in mesic grassland ecosystems.}, } @article {pmid20580847, year = {2010}, author = {Geiger, MF and McCrary, JK and Schliewen, UK}, title = {Not a simple case - A first comprehensive phylogenetic hypothesis for the Midas cichlid complex in Nicaragua (Teleostei: Cichlidae: Amphilophus).}, journal = {Molecular phylogenetics and evolution}, volume = {56}, number = {3}, pages = {1011-1024}, doi = {10.1016/j.ympev.2010.05.015}, pmid = {20580847}, issn = {1095-9513}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Bayes Theorem ; Cichlids/anatomy & histology/*classification/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genetic Speciation ; Genotype ; Models, Genetic ; Nicaragua ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Nicaraguan Midas cichlids from crater lakes have recently attracted attention as potential model systems for speciation research, but no attempt has been made to comprehensively reconstruct phylogenetic relationships of this highly diverse and recently evolved species complex. We present a first AFLP (2793 loci) and mtDNA based phylogenetic hypothesis including all described and several undescribed species from six crater lakes (Apoyeque, Apoyo, Asososca Leon, Masaya, Tiscapa and Xiloá), the two great Lakes Managua and Nicaragua and the San Juan River. Our analyses demonstrate that the relationships between the Midas cichlid members are complex, and that phylogenetic information from different markers and methods do not always yield congruent results. Nevertheless, monophyly support for crater lake assemblages from Lakes Apoyeque, Apoyo, A. Leon is high as compared to those from L. Xiloá indicating occurrence of sympatric speciation. Further, we demonstrate that a 'three species' concept for the Midas cichlid complex is inapplicable and consequently that an individualized and voucher based approach in speciation research of the Midas cichlid complex is necessary at least as long as there is no comprehensive revision of the species complex available.}, } @article {pmid20571577, year = {2010}, author = {Xiong, Y and Yao, S and Müller, R and Kaupp, M and Driess, M}, title = {From silicon(II)-based dioxygen activation to adducts of elusive dioxasiliranes and sila-ureas stable at room temperature.}, journal = {Nature chemistry}, volume = {2}, number = {7}, pages = {577-580}, pmid = {20571577}, issn = {1755-4349}, mesh = {Crystallography, X-Ray ; Methane/analogs & derivatives/chemistry ; Molecular Conformation ; Oxygen/*chemistry ; Silanes/*chemistry ; Silicon/*chemistry ; Temperature ; Urea/*chemistry ; }, abstract = {Dioxygen activation for the subsequent oxygenation of organic substrates that involves cheap and environmentally friendly chemical elements is at the cutting edge of chemical research. As silicon is a non-toxic and highly oxophilic element, the use of silylenes could be attractive for facile dioxygen activation to give dioxasiliranes with a SiO(2)-peroxo ring as versatile oxo-transfer reagents. However, the latter are elusive species, and have been generated and studied only in argon matrices at -233 degrees C. Recently, it was demonstrated that unstable silicon species can be isolated by applying the concept of donor-acceptor stabilization. We now report the first synthesis and crystallographic characterization of dioxasiliranes stabilized by N-heterocyclic carbenes that feature a three-membered SiO(2)-peroxide ring, isolable at room temperature. Unexpectedly, these can undergo internal oxygen transfer in toluene solution at ambient temperature to give a unique complex of cyclic sila-urea with C=O --> Si=O interaction and the shortest Si=O double-bond distance reported to date.}, } @article {pmid20561974, year = {2010}, author = {Dress, A and Moulton, V and Steel, M and Wu, T}, title = {Species, clusters and the 'Tree of life': a graph-theoretic perspective.}, journal = {Journal of theoretical biology}, volume = {265}, number = {4}, pages = {535-542}, doi = {10.1016/j.jtbi.2010.05.031}, pmid = {20561974}, issn = {1095-8541}, mesh = {*Biological Evolution ; Cluster Analysis ; *Models, Biological ; Phylogeny ; Species Specificity ; }, abstract = {A hierarchical structure describing the inter-relationships of species has long been a fundamental concept in systematic biology, from Linnean classification through to the more recent quest for a 'Tree of Life'. In this paper we use an approach based on discrete mathematics to address a basic question: could one delineate this hierarchical structure in nature purely by reference to the 'genealogy' of present-day individuals, which describes how they are related with one another by ancestry through a continuous line of descent? We describe several mathematically precise ways by which one can naturally define collections of subsets of present day individuals so that these subsets are nested (and so form a tree) based purely on the directed graph that describes the ancestry of these individuals. We also explore the relationship between these and related clustering constructions.}, } @article {pmid20560032, year = {2010}, author = {Sánchez-Ron, JM}, title = {Rebuilding the heart in Darwin's year: stem cell therapies in a Darwinian context.}, journal = {Journal of cardiovascular translational research}, volume = {3}, number = {1}, pages = {8-12}, pmid = {20560032}, issn = {1937-5395}, mesh = {Anniversaries and Special Events ; Atrophy ; Cardiovascular Diseases/genetics/pathology/physiopathology/*surgery ; *Evolution, Molecular ; *Genetic Fitness ; History, 19th Century ; Humans ; Myocardium/*pathology ; *Regeneration/genetics ; *Stem Cell Transplantation ; *Translational Research, Biomedical ; }, abstract = {The present paper tries to honour Charles Darwin's memory in the year in which the world celebrates the 200 anniversary of his birth and the 150 of the publication of The Origin of Species. After pointing out that the basis of his theory of evolution, "improvement of species", is a time-dependent concept, commenting on the role that atrophied organs played in Darwin's work and relating this with Darwinian medicine, it is suggested that stem cell and cardiovascular therapies could be perhaps connected with some of the ideas and possibilities already envisaged by Darwin and mentioned in one of his books, The Variation of Animals and Plants under Domestication (1868).}, } @article {pmid20524589, year = {2010}, author = {Kropp, BR and Matheny, PB and Nanagyulyan, SG}, title = {Phylogenetic taxonomy of the Inocybe splendens group and evolution of supersection "Marginatae".}, journal = {Mycologia}, volume = {102}, number = {3}, pages = {560-573}, doi = {10.3852/08-032}, pmid = {20524589}, issn = {0027-5514}, mesh = {Agaricales/*classification/*genetics ; Cell Nucleus/genetics ; DNA, Fungal/analysis/genetics ; DNA, Ribosomal/analysis ; *Evolution, Molecular ; Molecular Sequence Data ; North America ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {A phylogenetic and taxonomic study of the Inocybe splendens complex in western North America is presented. Our analysis indicates that western North American and European specimens referable to I. splendens sensu lato cluster into eight clades and that European and western North American representatives of this taxon are not conspecific. Section Splendentes and supersection "Marginatae" of Inocybe, smooth-spored taxa characterized by a syndrome of unique developmental characters (entirely or mostly pruinose stipe, absence of cortina, frequent presence of marginate basal bulb) are not monophyletic. The species concept for I. splendens is discussed, and a lectotype for I. splendens sensu Heim is designated. Two new species, I. monticola and I. praecox, are illustrated and described. The poorly known species I. bakeri is redescribed from type material, and a key for 22 species is provided for identification of these and other non-reddening species with smooth spores and a caulocystidiate stipe reported from North America and Europe.}, } @article {pmid20525191, year = {2010}, author = {Rotkopf, R and Abramsky, Z and Ovadia, O}, title = {Conservation genetics of a rare Gerbil species: a comparison of the population genetic structures and demographic histories of the locally rare Pygmy Gerbil and the common Anderson's Gerbil.}, journal = {BMC ecology}, volume = {10}, number = {}, pages = {15}, pmid = {20525191}, issn = {1472-6785}, mesh = {Animals ; Bayes Theorem ; *Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Female ; *Genetic Variation ; *Genetics, Population ; Gerbillinae/*genetics ; Haplotypes ; Israel ; Linkage Disequilibrium ; Male ; Phenotype ; Population Density ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: One of the major challenges in evolutionary biology is identifying rare species and devising management plans to protect them while also sustaining their genetic diversity. However, in attempting a broad understanding of rarity, single-species studies provide limited insights because they do not reveal whether the factors that affect rare species differ from those that affect more common species. To illustrate this important concept and to arrive at a better understanding of the form of rarity characterizing the rare Gerbillus henleyi, we explored its population genetic structure alongside that of the locally common Gerbillus andersoni allenbyi. We trapped gerbils in several locations in Israel's western and inner Negev sand dunes. We then extracted DNA from ear samples, and amplified two mitochondrial sequences: the control region (CR) and the cytochrome oxidase 2 gene (CO2).

RESULTS: Nucleotide diversity was low for all sequences, especially for the CR of G. a. allenbyi, which showed no diversity. We could not detect any significant population genetic structure in G. henleyi. In contrast, G. a. allenbyi's CO2 sequence showed significant population genetic structure. Pairwise PhiPT comparisons showed low values for G. henleyi but high values for G. a. allenbyi. Analysis of the species' demographic history indicated that G. henleyi's population size has not changed recently, and is under the influence of an ongoing bottleneck. The same analysis for G. a. allenbyi showed that this species has undergone a recent population expansion.

CONCLUSIONS: Comparing the two species, the populations of G. a. allenbyi are more isolated from each other, likely due to the high habitat specificity characterizing this species. The bottleneck pattern found in G. henleyi may be the result of competition with larger gerbil species. This result, together with the broad habitat use and high turnover rate characterizing G. henleyi, may explain the low level of differentiation among its populations. The evidence for a recent population expansion of G. a. allenbyi fits well with known geomorphological data about the formation of the Negev sand dunes and paleontological data about this species' expansion throughout the Levant. In conclusion, we suggest that adopting a comparative approach as presented here can markedly improve our understanding of the causes and effects of rarity, which in turn can allow us to better protect biodiversity patterns.}, } @article {pmid20514523, year = {2010}, author = {Monroe, MJ and Bokma, F}, title = {Punctuated equilibrium in a neontological context.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {129}, number = {2-3}, pages = {103-111}, pmid = {20514523}, issn = {1611-7530}, mesh = {Animals ; Ecosystem ; Extinction, Biological ; Fossils ; Gene Expression Profiling ; *Genetic Speciation ; Genetics, Population ; *Models, Genetic ; Phylogeny ; Plants ; Population Density ; Selection, Genetic/physiology ; Time Factors ; }, abstract = {The theory of punctuated equilibrium, which proposes that biological species evolve rapidly when they originate rather than gradually over time, has sparked intense debate between palaeontologists and evolutionary biologists about the mode of character evolution and the importance of natural selection. Difficulty in interpreting the fossil record prevented consensus, and it remains disputed as to what extent gradual change in established species is responsible for phenotypic differences between species. Against the historical background of the concept of evolution concentrated in speciation events, we review attempts to investigate tempo and mode of evolution using present-day species since the introduction of the theory of punctuated equilibrium in 1972. We discuss advantages, disadvantages, and prospects of using neontological data, methodological advances, and the findings of some recent studies.}, } @article {pmid20509012, year = {2010}, author = {Levy, A}, title = {Pattern, process and the evolution of meaning: species and units of selection.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {129}, number = {2-3}, pages = {159-166}, pmid = {20509012}, issn = {1611-7530}, mesh = {Adaptation, Biological ; *Biological Evolution ; Biology/classification ; Genetic Speciation ; *Phenotype ; *Selection, Genetic ; Species Specificity ; *Terminology as Topic ; }, abstract = {Many of the fundamental concepts of biology lack consensual, precise definitions. Partly, this is due to a contrast between our discrete language and the continuous character of nature. Some debates over these concepts are confounded by the use of the same terms with different specific meanings, indicating a possible need for an expanded scientific lexicon. Words have their own histories, and frequently scientific terms with a vernacular origin retain associated vestigial meanings. Even terms newly coined within science have histories and changing meanings, which can lead to confusion among debaters. Debates over concepts are further confounded when the same terms are used in different fields of biology, with distinct (even conflicting) objectives, and by biologists with different approaches and perspectives. I illustrate these issues by considering the debate over the concept of species and the unit of selection.}, } @article {pmid20498705, year = {2010}, author = {Birky, CW and Adams, J and Gemmel, M and Perry, J}, title = {Using population genetic theory and DNA sequences for species detection and identification in asexual organisms.}, journal = {PloS one}, volume = {5}, number = {5}, pages = {e10609}, pmid = {20498705}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Chlorophyta/genetics ; Fungi/genetics ; Genetic Speciation ; *Genetics, Population ; Heterotrophic Processes/genetics ; Mites/genetics ; Oligochaeta/genetics ; Phylogeny ; *Population Dynamics ; Reproduction, Asexual/*genetics ; Rotifera/genetics ; Species Specificity ; }, abstract = {BACKGROUND: It is widely agreed that species are fundamental units of biology, but there is little agreement on a definition of species or on an operational criterion for delimiting species that is applicable to all organisms.

We focus on asexual eukaryotes as the simplest case for investigating species and speciation. We describe a model of speciation in asexual organisms based on basic principles of population and evolutionary genetics. The resulting species are independently evolving populations as described by the evolutionary species concept or the general lineage species concept. Based on this model, we describe a procedure for using gene sequences from small samples of individuals to assign them to the same or different species. Using this method of species delimitation, we demonstrate the existence of species as independent evolutionary units in seven groups of invertebrates, fungi, and protists that reproduce asexually most or all of the time.

CONCLUSIONS/SIGNIFICANCE: This wide evolutionary sampling establishes the general existence of species and speciation in asexual organisms. The method is well suited for measuring species diversity when phenotypic data are insufficient to distinguish species, or are not available, as in DNA barcoding and environmental sequencing. We argue that it is also widely applicable to sexual organisms.}, } @article {pmid20465589, year = {2010}, author = {Becheler, R and Diekmann, O and Hily, C and Moalic, Y and Arnaud-Haond, S}, title = {The concept of population in clonal organisms: mosaics of temporally colonized patches are forming highly diverse meadows of Zostera marina in Brittany.}, journal = {Molecular ecology}, volume = {19}, number = {12}, pages = {2394-2407}, doi = {10.1111/j.1365-294X.2010.04649.x}, pmid = {20465589}, issn = {1365-294X}, mesh = {DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; France ; *Genetics, Population ; Microsatellite Repeats ; Models, Genetic ; Phenotype ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; Zosteraceae/*genetics ; }, abstract = {Seagrasses structure some of the world's key coastal ecosystems presently in decline due to human activities and global change. The ability to cope with environmental changes and the possibilities for shifts in distribution range depend largely on their evolvability and dispersal potential. As large-scale data usually show strong genetic structure for seagrasses, finer-grained work is needed to understand the local processes of dispersal, recruitment and colonization that could explain the apparent lack of exchange across large distances. We aimed to assess the fine-grained genetic structure of one of the most important and widely distributed seagrasses, Zostera marina, from seven meadows in Brittany, France. Both classic population genetics and network analysis confirmed a pattern of spatial segregation of polymorphism at both regional and local scales. One location exhibiting exclusively the variety 'angustifolia' did not appear more differentiated than the others, but instead showed a central position in the network analysis, confirming the status of this variety as an ecotype. This phenotypic diversity and the high allelic richness at nine microsatellites (2.33-9.67 alleles/locus) compared to levels previously reported across the distribution range, points to Brittany as a centre of diversity for Z. marina at both genetic and phenotypic levels. Despite dispersal potential of several 100 m, a significant pattern of genetic differentiation, even at fine-grained scale, revealed 'genetic patchiness'. Meadows seem to be composed of a mosaic of clones with distinct origins in space and time, a result that calls into question the accuracy of the concept of populations for such partially clonal species.}, } @article {pmid20452218, year = {2010}, author = {Didelot, X and Maiden, MC}, title = {Impact of recombination on bacterial evolution.}, journal = {Trends in microbiology}, volume = {18}, number = {7}, pages = {315-322}, pmid = {20452218}, issn = {1878-4380}, support = {087622/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/*genetics/*growth & development ; *Evolution, Molecular ; Gene Flow ; *Recombination, Genetic ; }, abstract = {Genetic exchange plays a defining role in the evolution of many bacteria. The recent accumulation of nucleotide sequence data from multiple members of diverse bacterial genera has facilitated comparative studies that have revealed many features of this process. Here we focus on genetic exchange that has involved homologous recombination and illustrate how nucleotide sequence data have furthered our understanding of: (i) the frequency of recombination; (ii) the impact of recombination in different parts of the genome; and (iii) patterns of gene flow within bacterial populations. Summarizing the results obtained for a range of bacteria, we survey evidence indicating that the extent and nature of recombination vary widely among microbiological species and often among lineages assigned to the same microbiological species. These results have important implications in studies ranging from epidemiological investigations to examination of the bacterial species problem.}, } @article {pmid20439286, year = {2010}, author = {Mallet, J}, title = {Group selection and the development of the biological species concept.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1547}, pages = {1853-1863}, pmid = {20439286}, issn = {1471-2970}, mesh = {Animals ; Biological Evolution ; Female ; *Genetic Speciation ; Genetics/history ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Male ; *Models, Genetic ; *Selection, Genetic ; }, abstract = {The development of what became known as the biological species concept began with a paper by Theodosius Dobzhansky in 1935, and was amplified by a mutualistic interaction between Dobzhansky, Alfred Emerson and Ernst Mayr after the second world war. By the 1950s and early 1960s, these authors had developed an influential concept of species as coadapted genetic complexes at equilibrium. At this time many features of species were seen as group advantages maintained by selection to avoid breakdown of beneficial coadaptation and the 'gene pool'. Speciation thus seemed difficult. It seemed to require, more so than today, an external deus ex machina, such as allopatry or the founder effect, rather than ordinary within-species processes of natural selection, sexual selection, drift and gene flow. In the mid-1960s, the distinctions between group and individual selection were clarified. Dobzhansky and Mayr both understood the implications, but their views on species changed little. These group selectionist ideas now seem peculiar, and are becoming distinctly less popular today. Few vestiges of group selectionism and species-level adaptationism remain in recent reviews of speciation. One wonders how many of our own cherished views on evolution will seem as odd to future biologists.}, } @article {pmid20437959, year = {2010}, author = {Richardson, PJ and Lundholm, JT and Larson, DW}, title = {Natural analogues of degraded ecosystems enhance conservation and reconstruction in extreme environments.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {20}, number = {3}, pages = {728-740}, doi = {10.1890/08-1092.1}, pmid = {20437959}, issn = {1051-0761}, mesh = {*Conservation of Natural Resources ; *Ecosystem ; *Environmental Restoration and Remediation ; Mining ; Ontario ; }, abstract = {Ecosystem rehabilitation strategies are grounded in the concept that coexisting species fit their environments as an outcome of natural selection operating over ecological and evolutionary timescales. From this perspective, re-creation of historical environmental filters on community assembly is a necessary first step to recovering biodiversity within degraded ecosystems; however, this approach is often not feasible in severely damaged environments where extensive physiochemical changes cannot be reversed. Under such circumstances management goals may shift from restoring historical conditions to reconstructing entirely new ecosystems or replicating natural ecosystems that may be locally novel but of regional conservation importance. This latter goal may be achieved by introducing to damaged sites species already adapted to filters maintaining the degraded state, through targeting assemblages from natural ecosystems biophysically analogous to the degraded state, here termed "degraded-state analogue" (DSA) ecosystems. This hypothesis predicts that, in high-stress sites where recruitment of previous inhabitants is strongly microsite-limited, DSA species will be primarily propagule-limited; furthermore, communities invaded by DSA species should shift in structure to reflect properties associated with high-value DSA target ecosystems. We tested these predictions by experimentally sowing long-abandoned limestone quarry floors with 18 perennial grass and forb species characteristic of rare natural limestone pavements called "alvars." Alvar species established successfully under a range of microsite conditions manipulated to alter suspected constraints on colonization, including nitrogen deficiency, excessive CaCO3, and competition with weeds. Alvar species performed equivalently to seeded weed species known to thrive on quarry floors. Resident communities doubled in species richness following alvar species addition, supporting 17-20 species/0.18 m2 (95% confidence interval) and providing refuge to regionally restricted or threatened species including Iris lacustris, Solidago ptarmicoides, and Liatris cylindracea. In contrast, maximum-diversity reference plots on a pristine alvar supported 20-23 species/0.18 m2. Strong propagule limitation but weak microsite constraints on quarry colonization by alvar species combined with establishment of species-rich communities comparable to natural alvar biodiversity hot spots confirms that targeting DSA assemblages in ecosystem reconstruction can promote both efficient site colonization and ex situ biodiversity conservation within difficult-to-restore anthropogenic wastelands.}, } @article {pmid20433686, year = {2010}, author = {Furman, A and Postawa, T and Oztunç, T and Coraman, E}, title = {Cryptic diversity of the bent-wing bat, Miniopterus schreibersii (Chiroptera: Vespertilionidae), in Asia Minor.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {121}, pmid = {20433686}, issn = {1471-2148}, mesh = {Animals ; Chiroptera/classification/*genetics/physiology ; DNA, Mitochondrial ; Echolocation ; Europe ; Genetics, Population ; Microsatellite Repeats ; Turkey ; }, abstract = {BACKGROUND: Two or more species are cryptic, if they are morphologically similar, biologically distinct, and misclassified as a single species. Cryptic species complexes were recently discovered within many bat species and we suspect that the bent-wing bat, Miniopterus schreibersii, found in Europe, northern Africa, and Asia Minor, could also form such a complex. Populations of M. schreibersii decline in most of the European countries and the species is currently listed as Near Threatened in the IUCN Red List. Finding that M. schreibersii is not a single species, but a species complex, would have a considerable impact on its conservation strategies, as the abundance of each component taxon would be much smaller than the one estimated for the nominal species.

RESULTS: Miniopterus schreibersii in Asia Minor consists of two genetically diverged lineages, which are reciprocally monophyletic on three mitochondrial DNA markers, have a diagnostic set of multilocus allele frequencies, and show a marked difference in their population structures. The lineages differ slightly in their size, wing shape, and echolocation call parameters. Although these differences are sufficient to discriminate between the lineages, they are not fully diagnostic in reference to individuals. We suggest that the lineages endured the major Northern Hemisphere glaciations in different glacial refugia and colonized Asia Minor after the last glacial maximum. The lineages are allopatric, which is neither delineated by the presence of geographical barriers nor associated with the specific climatic conditions, and which we link to competitive exclusion.

CONCLUSIONS: The distinctions between the lineages comply with most of the criteria required for species delineation imposed by various species concepts. Accordingly, we conclude that M. schreibersii in Asia Minor is represented by two cryptic species. Our results imply that the distributional range of the nominal species is almost exclusively limited to Europe and the coastal zones of Asia Minor. As populations of M. schreibersii seem to be much smaller than currently assumed, conservation strategies regarding this taxon need to be revised. The exact distributional range and the vulnerability of the suggested sister species to M. schreibersii is yet to be assessed.}, } @article {pmid20429934, year = {2010}, author = {Renn, SC and Machado, HE and Jones, A and Soneji, K and Kulathinal, RJ and Hofmann, HA}, title = {Using comparative genomic hybridization to survey genomic sequence divergence across species: a proof-of-concept from Drosophila.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {271}, pmid = {20429934}, issn = {1471-2164}, mesh = {Animals ; Base Sequence ; *Comparative Genomic Hybridization ; Drosophila/*genetics ; Drosophila melanogaster/*genetics ; Genome ; Microarray Analysis ; }, abstract = {BACKGROUND: Genome-wide analysis of sequence divergence among species offers profound insights into the evolutionary processes that shape lineages. When full-genome sequencing is not feasible for a broad comparative study, we propose the use of array-based comparative genomic hybridization (aCGH) in order to identify orthologous genes with high sequence divergence. Here we discuss experimental design, statistical power, success rate, sources of variation and potential confounding factors. We used a spotted PCR product microarray platform from Drosophila melanogaster to assess sequence divergence on a gene-by-gene basis in three fully sequenced heterologous species (D. sechellia, D. simulans, and D. yakuba). Because complete genome assemblies are available for these species this study presents a powerful test for the use of aCGH as a tool to measure sequence divergence.

RESULTS: We found a consistent and linear relationship between hybridization ratio and sequence divergence of the sample to the platform species. At higher levels of sequence divergence (< 92% sequence identity to D. melanogaster) approximately 84% of features had significantly less hybridization to the array in the heterologous species than the platform species, and thus could be identified as "diverged". At lower levels of divergence (>or= 97% identity), only 13% of genes were identified as diverged. While approximately 40% of the variation in hybridization ratio can be accounted for by variation in sequence identity of the heterologous sample relative to D. melanogaster, other individual characteristics of the DNA sequences, such as GC content, also contribute to variation in hybridization ratio, as does technical variation.

CONCLUSIONS: Here we demonstrate that aCGH can accurately be used as a proxy to estimate genome-wide divergence, thus providing an efficient way to evaluate how evolutionary processes and genomic architecture can shape species diversity in non-model systems. Given the increased number of species for which microarray platforms are available, comparative studies can be conducted for many interesting lineages in order to identify highly diverged genes that may be the target of natural selection.}, } @article {pmid20414245, year = {2010}, author = {Wassenaar, J and Jansen, E and van Zeist, WJ and Bickelhaupt, FM and Siegler, MA and Spek, AL and Reek, JN}, title = {Catalyst selection based on intermediate stability measured by mass spectrometry.}, journal = {Nature chemistry}, volume = {2}, number = {5}, pages = {417-421}, pmid = {20414245}, issn = {1755-4349}, mesh = {Acetates/chemistry ; Alkylation ; Allyl Compounds/chemistry ; Catalysis ; Ligands ; Mass Spectrometry/*methods ; Models, Molecular ; Molecular Structure ; Palladium/chemistry ; Phosphines/chemistry ; }, abstract = {The power of natural selection through survival of the fittest is nature's ultimate tool for the improvement and advancement of species. To apply this concept in catalyst development is attractive and may lead to more rapid discoveries of new catalysts for the synthesis of relevant targets, such as pharmaceuticals. Recent advances in ligand synthesis using combinatorial methods have allowed the generation of a great diversity of catalysts. However, selection methods are few in number. We introduce a new selection method that focuses on the stability of catalytic intermediates measured by mass spectrometry. The stability of the intermediate relates inversely to the reactivity of the catalyst, which forms the basis of a catalyst-screening protocol in which less-abundant species represent the most-active catalysts, 'the survival of the weakest'. We demonstrate this concept in the palladium-catalysed allylic alkylation reaction using diphosphine and IndolPhos ligands and support our results with high-level density functional theory calculations.}, } @article {pmid20394765, year = {2010}, author = {Kang, Y and Chesson, P}, title = {Relative nonlinearity and permanence.}, journal = {Theoretical population biology}, volume = {78}, number = {1}, pages = {26-35}, doi = {10.1016/j.tpb.2010.04.002}, pmid = {20394765}, issn = {1096-0325}, mesh = {Animals ; *Competitive Behavior ; Gene Frequency ; Humans ; Models, Genetic ; Models, Statistical ; *Nonlinear Dynamics ; *Population Dynamics ; Population Growth ; *Predatory Behavior ; Systems Theory ; }, abstract = {We modify the commonly used invasibility concept for coexistence of species to the stronger concept of uniform invasibility. For two-species discrete-time competition and predator-prey models, we use this concept to find broad easily checked sufficient conditions for the rigorous concept of permanent coexistence. With these results, permanent coexistence becomes a tractable concept for many discrete-time population models. To understand how these conditions apply to nonpoint attractors, we generalize the concept of relative nonlinearity and use it to show how population fluctuations affect the long-term low-density growth rate ("the invasion rate") of a species when it is invading the system consisting of the other species ("the resident") at a single-species attractor. The concept of relative nonlinearity defines circumstances when this invasion rate is increased or decreased by resident population fluctuations arising from a nonpoint attractor. The presence and sign of relative nonlinearity is easily checked in models of interacting species. When relative nonlinearity is zero or positive, fluctuations cannot decrease the invasion rate. It follows that permanence is then determined by invasibility of the resident's fixed points. However, when relative nonlinearity is negative, invasibility, and hence permanent coexistence, can be undermined by resident population fluctuations. These results are illustrated with specific two-species competition and predator-prey models of generic forms.}, } @article {pmid20368582, year = {2010}, author = {Abdel-Wahab, O and Levine, RL}, title = {Metabolism and the leukemic stem cell.}, journal = {The Journal of experimental medicine}, volume = {207}, number = {4}, pages = {677-680}, pmid = {20368582}, issn = {1540-9538}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Cholecalciferol/pharmacology/therapeutic use ; Glutarates/metabolism ; Hematopoiesis/drug effects/*physiology ; Hematopoietic Stem Cells/cytology/metabolism ; Humans ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Iron Chelating Agents/pharmacology/therapeutic use ; Isocitrate Dehydrogenase/genetics ; JNK Mitogen-Activated Protein Kinases/metabolism ; Leukemia/drug therapy/genetics/*metabolism/*pathology ; Leukemia, Myeloid, Acute/drug therapy/genetics/metabolism ; Models, Biological ; Mutation, Missense/genetics ; NADP/metabolism ; Neoplastic Stem Cells/cytology/*metabolism ; Reactive Oxygen Species/*metabolism ; }, abstract = {Acute leukemias are clonal disorders of hematopoiesis wherein a leukemic stem cell (LSC) acquires mutations that confer the capacity for unlimited self-renewal, impaired hematopoietic differentiation, and enhanced proliferation to the leukemic clone. Many recent advances in understanding the biology of leukemia have come from studies defining specific genetic and epigenetic abnormalities in leukemic cells. Three recent articles, however, further our understanding of leukemia biology by elucidating specific abnormalities in metabolic pathways in leukemic hematopoiesis. These studies potentially converge on the concept that modulation of reactive oxygen species (ROS) abundance may influence the pathogenesis and treatment of acute myeloid leukemia (AML).}, } @article {pmid20339288, year = {2009}, author = {Kupriyanova, L}, title = {Cytogenetic and genetic trends in the evolution of unisexual lizards.}, journal = {Cytogenetic and genome research}, volume = {127}, number = {2-4}, pages = {273-279}, doi = {10.1159/000303325}, pmid = {20339288}, issn = {1424-859X}, mesh = {Aneuploidy ; Animals ; *Biological Evolution ; Chimera/genetics ; Chromosomes/genetics ; *Cytogenetics ; *Evolution, Molecular ; Female ; Genome/genetics ; Lizards/*genetics ; Male ; Mosaicism ; Parthenogenesis/*genetics ; Sex Chromosomes/genetics ; }, abstract = {Extensive karyological, allozyme and molecular genetic analyses of many parthenogenetic lizards confirm the origin of these species by hybridization. The concept of reticulate (hybridogeneous) speciation based on 3 interrelated phenomena such as hybridization-unisexuality-polyploidy has been elaborated. Cytogenetic and genetic variability and some regular trends in the evolution of hybrid unisexual species have been demonstrated. Cytogenetic investigations of unisexual-bisexual complex lizards of the genus Darevskia (formerly Lacerta) in the family Lacertidae suggest that some characteristics of their karyotypes play a role in the evolution of parthenogenesis. The maternal species with advanced w sex microchromosomes (Zw type) appeared to be successful in hybridization and produced the diploid unisexual species. The polyploid back-cross hybrids between said diploids and bisexual parent species exhibited many chromosome aberrations which were associated with their complete or partial sterility. In addition, the karyotype and the structure of mitotic and meiotic lampbrush chromosomes in 2 species and in some back-cross hybrids of this unisexual-bisexual complex have been examined here using molecular cytogenetic techniques. The genomic and functional disturbances, genomic interactions between homeologous chromosomes, and possibly both genomic imprinting and the presence of mobile elements are some cytogenetic mechanisms that increase genetic diversity in hybrid parthenogenetic species.}, } @article {pmid20307672, year = {2010}, author = {Förschler, MI and Khoury, F and Bairlein, F and Aliabadian, M}, title = {Phylogeny of the mourning wheatear Oenanthe lugens complex.}, journal = {Molecular phylogenetics and evolution}, volume = {56}, number = {2}, pages = {758-767}, doi = {10.1016/j.ympev.2010.03.022}, pmid = {20307672}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Haplotypes ; Likelihood Functions ; Male ; Middle East ; Passeriformes/anatomy & histology/classification/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The phylogenetic relationship of many species and subspecies within the genus Oenanthe (wheatears) is still debated. Only recently molecular approaches have been used to clarify their basal taxonomy. One of the main unsolved groups is summarized under the name mourning wheatear O. lugens, which comprises depending on the underlying species concept 3-8 different taxa. These include the wheatears of the subspecies group lugens (halophila, lugens, persica), the subspecies group lugubris (lugubris, schalowi, vauriei), and the subspecies group lugentoides (lugentoides, boscaweni). In order to shed light on this unsolved issue we studied the taxonomy of the mourning wheatear complex by means of molecular markers and comparative morphometry. We found reasonable evidence to follow a narrow species concept treating all the three subspecies groups of the mourning wheatear in future as three independent taxonomic entities (super-species O. lugens, O. lugentoides, O. lugubris). Further within the subspecies group O. lugens we suggest treating halophila and lugens as members of the polytypic species O. lugens, while the Persian mourning wheatear O. persica merits the status of an independent monotypic species, endemic to the Iranian Plateau. Genetic and morphometric characters support a long separation of this form (a half to one Million years). For the black form "basalti" from Syria and Jordan our molecular data indicates a close relationship to lugens and this form is therefore probably best treated as a colour morph of lugens, adapted to the local habitat conditions. However, future behavioural studies have to show if there exist prezygotic barriers between both forms.}, } @article {pmid20206957, year = {2010}, author = {Bernard, HU and Burk, RD and Chen, Z and van Doorslaer, K and zur Hausen, H and de Villiers, EM}, title = {Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments.}, journal = {Virology}, volume = {401}, number = {1}, pages = {70-79}, pmid = {20206957}, issn = {1096-0341}, support = {R01 CA078527/CA/NCI NIH HHS/United States ; U01 CA078527/CA/NCI NIH HHS/United States ; CA78527/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; DNA, Viral/genetics ; Humans ; Papillomaviridae/*classification/genetics ; Papillomavirus Infections/veterinary/*virology ; Sequence Analysis, DNA ; }, abstract = {We present an expansion of the classification of the family Papillomaviridae, which now contains 29 genera formed by 189 papillomavirus (PV) types isolated from humans (120 types), non-human mammals, birds and reptiles (64, 3 and 2 types, respectively). To accommodate the number of PV genera exceeding the Greek alphabet, the prefix "dyo" is used, continuing after the Omega-PVs with Dyodelta-PVs. The current set of human PVs is contained within five genera, whereas mammalian, avian and reptile PVs are contained within 20, 3 and 1 genera, respectively. We propose standardizations to the names of a number of animal PVs. As prerequisite for a coherent nomenclature of animal PVs, we propose founding a reference center for animal PVs. We discuss that based on emerging species concepts derived from genome sequences, PV types could be promoted to the taxonomic level of species, but we do not recommend implementing this change at the current time.}, } @article {pmid20206774, year = {2010}, author = {Landires, I}, title = {The post-Darwinist concept of species: a place for Lamarck?.}, journal = {Lancet (London, England)}, volume = {375}, number = {9717}, pages = {806}, doi = {10.1016/S0140-6736(10)60346-7}, pmid = {20206774}, issn = {1474-547X}, mesh = {Animals ; *Biological Evolution ; *Epigenesis, Genetic ; Humans ; *Selection, Genetic ; }, } @article {pmid20204586, year = {2010}, author = {Hunter, RP}, title = {Interspecies allometric scaling.}, journal = {Handbook of experimental pharmacology}, volume = {}, number = {199}, pages = {139-157}, doi = {10.1007/978-3-642-10324-7_6}, pmid = {20204586}, issn = {0171-2004}, mesh = {Animals ; Animals, Wild ; Animals, Zoo ; Basal Metabolism ; Birds ; Body Weight ; Cats ; Cattle ; *Drug Delivery Systems ; Drug Therapy/*methods ; Female ; Goats ; Humans ; Kinetics ; Male ; *Metabolic Clearance Rate ; Pharmacokinetics ; Rabbits ; Sheep ; Species Specificity ; Veterinary Medicine/*methods ; }, abstract = {Lack of approved pharmaceutical agents and very limited pharmacokinetic data in the scientific literature for exotic, wildlife, and zoo species are a major issue for veterinarians treating these species. There are fewer than 15 compounds approved in the United States for zoo and wildlife species compared to nearly 300 drugs licensed for cattle. Zoo veterinarians are therefore required to extrapolate the use of approved agents (veterinary or human) to nonapproved species, often with little or no scientific basis to support drug or dose schedule selection. In general, species differences in drug absorption, metabolism, distribution, and excretion have been well documented for domestic species. However, there has been limited research to provide similar data for nondomestic species. Consequently, with the possible exception of pet bird species, there is little published information on the pharmacokinetic parameters of drugs in nondomestic species. Additionally, because of the commercial value of many zoo species, the traditional method of "trial and error" for drug and dose selection and related compliance issues is often inappropriate. There is an understandable concern, whereby the zoo veterinarian does not wish to be the first to administer an agent or formulation in an untested species. "One medicine" is a central concept in treating zoo species, in that vertebrate species are generally more similar than dissimilar. However, drug absorption can vary within as well as between species. Considering the anatomical differences between true monogastrics (canine and feline species), hind-gut fermentors (rodents, rabbits, horses, and elephants), fore-gut fermentors (Colobus monkeys and kangaroos), and ruminants (cattle, goats, sheep, and antelope), the potential for differences in pharmacokinetic profiles are marked. Moreover, there are potential differences between organisms in a single class. An example is the ability of several snake species to up- and down-regulate their digestive systems. This renders the time course of oral drug absorption dependent on both body temperature and time after feeding. Plasma protein binding may vary considerably between species and may also be temperature dependent. This is very significant when treating poikilothermic (reptiles, amphibians, and fish) species and when conducting pharmacokinetic studies with highly protein-bound drugs. The large body sizes of some zoo species create additional considerations for treatment with drugs and can place significant limitations on delivery of an effective drug dose.}, } @article {pmid20204430, year = {2010}, author = {Kuhn, JH and Jahrling, PB}, title = {Clarification and guidance on the proper usage of virus and virus species names.}, journal = {Archives of virology}, volume = {155}, number = {4}, pages = {445-453}, pmid = {20204430}, issn = {1432-8798}, support = {Z01 AI001025-02//Intramural NIH HHS/United States ; }, mesh = {Classification/*methods ; *Terminology as Topic ; Viruses/*classification ; }, abstract = {A pivotal step in the development of a consistent nomenclature for virus classification was the introduction of the virus species concept by the International Committee on Taxonomy of Viruses (ICTV) in 1991. Yet, almost two decades later, many virologists still are unable to differentiate between virus species and actual viruses. Here we attempt to explain the origin of this confusion, clarify the difference between taxa and physical entities, and suggest simple measures that could be implemented by ICTV Study Groups to make virus taxonomy and nomenclature more accessible to laboratory virologists.}, } @article {pmid20198135, year = {2009}, author = {Nagy, LG and Kocsubé, S and Papp, T and Vágvölgyi, C}, title = {Phylogeny and character evolution of the coprinoid mushroom genus Parasola as inferred from LSU and ITS nrDNA sequence data.}, journal = {Persoonia}, volume = {22}, number = {}, pages = {28-37}, pmid = {20198135}, issn = {1878-9080}, abstract = {Phylogenetic relationships, species concepts and morphological evolution of the coprinoid mushroom genus Parasola were studied. A combined dataset of nuclear ribosomal ITS and LSU sequences was used to infer phylogenetic relationships of Parasola species and several outgroup taxa. Clades recovered in the phylogenetic analyses corresponded well to morphologically discernable species, although in the case of P. leiocephala, P. lilatincta and P. plicatilis amended concepts proved necessary. Parasola galericuliformis and P. hemerobia are shown to be synonymous with P. leiocephala and P. plicatilis, respectively. By mapping morphological characters on the phylogeny, it is shown that the emergence of deliquescent Parasola taxa was accompanied by the development of pleurocystidia, brachybasidia and a plicate pileus. Spore shape and the position of the germ pore on the spores showed definite evolutionary trends within the group: from ellipsoid the former becomes more voluminous and heart-shaped, the latter evolves from central to eccentric in taxa referred to as 'crown' Parasola species. The results are discussed and compared to other Coprinus s.l. and Psathyrella taxa. Homoplasy and phylogenetic significance of various morphological characters, as well as indels in ITS and LSU sequences, are also evaluated.}, } @article {pmid20140034, year = {2010}, author = {Mayr, E}, title = {Commemorating the 20th century Darwin: Ernst Mayr's words and thoughts, five years later. Interview by Rob J. Kulathinal.}, journal = {Genome}, volume = {53}, number = {2}, pages = {157-159}, doi = {10.1139/g09-094}, pmid = {20140034}, issn = {1480-3321}, mesh = {Animals ; *Biological Evolution ; *Selection, Genetic ; Species Specificity ; }, abstract = {It has been five years since Ernst Mayr, one of the most influential evolutionary biologists of the last century, passed away. Mayr's seminal work as a naturalist and, in particular, as a bird systematist allowed him to approach the species problem in a revolutionary way. As a leading architect of the Modern Evolutionary Synthesis, Mayr helped integrate Darwinian theory with the broad fields of systematics and genetics. We pay tribute to this legend by publishing an interview taken shortly before his death.}, } @article {pmid20139118, year = {2010}, author = {Wieneke, H and Spencker, S and Svendsen, JH and Martinez, JG and Strohmer, B and Toivonen, L and Le Marec, H and Garcia, J and Kaup, B and Soykan, O and Corrado, D and Siffert, W}, title = {Polymorphisms associated with ventricular tachyarrhythmias: rationale, design, and endpoints of the 'diagnostic data influence on disease management and relation of genomics to ventricular tachyarrhythmias in implantable cardioverter/defibrillator patients (DISCOVERY)' study.}, journal = {Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology}, volume = {12}, number = {3}, pages = {424-429}, doi = {10.1093/europace/eup444}, pmid = {20139118}, issn = {1532-2092}, mesh = {Chromogranins ; *Defibrillators, Implantable ; GTP-Binding Protein alpha Subunits, Gq-G11/genetics ; GTP-Binding Protein alpha Subunits, Gs/genetics ; Genetic Markers ; Genetic Predisposition to Disease/epidemiology ; Genetic Testing ; *Genome-Wide Association Study ; Heterotrimeric GTP-Binding Proteins/genetics ; Humans ; Longitudinal Studies ; Multicenter Studies as Topic ; *Polymorphism, Single Nucleotide ; Risk Factors ; Tachycardia, Ventricular/*diagnosis/epidemiology/*genetics/therapy ; }, abstract = {Implantable cardioverter-defibrillator (ICD) therapy is effective in primary and secondary prevention for patients who are at high risk of sudden cardiac death. However, the current risk stratification of patients who may benefit from this therapy is unsatisfactory. Single nucleotide polymorphisms (SNPs) are DNA sequence variations occurring when a single nucleotide in the genome differs among members of a species. A novel concept has emerged being that these common genetic variations might modify the susceptibility of a certain population to specific diseases. Thus, genetic factors may also modulate the risk for arrhythmias and sudden cardiac death, and identification of common variants could help to better identify patients at risk. The DISCOVERY study is an interventional, longitudinal, prospective, multi-centre diagnostic study that will enrol 1287 patients in approximately 80 European centres. In the genetic part of the DISCOVERY study, candidate gene polymorphisms involved in coding of the G-protein subunits will be correlated with the occurrence of ventricular arrhythmias in patients receiving an ICD for primary prevention. Furthermore, in order to search for additional sequence variants contributing to ventricular arrhythmias, a genome-wide association study will be conducted if sufficient a priori evidence can be gathered. In the second part of the study, associations of SNPs with ventricular arrhythmias will be sought and a search for potential new biological arrhythmic pathways will be investigated. As it is a diagnostic study, DISCOVERY will also investigate the impact of long-term device diagnostic data on the management of patients suffering from chronic cardiac disease as well as medical decisions made regarding their treatment.}, } @article {pmid20133593, year = {2010}, author = {Denef, VJ and Kalnejais, LH and Mueller, RS and Wilmes, P and Baker, BJ and Thomas, BC and VerBerkmoes, NC and Hettich, RL and Banfield, JF}, title = {Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {6}, pages = {2383-2390}, pmid = {20133593}, issn = {1091-6490}, mesh = {Bacteria/classification/*genetics/growth & development ; Bacterial Proteins/analysis/genetics ; Biodiversity ; Biofilms ; California ; Cluster Analysis ; *Ecosystem ; Evolution, Molecular ; Genetic Variation ; Genome, Bacterial/*genetics ; Genomics/*methods ; Genotype ; Geography ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 23S/genetics ; }, abstract = {Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups of Leptospirillum group II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry-based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the approximately 15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies.}, } @article {pmid20067487, year = {2010}, author = {Cushman, SA and McKelvey, KS and Noon, BR and McGarigal, K}, title = {Use of abundance of one species as a surrogate for abundance of others.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {24}, number = {3}, pages = {830-840}, doi = {10.1111/j.1523-1739.2009.01396.x}, pmid = {20067487}, issn = {1523-1739}, mesh = {Animals ; *Biodiversity ; Birds/*classification ; Cluster Analysis ; *Conservation of Natural Resources ; Environmental Monitoring ; }, abstract = {Indicator species concepts have a long history in conservation biology. Arguments in favor of these approaches generally stress expediency and assume efficacy. We tested the premise that the abundance patterns of one species can be used to infer those of other species. Our data consisted of 72,495 bird observations on 55 species across 1046 plots distributed across 30 sub basins. We analyzed abundance patterns at two spatial scales (plot and sub basin) and for empirical and a priori grouping. There were few significant indicator relationships at either scale or under either grouping rule, and those few we found did not explain a substantial portion of the abundance of other species. Coupled with the lack of proven efficacy for species surrogacy in the literature, our results indicate the utility of indicators and similar types of surrogate approaches must be demonstrated rather than assumed.}, } @article {pmid20061950, year = {2010}, author = {Millard, AL and Mueller, NJ}, title = {Critical issues related to porcine xenograft exposure to human viruses: lessons from allotransplantation.}, journal = {Current opinion in organ transplantation}, volume = {15}, number = {2}, pages = {230-235}, doi = {10.1097/MOT.0b013e328336b8f9}, pmid = {20061950}, issn = {1531-7013}, mesh = {Adenoviruses, Human/immunology/pathogenicity ; Animals ; Cytomegalovirus/immunology/pathogenicity ; Cytopathogenic Effect, Viral ; Enterovirus B, Human/immunology/pathogenicity ; Graft Rejection/immunology/prevention & control/*virology ; *Graft Survival ; Hepacivirus/immunology/pathogenicity ; Herpesvirus 1, Human/immunology/pathogenicity ; Herpesvirus 2, Human/immunology/pathogenicity ; Humans ; Influenza A virus/immunology/pathogenicity ; Species Specificity ; Swine ; *Transplantation Tolerance ; Transplantation, Heterologous/*immunology ; Virus Diseases/immunology/prevention & control/*virology ; }, abstract = {PURPOSE OF REVIEW: Xenotransplantation of tissues from swine into humans poses the threat of bidirectional transfer of porcine or human microorganisms to the recipient or to the xenograft, respectively. This review focuses on recipient-derived infection. Recent data are reviewed that assess the susceptibility of porcine cells to human viruses. On the basis of the experience in allotransplantation, potential consequences for the xenograft are discussed.

RECENT FINDINGS: Traditionally, research on xenoses has focused on donor, that is pig-derived, infections. Efforts to exclude pathogens from pig donors have been successful with notable exceptions such as the genetically encoded porcine endogenous retrovirus. Intrinsic resistance of many viruses to infect cells from a different species has been assumed and may confer an advantage for a xenograft. Recent studies, however, have demonstrated the ability of a number of human viruses relevant in allotransplantation to infect porcine cells. Infection was associated with cytopathogenicity as well as cellular changes promoting adhesion and transmigration of human cells or a procoagulant stage.

SUMMARY: Successful infection of porcine cells with human viruses has challenged the concept of species specificity. For some viruses, infection resulted in production of infective progenies and is associated with cytopathogenicity. Cellular alterations potentially enhance the risk for graft damage, rejection or coagulation abnormalities.}, } @article {pmid20058861, year = {2010}, author = {Russell, LE and Fallas, JA and Hartgerink, JD}, title = {Selective assembly of a high stability AAB collagen heterotrimer.}, journal = {Journal of the American Chemical Society}, volume = {132}, number = {10}, pages = {3242-3243}, pmid = {20058861}, issn = {1520-5126}, support = {T90 DK070121/DK/NIDDK NIH HHS/United States ; T90 DK070121-05/DK/NIDDK NIH HHS/United States ; 5 T90 DK070121-05/DK/NIDDK NIH HHS/United States ; }, mesh = {Biomimetic Materials/chemistry ; Calorimetry, Differential Scanning ; Circular Dichroism ; Collagen/*chemistry ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Peptides/chemistry ; Protein Structure, Quaternary ; Protein Structure, Secondary ; }, abstract = {How collagen is able to obtain control of helix composition and register is poorly understood yet is critical for determining the structure and properties of the most abundant protein in the human body. In humans there are 28 known types of collagen that can form homotrimeric (AAA) or heterotrimeric (AAB and ABC) compositions. Additionally, because of a single amino acid offset between peptide chains in the triple helix, distinct heterotrimers of different registers can be formed. In this communication we describe an AAB collagen heterotrimer with controlled composition and register. This is the first report of a collagen heterotrimer whose thermal stability is greater than that of any of its component parts and therefore is the dominant species in solution. The design concept is simple: combination of peptides who follow the canonical (X-Y-Gly)(n) amino acid repeat in a 2:1 ratio in which the more abundant peptide has a charge 1/2 and opposite of the other should result in the formation of an AAB heterotrimeric collagen helix. This will be the dominant species because it is neutral (zwitterionic) while homotrimers should be destabilized because of charge repulsion. Here we show by circular dichroism, differential scanning calorimetry, and NMR that, in a 2:1 mixture of the peptides (EOGPOG)(5) and (PRG)(10), the AAB heterotrimer is the dominant structure in solution and melts 10 degrees C higher in temperature than the next most stable species.}, } @article {pmid21594118, year = {2010}, author = {Taekul, C and Johnson, NF and Masner, L and Polaszek, A and Rajmohana K, }, title = {World species of the genus Platyscelio Kieffer (Hymenoptera: Platygastridae).}, journal = {ZooKeys}, volume = {}, number = {50}, pages = {97-126}, pmid = {21594118}, issn = {1313-2970}, abstract = {The genus Platyscelio Kieffer (Hymenoptera: Platygastridae, Scelioninae) is a widespread group in the Old World, found from West Africa to northern Queensland, Australia. The species concepts are revised and a key to world species is presented. The genus is comprised of 6 species, including 2 known species which are redescribed: Platyscelioafricanus Risbec (Benin, Cameroon, Central African Republic, Ghana, Guinea, Guinea-Bissau, Ivory Coast, Kenya, Mozambique, Nigeria, Sierra Leone, South Africa, Tanzania, Togo, Uganda, Yemen, Zimbabwe); and Platysceliopulchricornis Kieffer (Australia, Bangladesh, China, India, Indonesia, Japan, Malaysia, Papua New Guinea, Philippines, Solomon Islands, Taiwan, Thailand, Vanuatu, Vietnam). Five species-group names are considered to be junior synonyms of Platysceliopulchricornis: Platyscelioabnormis Crawford syn. n., Platysceliodunensis Mukerjee syn. n., Platysceliomirabilis Dodd syn. n., Platysceliopunctatus Kieffer syn. n., and Platysceliowilcoxi Fullaway. The following species are hypothesized and described as new taxa: Platyscelioarcuatus Taekul & Johnson, sp. n. (Western Australia); Platysceliomysterium Taekul & Johnson, sp. n. (Zimbabwe, Botswana, South Africa); Platysceliomzantsi Taekul & Johnson, sp. n. (South Africa); and Platysceliostriga Taekul & Johnson, sp. n. (Western Australia).}, } @article {pmid20033830, year = {2010}, author = {Jensen, PR}, title = {Linking species concepts to natural product discovery in the post-genomic era.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {37}, number = {3}, pages = {219-224}, pmid = {20033830}, issn = {1476-5535}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; GM085770/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/*classification/genetics/*metabolism ; Biological Products/*isolation & purification ; Classification ; DNA, Bacterial/*genetics ; *Genetic Variation ; RNA, Ribosomal, 16S/*genetics ; Species Specificity ; }, abstract = {A widely accepted species concept for bacteria has yet to be established. As a result, species designations are inconsistently applied and tied to what can be considered arbitrary metrics. Increasing access to DNA sequence data and clear evidence that bacterial genomes are dynamic entities that include large numbers of horizontally acquired genes have added a new level of insight to the ongoing species concept debate. Despite uncertainties over how to apply species concepts to bacteria, there is clear evidence that sequence-based approaches can be used to resolve cohesive groups that maintain the properties of species. This cohesion is clearly evidenced in the genus Salinispora, where three species have been discerned despite very close relationships based on 16S rRNA sequence analysis. The major phenotypic differences among the three species are associated with secondary metabolite production, which occurs in species-specific patterns. These patterns are maintained on a global basis and provide evidence that secondary metabolites have important ecological functions. These patterns also suggest that an effective strategy for natural product discovery is to target the cultivation of new Salinispora taxa. Alternatively, bioinformatic analyses of biosynthetic genes provide opportunities to predict secondary metabolite novelty and reduce the redundant isolation of well-known metabolites. Although much remains to be learned about the evolutionary relationships among bacteria and how fundamental units of diversity can be resolved, genus and species descriptions remain the most effective method of scientific communication.}, } @article {pmid20022399, year = {2010}, author = {Mokini, Z and Marcovecchio, ML and Chiarelli, F}, title = {Molecular pathology of oxidative stress in diabetic angiopathy: role of mitochondrial and cellular pathways.}, journal = {Diabetes research and clinical practice}, volume = {87}, number = {3}, pages = {313-321}, doi = {10.1016/j.diabres.2009.11.018}, pmid = {20022399}, issn = {1872-8227}, mesh = {Diabetic Angiopathies/*metabolism ; Humans ; Hyperglycemia/*metabolism ; Ion Channels/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; Oxidative Stress/*physiology ; Uncoupling Protein 1 ; }, abstract = {Diabetes mellitus is characterized by chronic hyperglycaemia and a significant risk of developing micro- and macrovascular complications. Growing evidence suggests that increased oxidative stress, induced by several hyperglycaemia-activated pathways, is a key factor in the pathogenesis of endothelial dysfunction and vascular disease. Reactive oxidant molecules, which are produced at a high rate in the diabetic milieu, can cause oxidative damage of many cellular components and activate several pathways linked with inflammation and apoptosis. Among the mechanisms involved in oxidative stress generation, mitochondria and uncoupling proteins are of particular interest and there is growing evidence suggesting their pivotal role in the pathogenesis of diabetic complications. Other important cellular sources of oxidants include nicotinamide adenine dinucleotide phosphate oxidases and uncoupling endothelial nitric oxide synthase. In addition, diabetes is associated with reduced antioxidant defences, which generally contrast the deleterious effect of oxidant species. This concept underlines a potential beneficial role of antioxidant therapy for the prevention and treatment of diabetic vascular disease. However, large scale trials with classical antioxidants have failed to show a significant effect on major cardiovascular events, thus underlying the need of further investigations in order to develop therapies to prevent and/or delay the development of micro- and macrovascular complications.}, } @article {pmid20005655, year = {2010}, author = {Van Regenmortel, MH}, title = {Logical puzzles and scientific controversies: the nature of species, viruses and living organisms.}, journal = {Systematic and applied microbiology}, volume = {33}, number = {1}, pages = {1-6}, doi = {10.1016/j.syapm.2009.11.001}, pmid = {20005655}, issn = {1618-0984}, mesh = {Classification ; *Genetic Speciation ; Species Specificity ; Viruses/*genetics ; }, abstract = {In the past, biologists believed that species were stable and permanent entities and they viewed them as natural kinds which, like the chemical elements, exist in nature independently of any human conceptualization. After Darwin, biologists came to accept that species were the products of evolution and natural selection and were not immutable natural kinds. Different definitions of the species category are discussed, in particular the concept of cluster class as a family resemblance concept. In order to resolve what has become known as the species problem, it is necessary to distinguish between species as concrete entities and species as abstract entities. A species can be an abstract concept but the concept also refers to specific objects in space and time, namely the organisms studied by biologists. The nature of viruses is discussed and the difference between a virus and a virus particle is emphasized. The category "virus species" is defined as a cluster class and the task of defining a virus species is distinguished from the task of identifying the members of a species using diagnostic criteria. Such an identification is feasible only when the species taxon has been established beforehand on the basis of several genotypic and phenotypic characters. It is argued that viruses are genetic parasites rather than living organisms and that they have no place in the tree of life. This interpretation is based on an analysis of the properties of living agents and living organisms.}, } @article {pmid20002252, year = {2010}, author = {Martínez-Gordillo, D and Rojas-Soto, O and Espinosa de los Monteros, A}, title = {Ecological niche modelling as an exploratory tool for identifying species limits: an example based on Mexican muroid rodents.}, journal = {Journal of evolutionary biology}, volume = {23}, number = {2}, pages = {259-270}, doi = {10.1111/j.1420-9101.2009.01897.x}, pmid = {20002252}, issn = {1420-9101}, mesh = {Algorithms ; Animals ; *Ecosystem ; Mexico ; *Models, Biological ; *Muridae ; }, abstract = {Niche conservatism theory suggests that recently diverged sister species share the same ecological niche. However, if the ecological niche evolves as part of the speciation process, the ecological pattern could be useful for recognizing cryptic species. In a broad sense systematists agree that the niche characters could be used for species differentiation. However, to date such characters have been ignored. We used the genetic algorithm for rule-set production for modelling the ecological niche as a means of inferring ecological divergence in allopatric populations of muroid rodents for which taxonomic identity is uncertain. Our results show that niche differentiation is significant in most of the identified phylogroups. The differentiation is likely associated with natural evolutionary units, which can be identified by applying species concepts based on phylogenetic and ecological patterns (e.g. phylogenetic, cohesive, evolutionary). Even so, the role of the niche partition within phylogenetic reconstruction may be a limited one.}, } @article {pmid19932183, year = {2010}, author = {Torres, I and García, AM and Hernández, O and González, A and McEwen, JG and Restrepo, A and Arango, M}, title = {Presence and expression of the mating type locus in Paracoccidioides brasiliensis isolates.}, journal = {Fungal genetics and biology : FG & B}, volume = {47}, number = {4}, pages = {373-380}, doi = {10.1016/j.fgb.2009.11.005}, pmid = {19932183}, issn = {1096-0937}, mesh = {DNA Primers/genetics ; DNA, Fungal/chemistry/genetics ; *Gene Expression ; Genes, Mating Type, Fungal/*genetics ; Molecular Sequence Data ; Paracoccidioides/*genetics/physiology ; Polymerase Chain Reaction/methods ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Paracoccidioides brasiliensis has been classified in the phylum Ascomycota, order Onygenales, family Ajellomycetaceae, even in the absence of a known sexual cycle or mating system. The objective of this work was to determine the presence of the mating type locus in 71 P. brasiliensis isolates from various sources. A PCR assay using specific primers for the MAT 1 gene was developed and applied for the detection of such genes. Two heterothallic groups (MAT1-1 or MAT1-2) were recognized and, in some isolates, gene expression was confirmed indicating the existence of a basal gene expression. The distribution of two mating type loci in the studied population suggested that sexual reproduction might occur in P. brasiliensis. This finding points towards the possibility of applying a more precise definition of the concept of biological species to P. brasiliensis. Further studies should be conducted to confirm the sexual capacity of this fungus and its implications among phylogenetic species and geographical distribution.}, } @article {pmid19914306, year = {2010}, author = {Lievens, B and van Kerckhove, S and Justé, A and Cammue, BP and Honnay, O and Jacquemyn, H}, title = {From extensive clone libraries to comprehensive DNA arrays for the efficient and simultaneous detection and identification of orchid mycorrhizal fungi.}, journal = {Journal of microbiological methods}, volume = {80}, number = {1}, pages = {76-85}, doi = {10.1016/j.mimet.2009.11.004}, pmid = {19914306}, issn = {1872-8359}, mesh = {Basidiomycota/*classification/genetics/*isolation & purification ; DNA Primers/genetics ; DNA, Fungal/genetics ; Gene Library ; Molecular Sequence Data ; Mycological Typing Techniques ; Mycorrhizae/classification/genetics/*isolation & purification ; Oligonucleotide Array Sequence Analysis/*methods ; Orchidaceae/*microbiology ; Phylogeny ; }, abstract = {A DNA array was developed from extensive clone library sequence data sets for the assessment of dominant members of mycorrhizal fungi that associate with terrestrial orchid species. As a-proof-of-concept, the array was developed for the basidiomycetous mycorrhizal partners from three closely related perennial Orchis species, including Orchis anthropophora, O. militaris and O. purpurea. Based on internal transcribed spacer regions, oligonucleotides were developed for seven operational taxonomic units (OTUs; defined as groups of sequences sharing at least 97% sequence similarity), corresponding to members of the Tulasnellaceae family. In order to cover a broader spectrum of tulasnelloid fungi, oligonucleotides were as well developed for two subsets of closely related OTUs. The array was evaluated using multiple primer pairs. In addition, hybridization results were validated by recovery and sequencing of the hybridized amplicons as well as by hybridizing reference DNA samples. Considering the unlimited expansion possibilities of DNA arrays to include specific detector oligonucleotides for other and more microorganisms, the method described here has the major advantage that it provides a powerful, rapid and cost-effective way for the simultaneous detection and identification of a wide range of orchid mycorrhizae. The design, development and advantages of the array are discussed in relation to its potential for future research in mycorrhizal ecology.}, } @article {pmid19911158, year = {2010}, author = {Zou, J and Zhu, J and Huang, S and Tian, E and Xiao, Y and Fu, D and Tu, J and Fu, T and Meng, J}, title = {Broadening the avenue of intersubgenomic heterosis in oilseed Brassica.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {120}, number = {2}, pages = {283-290}, pmid = {19911158}, issn = {1432-2242}, mesh = {Brassica napus/*genetics ; *Genome, Plant ; Hybrid Vigor/*genetics ; Hybridization, Genetic ; }, abstract = {Accumulated evidence has shown that each of the three basic Brassica genomes (A, B and C) has undergone profound changes in different species, and has led to the concept of the "subgenome". Significant intersubgenomic heterosis was observed in hybrids between traditional Brassica napus and first generation lines of new type B. napus. The latter were produced by the partial introgression of subgenomic components from different species into B. napus. To increase the proportion of exotic subgenomic components and thus achieve stronger heterosis, lines of first generation new type B. napus were intercrossed with each other, and subjected to intensive marker-assisted selection to develop the second generation of new type B. napus. The second generation showed better agronomic traits and a higher proportion of introgression of subgenomic components than did the first generation. Compared with the commercial hybrid and the hybrids produced with the first generation new type B. napus, the novel hybrids showed stronger heterosis for seed yield during the 2 years of field trials. The extent of heterosis showed a significant positive correlation with the introgressed subgenomic components in the parental new type B. napus. To increase the content of the exotic subgenomic components further and to allow sustainable breeding of novel lines of new type B. napus, we initiated the development of a gene pool for new type B. napus that contained a substantial amount of genetic variation in the A(r) and C(c) genome. We discuss new approaches to broaden the avenue of intersubgenomic heterosis in oilseed Brassica.}, } @article {pmid19891628, year = {2010}, author = {Sobel, JM and Chen, GF and Watt, LR and Schemske, DW}, title = {The biology of speciation.}, journal = {Evolution; international journal of organic evolution}, volume = {64}, number = {2}, pages = {295-315}, doi = {10.1111/j.1558-5646.2009.00877.x}, pmid = {19891628}, issn = {1558-5646}, mesh = {*Biological Evolution ; Ecology ; Mutation ; Species Specificity ; }, abstract = {Since Darwin published the "Origin," great progress has been made in our understanding of speciation mechanisms. The early investigations by Mayr and Dobzhansky linked Darwin's view of speciation by adaptive divergence to the evolution of reproductive isolation, and thus provided a framework for studying the origin of species. However, major controversies and questions remain, including: When is speciation nonecological? Under what conditions does geographic isolation constitute a reproductive isolating barrier? and How do we estimate the "importance" of different isolating barriers? Here, we address these questions, providing historical background and offering some new perspectives. A topic of great recent interest is the role of ecology in speciation. "Ecological speciation" is defined as the case in which divergent selection leads to reproductive isolation, with speciation under uniform selection, polyploid speciation, and speciation by genetic drift defined as "nonecological." We review these proposed cases of nonecological speciation and conclude that speciation by uniform selection and polyploidy normally involve ecological processes. Furthermore, because selection can impart reproductive isolation both directly through traits under selection and indirectly through pleiotropy and linkage, it is much more effective in producing isolation than genetic drift. We thus argue that natural selection is a ubiquitous part of speciation, and given the many ways in which stochastic and deterministic factors may interact during divergence, we question whether the ecological speciation concept is useful. We also suggest that geographic isolation caused by adaptation to different habitats plays a major, and largely neglected, role in speciation. We thus provide a framework for incorporating geographic isolation into the biological species concept (BSC) by separating ecological from historical processes that govern species distributions, allowing for an estimate of geographic isolation based upon genetic differences between taxa. Finally, we suggest that the individual and relative contributions of all potential barriers be estimated for species pairs that have recently achieved species status under the criteria of the BSC. Only in this way will it be possible to distinguish those barriers that have actually contributed to speciation from those that have accumulated after speciation is complete. We conclude that ecological adaptation is the major driver of reproductive isolation, and that the term "biology of speciation," as proposed by Mayr, remains an accurate and useful characterization of the diversity of speciation mechanisms.}, } @article {pmid19886199, year = {2009}, author = {Belekhova, MG and Chudinova, TV and Kenigfest, NB}, title = {[Metabolic activity of thalamic and telencephalic auditory centers in the pigeon].}, journal = {Zhurnal evoliutsionnoi biokhimii i fiziologii}, volume = {45}, number = {5}, pages = {511-517}, pmid = {19886199}, issn = {0044-4529}, mesh = {Animals ; Auditory Cortex/cytology/*enzymology ; Carbon Monoxide/metabolism ; Columbidae/*metabolism ; Electron Transport Complex IV/*metabolism ; Reptiles ; Thalamus/cytology/*enzymology ; }, abstract = {Distribution of activity of the mitochondrial oxidative enzyme cytochrome oxidase C was studied in the thalamic (Ov) and telencephalic (field L) auditory centers in pigeons. The CO activity level has been shown to differ in the central (core) and peripheral (belt) subdivisions of these centers: the high CO activity in the former (nCe, L2) and the much lower or absent in the latter (Ovl, Ovm, SPO). Comparison of our data with those of various avian and reptile species confirms the concept of the common plan of rostral auditory centers in sauropsid amniotes by the principle of the center-periphery (core-belt), which is characteristic of the corresponding mammalian centers. The separation of the central and peripheral parts of these centers is better pronounced in birds than in reptiles.}, } @article {pmid19847472, year = {2010}, author = {Rico, A and Geber-Corrêa, R and Campos, PS and Garcia, MV and Waichman, AV and van den Brink, PJ}, title = {Effect of parathion-methyl on Amazonian fish and freshwater invertebrates: a comparison of sensitivity with temperate data.}, journal = {Archives of environmental contamination and toxicology}, volume = {58}, number = {3}, pages = {765-771}, pmid = {19847472}, issn = {1432-0703}, mesh = {Animals ; Brazil ; *Fishes ; Fresh Water ; Hydrogen-Ion Concentration ; Insecticides/*toxicity ; Invertebrates/*drug effects ; Lethal Dose 50 ; Methyl Parathion/*toxicity ; Toxicity Tests, Acute ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Parathion-methyl is an organophosphorous insecticide that is widely used in agricultural production sites in the Amazon. The use of this pesticide might pose a potential risk for the biodiversity and abundance of fish and invertebrate species inhabiting aquatic ecosystems adjacent to the agricultural fields. Due to a lack of toxicity data for Amazonian species, safe environmental concentrations used to predict the ecological risks of parathion-methyl in the Amazon are based on tests performed with temperate species, although it is unknown whether the sensitivity of temperate species is representative for those of Amazonian endemic species. To address this issue, the acute toxic effect (LC(50)-96 h) of parathion-methyl was assessed on seven fish and five freshwater invertebrate species endemic to the Amazon. These data were used to compare their pesticide sensitivity with toxicity data for temperate species collected from the literature. The interspecies sensitivity was compared using the Species Sensitivity Distribution (SSD) concept. The results of this study suggest that Amazonian species are no more, or less, sensitive to parathion-methyl than their temperate counterparts, with LC(50) values ranging from 2900 to 7270 microg/L for fish and from 0.3 to 319 microg/L for freshwater arthropods. Consequently, this evaluation supports the initial use of toxicity data of temperate fish and freshwater invertebrate species for assessing the effects of parathion-methyl on Amazonian freshwater ecosystems.}, } @article {pmid19847207, year = {2010}, author = {Auguet, JC and Barberan, A and Casamayor, EO}, title = {Global ecological patterns in uncultured Archaea.}, journal = {The ISME journal}, volume = {4}, number = {2}, pages = {182-190}, doi = {10.1038/ismej.2009.109}, pmid = {19847207}, issn = {1751-7370}, mesh = {Archaea/classification/genetics/*physiology ; DNA, Ribosomal/genetics ; *Ecosystem ; Multivariate Analysis ; Phylogeny ; Plankton/classification/genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {We have applied a global analytical approach to uncultured Archaea that for the first time reveals well-defined community patterns along broad environmental gradients and habitat types. Phylogenetic patterns and the environmental factors governing the creation and maintenance of these patterns were analyzed for c. 2000 archaeal 16S rRNA gene sequences from 67 globally distributed studies. The sequences were dereplicated at 97% identity, grouped into seven habitat types, and analyzed with both Unifrac (to explore shared phylogenetic history) and multivariate regression tree (that considers the relative abundance of the lineages or taxa) approaches. Both phylogenetic and taxon-based approaches showed salinity and not temperature as one of the principal driving forces at the global scale. Hydrothermal vents and planktonic freshwater habitats emerged as the largest reservoirs of archaeal diversity and consequently are promising environments for the discovery of new archaeal lineages. Conversely, soils were more phylogenetically clustered and archaeal diversity was the result of a high number of closely related phylotypes rather than different lineages. Applying the ecological concept of 'indicator species', we detected up to 13 indicator archaeal lineages for the seven habitats prospected. Some of these lineages (that is, hypersaline MSBL1, marine sediment FCG1 and freshwater plSA1), for which ecological importance has remained unseen to date, deserve further attention as they represent potential key archaeal groups in terms of distribution and ecological processes. Hydrothermal vents held the highest number of indicator lineages, suggesting it would be the earliest habitat colonized by Archaea. Overall, our approach provided ecological support for the often arbitrary nomenclature within uncultured Archaea, as well as phylogeographical clues on key ecological and evolutionary aspects of archaeal biology.}, } @article {pmid19827675, year = {2009}, author = {Severin, FF and Skulachev, VP}, title = {[Programmed cell death as a target to interrupt the aging program].}, journal = {Advances in gerontology = Uspekhi gerontologii}, volume = {22}, number = {1}, pages = {37-48}, pmid = {19827675}, issn = {1561-9125}, mesh = {Aging/genetics/*physiology ; Animals ; Antioxidants/physiology ; Apoptosis/genetics/*physiology ; Cellular Senescence/genetics/physiology ; Genome ; Mitochondria/physiology ; Models, Biological ; Mutation ; Oxygen Consumption/physiology ; Reactive Oxygen Species/metabolism ; }, abstract = {There are two opposite points of view on aging of organisms. The canonic concept assumes that aging is a stochastic process consisting in age-dependent accumulation of occasional injuries in living systems. However, many pieces of evidence are recently obtained in favor of the alternative scheme suggesting that aging is genetically programmed being the final step of ontogenesis. The latter concept predicts that (i) non-aging species should exist who has lost the aging program and (ii) the program in question can experimentally be interrupted by manipulating with corresponding genes or by low molecules operating as inhibitors of execution of aging program. In this paper, we summarize observations which are consistent with two above predictions. In both cases, interruption of the aging program is based upon inhibition of programmed cell death (apoptosis) mediated by mitochondrial reactive oxygen species (ROS). It is stated that the main difference between young and old multicellular organisms consists in the cellularity, i. e. in number of functional cells in organs or tissues rather than in quality of these cells. The cellularity decreases due to domination of apoptosis over proliferation in aging organisms. This means that apoptosis appears to be the basis for aging program. A pharmacological approach to switch off the aging program is considered, which is used mitochondria-targeted antioxidants and uncouplers. Such compounds prevent mitochondrial oxidative stress increasing with age and stimulating the age-dependent apoptosis.}, } @article {pmid19825944, year = {2009}, author = {Suzuki, G}, title = {Recent progress in plant reproduction research: the story of the male gametophyte through to successful fertilization.}, journal = {Plant & cell physiology}, volume = {50}, number = {11}, pages = {1857-1864}, doi = {10.1093/pcp/pcp142}, pmid = {19825944}, issn = {1471-9053}, mesh = {*Fertilization ; *Gametogenesis, Plant ; *Plant Development ; Plant Infertility ; Pollen/*growth & development ; Species Specificity ; }, abstract = {Sexual reproduction is an important biological event not only for evolution but also for breeding in plants. It is a well known fact that Charles Darwin (1809-1882) was interested in the reproduction system of plants as part of his concept of 'species' and 'evolution.' His keen observation and speculation is timeless even in the current post-genome era. In the Darwin anniversary year of 2009, I have summarized recent molecular genetic studies of plant reproduction, focusing especially on male gametophyte development, pollination and fertilization. We are just beginning to understand the molecular mechanisms of the elaborate reproduction system in flowering plants, which have been a mystery for >100 years.}, } @article {pmid19822887, year = {2009}, author = {Park, SJ and Mehrad, B}, title = {Innate immunity to Aspergillus species.}, journal = {Clinical microbiology reviews}, volume = {22}, number = {4}, pages = {535-551}, pmid = {19822887}, issn = {1098-6618}, support = {R01 HL073848/HL/NHLBI NIH HHS/United States ; HL73848/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Aspergillosis/*immunology/microbiology ; Aspergillus/*immunology ; Host-Pathogen Interactions/immunology ; Humans ; Immunity, Innate ; }, abstract = {All humans are continuously exposed to inhaled Aspergillus conidia, yet healthy hosts clear the organism without developing disease and without the development of antibody- or cell-mediated acquired immunity to this organism. This suggests that for most healthy humans, innate immunity is sufficient to clear the organism. A failure of these defenses results in a uniquely diverse set of illnesses caused by Aspergillus species, which includes diseases caused by the colonization of the respiratory tract, invasive infection, and hypersensitivity. A key concept in immune responses to Aspergillus species is that the susceptibilities of the host determine the morphological form, antigenic structure, and physical location of the fungus. In this review, we summarize the current literature on the multiple layers of innate defenses against Aspergillus species that dictate the outcome of this host-microbe interaction.}, } @article {pmid19818799, year = {2009}, author = {Ricotta, C and Szeidl, L}, title = {Diversity partitioning of Rao's quadratic entropy.}, journal = {Theoretical population biology}, volume = {76}, number = {4}, pages = {299-302}, doi = {10.1016/j.tpb.2009.10.001}, pmid = {19818799}, issn = {1096-0325}, mesh = {*Biodiversity ; Ecology ; *Entropy ; }, abstract = {Many applications of diversity indices are only valid if they are first transformed into their equivalent number of species. These equivalent numbers of species can be multiplicatively partitioned into independent alpha, beta and gamma components, and can be formed into mathematically consistent similarity measures. The utility of beta diversity and similarity measures that incorporate information about the degree of ecological dissimilarity between species is becoming increasingly recognized. The concept of equivalent number of species is here extended to Rao's quadratic entropy, opening the way to methods of diversity partitioning that take into account taxonomic or ecological differences between species.}, } @article {pmid19793206, year = {2011}, author = {Beifuss, B and Bezold, G and Gottlöber, P and Borelli, C and Wagener, J and Schaller, M and Korting, HC}, title = {Direct detection of five common dermatophyte species in clinical samples using a rapid and sensitive 24-h PCR-ELISA technique open to protocol transfer.}, journal = {Mycoses}, volume = {54}, number = {2}, pages = {137-145}, doi = {10.1111/j.1439-0507.2009.01771.x}, pmid = {19793206}, issn = {1439-0507}, support = {R01 DE017514-01/DE/NIDCR NIH HHS/United States ; }, mesh = {Arthrodermataceae/genetics/*isolation & purification ; DNA Primers/genetics ; DNA, Fungal/analysis/genetics ; Dermatomycoses/*microbiology ; Enzyme-Linked Immunosorbent Assay/*methods ; Humans ; Molecular Sequence Data ; Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; }, abstract = {Identification of dermatophytes is usually based on morphological characteristics determined by time-consuming microscopic and cultural examinations. An effective PCR-ELISA method has been developed for rapid detection of dermatophyte species directly from clinical specimens within 24 h. Isolated genomic DNA of skin scrapings and nail samples from patients with suspected dermatophyte infections is amplified with species-specific digoxigenin-labelled primers targeting the topoisomerase II gene. The subsequent ELISA procedure with biotin-labelled probes allows a sensitive and specific identification of the five common dermatophytes -Trichophyton rubrum, T. interdigitale, T. violaceum, Microsporum canis and Epidermophyton floccosum. PCR-ELISA, based on the new polyphasic species concept, was assessed using 204 microscopy-positive samples in two university mycological laboratories in Munich and Tübingen, and 316 consecutive specimens - regardless of mycological findings - in a dermatological practice laboratory in Neu-Ulm. One of the five dermatophytes was confirmed by PCR-ELISA in 163 of 204 (79.9%) of the clinical samples from the university hospitals found positive using microscopy. Culture was positive for dermatophytes in 59.8% of the same cases. A significant difference between these two methods could be demonstrated using the McNemar test (P < 0.005). Analysis of specimens from Neu-Ulm confirmed the results in a dermatological practice laboratory as 25.0% of the specimens had positive PCR results, whereas only 7.3% were positive according to culture. Direct DNA isolation from clinical specimens and the PCR-ELISA method employed in this study provide a rapid, reproducible and sensitive tool for detection and discrimination of five major dermatophytes at species level, independent of morphological and biochemical characteristics.}, } @article {pmid19779746, year = {2009}, author = {Staley, JT}, title = {Universal species concept: pipe dream or a step toward unifying biology?.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {36}, number = {11}, pages = {1331-1336}, pmid = {19779746}, issn = {1476-5535}, mesh = {Archaea/*classification ; Bacteria/*classification ; Genetic Speciation ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 5S/chemistry/genetics ; Species Specificity ; }, abstract = {The Universal Tree of Life, which is based on phylogenetic analysis of the RNA sequence from the small ribosomal subunit, was a breakthrough in understanding the relatedness among all living organisms. The result has had a major impact on taxonomy by separating life into three domains: Eukarya, Bacteria, and Archaea. Indeed, microbiologists have used the 16S ribosomal RNA (rRNA) of the small ribosomal subunit to construct the hierarchical classification of Bacteria and Archaea from the level of domain to genus. However, the 16S rRNA of the Bacteria and Archaea and the corresponding 18S rRNA of the Eukarya are too highly conserved to be useful phylogenetically at the species level. For this reason, I propose that biologists adopt a phylogenomic species concept that utilizes both phylogenetic analyses of less highly conserved genes and proteins as well as genomic analyses for the circumscription of species. If biologists adopt a phylogenomic concept for species, the classification of all living organisms from domain to species could be completed. Furthermore, this universal species concept could help provide a more equitable circumscription among all species, as well as aid in the unification of biologists and biology.}, } @article {pmid19772926, year = {2010}, author = {Pfenninger, M and Véla, E and Jesse, R and Elejalde, MA and Liberto, F and Magnin, F and Martínez-Ortí, A}, title = {Temporal speciation pattern in the western Mediterranean genus Tudorella P. Fischer, 1885 (Gastropoda, Pomatiidae) supports the Tyrrhenian vicariance hypothesis.}, journal = {Molecular phylogenetics and evolution}, volume = {54}, number = {2}, pages = {427-436}, doi = {10.1016/j.ympev.2009.09.024}, pmid = {19772926}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genetic Speciation ; Geography ; Mediterranean Region ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; Snails/classification/*genetics ; }, abstract = {The land snail genus Tudorella shows a peculiar disjunct distribution around the western Mediterranean coasts. Despite high phenotypic plasticity, only two species with a disputed number of subspecific taxa are currently recognised. We delimited the species with mitochondrial (COI & 16S) and nuclear (ITS-1) markers based on the unified species concept and suggested that there are eight species in the genus, two of them currently undescribed. Applying Bayesian phylogenetic model selection, we tested four different biogeographic hypotheses that could be causal for the current distribution pattern of extant Tudorella species. A scenario involving vicariance events resulting from the repeated splits of the Tyrrhenian plate with subsequent dispersal events over land bridges during the Pliocene received greatest support in the data.}, } @article {pmid19766011, year = {2010}, author = {Zhang, TT and Jiang, YQ and Zhou, H and Yang, WX}, title = {Ultrastructural observation on genesis and morphology of cortical granules in Macrobrachium nipponense (Crustacea, Caridea).}, journal = {Micron (Oxford, England : 1993)}, volume = {41}, number = {1}, pages = {59-64}, doi = {10.1016/j.micron.2009.08.004}, pmid = {19766011}, issn = {1878-4291}, mesh = {Animals ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Oocytes/*ultrastructure ; Palaemonidae/*ultrastructure ; Secretory Vesicles/*ultrastructure ; }, abstract = {Cortical granules are secretory vesicles in oocytes that develop from the Golgi complex. In the freshwater shrimp, Macrobrachium nipponense, mitochondria participates in the formation of cortical granules. We investigated the structural changes of mitochondria and the distribution cortical granules in different stages of oocyte development. Transmission electron microscopy provided evidence for the involvement of mitochondria and a particular spiral lamellar organization and an electron-lucent area in internal cortical granules. The ooplasm provided material for the cortical granules in early oocyte development. We demonstrated that mitochondria play a role in coalescence and maturation of cortical granules in this species. Additionally, a concept of cortical granules regarded as a functional integration is put forward. The genesis of shrimp cortical granules exhibited a particular pathway of maturation. The outer shape and inner organization considering different taxa suggested general as well as specific features of the development of cortical granules.}, } @article {pmid19758430, year = {2009}, author = {Davey, MW and Graham, NS and Vanholme, B and Swennen, R and May, ST and Keulemans, J}, title = {Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {436}, pmid = {19758430}, issn = {1471-2164}, support = {BB/E01772X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/B/1356X/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E022758/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G17764/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G18881/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Cold Temperature ; Comparative Genomic Hybridization ; DNA, Plant/genetics ; *Droughts ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Plant ; Genes, Plant ; *Genome, Plant ; Musa/*genetics ; *Oligonucleotide Array Sequence Analysis ; Oryza/genetics ; Quantitative Trait Loci ; }, abstract = {BACKGROUND: 'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip(R) microarrays to profile the response of the banana (Musa spp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed Musa transcripts.

RESULTS: Following cross-hybridisation of Musa gDNA to the Rice GeneChip(R) Genome Array, ~33,700 gene-specific probe-sets had a sufficiently high degree of homology to be retained for transcriptomic analyses. In a proof-of-concept approach, pooled RNA representing a single biological replicate of control and drought stressed leaves of the Musa cultivar 'Cachaco' were hybridised to the Affymetrix Rice Genome Array. A total of 2,910 Musa gene homologues with a >2-fold difference in expression levels were subsequently identified. These drought-responsive transcripts included many functional classes associated with plant biotic and abiotic stress responses, as well as a range of regulatory genes known to be involved in coordinating abiotic stress responses. This latter group included members of the ERF, DREB, MYB, bZIP and bHLH transcription factor families. Fifty-two of these drought-sensitive Musa transcripts were homologous to genes underlying QTLs for drought and cold tolerance in rice, including in 2 instances QTLs associated with a single underlying gene. The list of drought-responsive transcripts also included genes identified in publicly-available comparative transcriptomics experiments.

CONCLUSION: Our results demonstrate that despite the general paucity of nucleotide sequence data in Musa and only distant phylogenetic relations to rice, gDNA probe-based cross-hybridisation to the Rice GeneChip(R) is a highly promising strategy to study complex biological responses and illustrates the potential of such strategies for gene discovery in non-model species.}, } @article {pmid19740893, year = {2010}, author = {Sparholt, H and Cook, RM}, title = {Sustainable exploitation of temperate fish stocks.}, journal = {Biology letters}, volume = {6}, number = {1}, pages = {124-127}, pmid = {19740893}, issn = {1744-957X}, mesh = {Animals ; Atlantic Ocean ; Biomass ; Conservation of Natural Resources/*methods/statistics & numerical data ; *Ecosystem ; Fisheries/*methods/statistics & numerical data ; Fishes/*growth & development ; *Models, Theoretical ; }, abstract = {The theory of maximum sustainable yield (MSY) underpins many fishery management regimes and is applied principally as a single species concept. Using a simple dynamic biomass production model we show that MSY can be identified from a long time series of multi-stock data at a regional scale in the presence of species interactions and environmental change. It suggests that MSY is robust and calculable in a multispecies environment, offering a realistic reference point for fishery management. Furthermore, the demonstration of the existence of MSY shows that it is more than a purely theoretical concept. There has been an improvement in the status of stocks in the Northeast Atlantic, but our analysis suggests further reductions in fishing effort would improve long-term yields.}, } @article {pmid19739370, year = {2009}, author = {Reynolds, RJ and Westbrook, MJ and Rohde, AS and Cridland, JM and Fenster, CB and Dudash, MR}, title = {Pollinator specialization and pollination syndromes of three related North American Silene.}, journal = {Ecology}, volume = {90}, number = {8}, pages = {2077-2087}, doi = {10.1890/08-1141.1}, pmid = {19739370}, issn = {0012-9658}, mesh = {Animals ; Bees/physiology ; Flowers/*anatomy & histology/physiology ; Moths/physiology ; Pollination/*physiology ; Silene/*physiology ; Species Specificity ; }, abstract = {Community and biogeographic surveys often conclude that plant-pollinator interactions are highly generalized. Thus, a central implication of the pollination syndrome concept, that floral trait evolution occurs primarily via specialized interactions of plants with their pollinators, has been questioned. However, broad surveys may not distinguish whether flower visitors are actual pollen vectors and hence lack power to assess the relationship between syndrome traits and the pollinators responsible for their evolution. Here we address whether the floral traits of three closely related hermaphroditic Silene spp. native to eastern North America (S. caroliniana, S. virginica, and S. stellata) correspond to predicted specialized pollination based on floral differences among the three species and the congruence of these floral features with recognized pollination syndromes. A nocturnal/diurnal pollinator exclusion experiment demonstrated that all three Silene spp. have diurnal pollinators, and only S. stellata has nocturnal pollinators. Multiyear studies of visitation rates demonstrated that large bees, hummingbirds, and nocturnal moths were the most frequent pollinators of S. caroliniana, S. virginica, and S. stellata, respectively. Estimates of pollen grains deposited and removed per visit generally corroborated the visitation rate results for all three species. However, the relatively infrequent diurnal hawkmoth pollinators of S. caroliniana were equally effective and more efficient than the most frequent large bee visitors. Pollinator importance (visitation X deposition) of each of the animal visitors to each species was estimated and demonstrated that in most years large bees and nocturnal moths were the most important pollinators of S. caroliniana and S. stellata, respectively. By quantifying comprehensive aspects of the pollination process we determined that S. virginica and S. stellata were specialized on hummingbirds and nocturnal moths, respectively, and S. caroliniana was the least specialized with diurnal hawkmoth and large bee pollinators. Compared across the Silene species, divergent floral character states are consistent with increasing the attraction and/or pollen transfer efficiency of their respective major pollinators, which suggests that the pollinators are past and/or contemporary selective agents for floral trait evolution in these three Silene species. We conclude that the pollination syndrome concept allows us to effectively relate the functional significance of floral morphology to the major pollinators of these Silene species.}, } @article {pmid19714881, year = {2009}, author = {Honys, D and Rĕnák, D and Feciková, J and Jedelský, PL and Nebesárová, J and Dobrev, P and Capková, V}, title = {Cytoskeleton-associated large RNP complexes in tobacco male gametophyte (EPPs) are associated with ribosomes and are involved in protein synthesis, processing, and localization.}, journal = {Journal of proteome research}, volume = {8}, number = {4}, pages = {2015-2031}, doi = {10.1021/pr8009897}, pmid = {19714881}, issn = {1535-3893}, mesh = {Chromatography, High Pressure Liquid ; Cytoskeleton/*metabolism ; Germ Cells/*metabolism ; Plant Proteins/metabolism ; Pollen/metabolism ; Pollen Tube/metabolism ; Protein Biosynthesis ; Ribonucleoproteins/analysis/*metabolism ; Ribosomes/*metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tobacco/*metabolism ; }, abstract = {The progamic phase of male gametophyte development involves activation of synthetic and catabolic processes required for the rapid growth of the pollen tube. It is well-established that both transcription and translation play an important role in global and specific gene expression patterns during pollen maturation. On the contrary, germination of many pollen species has been shown to be largely independent of transcription but vitally dependent on translation of stored mRNAs. Here, we report the first structural and proteomic data about large ribonucleoprotein particles (EPPs) in tobacco male gametophyte. These complexes are formed in immature pollen where they contain translationally silent mRNAs. Although massively activated at the early progamic phase, they also serve as a long-term storage of mRNA transported along with the translational machinery to the tip region. Moreover, EPPs were shown to contain ribosomal subunits, rRNAs and a set of mRNAs. Presented results extend our view of EPP complexes from mere RNA storage and transport compartment in particular stages of pollen development to the complex and well-organized machinery devoted to mRNA storage, transport and subsequent controlled activation resulting in protein synthesis, processing and precise localization. Such an organization is extremely useful in fast tip-growing pollen tube. There, massive and orchestrated protein synthesis, processing, and transport must take place in accurately localized regions. Moreover, presented complex role of EPPs in tobacco cytoplasmic mRNA and protein metabolism makes them likely to be active in another plant species too. Expression of vast majority of the closest orthologues of EPP proteins also in Arabidopsis male gametophyte further extends this concept from tobacco to Arabidopsis, the model species with advanced tricellular pollen.}, } @article {pmid19695787, year = {2010}, author = {Woodley, MA}, title = {Is Homo sapiens polytypic? Human taxonomic diversity and its implications.}, journal = {Medical hypotheses}, volume = {74}, number = {1}, pages = {195-201}, doi = {10.1016/j.mehy.2009.07.046}, pmid = {19695787}, issn = {1532-2777}, mesh = {Animals ; Biological Evolution ; Classification ; Ethnicity ; Extinction, Biological ; Hominidae/*classification ; Humans ; Models, Biological ; Models, Theoretical ; Phylogeny ; Species Specificity ; }, abstract = {The term race is a traditional synonym for subspecies, however it is frequently asserted that Homo sapiens is monotypic and that what are termed races are nothing more than biological illusions. In this manuscript a case is made for the hypothesis that H. sapiens is polytypic, and in this way is no different from other species exhibiting similar levels of genetic and morphological diversity. First it is demonstrated that the four major definitions of race/subspecies can be shown to be synonymous within the context of the framework of race as a correlation structure of traits. Next the issue of taxonomic classification is considered where it is demonstrated that H. sapiens possesses high levels morphological diversity, genetic heterozygosity and differentiation (F(ST)) compared to many species that are acknowledged to be polytypic with respect to subspecies. Racial variation is then evaluated in light of the phylogenetic species concept, where it is suggested that the least inclusive monophyletic units exist below the level of species within H. sapiens indicating the existence of a number of potential human phylogenetic species; and the biological species concept, where it is determined that racial variation is too small to represent differentiation at the level of biological species. Finally the implications of this are discussed in the context of anthropology where an accurate picture of the sequence and timing of events during the evolution of human taxa are required for a complete picture of human evolution, and medicine, where a greater appreciation of the role played by human taxonomic differences in disease susceptibility and treatment responsiveness will save lives in the future.}, } @article {pmid19689803, year = {2009}, author = {Mans, JJ and von Lackum, K and Dorsey, C and Willis, S and Wallet, SM and Baker, HV and Lamont, RJ and Handfield, M}, title = {The degree of microbiome complexity influences the epithelial response to infection.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {380}, pmid = {19689803}, issn = {1471-2164}, support = {R01 DE011111/DE/NIDCR NIH HHS/United States ; R01 DE016715/DE/NIDCR NIH HHS/United States ; DE07200/DE/NIDCR NIH HHS/United States ; R01 DE11111/DE/NIDCR NIH HHS/United States ; T32 DE007200/DE/NIDCR NIH HHS/United States ; R01 DE16715/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteroidaceae Infections/genetics/metabolism ; Cell Line ; Coculture Techniques ; *Gene Expression Profiling ; Gene Expression Regulation ; Gingiva/metabolism/*microbiology ; *Host-Pathogen Interactions ; Humans ; Keratinocytes/metabolism/*microbiology ; *Metagenome ; Oligonucleotide Array Sequence Analysis ; Porphyromonas gingivalis/pathogenicity ; Streptococcal Infections/genetics/metabolism ; Streptococcus gordonii/pathogenicity ; }, abstract = {BACKGROUND: The human microflora is known to be extremely complex, yet most pathogenesis research is conducted in mono-species models of infection. Consequently, it remains unclear whether the level of complexity of a host's indigenous flora can affect the virulence potential of pathogenic species. Furthermore, it remains unclear whether the colonization by commensal species affects a host cell's response to pathogenic species beyond the direct physical saturation of surface receptors, the sequestration of nutrients, the modulation of the physico-chemical environment in the oral cavity, or the production of bacteriocins. Using oral epithelial cells as a model, we hypothesized that the virulence of pathogenic species may vary depending on the complexity of the flora that interacts with host cells.

RESULTS: This is the first report that determines the global epithelial transcriptional response to co-culture with defined complex microbiota. In our model, human immortalized gingival keratinocytes (HIGK) were infected with mono- and mixed cultures of commensal and pathogenic species. The global transcriptional response of infected cells was validated and confirmed phenotypically. In our model, commensal species were able to modulate the expression of host genes with a broad diversity of physiological functions and antagonize the effect of pathogenic species at the cellular level. Unexpectedly, the inhibitory effect of commensal species was not correlated with its ability to inhibit adhesion or invasion by pathogenic species.

CONCLUSION: Studying the global transcriptome of epithelial cells to single and complex microbial challenges offers clues towards a better understanding of how bacteria-bacteria interactions and bacteria-host interactions impact the overall host response. This work provides evidence that the degree of complexity of a mixed microbiota does influence the transcriptional response to infection of host epithelial cells, and challenges the current dogma regarding the potential versus the actual pathogenicity of bacterial species. These findings support the concept that members of the commensal oral flora have evolved cellular mechanisms that directly modulate the host cell's response to pathogenic species and dampen their relative pathogenicity.}, } @article {pmid19671194, year = {2009}, author = {Chou, FC and Sytwu, HK}, title = {Overexpression of thioredoxin in islets transduced by a lentiviral vector prolongs graft survival in autoimmune diabetic NOD mice.}, journal = {Journal of biomedical science}, volume = {16}, number = {1}, pages = {71}, pmid = {19671194}, issn = {1423-0127}, mesh = {Animals ; Apoptosis/drug effects ; Cell Survival ; Cells, Cultured/cytology/drug effects/metabolism ; Diabetes Mellitus, Type 1/*surgery ; Female ; Genes, Reporter ; Genetic Vectors/*therapeutic use ; Graft Survival ; Humans ; Hydrogen Peroxide/toxicity ; Insulin/metabolism ; Insulin Secretion ; Intracellular Signaling Peptides and Proteins/genetics/*physiology ; Islets of Langerhans/drug effects/*metabolism/ultrastructure ; *Islets of Langerhans Transplantation ; Male ; Membrane Proteins ; Mice ; Mice, Inbred NOD ; Reactive Oxygen Species/metabolism ; Recombinant Fusion Proteins/physiology ; Transduction, Genetic ; }, abstract = {UNLABELLED: Pancreatic islet transplantation is considered an appropriate treatment to achieve insulin independence in type I diabetic patients. However, islet isolation and transplantation-induced oxidative stress and autoimmune-mediated destruction are still the major obstacles to the long-term survival of graft islets in this potential therapy. To protect islet grafts from inflammatory damage and prolong their survival, we transduced islets with an antioxidative gene thioredoxin (TRX) using a lentiviral vector before transplantation. We hypothesized that the overexpression of TRX in islets would prolong islet graft survival when transplanted into diabetic non-obese diabetic (NOD) mice.

METHODS: Islets were isolated from NOD mice and transduced with lentivirus carrying TRX (Lt-TRX) or enhanced green fluorescence protein (Lt-eGFP), respectively. Transduced islets were transplanted under the left kidney capsule of female diabetic NOD mice, and blood glucose concentration was monitored daily after transplantation. The histology of the islet graft was assessed at the end of the study. The protective effect of TRX on islets was investigated.

RESULTS: The lentiviral vector effectively transduced islets without altering the glucose-stimulating insulin-secretory function of islets. Overexpression of TRX in islets reduced hydrogen peroxide-induced cytotoxicity in vitro. After transplantation into diabetic NOD mice, euglycemia was maintained for significantly longer in Lt-TRX-transduced islets than in Lt-eGFP-transduced islets; the mean graft survival was 18 vs. 6.5 days (n = 9 and 10, respectively, p < 0.05).

CONCLUSION: We successfully transduced the TRX gene into islets and demonstrated that these genetically modified grafts are resistant to inflammatory insult and survived longer in diabetic recipients. Our results further support the concept that the reactive oxygen species (ROS) scavenger and antiapoptotic functions of TRX are critical to islet survival after transplantation.}, } @article {pmid19668363, year = {2009}, author = {Harper, JT and Gile, GH and James, ER and Carpenter, KJ and Keeling, PJ}, title = {The inadequacy of morphology for species and genus delineation in microbial eukaryotes: an example from the parabasalian termite symbiont coronympha.}, journal = {PloS one}, volume = {4}, number = {8}, pages = {e6577}, pmid = {19668363}, issn = {1932-6203}, mesh = {Animals ; Isoptera/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Species Specificity ; *Symbiosis ; Trichomonadida/classification/*isolation & purification ; }, abstract = {BACKGROUND: For the majority of microbial eukaryotes (protists, algae), there is no clearly superior species concept that is consistently applied. In the absence of a practical biological species concept, most species and genus level delineations have historically been based on morphology, which may lead to an underestimate of the diversity of microbial eukaryotes. Indeed, a growing body of molecular evidence, such as barcoding surveys, is beginning to support the conclusion that significant cryptic species diversity exists. This underestimate of diversity appears to be due to a combination of using morphology as the sole basis for assessing diversity and our inability to culture the vast majority of microbial life. Here we have used molecular markers to assess the species delineations in two related but morphologically distinct genera of uncultivated symbionts found in the hindgut of termites.

Using single-cell isolation and environmental PCR, we have used a barcoding approach to characterize the diversity of Coronympha and Metacoronympha symbionts in four species of Incisitermes termites, which were also examined using scanning electron microscopy and light microcopy. Despite the fact that these genera are significantly different in morphological complexity and structural organisation, we find they are two life history stages of the same species. At the same time, we show that the symbionts from different termite hosts show an equal or greater level of sequence diversity than do the hosts, despite the fact that the symbionts are all classified as one species.

CONCLUSIONS/SIGNIFICANCE: The morphological information used to describe the diversity of these microbial symbionts is misleading at both the genus and species levels, and led to an underestimate of species level diversity as well as an overestimate of genus level diversity. The genus 'Metacoronympha' is invalid and appears to be a life history stage of Coronympha, while the single recognized species of Coronympha octonaria inhabiting these four termites is better described as four distinct species.}, } @article {pmid19666992, year = {2009}, author = {Dunn, KA and Bielawski, JP and Ward, TJ and Urquhart, C and Gu, H}, title = {Reconciling ecological and genomic divergence among lineages of listeria under an "extended mosaic genome concept".}, journal = {Molecular biology and evolution}, volume = {26}, number = {11}, pages = {2605-2615}, doi = {10.1093/molbev/msp176}, pmid = {19666992}, issn = {1537-1719}, mesh = {*Evolution, Molecular ; Genome, Bacterial/*genetics ; Listeria/*genetics ; Phylogeny ; }, abstract = {There is growing evidence for a discontinuity between genomic and ecological divergence in several groups of bacteria. This evidence is difficult to reconcile with the traditional concept that ecologically divergent species maintain a cohesive gene pool isolated from other gene pools by barriers to homologous recombination (HR). There have been several innovative models of bacterial divergence that permit such discontinuity; we refer to these, collectively, as "mosaic genome concepts" (MGCs). These concepts remain a point of contention. Here, we undertake an investigation among ecologically divergent lineages of genus Listeria, and report our assessment of both niche-specific selection pressure and HR in their core genome. We find evidence of a mosaic Listeria core genome. Some core genes appear to have been free to recombine across ecologically divergent lineages or across named species. In contrast, other core genes have histories consistent with the expected organism relationships and have evolved under niche-specific selective pressures. The products of some of those genes can even be linked to metabolic phenotypes with ecological significance. This finding indicates a potentially strong connection between ecological divergence and core-genome evolution, even among lineages that also experience frequent recombination. Based on these findings, we propose an expanded role for natural selection in core-genome evolution under the MGC.}, } @article {pmid19656960, year = {2009}, author = {Darr, S and Madisch, I and Hofmayer, S and Rehren, F and Heim, A}, title = {Phylogeny and primary structure analysis of fiber shafts of all human adenovirus types for rational design of adenoviral gene-therapy vectors.}, journal = {The Journal of general virology}, volume = {90}, number = {Pt 12}, pages = {2849-2854}, doi = {10.1099/vir.0.014514-0}, pmid = {19656960}, issn = {1465-2099}, mesh = {Adenoviruses, Human/*chemistry/genetics/metabolism ; Amino Acid Motifs ; Capsid Proteins/*chemistry/genetics/metabolism ; *Drug Design ; Genetic Therapy/*methods ; Genetic Vectors/*chemistry/genetics ; Humans ; Mutation ; *Phylogeny ; Protein Conformation ; Receptors, Virus/metabolism ; }, abstract = {The fiber shaft of human adenoviruses (HAdVs) is essential for bringing the penton base into proximity to the secondary cellular receptor. Fiber shaft sequences of all 53 HAdV types were studied. Phylogeny of the fiber shaft revealed clustering corresponding to the HAdV species concept. An intraspecies recombination hot spot was found at the shaft/knob boundary, a highly conserved sequence stretch. For example, HAdV-D20 clustered with HAdV-D23 in the fiber shaft, but with HAdV-D47 in the fiber knob. Although all shafts exhibited the typical pseudorepeats, amino acid sequence identity was found to be as high as 92 % (interspecies) and 54 % (intraspecies). In contrast to a previous study, a flexibility motif (KXGGLXFD/N) was found in eight HAdV-D types, whereas the putative heparan sulfate-binding site (KKTK) was only found in species HAdV-C. Our results suggest that pseudotyping of gene-therapy vectors at the shaft/knob boundary is feasible, but that flexibility data of shafts should be considered.}, } @article {pmid19641601, year = {2009}, author = {Göker, M and García-Blázquez, G and Voglmayr, H and Tellería, MT and Martín, MP}, title = {Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora.}, journal = {PloS one}, volume = {4}, number = {7}, pages = {e6319}, pmid = {19641601}, issn = {1932-6203}, mesh = {DNA, Fungal ; Likelihood Functions ; Peronospora/*classification/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms.

METHODOLOGY: Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews.

CONCLUSIONS: A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence.}, } @article {pmid19627369, year = {2009}, author = {Kim, JK and Negovetich, NJ and Forrest, HL and Webster, RG}, title = {Ducks: the "Trojan horses" of H5N1 influenza.}, journal = {Influenza and other respiratory viruses}, volume = {3}, number = {4}, pages = {121-128}, pmid = {19627369}, issn = {1750-2659}, support = {HHSN266200700005C/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Disease Reservoirs ; Ducks/*virology ; Influenza A Virus, H5N1 Subtype/*isolation & purification ; Influenza in Birds/*epidemiology/transmission/*virology ; }, abstract = {Wild ducks are the main reservoir of influenza A viruses that can be transmitted to domestic poultry and mammals, including humans. Of the 16 hemagglutinin (HA) subtypes of influenza A viruses, only the H5 and H7 subtypes cause highly pathogenic (HP) influenza in the natural hosts. Several duck species are naturally resistant to HP Asian H5N1 influenza viruses. These duck species can shed and spread virus from both the respiratory and intestinal tracts while showing few or no disease signs. While the HP Asian H5N1 viruses are 100% lethal for chickens and other gallinaceous poultry, the absence of disease signs in some duck species has led to the concept that ducks are the "Trojan horses" of H5N1 in their surreptitious spread of virus. An important unresolved issue is whether the HP H5N1 viruses are maintained in the wild duck population of the world. Here, we review the ecology and pathobiology of ducks infected with influenza A viruses and ducks' role in the maintenance and spread of HP H5N1 viruses. We also identify the key questions about the role of ducks that must be resolved in order to understand the emergence and control of pandemic influenza. It is generally accepted that wild duck species can spread HP H5N1 viruses, but there is insufficient evidence to show that ducks maintain these viruses and transfer them from one generation to the next.}, } @article {pmid19596455, year = {2009}, author = {Borghuis, A and van Groenendael, J and Madsen, O and Ouborg, J}, title = {Phylogenetic analyses of the leaf beetle genus Galerucella: evidence for host switching at speciation?.}, journal = {Molecular phylogenetics and evolution}, volume = {53}, number = {2}, pages = {361-367}, doi = {10.1016/j.ympev.2009.07.005}, pmid = {19596455}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Coleoptera/classification/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genetic Speciation ; Likelihood Functions ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {It is still the subject of lively debate whether sympatric speciation is a general mode of speciation as opposed to allopatric speciation. In herbivorous insects, host switching, i.e. colonization of, and adaptation to, a new host by a herbivore, has been proposed as one of the driving mechanisms of sympatric speciation. Evidence for host switching as a speciation driving mechanism can be inferred from phylogenies of herbivores and host plants: if the host plant phylogeny is randomly distributed over the herbivore phylogeny, this indicates host switching. The Chrysomelid beetle genus Galerucella is a good taxon to study for evidence of host switching, because several closely related Galerucella species form sympatric species complexes associated with various unrelated plant species. Here we present the phylogenetic relationships of 10 species in the genus Galerucella, based on the mitochondrial gene fragments of the NADH-2 (410 bp) and CO-I (659 bp) genes, and analyzed with Bayesian, Maximum Likelihood and Maximum Parsimony methods. The resulting molecular phylogenetic tree proved to be largely congruent with morphologically based taxonomy. The host-associated taxa of the Galerucellanymphaeae species complex are not defined as distinct gene pools under the phylogenetic species concept (PSC), however, the species complex as a whole is. Two results indicate the contribution of host switching to the speciation of Galerucella: (1) the host-associated taxa of the G. nymphaeae species complex have diverged very recently and (2) constrained ML analyses showed that host use constraints led to a significantly different Galerucella tree compared to unconstrained analyses. This evidence for host switching, together with the observation that several sister taxa using unrelated host plants live in sympatry, suggests that sympatric speciation by host race formation can be an important mode of speciation in this genus.}, } @article {pmid19592529, year = {2009}, author = {Caron, DA and Countway, PD and Savai, P and Gast, RJ and Schnetzer, A and Moorthi, SD and Dennett, MR and Moran, DM and Jones, AC}, title = {Defining DNA-based operational taxonomic units for microbial-eukaryote ecology.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {18}, pages = {5797-5808}, pmid = {19592529}, issn = {1098-5336}, mesh = {Atlantic Ocean ; Classification/*methods ; Computational Biology/*methods ; DNA, Ribosomal/*genetics ; *Ecosystem ; Eukaryotic Cells/*classification ; Molecular Sequence Data ; Pacific Ocean ; RNA, Ribosomal, 18S/*genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.}, } @article {pmid19573870, year = {2009}, author = {Quintyn, C}, title = {The naming of new species in hominin evolution: A radical proposal--A temporary cessation in assigning new names.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {60}, number = {4}, pages = {307-341}, doi = {10.1016/j.jchb.2009.05.001}, pmid = {19573870}, issn = {1618-1301}, mesh = {Animals ; *Biological Evolution ; Fossils ; Genetic Speciation ; Hominidae/*genetics ; Humans ; Paleontology/methods ; *Phylogeny ; *Terminology as Topic ; }, abstract = {The species problem is one of the most complex and enduring problems plaguing evolutionary biology in general and human paleontology in particular. In the past 50 years, conceptions of species have diverged and speciated analogous to the present, largely accepted view of the hominin phylogeny. Conventional wisdom supports a "bushy" hominin phylogeny. However, chaos reigns because there is no agreed-upon methodology used to delimit species taxa in paleontology. This dispute is complicated by the ever-present intraspecific and interspecific morphological variation, which is itself exacerbated by other types of variation, including behavioral, ecological, geographical and temporal. When two or more of these forms of variation are used to delimit "new" extant or fossil species, any decision arrived at might be construed as arbitrary. This paper proposes that temporary cessation in assigning new names should be considered based on several critical problems: (1) the explosion of conceptions of a "species" arising from disagreements regarding species definitions, (2) differing interpretations of population variation, which lead to difficulty in interpreting hybridization in nature, leading in turn to the underestimation or overestimation of species, (3) the problem of modes of speciation being confounded with criteria used to distinguish among species, e.g., punctuated equilibrium posits high-speciation rates, and (4) the most common of all human traits, vanity.}, } @article {pmid19563451, year = {2009}, author = {Barrett, LG and Kniskern, JM and Bodenhausen, N and Zhang, W and Bergelson, J}, title = {Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences.}, journal = {The New phytologist}, volume = {183}, number = {3}, pages = {513-529}, doi = {10.1111/j.1469-8137.2009.02927.x}, pmid = {19563451}, issn = {1469-8137}, mesh = {Biological Evolution ; Ecosystem ; *Host-Pathogen Interactions ; Plants/*microbiology ; Species Specificity ; Virulence ; }, abstract = {Ecological, evolutionary and molecular models of interactions between plant hosts and microbial pathogens are largely based around a concept of tightly coupled interactions between species pairs. However, highly pathogenic and obligate associations between host and pathogen species represent only a fraction of the diversity encountered in natural and managed systems. Instead, many pathogens can infect a wide range of hosts, and most hosts are exposed to more than one pathogen species, often simultaneously. Furthermore, outcomes of pathogen infection vary widely because host plants vary in resistance and tolerance to infection, while pathogens are also variable in their ability to grow on or within hosts. Environmental heterogeneity further increases the potential for variation in plant host-pathogen interactions by influencing the degree and fitness consequences of infection. Here, we describe these continua of specificity and virulence inherent within plant host-pathogen interactions. Using this framework, we describe and contrast the genetic and environmental mechanisms that underlie this variation, outline consequences for epidemiology and community structure, explore likely ecological and evolutionary drivers, and highlight several key areas for future research.}, } @article {pmid19557335, year = {2009}, author = {ZHANG, J and WANG, J and XIA, T and ZHOU, S}, title = {DNA barcoding: species delimitation in tree peonies.}, journal = {Science in China. Series C, Life sciences}, volume = {52}, number = {6}, pages = {568-578}, doi = {10.1007/s11427-009-0069-5}, pmid = {19557335}, issn = {1006-9305}, mesh = {Classification/*methods ; Computational Biology/*methods ; DNA, Plant/analysis/genetics ; Evolution, Molecular ; *Paeonia/classification/genetics ; Phylogeny ; }, abstract = {Delimitations of species are crucial for correct and precise identification of taxa. Unfortunately "species" is more a subjective than an objective concept in taxonomic practice due to difficulties in revealing patterns of infra- or inter-specific variations. Molecular phylogenetic studies at the population level solve this problem and lay a sound foundation for DNA barcoding. In this paper we exemplify the necessity of adopting a phylogenetic concept of species in DNA barcoding for tree peonies (Paeonia sect. Moutan). We used 40 samples representing all known populations of rare and endangered species and several populations of widely distributed tree peonies. All currently recognized species and major variants have been included in this study. Four chloroplast gene fragments, i.e. ndhF, rps16-trnQ, trnL-F and trnS-G (a total of 5040 characters, 96 variable and 69 parsimony-informative characters) and one variable and single-copy nuclear GPAT gene fragment (2093-2197 bp, 279 variable and 148 parsimony-informative characters) were used to construct phylogenetic relationships among the taxa. The evolutionary lineages revealed by the nuclear gene and the chloroplast genes are inconsistent with the current circumscriptions of P. decomposita, P. jishanensis, P. qiui, and P. rockii based on morphology. The inconsistencies come from (1) significant chloroplast gene divergence but little nuclear GPAT gene divergence among population systems of P. decomposita + P. rockii, and (2) well-diverged nuclear GPAT gene but little chloroplast gene divergence between P. jishanensis and P. qiui. The incongruence of the phylogenies based on the chloroplast genes and the nuclear GPAT gene is probably due to the chloroplast capture event in evolutionary history, as no reproductive barriers exist to prevent inter-specific hybridization. We also evaluated the suitability of these genes for use as DNA barcodes for tree peonies. The variability of chloroplast genes among well-defined species or population systems of a species complex is 4.82 times the figure within the groups, and the GPAT gene is twice as variable between the groups as within the groups. The number of completely divergent sites is sufficient to mark the two subsections, the two species in subsection Delavayanae, and the well-divergent species in subsection Vaginatae. But the genes currently used either from the chloroplast genome or from the nuclear genome alone cannot correctly assign samples of P. decomposita, P. jishanensis, P. qiui, or P. rockii to the species as currently defined. We conclude that (1) DNA barcoding should be based on prior phylogenetic studies to understand the evolutionary lineages and how well the taxonomic species correspond to the lineages; (2) it is unlikely to find a single short fragment as a barcode for every plant and such a fragment could result in misidentification when a chloroplast capture event happened in the evolutionary history of plants like tree peonies; and (3) we suggest striving for a universal marker at the familial level and locally universal barcodes within a family instead of looking for a universal barcode for all plants.}, } @article {pmid19556257, year = {2009}, author = {Mayer, VE and Voglmayr, H}, title = {Mycelial carton galleries of Azteca brevis (Formicidae) as a multi-species network.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1671}, pages = {3265-3273}, pmid = {19556257}, issn = {0962-8452}, mesh = {Animals ; Ants/genetics/*physiology ; Ascomycota/isolation & purification/*physiology/ultrastructure ; Behavior, Animal ; Biodiversity ; Mycelium/genetics/*physiology/ultrastructure ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Apart from growing fungi for nutrition, as seen in the New World Attini, ants cultivate fungi for reinforcement of the walls of their nests or tunnel-shaped runway galleries. These fungi are grown on organic material such as bark, epiphylls or trichomes, and form stable 'carton structures'. In this study, the carton of the runway galleries built by Azteca brevis (Formicidae, Dolichoderinae) on branches of Tetrathylacium macrophyllum (Flacourtiaceae) is investigated. For the first time, molecular tools are used to address the biodiversity and phylogenetic affinities of fungi involved in tropical ant carton architecture, a previously neglected ant-fungus mutualism. The A. brevis carton involves a complex association of several fungi. All the isolated fungi were unequivocally placed within the Chaetothyriales by DNA sequence data. Whereas five types of fungal hyphae were morphologically distinguishable, our DNA data showed that more species are involved, applying a phylogenetic species concept based on DNA phylogenies and hyphal morphology. In contrast to the New World Attini with their many-to-one (different ant species-one fungal cultivar) pattern, and temperate Lasius with a one-to-two (one ant species-two mutualists) or many-to-one (different ant species share the same mutualist) system, the A. brevis-fungi association is a one-to-many multi-species network. Vertical fungus transmission has not yet been found, indicating that the A. brevis-fungi interaction is rather generalized.}, } @article {pmid19520805, year = {2009}, author = {Sangster, G}, title = {Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1670}, pages = {3185-3191}, pmid = {19520805}, issn = {0962-8452}, mesh = {Animals ; Birds/*classification ; Classification/methods ; *Phylogeny ; Species Specificity ; }, abstract = {The impact and significance of modern taxonomy on other fields in biology have been subjects of much debate. It has been proposed that increasing numbers of vertebrate species are largely owing to 'taxonomic inflation'. According to this hypothesis, newly recognized species result from reinterpretations of species limits based on phylogenetic species concepts (PSCs) rather than from new discoveries. Here, I examine 747 proposals to change the taxonomic rank of birds in the period 1950-2007. The trend to recognize more species of birds started at least two decades before the introduction of PSCs. Most (84.6%) newly recognized species were supported by new taxonomic data. Proposals to recognize more species resulted from application of all six major taxonomic criteria. Many newly recognized species (63.4%) were not based exclusively on PSC-based criteria (diagnosability, monophyly and exclusive coalescence of gene trees). Therefore, this study finds no empirical support for the idea that the increase in species is primarily epistemological rather than data-driven. This study shows that previous claims about the causes and effects of taxonomic inflation lack empirical support. I argue that a more appropriate term for the increase in species is 'taxonomic progress'.}, } @article {pmid19518206, year = {2009}, author = {Mukherji, S}, title = {Fixed points and boundary layers in asymmetric simple exclusion processes.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {79}, number = {4 Pt 1}, pages = {041140}, doi = {10.1103/PhysRevE.79.041140}, pmid = {19518206}, issn = {1539-3755}, abstract = {In this paper, we show how a fixed-point-based boundary layer analysis can be used to understand phases and phase transitions in asymmetric simple exclusion processes (ASEPs) with open boundaries. In order to illustrate this method, we choose a two-species ASEP which has interesting phase transitions not seen in the one-species case. We also apply this method to the single-species problem where the analysis is simple but nevertheless quite insightful.}, } @article {pmid19485120, year = {2009}, author = {Kosoff, RE and Chen, CY and Wooster, GA and Getchell, RG and Bowser, PR and Clifford, A and Craig, JL and Lim, P and Wetzlich, SE and Craigmill, AL and Tell, LA}, title = {Florfenicol residues in three species of fish after 10-day oral dosing in feed.}, journal = {Journal of aquatic animal health}, volume = {21}, number = {1}, pages = {8-13}, doi = {10.1577/H08-013.1}, pmid = {19485120}, issn = {0899-7659}, mesh = {Administration, Oral ; Animal Feed ; Animals ; Anti-Bacterial Agents/*metabolism ; *Drug Residues ; Perciformes/*metabolism ; Species Specificity ; Thiamphenicol/*analogs & derivatives/metabolism ; }, abstract = {Nile tilapia Oreochromis niloticus, walleye Sander vitreus, and hybrid striped bass (female white bass Morone chrysops x male striped bass M. saxatilis) were medicated with florfenicol (AQUAFLOR type A medicated article; Schering-Plough Animal Health, Summit, New Jersey) via a medicated ration of 10 mg florfenicol x kg fish body weight(-1) d(-1) for 10 d to compare the elimination kinetics of the test article. This study was part of a larger effort in support of a species grouping concept that could contribute to the regulatory approval process for therapeutic compounds for cultured fishes. The trials in this study were conducted at the ideal water temperature for each species and at the temperature 5 degrees C lower than the ideal. The test temperatures were 30 degrees C and 25 degrees C for Nile tilapia, 25 degrees C and 20 degrees C for both walleyes and hybrid striped bass. In all cases, the elimination kinetics of florfenicol were more rapid at higher temperatures. The time to reach the tolerance of 1 microg/g in muscle-skin, as set by the U.S. Food and Drug Administration for channel catfish Ictalurus punctatus and salmonids, ranged from 6.1 to 4.1 d for Nile tilapia, from 12.6 to 9.7 d for walleyes, and from 2.6 to 0.7 d for hybrid striped bass at temperatures between 20 degrees C and 30 degrees C.}, } @article {pmid19467004, year = {2009}, author = {Taylor, MG and Rhodes, M and Gelman, SA}, title = {Boys will be boys; cows will be cows: children's essentialist reasoning about gender categories and animal species.}, journal = {Child development}, volume = {80}, number = {2}, pages = {461-481}, pmid = {19467004}, issn = {1467-8624}, support = {R01 HD036043-09A1/HD/NICHD NIH HHS/United States ; R56 HD036043/HD/NICHD NIH HHS/United States ; R01 HD036043-06/HD/NICHD NIH HHS/United States ; R01 HD036043-08/HD/NICHD NIH HHS/United States ; R01 HD036043-07/HD/NICHD NIH HHS/United States ; HD-36043/HD/NICHD NIH HHS/United States ; R01 HD036043/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; Age Factors ; Child ; *Child Development ; Child, Preschool ; *Cognition ; *Concept Formation ; Female ; *Gender Identity ; Humans ; Male ; Neuropsychological Tests ; Terminology as Topic ; }, abstract = {Two studies (N = 456) compared the development of concepts of animal species and human gender, using a switched-at-birth reasoning task. Younger children (5- and 6-year-olds) treated animal species and human gender as equivalent; they made similar levels of category-based inferences and endorsed similar explanations for development in these 2 domains. In contrast, 10-year-olds and adults treated gender and species concepts as distinct from one another. They viewed gender-linked behavioral properties as open to environmental influence and endorsed environment-based mechanisms to explain gender development. At all ages, children demonstrated differentiated reasoning about physical and behavioral properties, although this differentiation became more stable with age. The role of psychological essentialism in guiding conceptual development is discussed.}, } @article {pmid19457189, year = {2009}, author = {Irwin, DE}, title = {Incipient ring speciation revealed by a migratory divide.}, journal = {Molecular ecology}, volume = {18}, number = {14}, pages = {2923-2925}, doi = {10.1111/j.1365-294X.2009.04211.x}, pmid = {19457189}, issn = {1365-294X}, mesh = {Animals ; *Genetic Speciation ; *Genetics, Population ; Geography ; Hybridization, Genetic ; Passeriformes/anatomy & histology/*genetics ; Phylogeny ; }, abstract = {Ever since Ernst Mayr (1942) called ring species the 'perfect demonstration of speciation', they have attracted much interest from researchers examining how two species evolve from one. In a ring species, two sympatric and reproductively isolated forms are connected by a long chain of intermediate populations that encircle a geographic barrier. Ring species have the potential to demonstrate that speciation can occur without complete geographic isolation, in contrast to the classic model of allopatric speciation. They also allow researchers to examine the causes of reproductive isolation in the contact zone and to use spatial variation to infer the steps by which speciation occurs. According to the classical definition, a ring species must have (i) gradual variation through a chain of populations connecting two divergent and sympatric forms, and (ii) complete or nearly complete reproductive isolation between the terminal forms. But evolutionary biologists now recognize that the process of speciation might often occur with some periods of geographic contact and hybridization between diverging forms; during these phases, even partial reproductive isolation can limit gene flow and permit further divergence to occur. In this issue Bensch et al. (2009) make an exciting and important contribution by extending the ring species concept to a case in which the divergence is much younger and not yet advanced to full reproductive isolation. Their study of geographic variation in willow warblers (Phylloscopus trochilus; Fig. 1) provides a beautiful example of gradual variation through a ring of populations connecting two forms that are partially reproductively isolated where they meet, possibly due to divergent migratory behaviours of the terminal forms.}, } @article {pmid19457050, year = {2009}, author = {Caron, DA}, title = {Past President's address: protistan biogeography: why all the fuss?.}, journal = {The Journal of eukaryotic microbiology}, volume = {56}, number = {2}, pages = {105-112}, doi = {10.1111/j.1550-7408.2008.00381.x}, pmid = {19457050}, issn = {1550-7408}, mesh = {Adaptation, Physiological ; *Biodiversity ; *Biological Evolution ; Ecology ; Ecosystem ; Eukaryota/*classification/*genetics/physiology ; Microbiology ; Parasitology ; Phylogeny ; Phylogeography ; }, abstract = {Conflicting hypotheses regarding the distribution of protistan species on our planet have led to rather impassioned arguments in the recent literature, and heated discussions at scientific meetings. Both sides of this debate have mounted seemingly credible arguments for endemism on the one hand, or ubiquitous dispersal of protists on the other. At present, the controversy appears unending, perhaps because it is fueled by a convergence of unresolvable issues involving the enormous phylogenetic breadth of species presently encompassed by the term "protist," the application of multiple species concepts to these taxa, the inability of extant techniques and technology to plumb the depths of microbial diversity in natural ecosystems, and a lack of knowledge regarding the relationship between dispersal rates and rates of evolution of protists. These issues have made it difficult to erect and test hypotheses concerning the distribution of protists. In the absence of definitive experimental or observational information, preconceived attitudes regarding protistan distributions have dominated the interpretation of the available data. On the positive side, the debate has led to the development and application of new approaches to the study of protistan diversity, and stimulated discussions involving how (and why) we define protistan species.}, } @article {pmid19453735, year = {2009}, author = {Scopece, G and Musacchio, A and Widmer, A and Cozzolino, S}, title = {Contrasting thoughts about deceptive orchids: a response to Sobel and Randle.}, journal = {Evolution; international journal of organic evolution}, volume = {63}, number = {8}, pages = {2205-2209}, doi = {10.1111/j.1558-5646.2009.00693.x}, pmid = {19453735}, issn = {1558-5646}, mesh = {*Biological Evolution ; Botany/*methods ; Magnoliopsida/classification/*genetics/*growth & development ; Pollination ; }, abstract = {Sobel and Randle (2009) challenge several methodological choices in the comparative study of the evolution of reproductive isolation in Mediterranean deceptive orchids of Scopece et al. (2007) including the species concept used and the selection of taxa, together with the perceived comparison of clades of different ages. They further criticize that pollinator information was taken from the literature and that two different methods were used to estimate pollinator specificity in food-deceptive and sexually deceptive orchids, respectively. Here we reply to these challenges.}, } @article {pmid19411599, year = {2009}, author = {Doolittle, WF and Zhaxybayeva, O}, title = {On the origin of prokaryotic species.}, journal = {Genome research}, volume = {19}, number = {5}, pages = {744-756}, doi = {10.1101/gr.086645.108}, pmid = {19411599}, issn = {1088-9051}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Biodiversity ; Ecosystem ; *Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Genomics ; Species Specificity ; }, abstract = {The notion that all prokaryotes belong to genomically and phenomically cohesive clusters that we might legitimately call "species" is a contentious one. At issue are (1) whether such clusters actually exist; (2) what species definition might most reliably identify them, if they do; and (3) what species concept -- by which is meant a genetic and ecological theory of speciation -- might best explain species existence and rationalize a species definition, if we could agree on one. We review existing theories and some relevant data. We conclude that microbiologists now understand in some detail the various genetic, population, and ecological processes that effect the evolution of prokaryotes. There will be on occasion circumstances under which these, working together, will form groups of related organisms sufficiently like each other that we might all agree to call them "species," but there is no reason that this must always be so. Thus, there is no principled way in which questions about prokaryotic species, such as how many there are, how large their populations are, or how globally they are distributed, can be answered. These questions can, however, be reformulated so that metagenomic methods and thinking will meaningfully address the biological patterns and processes whose understanding is our ultimate target.}, } @article {pmid19398445, year = {2009}, author = {Hopper, SD}, title = {Taxonomic turmoil down-under: recent developments in Australian orchid systematics.}, journal = {Annals of botany}, volume = {104}, number = {3}, pages = {447-455}, pmid = {19398445}, issn = {1095-8290}, mesh = {Australia ; Orchidaceae/*classification/genetics ; Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: The issue of determining the most appropriate rank for each accepted taxon fuels ongoing controversy throughout systematics. The particularly marked escalation of such issues in modern Australian orchid systematics merits examination, not only because of wider implications in taxonomy but also because of direct effects on studies of comparative biology and conservation management.

SCOPE: This paper briefly reviews the causes of recent taxonomic turmoil for Australian orchids and outlines new research opportunities and conservation implications arising from an improved understanding of their molecular phylogenetics.

CONCLUSIONS: DNA sequencing and intensified field work have contributed towards a much improved understanding of Australian orchid systematics. Great progress has been made in discerning monophyletic groups or clades. Fresh interpretations of morphological evolution have been made possible by comparisons with the results of DNA analyses. Significant conceptual shifts from polymorphic species concepts to biological and phylogenetic concepts have also elevated the discovery and description of new species. Consequently, over the past decade, the number of Australian orchid species recognized by taxonomists has risen from approx. 900 to 1200. Similarly, the number of genera recognized by some taxonomists has increased from 110 to 192, resulting in 45% of Australian species/subspecies being assigned a new generic epithet since 2000. At higher taxonomic levels, much of the recent controversy in Australian orchid systematics reflects a divergence in views about where to split and assign formal names within unequivocally monophyletic groups. Differences regarding typification in the case of Caladenia have added additional confusion and complexity. However, new insights into and research opportunities concerning speciation processes in orchids have arisen from the wealth of new data and discrimination of species. Robustly supported molecular analyses of most clades enable comparative biological studies of Australian orchids to be conducted as never before. Outstanding subjects exist for exploring pollination by sexual deception and understanding the intricacies of mycorrhizal relationships and orchid conservation biology.}, } @article {pmid19393769, year = {2010}, author = {Fargette, M and Berthier, K and Richaud, M and Lollier, V and Franck, P and Hernandez, A and Frutos, R}, title = {Crosses prior to parthenogenesis explain the current genetic diversity of tropical plant-parasitic Meloidogyne species (Nematoda: Tylenchida).}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {10}, number = {6}, pages = {807-814}, doi = {10.1016/j.meegid.2009.04.013}, pmid = {19393769}, issn = {1567-7257}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Biodiversity ; *Crosses, Genetic ; Evolution, Molecular ; Genes, Mitochondrial/genetics ; Genetic Speciation ; *Genetic Variation ; Parthenogenesis/*genetics/physiology ; Phylogeny ; Plant Diseases/genetics/parasitology ; Secernentea Infections/parasitology ; Species Specificity ; Tropical Climate ; Tylenchoidea/classification/*genetics ; }, abstract = {The tropical and subtropical parthenogenetic plant-parasitic nematodes Meloidogyne are polyphagous major agricultural pests. Implementing proper pest management approaches requires a good understanding of mechanisms, population structure, evolutionary patterns and species identification. A comparative analysis of the mitochondrial vs nuclear diversity was conducted on a selected set of Meloidogyne lines from various geographic origins. Mitochondrial co2-16S sequences and AFLP markers of total DNA were applied because of their ability to evidence discrete genetic variation between closely related isolates. Several distinct maternal lineages were present, now associated with different genetic backgrounds. Relative discordances were found when comparing mitochondrial and nuclear diversity patterns. These patterns are most likely related to crosses within one ancestral genetic pool, followed by the establishment of parthenogenesis. In this case, they mirror the genetic backgrounds of the original individuals. Another aspect could be that species emergence was recent or on process from this original genetic pool and that the relatively short time elapsed since then and before parthenogenesis settlement did not allow for lineage sorting. This could also be compatible with the hypothesis of hybrids between closely related species. This genetic pool would correspond to a species as defined by the species interbreeding concept, but also including the grey area of species boundaries. This complex process has implications on the way genotypic and phenotypic diversity should be addressed. The phenotype of parthenogenetic lines is at least for part determined by the ancestral amphimictic genetic background. A direct consequence is, therefore, in terms of risk management, the limited confidence one can have on the direct association of an agronomic threat to a simple typing or species delineation. Risk management strategies and tools must thus consider this complexity when designing quarantine implementation, resistance breeding programmes or molecular diagnostic.}, } @article {pmid19341148, year = {2009}, author = {Hall, SR and Becker, CR and Simonis, JL and Duffy, MA and Tessier, AJ and Cáceres, CE}, title = {Friendly competition: evidence for a dilution effect among competitors in a planktonic host-parasite system.}, journal = {Ecology}, volume = {90}, number = {3}, pages = {791-801}, doi = {10.1890/08-0838.1}, pmid = {19341148}, issn = {0012-9658}, mesh = {Animals ; Daphnia/*immunology/*parasitology ; Disease Outbreaks/veterinary ; *Ecosystem ; Host-Parasite Interactions/*physiology ; Immunity, Innate ; Multivariate Analysis ; Population Density ; Population Dynamics ; Seasons ; Time Factors ; Zooplankton/*physiology ; }, abstract = {The "dilution effect" concept in disease ecology offers the intriguing possibility that clever manipulation of less competent hosts could reduce disease prevalence in populations of more competent hosts. The basic concept is straightforward: host species vary in suitability (competence) for parasites, and disease transmission decreases when there are more incompetent hosts interacting with vectors or removing free-living stages of a parasite. However, host species also often interact with each other in other ecological ways, e.g., as competitors for resources. The net result of these simultaneous, multiple interactions (disease dilution and resource competition) is challenging to predict. Nonetheless, we see the signature of both roles operating concurrently in a planktonic host-parasite system. We document pronounced spatiotemporal variation in the size of epidemics of a virulent fungus (Metschnikowia bicuspidata) in Midwestern U.S. lake populations of a dominant crustacean grazer (Daphnia dentifera). We show that some of this variation is captured by changes in structure of Daphnia assemblages. Lake-years with smaller epidemics were characterized by assemblages dominated by less suitable hosts ("diluters," D. pulicaria and D. retrocurva, whose suitabilties were determined in lab experiments and field surveys) at the start of epidemics. Furthermore, within a season, less suitable hosts increased as epidemics declined. These observations are consistent with a dilution effect. However, more detailed time series analysis (using multivariate autoregressive models) of three intensively sampled epidemics show the signature of a likely interaction between dilution and resource competition between these Daphnia species. The net outcome of this interaction likely promoted termination of these fungal outbreaks. Should this outcome always arise in "friendly competition" systems where diluting hosts compete with more competent hosts? The answers to this question lie at a frontier of disease ecology.}, } @article {pmid19281950, year = {2009}, author = {Lopez, P and Bapteste, E}, title = {Molecular phylogeny: reconstructing the forest.}, journal = {Comptes rendus biologies}, volume = {332}, number = {2-3}, pages = {171-182}, doi = {10.1016/j.crvi.2008.07.003}, pmid = {19281950}, issn = {1768-3238}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Trees/*physiology ; }, abstract = {Phylogeny, be it morphological or molecular, has long tried to explain the extant biodiversity by the Tree of Species, which is a logical consequence of strict Darwinian evolutionary principles. Through constant improvement of both methods and data sets, some parts of this diversity have actually been demonstrated to be the result of a tree-like process. For some other parts, and especially for prokaryotes, different molecular markers have, however, produced different evolutionary trees, preventing the reconstruction of such a Tree. While technical artifacts could be blamed for these discrepancies, Lateral Gene Transfers are now largely held for responsible, and their existence requires an extension of the Darwinian framework, since genetic material is not always vertically inherited from parents to offspring. Through a variety of biological processes, sometimes large parts of DNA are exchanged between phylogenetically distant contemporary organisms, especially between those sharing the same environment. While mainly concerning prokaryotes, Lateral Gene Transfers have been also demonstrated to affect eukaryotes, and even multicellular ones, like plants or animals. Most of the time, these transfers allow important adaptations and the colonisation of new niches. The quantitative and qualitative importance of genetic transfers has thus severely challenged the very existence of a universal Tree of Species, since genetic connections, at least for microbes, seem more reticulated than tree-like. Even traditional biological concepts, like the concept of species, need to be re-evaluated in the light of recent discoveries. In short, instead of focusing on a elusive universal tree, biologists are now considering the whole forest corresponding to the multiple processes of inheritance, both vertical and horizontal. This constitutes the major challenge of evolutionary biology for the years to come.}, } @article {pmid19278444, year = {2009}, author = {Rybalka, N and Andersen, RA and Kostikov, I and Mohr, KI and Massalski, A and Olech, M and Friedl, T}, title = {Testing for endemism, genotypic diversity and species concepts in Antarctic terrestrial microalgae of the Tribonemataceae (Stramenopiles, Xanthophyceae).}, journal = {Environmental microbiology}, volume = {11}, number = {3}, pages = {554-565}, doi = {10.1111/j.1462-2920.2008.01787.x}, pmid = {19278444}, issn = {1462-2920}, mesh = {Antarctic Regions ; Base Sequence ; *Biodiversity ; Cluster Analysis ; DNA, Algal/chemistry/genetics ; DNA, Chloroplast/chemistry/genetics ; DNA, Intergenic ; Eukaryota/*classification/cytology/*isolation & purification ; Molecular Sequence Data ; Photosystem II Protein Complex/genetics ; Phylogeny ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; *Soil Microbiology ; }, abstract = {The genetic diversity of all available culture strains of the Tribonemataceae (Stramenopiles, Xanthophyceae) from Antarctica was assessed using the chloroplast-encoded psbA /rbcL spacer region sequences, a highly variable molecular marker, to test for endemism when compared with their closest temperate relatives. There was no species endemic for Antarctica, and no phylogenetic clade corresponded to a limited geographical region. However, species of the Tribonemataceae may have Antarctic populations that are distinct from those of other regions because the Antarctic strain spacer sequences were not identical to sequences from temperate regions. Spacer sequences from five new Antarctic isolates were identical to one or more previously available Antarctic strains, indicating that the Tribonemataceae diversity in Antarctic may be rather limited. Direct comparisons of the spacer sequences and phylogenetic analyses of the more conserved rbcL gene revealed that current morphospecies were inadequate to describe the actual biodiversity of the group. For example, the genus Xanthonema, as currently circumscribed, was paraphyletic. Fortunately, the presence of distinctive sequence regions within the psbA/rbcL spacer, together with differences in the rbcL phylogeny, provided significant autoapomorphic criteria to re-define the Tribonemataceae species.}, } @article {pmid19276111, year = {2009}, author = {Ionita-Laza, I and Lange, C and M Laird, N}, title = {Estimating the number of unseen variants in the human genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {13}, pages = {5008-5013}, pmid = {19276111}, issn = {1091-6490}, support = {R01 MH059532/MH/NIMH NIH HHS/United States ; R01 MH59532/MH/NIMH NIH HHS/United States ; }, mesh = {Databases, Genetic ; Ecology ; *Genetic Variation ; Genetics, Population ; Genome, Human/*genetics ; Humans ; *Models, Genetic ; Polymorphism, Single Nucleotide ; Population Groups/*genetics ; Sample Size ; }, abstract = {The different genetic variation discovery projects (The SNP Consortium, the International HapMap Project, the 1000 Genomes Project, etc.) aim to identify as much as possible of the underlying genetic variation in various human populations. The question we address in this article is how many new variants are yet to be found. This is an instance of the species problem in ecology, where the goal is to estimate the number of species in a closed population. We use a parametric beta-binomial model that allows us to calculate the expected number of new variants with a desired minimum frequency to be discovered in a new dataset of individuals of a specified size. The method can also be used to predict the number of individuals necessary to sequence in order to capture all (or a fraction of) the variation with a specified minimum frequency. We apply the method to three datasets: the ENCODE dataset, the SeattleSNPs dataset, and the National Institute of Environmental Health Sciences SNPs dataset. Consistent with previous descriptions, our results show that the African population is the most diverse in terms of the number of variants expected to exist, the Asian populations the least diverse, with the European population in-between. In addition, our results show a clear distinction between the Chinese and the Japanese populations, with the Japanese population being the less diverse. To find all common variants (frequency at least 1%) the number of individuals that need to be sequenced is small (approximately 350) and does not differ much among the different populations; our data show that, subject to sequence accuracy, the 1000 Genomes Project is likely to find most of these common variants and a high proportion of the rarer ones (frequency between 0.1 and 1%). The data reveal a rule of diminishing returns: a small number of individuals (approximately 150) is sufficient to identify 80% of variants with a frequency of at least 0.1%, while a much larger number (> 3,000 individuals) is necessary to find all of those variants. Finally, our results also show a much higher diversity in environmental response genes compared with the average genome, especially in African populations.}, } @article {pmid19271197, year = {2009}, author = {Thane Papke, R}, title = {A critique of prokaryotic species concepts.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {379-395}, doi = {10.1007/978-1-60327-853-9_22}, pmid = {19271197}, issn = {1064-3745}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; Biological Evolution ; Gene Transfer, Horizontal ; *Genetic Speciation ; Halorubrum/genetics ; Models, Genetic ; Phylogeny ; Selection, Genetic ; }, abstract = {Developments in DNA sequencing and population genetics analyses have revealed unanticipated complexity in prokaryotic variation. The observation that genetic traits are horizontally inherited at unexpected rates within and between closely related asexually reproducing lineages impacts our comprehension of prokaryotic evolution and ecology. As a result, the concepts that point to species as being discrete clusters or monophyletic lineages are at odds with most of the data, suggesting that taxon circumscription can only proceed by informed compromise, pragmatism, and subjectivity.}, } @article {pmid19271196, year = {2009}, author = {Riley, MA and Lizotte-Waniewski, M}, title = {Population genomics and the bacterial species concept.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {367-377}, pmid = {19271196}, issn = {1064-3745}, support = {R01 AI064588/AI/NIAID NIH HHS/United States ; R01 AI064588-01A2/AI/NIAID NIH HHS/United States ; R01 GM068657/GM/NIGMS NIH HHS/United States ; R01 GM068657-01A2/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genetic Speciation ; Genetics, Population ; Genomics ; Models, Genetic ; Phylogeny ; }, abstract = {In recent years, the importance of horizontal gene transfer (HGT) in bacterial evolution has been elevated to such a degree that many bacteriologists now question the very existence of bacterial species. If gene transfer is as rampant as comparative genomic studies have suggested, how could bacterial species survive such genomic fluidity? And yet, most bacteriologists recognize, and name, as species, clusters of bacterial isolates that share complex phenotypic properties. The Core Genome Hypothesis (CGH) has been proposed to explain this apparent paradox of fluid bacterial genomes associated with stable phenotypic clusters. It posits that there is a core of genes responsible for maintaining the species-specific phenotypic clusters observed throughout bacterial diversity and argues that, even in the face of substantial genomic fluidity, bacterial species can be rationally identified and named.}, } @article {pmid19271179, year = {2009}, author = {Bapteste, E and Boucher, Y}, title = {Epistemological impacts of horizontal gene transfer on classification in microbiology.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {55-72}, doi = {10.1007/978-1-60327-853-9_4}, pmid = {19271179}, issn = {1064-3745}, mesh = {Biological Evolution ; Classification/*methods ; *Gene Transfer, Horizontal ; Genetic Speciation ; *Genetics, Microbial ; Models, Genetic ; Philosophy ; Phylogeny ; }, abstract = {We describe the reasons why the newly recognized process of horizontal gene transfer (HGT) forces evolutionists who study classification and microbiology to go beyond the classical Darwinian framework. We recall the importance of processes in philosophical definitions of species and for taxonomical purposes in general. More precisely, we present a brief description of a possible transition from a thinking inspired by essentialism to eliminative pluralism in the species debate and we insist on a major philosophical lesson: that processes matter and that, consequently, HGT cannot be overlooked in microbial classification. We then expand the conclusions of eliminative pluralism to microbial classification, namely (i) that species are not real and (ii) that overlapping taxonomies are equally legitimate when they are based on real natural processes. We introduce alternatives to the traditional species concept and describe what we call evolutionary units. Two types of units can be described: coherent and composite. The former are sets of co-evolving genes, pathways, or organisms, which share the same phylogenetic origin, while the latter comprise genes, pathways, or organisms with component parts from multiple phylogenetic origins. These evolutionary units are either "mostly flexible" or "mostly rigid" in their genetic composition and we discuss how this dissimilarity could profoundly affect our systematics practice. In this chapter, we illustrate how much there is to learn from the reconstruction of the complex evolutionary histories of all evolutionary units - large or small - by giving up the notion of species for recombining microbes, and suggest replacing a unique nested hierarchy of life with a comprehensive database including overlapping taxonomical groups.}, } @article {pmid19271178, year = {2009}, author = {Lawrence, JG and Retchless, AC}, title = {The interplay of homologous recombination and horizontal gene transfer in bacterial speciation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {29-53}, doi = {10.1007/978-1-60327-853-9_3}, pmid = {19271178}, issn = {1064-3745}, support = {GM078092/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/classification/*genetics ; Biological Evolution ; Ecosystem ; *Gene Transfer, Horizontal ; *Genetic Speciation ; Genome, Bacterial ; Models, Genetic ; Mutation ; *Recombination, Genetic ; Selection, Genetic ; Time Factors ; }, abstract = {Bacteria experience recombination in two ways. In the context of the Biological Species concept, allelic exchange purges genic variability within bacterial populations as gene exchange mediates selective sweeps. In contrast, horizontal gene transfer (HGT) increases the size of the population's pan-genome by providing an influx of novel genetic material. Here we discuss the interplay of these two processes, with an emphasis on how they allow for the maintenance of genotypically cohesive bacterial populations, yet allow for the separation of these populations upon bacterial speciation. In populations that maintain genotypic similarity by frequent allelic exchange, horizontally transferred genes may initiate ecological barriers to genetic exchange. The resulting recombination interference allows for the accumulation of neutral mutations and, consequently, the imposition of a pre-mating barrier to gene transfer.}, } @article {pmid19258340, year = {2009}, author = {Herrera, J}, title = {Visibility vs. biomass in flowers: exploring corolla allocation in Mediterranean entomophilous plants.}, journal = {Annals of botany}, volume = {103}, number = {7}, pages = {1119-1127}, pmid = {19258340}, issn = {1095-8290}, mesh = {*Biomass ; Droughts ; Flowers/*growth & development/*physiology ; Mediterranean Region ; Plant Development ; Pollination/*physiology ; Water/metabolism ; }, abstract = {BACKGROUND AND AIMS: While pollinators may in general select for large, morphologically uniform floral phenotypes, drought stress has been proposed as a destabilizing force that may favour small flowers and/or promote floral variation within species.

METHODS: The general validity of this concept was checked by surveying a taxonomically diverse array of 38 insect-pollinated Mediterranean species. The interplay between fresh biomass investment, linear size and percentage corolla allocation was studied. Allometric relationships between traits were investigated by reduced major-axis regression, and qualitative correlates of floral variation explored using general linear-model MANOVA.

KEY RESULTS: Across species, flowers were perfectly isometrical with regard to corolla allocation (i.e. larger flowers were just scaled-up versions of smaller ones and vice versa). In contrast, linear size and biomass varied allometrically (i.e. there were shape variations, in addition to variations in size). Most floral variables correlated positively and significantly across species, except corolla allocation, which was largely determined by family membership and floral symmetry. On average, species with bilateral flowers allocated more to the corolla than those with radial flowers. Plant life-form was immaterial to all of the studied traits. Flower linear size variation was in general low among conspecifics (coefficients of variation around 10 %), whereas biomass was in general less uniform (e.g. 200-400 mg in Cistus salvifolius). Significant among-population differences were detected for all major quantitative floral traits.

CONCLUSIONS: Flower miniaturization can allow an improved use of reproductive resources under prevailingly stressful conditions. The hypothesis that flower size reflects a compromise between pollinator attraction, water requirements and allometric constraints among floral parts is discussed.}, } @article {pmid19255907, year = {2009}, author = {Samson, RA and Varga, J}, title = {What is a species in Aspergillus?.}, journal = {Medical mycology}, volume = {47 Suppl 1}, number = {}, pages = {S13-20}, doi = {10.1080/13693780802354011}, pmid = {19255907}, issn = {1460-2709}, mesh = {Animals ; Aspergillus/*classification/genetics/physiology ; DNA, Fungal/*genetics ; Genes, Fungal ; Humans ; Mycological Typing Techniques ; *Phylogeny ; Terminology as Topic ; }, abstract = {The various species concepts with emphasis on those which can be applied to Aspergillus and its teleomorphs are discussed. Any proposed new species should show evidence for evolutionary divergence from other taxa, particularly unique DNA characters at multiple loci and the polyphasic approach was suggested as the 'gold standard' for species delimitation using a combination of multilocus sequence data, morphological, physiological characteristics and ecological data. For species descriptions it is recommended to examine several gene sequences (e.g., ITS, calmodulin, beta-tubulin, actin) and submit them to recognized sequence databases. Dual naming of Aspergillus taxa with teleomorphs has been recommended where necessary. To avoid confusion, the 'List of Names in Current Use' is recommended as a reference for Aspergillus nomenclature. For clinical researchers who depend on one of the names, it was suggested to use the name 'complex' if identification is solely based on morphology, which cannot distinguish between closely related species. A protocol for naming new Aspergillus taxa is proposed, which include the deposition of type cultures in at least two recognized culture collections. If type cultures are not available the taxon can be declared invalid.}, } @article {pmid19244845, year = {2008}, author = {Miracle, ME}, title = {The significance of Temminck's work on biogeography: early nineteenth century natural history in Leiden, The Netherlands.}, journal = {Journal of the history of biology}, volume = {41}, number = {4}, pages = {677-716}, pmid = {19244845}, issn = {0022-5010}, mesh = {Animals ; Geography/*history ; History, 19th Century ; Museums/*history ; Natural History/*history ; Netherlands ; Zoology/history ; }, abstract = {C.J. Temminck, director of the Rijksmuseum van Natuurlijke Historie (now the National Museum of Natural History in Leiden) and a renowned ornithologist, gained his contemporary's respect thanks to the description of many new species and to his detailed monographs on birds. He also published a small number of works on biogeography describing the fauna of the Dutch colonies in South East Asia and Japan. These works are remarkable for two reasons. First, in them Temminck accurately described the species composition of poorly explored regions, like the Sunda Islands and Japan. Secondly, he formulated a new law on the geographical distribution of animals around the globe, based on the parallels he observed between the fauna from Europe, Asia and Japan. The underlying ideas that lead Temminck to this law were the type-concept, which he understood as the ideal morphological plan behind animal form, the unchanging character of the species and a strong belief in nature's divine design. During the first half of the nineteenth century, the type- and the species-concept, the origin and fixity of the species and the meaning of variations aroused heated discussions. When put in the context of his time, Temminck emerges as a scientist whose work was driven by the dominating scientific philosophy of the time in which he lived, under the influence of late eighteenth century natural history and of French empiricists, in particular, the great zoologist and paleontologist Georges Cuvier. Temminck's detailed descriptions of the Dutch East Indian fauna helped the great naturalists after him to understand nature's patterns and to propose comprehensive theories that explain its diversity.}, } @article {pmid19239678, year = {2009}, author = {Forsman, ZH and Barshis, DJ and Hunter, CL and Toonen, RJ}, title = {Shape-shifting corals: molecular markers show morphology is evolutionarily plastic in Porites.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {45}, pmid = {19239678}, issn = {1471-2148}, mesh = {Animals ; Anthozoa/anatomy & histology/classification/*genetics ; Bayes Theorem ; Biodiversity ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; *Evolution, Molecular ; Genetic Markers ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Corals are notoriously difficult to identify at the species-level due to few diagnostic characters and variable skeletal morphology. This 'coral species problem' is an impediment to understanding the evolution and biodiversity of this important and threatened group of organisms. We examined the evolution of the nuclear ribosomal internal transcribed spacer (ITS) and mitochondrial markers (COI, putative control region) in Porites, one of the most taxonomically challenging and ecologically important genera of reef-building corals.

RESULTS: Nuclear and mitochondrial markers were congruent, clearly resolving many traditionally recognized species; however, branching and mounding varieties were genetically indistinguishable within at least two clades, and specimens matching the description of 'Porites lutea' sorted into three genetically divergent groups. Corallite-level features were generally concordant with genetic groups, although hyper-variability in one group (Clade I) overlapped and obscured several others, and Synarea (previously thought to be a separate subgenus) was closely related to congeners despite its unique morphology. Scanning electron microscopy revealed subtle differences between genetic groups that may have been overlooked previously as taxonomic characters.

CONCLUSION: This study demonstrates that the coral skeleton can be remarkably evolutionarily plastic, which may explain some taxonomic difficulties, and obscure underlying patterns of endemism and diversity.}, } @article {pmid19236147, year = {2009}, author = {Nakamura, T and Wright, AA and Katz, JS and Bodily, KD and Sturz, BR}, title = {Abstract-concept learning carryover effects from the initial training set in pigeons (Columba livia).}, journal = {Journal of comparative psychology (Washington, D.C. : 1983)}, volume = {123}, number = {1}, pages = {79-89}, pmid = {19236147}, issn = {0735-7036}, support = {R01 MH072616/MH/NIMH NIH HHS/United States ; R01 DA010715-04/DA/NIDA NIH HHS/United States ; R01 MH061798/MH/NIMH NIH HHS/United States ; R01 MH061798-01A1/MH/NIMH NIH HHS/United States ; R01 MH061798-03/MH/NIMH NIH HHS/United States ; DA10715/DA/NIDA NIH HHS/United States ; MH-061798/MH/NIMH NIH HHS/United States ; R01 MH072616-02/MH/NIMH NIH HHS/United States ; MH-072616/MH/NIMH NIH HHS/United States ; R01 DA010715/DA/NIDA NIH HHS/United States ; R01 MH072616-01A2/MH/NIMH NIH HHS/United States ; R01 DA010715-05/DA/NIDA NIH HHS/United States ; R01 MH061798-02/MH/NIMH NIH HHS/United States ; R01 DA010715-04S1/DA/NIDA NIH HHS/United States ; R01 MH061798-05/MH/NIMH NIH HHS/United States ; R01 DA010715-03/DA/NIDA NIH HHS/United States ; R01 MH061798-04/MH/NIMH NIH HHS/United States ; R01 MH072616-01A2S1/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Aptitude ; *Association Learning ; Attention ; Color Perception ; *Columbidae ; *Concept Formation ; Discrimination Learning ; *Mental Recall ; *Pattern Recognition, Visual ; Reaction Time ; *Transfer, Psychology ; }, abstract = {Three groups of pigeons were trained in a same/different task with 32, 64, or 1,024 color-picture stimuli. They were tested with novel transfer pictures. The training-testing cycle was repeated with training-set doublings. The 32-item group learned the same/different task as rapidly as a previous 8-item group and transferred better than the 8-item group at the 32-item training set. The 64- and 1,024-item groups learned the task only somewhat slower than other groups, but their transfer was better and equivalent to baseline performances. These results show that pigeons trained with small sets (e.g., 8 items) have carryover effects that hamper transfer when the training set is expanded. Without carryover effects (i.e., initial transfer from the 32- and 64-item groups), pigeons show the same degree of transfer as rhesus and capuchin monkeys at these same set sizes. This finding has implications for the general ability of abstract-concept learning across species with different neural architectures.}, } @article {pmid19221132, year = {2009}, author = {Gomez, L and Li, B and Mewton, N and Sanchez, I and Piot, C and Elbaz, M and Ovize, M}, title = {Inhibition of mitochondrial permeability transition pore opening: translation to patients.}, journal = {Cardiovascular research}, volume = {83}, number = {2}, pages = {226-233}, doi = {10.1093/cvr/cvp063}, pmid = {19221132}, issn = {1755-3245}, mesh = {*Angioplasty, Balloon, Coronary ; Animals ; Cardiotonic Agents/*therapeutic use ; Cyclosporine/*therapeutic use ; Humans ; Mitochondria, Heart/*drug effects/metabolism ; Mitochondrial Membrane Transport Proteins/*antagonists & inhibitors/metabolism ; Mitochondrial Permeability Transition Pore ; Myocardial Contraction/drug effects ; Myocardial Infarction/metabolism/pathology/physiopathology/*therapy ; Myocardial Reperfusion Injury/metabolism/pathology/physiopathology/*prevention & control ; Myocardium/*metabolism/pathology ; Time Factors ; Treatment Outcome ; }, abstract = {A large body of experimental evidence indicates that during an acute myocardial infarction (AMI), tissue injury occurring after reperfusion represents a significant amount of the whole, irreversible damage. It is now recognized that mitochondrial permeability transition pore opening plays a crucial role in this specific component of myocardial infarction. Ischaemic postconditioning and cyclosporine A (CsA) have been shown to dramatically reduce infarct size in many animal species. Recent proof-of-concept clinical trials support the idea that lethal myocardial reperfusion injury is also of significant importance in patients with ongoing AMI, and that targeting mitochondrial permeability transition by either percutaneous coronary intervention postconditioning or CsA can reduce infarct size and improve the recovery of contractile function after reperfusion. Large-scale trials are ongoing to address whether these new treatments may improve clinical outcome in reperfused AMI patients.}, } @article {pmid19220367, year = {2009}, author = {Bowkett, AE}, title = {Recent captive-breeding proposals and the return of the ark concept to global species conservation.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {23}, number = {3}, pages = {773-776}, doi = {10.1111/j.1523-1739.2008.01157.x}, pmid = {19220367}, issn = {1523-1739}, mesh = {Animals ; Animals, Zoo/*physiology ; Breeding/*methods ; Conservation of Natural Resources/*methods/*trends ; *Endangered Species ; }, } @article {pmid19195395, year = {2008}, author = {Kim, GH and Han, HK and Lim, KJ}, title = {Taxonomic reappraisal of Antithamnion sparsum Tokida (Ceramiaceae, Rhodophyta).}, journal = {Journal of environmental biology}, volume = {29}, number = {4}, pages = {547-553}, pmid = {19195395}, issn = {0254-8704}, mesh = {Chromosomes/genetics ; DNA Primers/genetics ; DNA, Algal/genetics ; Genetic Markers ; Genetic Variation ; Korea ; Phylogeny ; Random Amplified Polymorphic DNA Technique ; Rhodophyta/*classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The taxonomic criterion of Antithamnion sparsum was reappraised in comparison with A. densum and A. defectum based on crossing experiments, morphological observation, chromosome study and Random Amplified Polymorphic DNA (RAPD) analysis. These species had a very similar morphology but were sexually isolated. The chromosome number was n = ca. 24 for A. densum, n = ca. 21 for A. defectum, and n = ca. 44 for A. sparsum. All isolates of A. sparsum and A. densum showed polysiphonia-type life history Asexual reproduction was induced by favorable environmental conditions. In A. sparsum, 1-2% of male plants developed mitotic tetrasporangia together with spermatangia. In A. densum, 5-10% of tetraspores developed into asexual tetrasporophytes. Phylogenetic relationships between these species were examined using RAPD analysis, and A. glanduliferum was used as an outgroup. A total of 167 polymorphic RAPD markers amplified from 15 different primers were analyzed. Results suggested that these species were closely related, with A. defectum placed in the middle of A. sparsum and A. densum. Chromosome study and RAPD analysis implied that A. sparsum first separated from A. defectum through polyploidization and later A. densum evolved. These species may present another example of the narrow species concept in the genus Antithamnion.}, } @article {pmid19182221, year = {2009}, author = {Jarvis, C and Cribb, P}, title = {Linnaean sources and concepts of orchids.}, journal = {Annals of botany}, volume = {104}, number = {3}, pages = {365-376}, doi = {10.1093/aob/mcp005}, pmid = {19182221}, issn = {1095-8290}, mesh = {Africa ; Americas ; Asia ; Europe ; History, 18th Century ; Orchidaceae/anatomy & histology/*classification ; Species Specificity ; Terminology as Topic ; }, abstract = {BACKGROUND: Linnaeus developed a robust system for naming plants and a useful, if mechanical, system for classifying them. His binomial nomenclature proved the catalyst for the rapid development of our knowledge of orchids, with his work on the family dating back to 1737 in the first edition of his Genera Plantarum. His first work devoted to orchids, indeed the first monograph of the family, was published in 1740 and formed the basis for his account in Species Plantarum, published in 1753, in which he gave a binomial name to each species. Given the overwhelming number of orchids, he included surprisingly few - only 62 mostly European species - in Species Plantarum, his seminal work on the plants of the world. This reflects the European origin of modern botany and the concentration of extra-European exploration on other matters, such as conquest, gold and useful plants. Nevertheless, the scope of Linnaeus' work is broad, including plants from as far afield as India, Japan, China and the Philippines to the east, and eastern Canada, the West Indies and northern South America to the west. In his later publications he described and named a further 45 orchids, mostly from Europe, South Africa and the tropical Americas.

SCOPE: The philosophical basis of Linnaeus' work on orchids is discussed and his contribution to our knowledge of the family assessed. His generic and species concepts are considered in the light of current systematic ideas, but his adoption of binomial nomenclature for all plants is his lasting legacy.}, } @article {pmid20525569, year = {2009}, author = {Baum, DA}, title = {Species as ranked taxa.}, journal = {Systematic biology}, volume = {58}, number = {1}, pages = {74-86}, doi = {10.1093/sysbio/syp011}, pmid = {20525569}, issn = {1076-836X}, mesh = {Animals ; *Classification ; Fossils ; Genetic Speciation ; Humans ; Hybridization, Genetic ; Phylogeny ; }, abstract = {Because species names play an important role in scientific communication, it is more important that species be understood to be taxa than that they be equated with functional ecological or evolutionary entities. Although most biologists would agree that taxa are composed of organisms that share a unique common history, 2 major challenges remain in developing a species-as-taxa concept. First, grouping: in the face of genealogical discordance at all levels in the taxonomic hierarchy, how can we understand the nature of taxa? Second, ranking: what criteria should be used to designate certain taxa in a nested series as being species? The grouping problem can be solved by viewing taxa as exclusive groups of organisms- sets of organisms that form a clade for a plurality of the genome (more than any conflicting set). However, no single objective criterion of species rank can be proposed. Instead, the species rank should be assigned by practitioners based on the semisubjective application of a set of species-ranking criteria. Although these criteria can be designed to yield species taxa that approximately match the ecological, evolutionary, and morphological entities that taxonomists have traditionally associated with the species rank, such a correspondence cannot be enforced without undermining the assumption that species are taxa. The challenge and art of monography is to use genealogical and other kinds of data to assign all organisms to one and only one species-ranked taxon. Various implications of the species-as-ranked-taxa view are discussed, including the synchronic nature of taxa, fossil species, the treatment of hybrids, and species nomenclature. I conclude that, although challenges remain, adopting the view that species are ranked taxa will facilitate a much-needed revolution in taxonomy that will allow it to better serve the biodiversity informatic needs of the 21st century.}, } @article {pmid19121213, year = {2009}, author = {Garnica, S and Weiss, M and Oertel, B and Ammirati, J and Oberwinkler, F}, title = {Phylogenetic relationships in Cortinarius, section Calochroi, inferred from nuclear DNA sequences.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {1}, pmid = {19121213}, issn = {1471-2148}, mesh = {Cell Nucleus/genetics ; Central America ; Cortinarius/classification/*genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Europe ; Evolution, Molecular ; North America ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Section Calochroi is one of the most species-rich lineages in the genus Cortinarius (Agaricales, Basidiomycota) and is widely distributed across boreo-nemoral areas, with some extensions into meridional zones. Previous phylogenetic studies of Calochroi (incl. section Fulvi) have been geographically restricted; therefore, phylogenetic and biogeographic relationships within this lineage at a global scale have been largely unknown. In this study, we obtained DNA sequences from a nearly complete taxon sampling of known species from Europe, Central America and North America. We inferred intra- and interspecific phylogenetic relationships as well as major morphological evolutionary trends within section Calochroi based on 576 ITS sequences, 230 ITS + 5.8S + D1/D2 sequences, and a combined dataset of ITS + 5.8S + D1/D2 and RPB1 sequences of a representative subsampling of 58 species.

RESULTS: More than 100 species were identified by integrating DNA sequences with morphological, macrochemical and ecological data. Cortinarius section Calochroi was consistently resolved with high branch support into at least seven major lineages: Calochroi, Caroviolacei, Dibaphi, Elegantiores, Napi, Pseudoglaucopodes and Splendentes; whereas Rufoolivacei and Sulfurini appeared polyphyletic. A close relationship between Dibaphi, Elegantiores, Napi and Splendentes was consistently supported. Combinations of specific morphological, pigmentation and molecular characters appear useful in circumscribing clades.

CONCLUSION: Our analyses demonstrate that Calochroi is an exclusively northern hemispheric lineage, where species follow their host trees throughout their natural ranges within and across continents. Results of this study contribute substantially to defining European species in this group and will help to either identify or to name new species occurring across the northern hemisphere. Major groupings are in partial agreement with earlier morphology-based and molecular phylogenetic hypotheses, but some relationships were unexpected, based on external morphology. In such cases, their true affinities appear to have been obscured by the repeated appearance of similar features among distantly related species. Therefore, further taxonomic studies are needed to evaluate the consistency of species concepts and interpretations of morphological features in a more global context. Reconstruction of ancestral states yielded two major evolutionary trends within section Calochroi: (1) the development of bright pigments evolved independently multiple times, and (2) the evolution of abruptly marginate to flattened stipe bulbs represents an autapomorphy of the Calochroi clade.}, } @article {pmid21032942, year = {2009}, author = {Galera, A}, title = {[Lamarck and the adaptive conservation of life].}, journal = {Asclepio; archivo iberoamericano de historia de la medicina y antropologia medica}, volume = {61}, number = {2}, pages = {129-140}, doi = {10.3989/asclepio.2009.v61.i2.287}, pmid = {21032942}, issn = {0210-4466}, mesh = {*Beginning of Human Life ; *Biological Evolution ; Classification ; History, 19th Century ; History, 20th Century ; *Natural History/education/history ; *Origin of Life ; Quality of Life/psychology ; Religion and Science ; }, abstract = {This paper studies Lamarck's evolutionary thought through four analytic elements. Firstly, Lamarckian construction of a founding evolutionary archetype. Secondly, the interpretation of nature as a material system where the organic change represents a continuous process aimed at the adaptative conservation of life. Thirdly, the definition of a genealogical process on the origin of species which identifies the natural method. Fourthly, the redefinition of the concept of species applying the arguments of temporary relativity and individual instability.}, } @article {pmid19101057, year = {2009}, author = {Pannell, JR and Pujol, B}, title = {The paradoxical spread of a new Y chromosome - a novel explanation.}, journal = {Trends in ecology & evolution}, volume = {24}, number = {2}, pages = {59-63}, doi = {10.1016/j.tree.2008.09.013}, pmid = {19101057}, issn = {0169-5347}, mesh = {Animals ; *Evolution, Molecular ; Female ; Hybridization, Genetic ; Male ; Sex Chromosomes/physiology ; *Sex Determination Processes ; Sexual Behavior, Animal ; Y Chromosome/*physiology ; }, abstract = {Hybrid zones provide one of the more prickly challenges to the cherished biological species concept, which is based on reproductive isolation between species, because some hybrid zones occur in areas where recognised species come together and mate to produce viable progeny. By contrast, hybrid zones have repeatedly provided outstanding material for the study of evolution: they allow us to study ecological and genomic differences between recently diverged taxa; and they bring into sharp focus the interplay between migration, selection, recombination and drift. A new theoretical analysis now demonstrates that hybrid-zone dynamics provide a counterintuitive explanation for how a new chromosomal sex-determination system can evolve and spread across the landscape, displacing the ancestral system, even though it would be eliminated by natural selection in a single isolated population. This work thus provides a provocative resolution to a conundrum that has puzzled cytogeneticists and evolutionary biologists for years.}, } @article {pmid19049869, year = {2009}, author = {Irinyi, L and Kövics, GJ and Sándor, E}, title = {Taxonomical re-evaluation of Phoma-like soybean pathogenic fungi.}, journal = {Mycological research}, volume = {113}, number = {Pt 2}, pages = {249-260}, doi = {10.1016/j.mycres.2008.11.003}, pmid = {19049869}, issn = {0953-7562}, mesh = {Ascomycota/*genetics ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Evolution, Molecular ; Fungal Proteins/genetics ; Genes, Fungal ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Soybeans/*microbiology ; Species Specificity ; Tubulin/genetics ; }, abstract = {Coelomycetous fungi classified in Ascochyta, Phoma, and Phyllosticta have been recorded from spots on leaves and pods of soybeans. Based on the Genealogical Concordance Phylogenetic Species Concept, the authors suggest the re-evaluation of the taxonomic status of Phoma sojicola (syn.=Ascochyta sojicola) and Phyllosticta sojicola. In spite of the former delimitation of Phoma sojicola based on small differences in morphological features, it has proved to be identical to Phoma pinodella. Similarly, it was also confirmed that Phyllosticta sojicola was identical to Phoma exigua var. exigua. The authors supply tools for identification of Phoma-like fungi by combined conventional and molecular methods. Protein-encoding genes (tef1 and beta-tubulin) were successfully applied within the Phoma genus to infer phylogenetic relationships.}, } @article {pmid19040451, year = {2009}, author = {Jones, SE and McMahon, KD}, title = {Species-sorting may explain an apparent minimal effect of immigration on freshwater bacterial community dynamics.}, journal = {Environmental microbiology}, volume = {11}, number = {4}, pages = {905-913}, doi = {10.1111/j.1462-2920.2008.01814.x}, pmid = {19040451}, issn = {1462-2920}, mesh = {Bacteria/*classification/*isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Ecosystem ; Fresh Water/*microbiology ; Time Factors ; }, abstract = {Long distance atmospheric transport of bacterial cells is often implied as a driver of the apparent cosmopolitan distribution of bacterial taxa. Surprisingly, efforts to measure immigration in bacterial communities are rare. An 8-week time series of within-lake bacterial community composition and atmospheric deposition rates and composition were used to estimate the influence of immigration on bacterial community dynamics in two north temperate lakes. Characterization of bacterial community dynamics using automated ribosomal intergenic spacer analysis suggested moderate overlap in composition between the lakes and atmospherically deposited cells. However, taxa that appeared to be delivered by atmospheric deposition had a relatively minor influence on lake bacterial community dynamics. The weak influence of immigrating bacterial taxa suggests that a species-sorting concept best describes aquatic bacterial metacommunity dynamics.}, } @article {pmid19026972, year = {2008}, author = {Velasco, JD}, title = {Species concepts should not conflict with evolutionary history, but often do.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {39}, number = {4}, pages = {407-414}, doi = {10.1016/j.shpsc.2008.09.007}, pmid = {19026972}, issn = {1369-8486}, mesh = {*Biological Evolution ; *Classification ; *Genetic Speciation ; Models, Biological ; *Phylogeny ; Species Specificity ; }, abstract = {Many phylogenetic systematists have criticized the Biological Species Concept (BSC) because it distorts evolutionary history. While defences against this particular criticism have been attempted, I argue that these responses are unsuccessful. In addition, I argue that the source of this problem leads to previously unappreciated, and deeper, fatal objections. These objections to the BSC also straightforwardly apply to other species concepts that are not defined by genealogical history. What is missing from many previous discussions is the fact that the Tree of Life, which represents phylogenetic history, is independent of our choice of species concept. Some species concepts are consistent with species having unique positions on the Tree while others, including the BSC, are not. Since representing history is of primary importance in evolutionary biology, these problems lead to the conclusion that the BSC, along with many other species concepts, are unacceptable. If species are to be taxa used in phylogenetic inferences, we need a history-based species concept.}, } @article {pmid19023087, year = {2009}, author = {Catania, F and Wurmser, F and Potekhin, AA and Przybos, E and Lynch, M}, title = {Genetic diversity in the Paramecium aurelia species complex.}, journal = {Molecular biology and evolution}, volume = {26}, number = {2}, pages = {421-431}, pmid = {19023087}, issn = {1537-1719}, mesh = {Animals ; Cell Nucleus/genetics ; Evolution, Molecular ; Genetic Speciation ; *Genetic Variation ; Mitochondria/genetics ; Paramecium aurelia/classification/*genetics ; Phylogeny ; }, abstract = {Current understanding of the population genetics of free-living unicellular eukaryotes is limited, and the amount of genetic variability in these organisms is still a matter of debate. We characterized-reproductively and genetically-worldwide samples of multiple Paramecium species belonging to a cryptic species complex, Paramecium aurelia, whose species have been shown to be reproductively isolated. We found that levels of genetic diversity both in the nucleus and in the mitochondrion are substantial within groups of reproductively compatible P. aurelia strains but drop considerably when strains are partitioned according to their phylogenetic groupings. Our study reveals the existence of discrepancies between the mating behavior of a number of P. aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex.}, } @article {pmid19017061, year = {2008}, author = {Lahr, DJ and Bergmann, PJ and Lopes, SG}, title = {Taxonomic identity in microbial eukaryotes: a practical approach using the testate amoeba Centropyxis to resolve conflicts between old and new taxonomic descriptions.}, journal = {The Journal of eukaryotic microbiology}, volume = {55}, number = {5}, pages = {409-416}, doi = {10.1111/j.1550-7408.2008.00339.x}, pmid = {19017061}, issn = {1550-7408}, mesh = {Amoeba/*classification/isolation & purification/*ultrastructure ; Animals ; Biometry ; Brazil ; Fresh Water/*parasitology ; Microscopy, Electron, Scanning ; Rivers ; }, abstract = {The present work focuses on 12 taxa of the genus Centropyxis Stein, 1857 to explore the conflict between traditional and contemporary taxonomic practices. We examined the morphology, biometry, and ecology of 2,120 Centropyxis individuals collected from Tiete River, Sao Paulo, Brazil; with these new data we studied the consistency of previously described species, varieties, and forms. We encountered transitional forms of test morphology that undermine specific and varietal distinctions for three species and nine varieties. Biometrical analyses made comparing the organisms at the species level suggest a lack of separation between Centropyxis aculeata and Centropyxis discoides, and a possible distinction for Centropyxis ecornis based on spine characteristics. However, incongruence between recent and previous surveys makes taking any taxonomic-nomenclatural actions inadvisable, as they would only add to the confusion. We suggest an explicit and objective taxonomic practice in order to enhance our taxonomic and species concepts for microbial eukaryotes. This will allow more precise inferences of taxon identity for studies in other areas.}, } @article {pmid19004631, year = {2009}, author = {Gómez-Vallejo, V and Llop, J}, title = {Specific activity of [11C]CH3I synthesized by the "wet" method: main sources of non-radioactive carbon.}, journal = {Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine}, volume = {67}, number = {1}, pages = {111-114}, doi = {10.1016/j.apradiso.2008.09.012}, pmid = {19004631}, issn = {1872-9800}, mesh = {Carbon/*chemistry ; Carbon Dioxide ; Hydrocarbons, Iodinated/*chemical synthesis ; Isotope Labeling/*methods ; Methods ; Methylation ; Positron-Emission Tomography/methods ; Radioactivity ; }, abstract = {Positron emission tomography (PET) is a powerful molecular imaging technique based on the administration and detection of radioactive (positron emitting) species. In some applications, the concept of specific activity becomes especially important in order to prevent undesired pharmacological and/or toxic effects after injection of the radiotracer. Problems to obtain high specific activities are found when (11)C-labeled compounds are prepared by methylation following the so called "wet" method, which consists of a simple route but usually yields radiotracers highly diluted with the stable specie. In the present work, the main sources of contamination by stable carbon in the [(11)C]CH(3)I synthesis following the "wet" method have been analyzed and their individual contribution has been quantified. The results show that the most relevant contamination of CO(2) is generated during the bombardment process.}, } @article {pmid18978222, year = {2008}, author = {Packard, GC and Birchard, GF}, title = {Traditional allometric analysis fails to provide a valid predictive model for mammalian metabolic rates.}, journal = {The Journal of experimental biology}, volume = {211}, number = {Pt 22}, pages = {3581-3587}, doi = {10.1242/jeb.023317}, pmid = {18978222}, issn = {0022-0949}, mesh = {Algorithms ; Animals ; *Basal Metabolism ; Body Size/physiology ; Body Weight/physiology ; Mammals/*physiology ; *Models, Biological ; }, abstract = {The field of biological allometry was energized by the publication in 1997 of a theoretical model purporting to explain 3/4-power scaling of metabolic rate with body mass in mammals. This 3/4-power scaling exponent, which was first reported by Max Kleiber in 1932, has been derived repeatedly in empirical research by independent investigators and has come to be known as 'Kleiber's Law'. The exponent was estimated in virtually every instance, however, by fitting a straight line to logarithmic transformations of data and by then re-expressing the resulting equation in the arithmetic scale. Because this traditional method may yield inaccurate and misleading estimates for parameters in the allometric equation, we re-examined the comprehensive data set that led Savage and colleagues to reaffirm the view that the metabolic rate of mammals scales to the 3/4-power of body mass. We found that a straight line fitted to logged data for the basal metabolic rate (BMR) of mammals ranging in size from a 2.4 g shrew to a 3672 kg elephant does not satisfy assumptions underlying the analysis and that the allometric equation obtained by back-transformation underestimates BMR for the largest species in the sample. Thus, the concept of 3/4-power scaling of metabolic rate to body mass is not well supported because the underlying statistical model does not apply to mammalian species spanning the full range in body size. Our findings have important implications with respect to methods and results of other studies that used the traditional approach to allometric analysis.}, } @article {pmid18977366, year = {2009}, author = {Ju, S and DeAngelis, DL}, title = {The R* rule and energy flux in a plant-nutrient ecosystem.}, journal = {Journal of theoretical biology}, volume = {256}, number = {3}, pages = {326-332}, doi = {10.1016/j.jtbi.2008.10.002}, pmid = {18977366}, issn = {1095-8541}, mesh = {Carbon/metabolism ; *Ecosystem ; Energy Metabolism ; Food ; Models, Biological ; *Plant Development ; Plants/metabolism ; Soil ; Species Specificity ; }, abstract = {The R* rule predicts that the species that can survive in steady state at the lowest level of limiting resource, R*, excludes all other species. Simple models indicate that this concept is not necessarily consistent with Lotka's conjecture that an ecological system should evolve towards a state of maximum power, Max(G), where G is the power, or rate of biomass production of the system. To explore the relationship in detail, we used a published model of a plant-nutrient system in which a plant can use various strategies, S, of allocation of energy between foliage, roots, and wood. We found that the allocation strategy, S(MinR*), that leads to Min(N(pore*), where N(pore*) is a limiting nutrient in soil pore water in our model (and equivalent to R* in Tilman's notation), is the same as the strategy, S(MaxG_root), for which energy flux to roots is maximized. However, that allocation strategy is different from the strategy, S(MaxG), that produces maximum power, or maximum photosynthetic rate, for the plant system, Max(G). Hence, we conclude that Min(N(pore*) and Max(G) should not necessarily co-occur in an ecological system. We also examined which strategy, S(fit), was fittest; that is, eliminated any other strategies, when allowed to compete. The strategy S(fit) differed from S(MinR*, S(MaxG), and S(MaxG_root), which we demonstrated mathematically. We also considered the feasible situation in which a plant is able to positively influence external nutrient input to the system. Under such conditions, the strategy, S(MaxG_root), that maximizes energy flux to roots was the same as the strategy, S(MaxR*, that leads to maximum concentration of available nutrient in soil pore water, Max(N pore*), and not same as S(MinR*, for Min(N pore*).}, } @article {pmid18948119, year = {2009}, author = {González-Forero, M}, title = {Removing ambiguity from the biological species concept.}, journal = {Journal of theoretical biology}, volume = {256}, number = {1}, pages = {76-80}, doi = {10.1016/j.jtbi.2008.09.016}, pmid = {18948119}, issn = {1095-8541}, mesh = {Animals ; Biodiversity ; *Genetic Speciation ; Humans ; Models, Biological ; *Phylogeny ; Reproduction/physiology ; Species Specificity ; }, abstract = {The biological species concept (BSC) is a common way to define species although it is ambiguous even when strictly applied. I interpret it here syntactically in four different ways and show that one of them is more suitable than previously thought. The first interpretation (fully restricted) produces discrete, non-overlapping biological species with the inconvenience of being inapplicable when there is gradual evolution of reproductive isolation. The second (cohesion relaxed) and fourth (fully relaxed) interpretation are overly unrestricted to be useful. The third interpretation (isolation relaxed) overcomes the problem of gradual evolution of reproductive isolation at the cost of recognizing non-discrete, overlapping biological species. That is, some populations are members of more than one species. Non-discreteness, however, removes hand-waving in infamous difficulties of the BSC such as those with ring species, phyletic species, and syngameons. Moreover, it lets the BSC deal with introgression with no appeal to subjectivity. Therefore, precision in terms underlying the BSC provides an objective and still natural alternative to deal with gradual evolution of reproductive isolation.}, } @article {pmid18944917, year = {1998}, author = {Fawe, A and Abou-Zaid, M and Menzies, JG and Bélanger, RR}, title = {Silicon-mediated accumulation of flavonoid phytoalexins in cucumber.}, journal = {Phytopathology}, volume = {88}, number = {5}, pages = {396-401}, doi = {10.1094/PHYTO.1998.88.5.396}, pmid = {18944917}, issn = {0031-949X}, abstract = {The controversial role of silicon in plant disease resistance, described mostly as a passive mechanical protection, has been addressed. Conclusive evidence is presented that silicon is involved in the increased resistance of cucumber to powdery mildew by enhancing the antifungal activity of infected leaves. This antifungal activity was attributable to the presence of low-molecular-weight metabolites. One of these metabolites, described here as a phytoalexin, was identified as a flavonol aglycone rhamnetin (3,5,3',4'-tetrahydroxy-7-O-methoxyflavone). This is the first report of a phytoalexin for this chemical group in the plant kingdom and of a flavonol phytoalexin in cucumber, a chemical defense long believed to be nonexistent in the family Cucurbitaceae. The antifungal activity of leaf extracts was better expressed after acid hydrolysis, extending to another plant species the concept that some phytoalexins are synthesized as glycosylated phytoalexins or their precursors.}, } @article {pmid18944443, year = {2006}, author = {Giraud, T and Villaréal, LM and Austerlitz, F and Le Gac, M and Lavigne, C}, title = {Importance of the life cycle in sympatric host race formation and speciation of pathogens.}, journal = {Phytopathology}, volume = {96}, number = {3}, pages = {280-287}, doi = {10.1094/PHYTO-96-0280}, pmid = {18944443}, issn = {0031-949X}, abstract = {Numerous morphological species of pathogenic fungi have been shown to actually encompass several genetically isolated lineages, often specialized on different hosts and, thus, constituting host races or sibling species. In this article, we explore theoretically the importance of some aspects of the life cycle on the conditions of sympatric divergence of host races, particularly in fungal plant pathogens. Because the life cycles classically modeled by theoreticians of sympatric speciation correspond to those of free-living animals, sympatric divergence of host races requires the evolution of active assortative mating or of active host preference if mating takes place on the hosts. With some particular life cycles with restricted dispersal between selection on the host and mating, we show that divergence can occur in sympatry and lead to host race formation, or even speciation, by a mere process of specialization, with strong divergent adaptive selection. Neither active assortative mating nor active habitat choice is required in these cases, and this may explain why the phylo-genetic species concept seems more appropriate than the biological species concept in these organisms.}, } @article {pmid18943925, year = {2006}, author = {Samuels, GJ}, title = {Trichoderma: systematics, the sexual state, and ecology.}, journal = {Phytopathology}, volume = {96}, number = {2}, pages = {195-206}, doi = {10.1094/PHYTO-96-0195}, pmid = {18943925}, issn = {0031-949X}, abstract = {A chronology is presented that charts the development of a genus and species concept in Trichoderma. Eighty-nine species of Trichoderma have been named, and several species of Hypocrea have been linked to unnamed Trichoderma anamorphs. Eighty-three taxa of Trichoderma and their teleomorphs, Hypocrea spp., have been included in phylogenetic analyses, including 11 species of Hypocrea with unnamed Trichoderma anamorphs. Phylogenetic analyses show that Trichoderma and Hypocrea are congeneric. Trichoderma species not linked to Hypocrea teleomorphs are derived from among species that are linked to teleomorphs, indicating sexual and asexual lineages are not independent of each other. Many more species remain to be discovered and described. Molecular phylogenetic analyses have revealed the existence of more species than have been recognized on the basis of morphology alone. A suggestion is made to modify the International Code of Botanical Nomenclature to enable adoption of a single generic name for Trichoderma/Hypocrea, with Trichoderma being the older and more utilitarian name. As increasing numbers of species are studied, the few morphological characters of anamorph and teleomorph have reached their limit for defining species. DNA-based characters have assumed an indispensable role. Exploration of new niches, such as within tree trunks and new geographic locations, have resulted in a substantial increase in the number of species of Trichoderma. Trichoderma is usually considered a genus of free-living soil fungi but evidence suggests that Trichoderma species may be opportunistic, avirulent plant symbionts as well as parasites of other fungi. Members of the genus Trichoderma are universally present in soils, although individual species may be either cosmopolitan (e.g., T. harzianum) or limited (e.g., T. viride) in their geographic distribution. To facilitate identification of species, a list of correctly identified strains of Trichoderma and their GenBank numbers for sequences of translation-elongation factor EF-1alpha and internal transcribed spacer rDNA is provided.}, } @article {pmid18943689, year = {2007}, author = {Liu, B and Wasilwa, LA and Morelock, TE and O'Neill, NR and Correll, JC}, title = {Comparison of Colletotrichum orbiculare and Several Allied Colletotrichum spp. for mtDNA RFLPs, Intron RFLP and Sequence Variation, Vegetative Compatibility, and Host Specificity.}, journal = {Phytopathology}, volume = {97}, number = {10}, pages = {1305-1314}, doi = {10.1094/PHYTO-97-10-1305}, pmid = {18943689}, issn = {0031-949X}, abstract = {Based on spore morphology, appressorium development, sequence similarities of the rDNA, and similarities in amplified restriction fragment length polymorphism (AFLP), it has been proposed that Colletotrichum orbiculare, C. trifolii, C. lindemuthianum, and C. malvarum represent a single phylogenetic species, C. orbiculare. In the current study, the phylogenetic relationship among isolates in the C. orbiculare species complex was reassessed. In all, 72 isolates of C. orbiculare from cultivated cucurbit or weed hosts, C. trifolii from alfalfa, C. lindemuthianum from green bean, and C. malvarum from prickly sida (Sida spinosa) were examined for mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs), RFLPs and sequence variation of a 900-bp intron of the glutamine synthetase gene and a 200-bp intron of the glyceraldehyde-3-phosphate dehydrogenase gene, and vegetative compatibility. In addition, host specificity was examined in foliar inoculations on cucurbit, bean, and alfalfa hosts. Inoculations also were conducted on cucumber fruit. Genetically distinct isolates, based on vegetative compatibility, within the species complex (C. orbiculare, C. trifolii, and C. malvarum) had an identical mtDNA haplotype (haplotype A) when examined with each of three different restriction enzymes. Isolates of C. lindemuthianum had a very similar mtDNA haplotype to haplotype A, with a single polymorphism detected with the enzyme HaeIII. The four species represent a phylogenetically closely related group based on a statistical analysis of the 900- and 200-bp intron sequences. However, distinct RFLPs in the 900-bp intron were consistently associated with each species and could be used to qualitatively and quantitatively distinguish each species. Furthermore, each of the species showed distinct host specificity, with isolates of C. orbiculare (from cucurbits), C. lindemuthianum, and C. trifolii being pathogenic only on cucurbits, green bean, and alfalfa, respectively. Consequently, distinct and fixed nucleotide, or genotypic (intron sequences and RFLPs) and phenotypic (host specificity) characteristics can be used to distinguish C. orbiculare, C. lindemuthianum, and C. trifolii from one another; therefore, they should be recognized as distinct species. This species delineation is consistent with the most current species concepts in fungi. More isolates and further characterization is needed to determine whether C. orbiculare from cocklebur and C. malvarum represent distinct species. RFLPs of the 900-bp intron may represent a relatively inexpensive, reliable, and useful diagnostic tool for general species differentiation in the genus Colletotrichum.}, } @article {pmid18943418, year = {2006}, author = {Rolshausen, PE and Mahoney, NE and Molyneux, RJ and Gubler, WD}, title = {A Reassessment of the Species Concept in Eutypa lata, the Causal Agent of Eutypa Dieback of Grapevine.}, journal = {Phytopathology}, volume = {96}, number = {4}, pages = {369-377}, doi = {10.1094/PHYTO-96-0369}, pmid = {18943418}, issn = {0031-949X}, abstract = {Eutypa dieback is a vascular disease of several cultivated crops and trees worldwide. The attribution of the name to the agent responsible for branch dieback is ambiguous. Pathogenicity of Eutypa sp. first was reported on apricot and the causal agent was named E. armeniacae. However, no morphological differences were reported with the previously described E. lata, and some authors considered both species synonymous. Others regarded them as distinct species on the basis of pathogenesis and molecular analysis. We further investigated the relatedness of both species by phylogenetic analyses of the internal transcribed spacer region and beta-tubulin gene. These analyses included several other taxa placed in the same family (Diatrypaceae), and yielded three groups. The isolates referred to as E. lata in previous work clustered with Diatrype stigma in one group. Isolates of E. armeniacae and E. lata clustered in a second group, supporting the synonymy of these species. The third group included other Eutypa spp. supporting the polyphyletic origin of this genus. Measurements of conidia length and secondary metabolite production of isolates supported the phylogenetic analyses. Secondary metabolites appeared to be a synapomorphic character shared by several taxa including E. lata, E. armeniacae, E. laevata, and E. petrakii var. petrakii.}, } @article {pmid18943299, year = {2005}, author = {Andersen, B and Hansen, ME and Smedsgaard, J}, title = {Automated and Unbiased Image Analyses as Tools in Phenotypic Classification of Small-Spored Alternaria spp.}, journal = {Phytopathology}, volume = {95}, number = {9}, pages = {1021-1029}, doi = {10.1094/PHYTO-95-1021}, pmid = {18943299}, issn = {0031-949X}, abstract = {For more than 25 years, controversy has surrounded the characterization and differentiation of small-spored Alternaria spp. And, therefore, the application of names of several species that are involved in the pathology of diseases related to host-specific toxin production. The name A. alternata often has been broadly applied to various morphologically and chemically distinct groups of isolates from different hosts. The purpose of this study was to develop and evaluate automated and unbiased image analysis systems that will analyze different phenotypic characters and facilitate testing and application of the morphological species concept in Alternaria taxonomy. Host-specific toxin-producing Alternaria isolates assigned to five morpho-species were compared with representative isolates of morphologically distinct A. alternata. Combined results of growth rates at different temperatures, colony morphology, and metabolite profiles were found to be useful in characterization and differentiation of small-spored Alternaria spp. when standardized conditions are applied and representative isolates employed for comparison.}, } @article {pmid18936442, year = {2009}, author = {Costechareyre, D and Bertolla, F and Nesme, X}, title = {Homologous recombination in Agrobacterium: potential implications for the genomic species concept in bacteria.}, journal = {Molecular biology and evolution}, volume = {26}, number = {1}, pages = {167-176}, doi = {10.1093/molbev/msn236}, pmid = {18936442}, issn = {1537-1719}, mesh = {Bacteria/classification/genetics ; *Genetic Speciation ; Genome, Bacterial ; *Recombination, Genetic ; Rhizobium/classification/*genetics ; }, abstract = {According to current taxonomical rules, a bona fide bacterial species is a genomic species characterized by the genomic similarity of its members. It has been proposed that the genomic cohesion of such clusters may be related to sexual isolation, which limits gene flow between too divergent bacteria. Homologous recombination is one of the most studied mechanisms responsible for this genetic isolation. Previous studies on several bacterial models showed that recombination frequencies decreased exponentially with increasing DNA sequence divergence. In the present study, we investigated this relationship in the Agrobacterium tumefaciens species complex, which allowed us to focus on sequence divergence in the vicinity of the genetic boundaries of genomic species. We observed that the sensitivity of the recombination frequency to DNA divergence fitted a log-linear function until approximately 10% sequence divergence. The results clearly revealed that there was no sharp drop in recombination frequencies at the point where the sequence divergence distribution showed a "gap" delineating genomic species. The ratio of the recombination frequency in homogamic conditions relative to this frequency in heterogamic conditions, that is, sexual isolation, was found to decrease from 8 between the most distant strains within a species to 9 between the most closely related species, for respective increases from 4.3% to 6.4% mismatches in the marker gene chvA. This means that there was only a 1.13-fold decrease in recombination frequencies for recombination events at both edges of the species border. Hence, from the findings of this investigation, we conclude that--at least in this taxon--sexual isolation based on homologous recombination is likely not high enough to strongly hamper gene flow between species as compared with gene flow between distantly related members of the same species. The 70% relative binding ratio cutoff used to define bacterial species is likely correlated to only minor declines in homologous recombination frequencies. Consequently, the sequence diversity, as a mechanistic factor for the efficiency of recombination (as assayed in the laboratory), appears to play little role in the genetic cohesion of bacterial species, and thus, the genomic species definition for prokaryotes is definitively not reconcilable with the biological species concept for eukaryotes.}, } @article {pmid18852109, year = {2008}, author = {Galtier, N and Daubin, V}, title = {Dealing with incongruence in phylogenomic analyses.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1512}, pages = {4023-4029}, pmid = {18852109}, issn = {1471-2970}, mesh = {Bacteria/*genetics ; Databases, Genetic ; Gene Transfer, Horizontal/*genetics ; Genomics/*methods ; *Phylogeny ; *Research Design ; }, abstract = {Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent.We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.}, } @article {pmid18849002, year = {2008}, author = {Cabanne, GS and d'Horta, FM and Sari, EH and Santos, FR and Miyaki, CY}, title = {Nuclear and mitochondrial phylogeography of the Atlantic forest endemic Xiphorhynchus fuscus (Aves: Dendrocolaptidae): biogeography and systematics implications.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {760-773}, doi = {10.1016/j.ympev.2008.09.013}, pmid = {18849002}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; Brazil ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Flow ; *Genes, Mitochondrial ; *Genetic Speciation ; Genetics, Population ; Geography ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; Passeriformes/classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {We studied the intraspecific evolutionary history of the South American Atlantic forest endemic Xiphorhynchusfuscus (Aves: Dendrocolaptidae) to address questions such as: Was the diversification of this bird's populations associated to areas of avian endemism? Which models of speciation (i.e., refuges, river as barriers or geotectonism) explain the diversification within X. fuscus? Does the genetic data support subspecies as independent evolutionary units (species)? We used mitochondrial (n=34) and nuclear (n=68) DNA sequences of X. fuscus to study temporal and spatial relationships within and between populations. We described four main monophyletic lineages that diverged during the Pleistocene. The subspecies taxonomy did not match all the evolutionary lineages; subspecies atlanticus was the only one that represented a monophyletic and isolated lineage. The distribution of these lineages coincided with some areas of endemism for passerines, suggesting that those areas could be regions of biotic differentiation. The ancestor of X. fuscus diverged approximately 3 million years ago from Amazonian taxa and the phylogeographic pattern suggested that X. fuscus radiated from northeastern Brazil. Neither the riverine nor the geotectonic vicariance models are supported as the primary cause for diversification of geographic lineages, but rainforest contractions and expansions (ecological vicariance) can explain most of the spatial divergence observed in this species. Finally, analyses of gene flow and divergence time estimates suggest that the endangered subspecies atlanticus (from northeastern Brazil) can be considered a full species under the general lineage species concept.}, } @article {pmid18833759, year = {2008}, author = {Piatek, M and Vánky, K and Mossebo, DC and Piatek, J}, title = {Doassansiopsis caldesiae sp. nov. and Doassansiopsis tomasii: two remarkable smut fungi from Cameroon.}, journal = {Mycologia}, volume = {100}, number = {4}, pages = {662-672}, doi = {10.3852/07-189r}, pmid = {18833759}, issn = {0027-5514}, mesh = {Africa, Western ; Alismataceae/*microbiology ; Basidiomycota/chemistry/classification/cytology/*isolation & purification ; Cameroon ; Plant Diseases/*microbiology ; Plant Leaves/microbiology ; Spores, Fungal/chemistry/cytology ; }, abstract = {Three recent collections of Doassansiopsis from western Cameroon are assessed taxonomically. Doassansiopsis caldesiae M. Piatek & Vánky is described as a new species from infected leaves of Caldesia reniformis (D. Don) Makino. Its diagnostic characters are flat, nonthickened sori with spore balls as blackish, slightly elevated dots, more or less globoid spores, conspicuous cortical sterile cells and parasitism on Caldesia reniformis of family Alismataceae. The species is compared to another Doassansiopsis species on host plants belonging to family Alismataceae. Doassansiopsis tomasii Vánky is described from two localities on Nymphaea nouchali Burm.f. var. caerulea (Savigny) Verdc. (Nymphaeaceae), which represents the first report of this smut from Cameroon and western Africa. Similarities between this species and Doassansiopsis nymphaeae (Syd. & P. Syd.) Thirum. and D. ticonis M. Piepenbr. are outlined and the global distribution of the three taxa is mapped. The species concept in the genus Doassansiopsis is discussed, and a key to all known species of the genus is provided.}, } @article {pmid18825916, year = {2008}, author = {Filippova, NA}, title = {[Characteristic features of the ranks genus and subgenus, and an intercalary rank "species complex" in ixodid ticks (Acari: Ixodidae)].}, journal = {Parazitologiia}, volume = {42}, number = {4}, pages = {249-263}, pmid = {18825916}, issn = {0031-1847}, mesh = {Animals ; Arachnid Vectors/*anatomy & histology/*classification/microbiology ; Borrelia burgdorferi/physiology ; Female ; Host-Pathogen Interactions ; Humans ; Ixodidae/*anatomy & histology/*classification/microbiology ; Male ; Species Specificity ; }, abstract = {The work was carries our from the standpoint of the morphological conception of species. Vast collections of the Zoological Institute of the Russian Academy of Science testify to the existence of hiatuses in both genera and subgenera of Palearctic ixodids at all active phases of their ontogenesis. The fact that the subgenera of Palearctic genera have been well studies is notes, and composition of the subgenera is presented. The question of a taxonomic intercalary rank "species complex" is considered in detail in the context of the coevolution between some complexes of closely related species of ixodid ticks and some closely related species (genospecies, strains) of pathogens. The question of the taxonomic rank "species complex" in ixodid ticks as a phyletic species association is postulated on the basis of comparative ontogenetic data. Nomenclature status of the intercalary association "species complex" is specified in conformity with the fourth edition of the International Code of Zoological Nomenclature. Species composition of most studied complexes is presented. Some variants of morphological differentiation between species complexes within subgenus are considered. Significance of the taxonomic concept "species complex" for zoological. parasitological, and medical aspects of the ixodid ticks study was evaluated. Prognostic significance of the rank "species complex" for the study of the relationships between ixodid ticks and pathogens is discussed.}, } @article {pmid18812395, year = {2009}, author = {Riaño-Pachón, DM and Nagel, A and Neigenfind, J and Wagner, R and Basekow, R and Weber, E and Mueller-Roeber, B and Diehl, S and Kersten, B}, title = {GabiPD: the GABI primary database--a plant integrative 'omics' database.}, journal = {Nucleic acids research}, volume = {37}, number = {Database issue}, pages = {D954-9}, pmid = {18812395}, issn = {1362-4962}, mesh = {*Databases, Genetic ; Gene Expression Profiling ; *Genes, Plant ; *Genome, Plant ; Metabolomics ; Plant Proteins/chemistry/*genetics/metabolism ; Plants/metabolism ; Proteomics ; Software ; Systems Integration ; }, abstract = {The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different 'omics' fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text-based retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.}, } @article {pmid18810265, year = {2008}, author = {Silverman, J}, title = {Sentience and sensation.}, journal = {Lab animal}, volume = {37}, number = {10}, pages = {465-467}, doi = {10.1038/laban1008-465}, pmid = {18810265}, issn = {0093-7355}, mesh = {Animal Experimentation/*standards ; Animal Welfare/*standards ; Animals ; Animals, Laboratory ; Bioethics ; Pain/*prevention & control ; Sensation/*physiology ; }, abstract = {When animals are used in a biomedical research activity that may result in more than mild or momentary pain or distress, humanity, federal regulations and common sense direct us to use the least sentient species that can fulfill the aims of the research. The use of a less-sentient species is in line with the concept of Replacement, one of the well-known 3Rs of laboratory animal use. But what is a less-sentient species? Is a chimpanzee less sentient than a human; is a dog less sentient than a chimpanzee; and is a mouse less sentient than a dog? Does 'less sentient' imply that a species is less able to experience pain, is less intelligent or has less self-awareness? This essay will explore some of the relationships between sentience, pain and vertebrate phylogeny.}, } @article {pmid18781832, year = {2008}, author = {Bertrand, D and Lajoie, M and El-Mabrouk, N}, title = {Inferring ancestral gene orders for a family of tandemly arrayed genes.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {15}, number = {8}, pages = {1063-1077}, doi = {10.1089/cmb.2008.0025}, pmid = {18781832}, issn = {1557-8666}, mesh = {*Algorithms ; Animals ; Evolution, Molecular ; Gene Duplication ; Genome ; Humans ; Mice ; *Models, Genetic ; *Multigene Family ; Opossums ; Phylogeny ; Rats ; Receptors, Odorant/genetics ; }, abstract = {Tandemly arrayed genes (TAG) constitute a large fraction of most genomes and play important biological roles. They evolve through unequal recombination, which places duplicated genes next to the original ones (tandem duplications). Many algorithms have been proposed to infer a tandem duplication history for a TAG cluster. However, the presence of different transcriptional orientations in many clusters highlights the fact that processes such as inversions also contribute to their evolution. Moreover, existing algorithms are restricted to the study of TAGs evolution in a single species (only paralogous genes are considered). To circumvent these limitations, we consider an evolutionary model for TAGs involving duplication, gene loss, inversion, and speciation events. A general framework to infer ancestral gene orders that minimize the number of inversions in the whole evolutionary history is presented. At the methodological level, this paper integrates three approaches to genome evolution: the duplication tree reconstruction, the gene tree/species tree reconciliation theory, and the concept of inversion median used in order-based phylogeny reconstruction. An application on a cluster of olfactory receptor genes in four mammals is presented.}, } @article {pmid18757077, year = {2008}, author = {Boekhold, AE}, title = {Ecological risk assessment in legislation on contaminated soil in The Netherlands.}, journal = {The Science of the total environment}, volume = {406}, number = {3}, pages = {518-522}, doi = {10.1016/j.scitotenv.2008.07.018}, pmid = {18757077}, issn = {0048-9697}, mesh = {*Ecology ; Netherlands ; Risk Assessment ; *Soil Pollutants ; }, abstract = {Recently the Dutch soil policy was revised including new rules for the relocation of contaminated soil and dredged soil material. With these rules, new methods for ecotoxicological risk assessment were implemented. One of the new methods is the assessment of the local toxic pressure of mixtures, also known as the ms-PAF- method, based on the Species Sensitivity Distribution concept. The ms-PAF method is applied for risk assessment of spreading of dredged soil material on adjacent land. Its application will possibly be extended to the derivation of local soil quality standards relevant in the context of soil relocation. The application of the local toxic pressure will probably increase the reuse of contaminated soil and dredged soil material and hence will reduce the amounts considered to be unfit for use. With this method, local ecological risk limits are derived using pore water concentrations and effects on water organisms. Pore water concentrations are subsequently transferred to total soil concentrations using empirical relationships. The methodology does not impose upper limits for total soil concentrations. In soils with a high sorption capacity, total soil concentrations that are considered to be acceptable may be several times higher than the current Dutch intervention values. The possible introduction of the ms-PAF method will open the door to local soil relocation with soils containing large amounts of (semi-permanently soil bound) contaminants. Since the ms-PAF method is not yet properly validated, the lack of evidence of ecological effects using models like the ms-PAF method cannot be regarded as an indication for the absence of effects in reality. The Dutch soil quality decree would gain environmental ambition when the ms-PAF method was combined with a realistic upper limit on total soil concentrations. This would prevent contamination of land by means of soil relocation.}, } @article {pmid21585938, year = {2008}, author = {Mommer, L and Wagemaker, CA and DE Kroon, H and Ouborg, NJ}, title = {Unravelling below-ground plant distributions: a real-time polymerase chain reaction method for quantifying species proportions in mixed root samples.}, journal = {Molecular ecology resources}, volume = {8}, number = {5}, pages = {947-953}, doi = {10.1111/j.1755-0998.2008.02130.x}, pmid = {21585938}, issn = {1755-098X}, abstract = {Knowledge on below-ground plant distributions is almost lacking to date, despite the fact that such information would be very valuable in understanding below-ground competition and species-specific interactions, processes that are expected to shape community structure. Methods available so far for below-ground species determination have drawbacks that we tried to challenge. Some methods make use of differences in the chemical composition between species, but this is highly variable upon environmental factors. DNA-based techniques - far less dependent on chemical composition - such as polymerase chain reaction on internal transcribed spacer (ITS) primers can so far only determine presence-absence of a species in a mixed root sample. Here, we present a quantitative DNA-based technique that allows investigation of relative species abundances in experimental mixed root samples. We used quantitative real-time polymerase chain reaction (PCR) on species-specific markers obtained from intersimple sequence repeat (ISSR) analyses in root samples. This molecular technique is novel in the field of root ecology and its development overcame three challenges: (i) determination of species-specific DNA fragments, (ii) development and optimization of the real time PCR protocol, (iii) designing a data treatment method based on a modified delta-delta-cycle threshold (CT) analysis. The method gained robustness from using relative DNA abundances in species mixtures rather than absolute concentration readings. This requires accurate multispecies reference series as a calibration. Test samples with different known biomass ratios of all species showed proof of concept of this method. The pro's and contra's of this method are discussed in the light of its contribution to advancing ecological research on below-ground plant-plant interactions.}, } @article {pmid18752470, year = {2009}, author = {Mantena, SK and Vaughn, DP and Andringa, KK and Eccleston, HB and King, AL and Abrams, GA and Doeller, JE and Kraus, DW and Darley-Usmar, VM and Bailey, SM}, title = {High fat diet induces dysregulation of hepatic oxygen gradients and mitochondrial function in vivo.}, journal = {The Biochemical journal}, volume = {417}, number = {1}, pages = {183-193}, pmid = {18752470}, issn = {1470-8728}, support = {AA13395/AA/NIAAA NIH HHS/United States ; AA15172/AA/NIAAA NIH HHS/United States ; DK56336/DK/NIDDK NIH HHS/United States ; DK73775/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Cell Respiration/drug effects ; Cytochrome P-450 CYP2E1/metabolism ; Dietary Fats/*administration & dosage ; Fatty Liver/etiology/*metabolism/pathology ; Hypoxia/metabolism ; Liver/drug effects/*metabolism/pathology ; Male ; Membrane Potential, Mitochondrial/drug effects ; Mice ; Mice, Inbred C57BL ; Mitochondria, Liver/drug effects/*metabolism/pathology ; Mitochondrial Proteins/metabolism ; Nitric Oxide/pharmacology ; Nitric Oxide Synthase Type II/metabolism ; Oxidative Stress/drug effects ; Tyrosine/analogs & derivatives/metabolism ; }, abstract = {NAFLD (non-alcoholic fatty liver disease), associated with obesity and the cardiometabolic syndrome, is an important medical problem affecting up to 20% of western populations. Evidence indicates that mitochondrial dysfunction plays a critical role in NAFLD initiation and progression to the more serious condition of NASH (non-alcoholic steatohepatitis). Herein we hypothesize that mitochondrial defects induced by exposure to a HFD (high fat diet) contribute to a hypoxic state in liver and this is associated with increased protein modification by RNS (reactive nitrogen species). To test this concept, C57BL/6 mice were pair-fed a control diet and HFD containing 35% and 71% total calories (1 cal approximately 4.184 J) from fat respectively, for 8 or 16 weeks and liver hypoxia, mitochondrial bioenergetics, NO (nitric oxide)-dependent control of respiration, and 3-NT (3-nitrotyrosine), a marker of protein modification by RNS, were examined. Feeding a HFD for 16 weeks induced NASH-like pathology accompanied by elevated triacylglycerols, increased CYP2E1 (cytochrome P450 2E1) and iNOS (inducible nitric oxide synthase) protein, and significantly enhanced hypoxia in the pericentral region of the liver. Mitochondria from the HFD group showed increased sensitivity to NO-dependent inhibition of respiration compared with controls. In addition, accumulation of 3-NT paralleled the hypoxia gradient in vivo and 3-NT levels were increased in mitochondrial proteins. Liver mitochondria from mice fed the HFD for 16 weeks exhibited depressed state 3 respiration, uncoupled respiration, cytochrome c oxidase activity, and mitochondrial membrane potential. These findings indicate that chronic exposure to a HFD negatively affects the bioenergetics of liver mitochondria and this probably contributes to hypoxic stress and deleterious NO-dependent modification of mitochondrial proteins.}, } @article {pmid18707495, year = {2002}, author = {Grant, BR and Grant, PR}, title = {Lack of premating isolation at the base of a phylogenetic tree.}, journal = {The American naturalist}, volume = {160}, number = {1}, pages = {1-19}, doi = {10.1086/339987}, pmid = {18707495}, issn = {1537-5323}, abstract = {Darwin's finches in the Galápagos archipelago are an unusual example of adaptive radiation in that the basal split separates two lineages of warbler finches (Certhidea olivacea and Certhidea fusca) believed until recently to be only one species. The large genetic difference between them contrasts with their similarity in plumage, size, shape, and courtship behavior. They differ in song, which is a key factor in premating isolation of other sympatric Darwin's finches. We conducted playback experiments to see whether members of the population of C. olivacea on Santa Cruz Island would respond to songs of C. fusca from two islands, Genovesa and Pinta, and songs of C. olivacea from another island (Isabela). Another set of experiments was performed, using the same playback tapes, with C. fusca on Genovesa. Some members of both populations responded to all playbacks; therefore, the hypothesis of complete premating isolation on the basis of song is rejected. Discrimination between songs of the two lineages was inconsistent. We conclude that premating barriers to interbreeding among the tested populations have not arisen in the 1.5-2.0 m.yr. of their geographical isolation on different islands. This contrasts with strong premating barriers between more recently derived sympatric species. Early learning of song associated with morphology is later used in mate recognition. This explains why sympatric species that are vocally and morphologically distinct yet genetically less differentiated than Certhidea do not interbreed, whereas the Certhidea lineages that are genetically well differentiated but vocally and morphologically similar have no apparent premating barrier. We discuss this unusual situation in terms of the forces that have produced similarities and differences in song, morphology, and ecology and their relevance to phylogenetic and biological species concepts. Neither principles nor details are unique to Darwin's finches, and we conclude by pointing out strong parallels with some continental birds.}, } @article {pmid18707233, year = {2001}, author = {Vos, CC and Verboom, J and Opdam, PF and Ter Braak, CJ}, title = {Toward ecologically scaled landscape indices.}, journal = {The American naturalist}, volume = {157}, number = {1}, pages = {24-41}, doi = {10.1086/317004}, pmid = {18707233}, issn = {1537-5323}, abstract = {Nature conservation is increasingly based on a landscape approach rather than a species approach. Landscape planning that includes nature conservation goals requires integrated ecological tools. However, species differ widely in their response to landscape change. We propose a framework of ecologically scaled landscape indices that takes into account this variation. Our approach is based on a combination of field studies of spatially structured populations (metapopulations) and model simulations in artificial landscapes. From these, we seek generalities in the relationship among species features, landscape indices, and metapopulation viability. The concept of ecological species profiles is used to group species according to characteristics that are important in metapopulations' response to landscape change: individual area requirements as the dominant characteristic of extinction risk in landscape patches and dispersal distance as the main determinant of the ability to colonize patches. The ecological profiles and landscape indices are then integrated into two ecologically scaled landscape indices (ESLI): average patch carrying capacity and average patch connectivity. The field data show that the fraction of occupied habitat patches is correlated with the two ESLI. To put the ESLI into a perspective of metapopulation persistence, we determine the viability for six ecological profiles at different degrees of habitat fragmentation using a metapopulation model and computer-generated landscapes. The model results show that the fraction of occupied patches is a good indicator for metapopulation viability. We discuss how ecological profiles, ESLI, and the viability threshold can be applied for landscape planning and design in nature conservation.}, } @article {pmid18675366, year = {2008}, author = {Denise, TS and Ali, F and Kutty, SN and Meier, R}, title = {The need for specifying species concepts: How many species of silvered langurs (Trachypithecus cristatus group) should be recognized?.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {688-689}, doi = {10.1016/j.ympev.2008.06.020}, pmid = {18675366}, issn = {1095-9513}, mesh = {Animals ; Cercopithecidae/*classification/*genetics ; Genetic Markers ; *Genetic Speciation ; Genetics, Population ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, } @article {pmid18667078, year = {2008}, author = {Multigner, L and Kadhel, P and Pascal, M and Huc-Terki, F and Kercret, H and Massart, C and Janky, E and Auger, J and Jégou, B}, title = {Parallel assessment of male reproductive function in workers and wild rats exposed to pesticides in banana plantations in Guadeloupe.}, journal = {Environmental health : a global access science source}, volume = {7}, number = {}, pages = {40}, pmid = {18667078}, issn = {1476-069X}, mesh = {Adult ; *Agriculture ; Animals ; Cross-Sectional Studies ; Environmental Exposure/adverse effects ; Environmental Monitoring/methods ; Genitalia, Male/*drug effects ; Guadeloupe ; Humans ; Male ; Middle Aged ; Occupational Exposure/adverse effects ; Pesticides/*poisoning ; Rats ; Reproduction/*drug effects ; Semen/*drug effects ; Testosterone/metabolism ; }, abstract = {BACKGROUND: There is increasing evidence that reproductive abnormalities are increasing in frequency in both human population and among wild fauna. This increase is probably related to exposure to toxic contaminants in the environment. The use of sentinel species to raise alarms relating to human reproductive health has been strongly recommended. However, no simultaneous studies at the same site have been carried out in recent decades to evaluate the utility of wild animals for monitoring human reproductive disorders. We carried out a joint study in Guadeloupe assessing the reproductive function of workers exposed to pesticides in banana plantations and of male wild rats living in these plantations.

METHODS: A cross-sectional study was performed to assess semen quality and reproductive hormones in banana workers and in men working in non-agricultural sectors. These reproductive parameters were also assessed in wild rats captured in the plantations and were compared with those in rats from areas not directly polluted by humans.

RESULTS: No significant difference in sperm characteristics and/or hormones was found between workers exposed and not exposed to pesticide. By contrast, rats captured in the banana plantations had lower testosterone levels and gonadosomatic indices than control rats.

CONCLUSION: Wild rats seem to be more sensitive than humans to the effects of pesticide exposure on reproductive health. We conclude that the concept of sentinel species must be carefully validated as the actual nature of exposure may varies between human and wild species as well as the vulnerable time period of exposure and various ecological factors.}, } @article {pmid18664418, year = {2008}, author = {Morin, X and Lechowicz, MJ}, title = {Contemporary perspectives on the niche that can improve models of species range shifts under climate change.}, journal = {Biology letters}, volume = {4}, number = {5}, pages = {573-576}, pmid = {18664418}, issn = {1744-9561}, mesh = {*Ecosystem ; *Geography ; *Greenhouse Effect ; *Models, Biological ; }, abstract = {Pioneering efforts to predict shifts in species distribution under climate change used simple models based on the correlation between contemporary environmental factors and distributions. These models make predictions at coarse spatial scales and assume the constancy of present correlations between environment and distribution. Adaptive management of climate change impacts requires models that can make more robust predictions at finer spatio-temporal scales by accounting for processes that actually affect species distribution on heterogeneous landscapes. Mechanistic models of the distribution of both species and vegetation types have begun to emerge to meet these needs. We review these developments and highlight how recent advances in our understanding of relationships among the niche concept, species diversity and community assembly point the way towards more effective models for the impacts of global change on species distribution and community diversity.}, } @article {pmid18638390, year = {2008}, author = {Jungblut, PR and Holzhütter, HG and Apweiler, R and Schlüter, H}, title = {The speciation of the proteome.}, journal = {Chemistry Central journal}, volume = {2}, number = {}, pages = {16}, pmid = {18638390}, issn = {1752-153X}, abstract = {INTRODUCTION: In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function.

DISCUSSION: Optimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function.

CONCLUSION: To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today.}, } @article {pmid18612652, year = {2008}, author = {Clauss, M and Hofmann, RR and Streich, WJ and Fickel, J and Hummel, J}, title = {Higher masseter muscle mass in grazing than in browsing ruminants.}, journal = {Oecologia}, volume = {157}, number = {3}, pages = {377-385}, pmid = {18612652}, issn = {0029-8549}, mesh = {Animals ; Body Weight ; Diet/veterinary ; Feeding Behavior/*physiology ; Female ; Male ; Masseter Muscle/*anatomy & histology ; Phylogeny ; Poaceae/metabolism ; Regression Analysis ; Ruminants/*anatomy & histology/*physiology ; }, abstract = {Using cranioskeletal measurements, several studies have generated evidence that grazing ruminants have a more pronounced mastication apparatus, in terms of muscle insertion areas and protuberances, than browsing ruminants, with the resulting hypothesis that grazers should have larger, heavier chewing muscles than browsers. However, the only investigation of this so far [Axmacher and Hofmann (J Zool 215:463-473, 1988)] did not find differences between ruminant feeding types in the masseter muscle mass of 22 species. Here, we expand the dataset to 48 ruminant species. Regardless of phylogenetic control in the statistical treatment, there was a significant positive correlation of body mass and masseter mass, and also a significant association between percent grass in the natural diet and masseter mass. The results support the concept that ruminant species that ingest more grass have relatively larger masseter muscles, possibly indicating an increased requirement to overcome the resistance of grass forage. The comparative chewing resistance of different forage classes may represent a rewarding field of ecophysiological research.}, } @article {pmid18586729, year = {2008}, author = {Schulz, S and Stenzhorn, H and Boeker, M}, title = {The ontology of biological taxa.}, journal = {Bioinformatics (Oxford, England)}, volume = {24}, number = {13}, pages = {i313-21}, pmid = {18586729}, issn = {1367-4811}, mesh = {*Algorithms ; Animals ; Classification/*methods ; Humans ; Information Storage and Retrieval/*methods ; *Software ; *Terminology as Topic ; }, abstract = {MOTIVATION: The classification of biological entities in terms of species and taxa is an important endeavor in biology. Although a large amount of statements encoded in current biomedical ontologies is taxon-dependent there is no obvious or standard way for introducing taxon information into an integrative ontology architecture, supposedly because of ongoing controversies about the ontological nature of species and taxa.

RESULTS: In this article, we discuss different approaches on how to represent biological taxa using existing standards for biomedical ontologies such as the description logic OWL DL and the Open Biomedical Ontologies Relation Ontology. We demonstrate how hidden ambiguities of the species concept can be dealt with and existing controversies can be overcome. A novel approach is to envisage taxon information as qualities that inhere in biological organisms, organism parts and populations.

AVAILABILITY: The presented methodology has been implemented in the domain top-level ontology BioTop, openly accessible at http://purl.org/biotop. BioTop may help to improve the logical and ontological rigor of biomedical ontologies and further provides a clear architectural principle to deal with biological taxa information.}, } @article {pmid18583278, year = {2008}, author = {Abbott, RJ and Ritchie, MG and Hollingsworth, PM}, title = {Introduction. Speciation in plants and animals: pattern and process.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1506}, pages = {2965-2969}, pmid = {18583278}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; Gene Flow/*genetics ; *Genetic Speciation ; Hybridization, Genetic/*genetics ; Plants/*genetics ; Reproduction/genetics ; Species Specificity ; }, abstract = {Although approximately 150 years have passed since the publication of On the origin of species by means of natural selection, the definition of what species are and the ways in which species originate remain contentious issues in evolutionary biology. The biological species concept, which defines species as groups of interbreeding natural populations that are reproductively isolated from other such groups, continues to draw support. However, there is a growing realization that many animal and plant species can hybridize with their close relatives and exchange genes without losing their identity. On occasion, such hybridization can lead to the origin of new species. A key to understanding what species are and the ways in which they originate rests to a large extent on a detailed knowledge of the nature and genetics of factors that limit gene flow between species and the conditions under which such isolation originates. The collection of papers in this issue addresses these topics and deals as well with some specific issues of hybrid speciation and the causes of species radiations. The papers included arise from a 1-day symposium on speciation held during the Sixth Biennial Meeting of the Systematics Association at Edinburgh in August 2007. In this introduction, we provide some background to these papers and highlight some key points made. The papers make clear that highly significant advances to our understanding of animal and plant speciation are currently being made across the range of this topic.}, } @article {pmid18576666, year = {2008}, author = {Yan, D and Yang, L and Wang, Q}, title = {Alternative thermodiffusion interface for simultaneous speciation of organic and inorganic lead and mercury species by capillary GC-ICPMS using tri-n-propyl-lead chloride as an internal standard.}, journal = {Analytical chemistry}, volume = {80}, number = {15}, pages = {6104-6109}, doi = {10.1021/ac800347j}, pmid = {18576666}, issn = {1520-6882}, abstract = {An alternative thermodiffusion interface (TDI) was designed and constructed for the effective online coupling of capillary gas chromatography (cGC) and inductively coupled plasma mass spectrometry (ICPMS). Pb(2+), (CH3)3Pb(+), (C2H5)3Pb(+), Hg(2+), CH3Hg(+) and C2H5Hg(+) were derived as Pb(C4H9)4, (CH3)3PbC4H9, (C2H5)3PbC4H9, (C4H9)2Hg, CH3HgC4H9, and C2H5HgC4H9 when butyl magnesium bromide was employed as a derivatization reagent for a proof-of-concept study, avoiding the loss of their species specific information. All these derivatives together with the neutral fully saturated (CH3)4Pb and (C2H5)4Pb could be quantitatively separated within 7 min using a 15 m long capillary column, allowing the determination and speciation of organic and inorganic Pb and Hg species in a single run. The method detection limits (3sigma) for Me4Pb, Et4Pb, Me3Pb(3+), Pb(2+), MeHg(+), EtHg(+), and Hg(2+) are 0.07, 0.06, 0.04, 7.0, 0.09, 0.1, and 0.2 pg g(-1), respectively. Moreover, tri-n-propyl-lead chloride was synthesized and used as an alternative internal standard for the accurate and simultaneous speciation analysis of Pb and Hg in complicated environmental and biological samples for the first time. This cGC-TDI-ICPMS method was validated by analyzing Pb and Hg species in certified reference materials and then was applied to simultaneous speciation analysis of Pb and Hg in real-life samples. It is expected that these approaches can be extended to the speciation of other organometallic compounds after suitable modifications and so will aid in monitoring the occurrence, pathways, toxicity, and/or biological effects of these compounds in the environment and in organisms.}, } @article {pmid18565802, year = {2008}, author = {Aliouat-Denis, CM and Chabé, M and Demanche, C and Aliouat, el M and Viscogliosi, E and Guillot, J and Delhaes, L and Dei-Cas, E}, title = {Pneumocystis species, co-evolution and pathogenic power.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {8}, number = {5}, pages = {708-726}, doi = {10.1016/j.meegid.2008.05.001}, pmid = {18565802}, issn = {1567-1348}, mesh = {Animals ; *Biological Evolution ; Ecosystem ; Host-Pathogen Interactions ; Humans ; Immunocompetence ; Life Cycle Stages ; Lung/microbiology ; Pneumocystis/*classification/genetics/growth & development/*pathogenicity ; Pneumocystis Infections/*microbiology/pathology/transmission ; Rabbits ; Species Specificity ; }, abstract = {The genus Pneumocystis comprises uncultured, highly diversified microfungal organisms able to attach specifically to type-I alveolar epithelial cells and to proliferate in pulmonary alveoli provoking severe pneumonitis. The pathogenic potential of Pneumocystis species, especially of the human-associated Pneumocystis jirovecii, has stimulated a growing interest in these peculiar microfungi. However, a comprehensive understanding of basic biology and pathogenic power of Pneumocystis organisms calls for their recognition as natural, complex entities, without reducing them to their pathogenic role. For many years, the entity named "Pneumocystis carinii" was considered like an anecdotal pulmonary pathogen able to cause pneumonia in immunosuppressed hosts. Only for the last years, marked genetic divergence was documented among the Pneumocystis strains of different mammals. Cross-infection experiments showed that Pneumocystis species are stenoxenous parasites. Mainly on the basis of the Phylogenetic Concept of Species, Pneumocystis strains were considered as genuine species. Five species were described: P. carinii and Pneumocystis wakefieldiae in rats, P. jirovecii in humans, Pneumocystis murina in mice, and Pneumocystis oryctolagi in rabbits. They also present distinctive phenotypic features. Molecular techniques have revealed a high prevalence of Pneumocystis colonization in wild mammals, probably resulting from active airborne horizontal and vertical (transplacental or aerial) transmission mechanisms. Cophylogeny is the evolutionary pattern for Pneumocystis species, which dwelt in the lungs of mammals for more than 100 million years. Consistently, Pneumocystis organisms exhibit successful adaptation to colonize the lungs of both immunocompromised and healthy hosts that can act as infection reservoir. Pneumocystis pneumonia, rarely reported in wild mammals, seems to be a rather unfrequent event. A larger spectrum of Pneumocystis infections related to the heterogeneous level of immune defence found in natural populations, is, however, expected. Pneumocystis infection of immunocompetent hosts emerges therefore as a relevant issue to human as well as animal health.}, } @article {pmid18558605, year = {2008}, author = {Deepinder, F and Cocuzza, M and Agarwal, A}, title = {Should seminal oxidative stress measurement be offered routinely to men presenting for infertility evaluation?.}, journal = {Endocrine practice : official journal of the American College of Endocrinology and the American Association of Clinical Endocrinologists}, volume = {14}, number = {4}, pages = {484-491}, doi = {10.4158/EP.14.4.484}, pmid = {18558605}, issn = {1934-2403}, mesh = {Antioxidants/therapeutic use ; Humans ; Infertility, Male/diagnosis/drug therapy/*metabolism ; Male ; *Oxidative Stress ; Reactive Oxygen Species/*metabolism ; Semen/drug effects/*metabolism ; }, abstract = {OBJECTIVE: To determine if seminal oxidative stress measurement should be offered routinely to men presenting for infertility evaluation.

METHODS: We performed an extensive review of the English-language literature by searching MEDLINE for studies published between 1980 and 2007.

RESULTS: Research conducted during the last decade has provided growing support for the concept that excessive production of reactive oxygen species (ROS) is related to abnormal semen parameters and sperm damage. Routine semen analysis remains the backbone of clinical evaluation in male infertility, but determining the levels and sources of excessive ROS generation in semen is currently not included in the routine evaluation of subfertile men. However, the diagnostic and prognostic capabilities of seminal oxidative stress measurement exceed the capabilities of conventional sperm quality tests. An oxidative stress test may accurately discriminate between fertile and infertile men and identify those with a clinical diagnosis of male factor infertility who are likely to initiate a pregnancy if they are followed over a period of time. In addition, such a test can help select subgroups of patients with infertility in which oxidative stress is an important factor and those who may benefit from antioxidant supplementation. Although consensus is still required about the type and dosage of antioxidants to be used, rationale and evidence exist supporting their use in infertile men with elevated oxidative stress.

CONCLUSION: Consensus is growing about the clinical utility of seminal oxidative stress testing in infertility clinics, but standardization of protocols to measure ROS is crucial before introducing these tests into routine clinical practice.}, } @article {pmid18557640, year = {2008}, author = {Alape-Girón, A and Sanz, L and Escolano, J and Flores-Díaz, M and Madrigal, M and Sasa, M and Calvete, JJ}, title = {Snake venomics of the lancehead pitviper Bothrops asper: geographic, individual, and ontogenetic variations.}, journal = {Journal of proteome research}, volume = {7}, number = {8}, pages = {3556-3571}, doi = {10.1021/pr800332p}, pmid = {18557640}, issn = {1535-3893}, mesh = {Amino Acid Sequence ; Animals ; Animals, Newborn ; *Bothrops ; Chromatography, High Pressure Liquid ; Costa Rica ; Crotalid Venoms/*analysis ; Electrophoresis, Polyacrylamide Gel ; Molecular Sequence Data ; Proteome/*analysis ; Species Specificity ; }, abstract = {We report the comparative proteomic characterization of the venoms of adult and newborn specimens of the lancehead pitviper Bothrops asper from two geographically isolated populations from the Caribbean and the Pacific versants of Costa Rica. The crude venoms were fractionated by reverse-phase HPLC, followed by analysis of each chromatographic fraction by SDS-PAGE, N-terminal sequencing, MALDI-TOF mass fingerprinting, and collision-induced dissociation tandem mass spectrometry of tryptic peptides. The two B. asper populations, separated since the late Miocene or early Pliocene (8-5 mya) by the Guanacaste Mountain Range, Central Mountain Range, and Talamanca Mountain Range, contain both identical and different (iso)enzymes from the PLA 2, serine proteinase, and SVMP families. Using a similarity coefficient, we estimate that the similarity of venom proteins between the two B. asper populations may be around 52%. Compositional differences between venoms among different geographic regions may be due to evolutionary environmental pressure acting on isolated populations. To investigate venom variability among specimens from the two B. asper populations, the reverse-phase HPLC protein profiles of 15 venoms from Caribbean specimens and 11 venoms from snakes from Pacific regions were compared. Within each B. asper geographic populations, all major venom protein families appeared to be subjected to individual variations. The occurrence of intraspecific individual allopatric variability highlights the concept that a species, B. asper in our case, should be considered as a group of metapopulations. Analysis of pooled venoms of neonate specimens from Caribbean and Pacific regions with those of adult snakes from the same geographical habitat revealed prominent ontogenetic changes in both geographical populations. Major ontogenetic changes appear to be a shift from a PIII-SVMP-rich to a PI-SVMP-rich venom and the secretion in adults of a distinct set of PLA 2 molecules than in the neonates. In addition, the ontogenetic venom composition shift results in increasing venom complexity, indicating that the requirement for the venom to immobilize prey and initiate digestion may change with the size (age) of the snake. Besides ecological and taxonomical implications, the geographical venom variability reported here may have an impact in the treatment of bite victims and in the selection of specimens for antivenom production. The occurrence of intraspecies variability in the biochemical composition and symptomatology after envenomation by snakes from different geographical location and age has long been appreciated by herpetologist and toxinologists, though detailed comparative proteomic analysis are scarce. Our study represents the first detailed characterization of individual and ontogenetic venom protein profile variations in two geographical isolated B. asper populations, and highlights the necessity of using pooled venoms as a statistically representative venom for antivenom production.}, } @article {pmid18555737, year = {2008}, author = {Northoff, G and Panksepp, J}, title = {The trans-species concept of self and the subcortical-cortical midline system.}, journal = {Trends in cognitive sciences}, volume = {12}, number = {7}, pages = {259-264}, doi = {10.1016/j.tics.2008.04.007}, pmid = {18555737}, issn = {1364-6613}, mesh = {Animals ; Awareness/physiology ; Cerebral Cortex/*physiology ; Concept Formation/*physiology ; Consciousness/*physiology ; Humans ; Mammals ; Motivation ; Nerve Net/*physiology ; Orientation/*physiology ; Species Specificity ; }, abstract = {The nature of the self has been one of the central problems in philosophy and most recently in neuroscience. Here, we suggest that animals and humans share a 'core self' represented in homologous underlying neural networks. We argue that the core self might be constituted by an integrative neuronal mechanism that enables self-related processing (SRP). Because mammalian organisms are capable of relating bodily states, intrinsic brain states (e.g. basic attentional, emotional and motivational systems) and environmental stimuli to various life-supporting goal-orientations, SRP appears to be a core ability preserved across numerous species. Recent data suggest that SRP is operating via a central integrative neural system made up of subcortical-cortical midline structures (SCMSs), that are homologous across mammalian species.}, } @article {pmid18500746, year = {2008}, author = {Matthews, LJ and Rosenberger, AL}, title = {Taxon combinations, parsimony analysis (PAUP*), and the taxonomy of the yellow-tailed woolly monkey, Lagothrix flavicauda.}, journal = {American journal of physical anthropology}, volume = {137}, number = {3}, pages = {245-255}, doi = {10.1002/ajpa.20859}, pmid = {18500746}, issn = {1096-8644}, mesh = {Animals ; Atelinae/anatomy & histology/*classification ; *Phylogeny ; }, abstract = {The classifications of primates, in general, and platyrrhine primates, in particular, have been greatly revised subsequent to the rationale for taxonomic decisions shifting from one rooted in the biological species concept to one rooted solely in phylogenetic affiliations. Given the phylogenetic justification provided for revised taxonomies, the scientific validity of taxonomic distinctions can be rightly judged by the robusticity of the phylogenetic results supporting them. In this study, we empirically investigated taxonomic-sampling effects on a cladogram previously inferred from craniodental data for the woolly monkeys (Lagothrix). We conducted the study primarily through much greater sampling of species-level taxa (OTUs) after improving some character codings and under a variety of outgroup choices. The results indicate that alternative selections of species subsets from within genera produce various tree topologies. These results stand even after adjusting the character set and considering the potential role of interobserver disagreement. We conclude that specific taxon combinations, in this case, generic or species pairings, of the primary study group has a biasing effect in parsimony analysis, and that the cladistic rationale for resurrecting the Oreonax generic distinction for the yellow-tailed woolly monkey (Lagothrix flavicauda) is based on an artifact of idiosyncratic sampling within the study group below the genus level. Some recommendations to minimize the problem, which is prevalent in all cladistic analyses, are proposed.}, } @article {pmid18490978, year = {2006}, author = {Lee, S and Crous, PW and Wingfield, MJ}, title = {Pestalotioid fungi from Restionaceae in the Cape Floral Kingdom.}, journal = {Studies in mycology}, volume = {55}, number = {}, pages = {175-187}, pmid = {18490978}, issn = {0166-0616}, abstract = {Eight pestalotioid fungi were isolated from the Restionaceae growing in the Cape Floral Kingdom of South Africa. Sarcostroma restionis, Truncatella megaspora, T. restionacearum and T. spadicea are newly described. New records include Pestalotiopsis matildae, Sarcostroma lomatiae, Truncatella betulae and T. hartigii. To resolve generic affiliations, phylogenetic analyses were performed on ITS (ITS1, 5.8S, ITS2) and part of 28S rDNA. DNA data support the original generic concept of Truncatella, which encompasses Pestalotiopsis species having 3-septate conidia. The genus Sarcostroma is retained as separate from Seimatosporium.}, } @article {pmid18490976, year = {2006}, author = {Hunter, GC and Wingfield, BD and Crous, PW and Wingfield, MJ}, title = {A multi-gene phylogeny for species of Mycosphaerella occurring on Eucalyptus leaves.}, journal = {Studies in mycology}, volume = {55}, number = {}, pages = {147-161}, pmid = {18490976}, issn = {0166-0616}, abstract = {Species of the ascomycete genus Mycosphaerella are regarded as some of the most destructive leaf pathogens of a large number of economically important crop plants. Amongst these, approximately 60 Mycosphaerella spp. have been identified from various Eucalyptus spp. where they cause leaf diseases collectively known as Mycosphaerella Leaf Disease (MLD). Species concepts for this group of fungi remain confused, and hence their species identification is notoriously difficult. Thus, the introduction of DNA sequence comparisons has become the definitive characteristic used to distinguish species of Mycosphaerella. Sequences of the Internal Transcribed Spacer (ITS) region of the ribosomal RNA operon have most commonly been used to consider species boundaries in Mycosphaerella. However, sequences for this gene region do not always provide sufficient resolution for cryptic taxa. The aim of this study was, therefore, to use DNA sequences for three loci, ITS, Elongation factor 1-alpha (EF-1alpha) and Actin (ACT) to reconsider species boundaries for Mycosphaerella spp. from Eucalyptus. A further aim was to study the anamorph concepts and resolve the deeper nodes of Mycosphaerella, for which part of the Large Subunit (LSU) of the nuclear rRNA operon was sequenced. The ITS and EF-1alpha gene regions were found to be useful, but the ACT gene region did not provide species-level resolution in Mycosphaerella. A phylogeny of the combined DNA datasets showed that species of Mycosphaerella from Eucalyptus cluster in two distinct groups, which might ultimately represent discrete genera.}, } @article {pmid18490953, year = {2007}, author = {Samson, RA and Hong, S and Peterson, SW and Frisvad, JC and Varga, J}, title = {Polyphasic taxonomy of Aspergillus section Fumigati and its teleomorph Neosartorya.}, journal = {Studies in mycology}, volume = {59}, number = {}, pages = {147-203}, pmid = {18490953}, issn = {0166-0616}, abstract = {The taxonomy of Aspergillus section Fumigati with its teleomorph genus Neosartorya is revised. The species concept is based on phenotypic (morphology and extrolite profiles) and molecular (beta-tubulin and calmodulin gene sequences) characters in a polyphasic approach. Four new taxa are proposed: N. australensis N. ferenczii, N. papuaensis and N. warcupii. All newly described and accepted species are illustrated. The section consists of 33 taxa: 10 strictly anamorphic Aspergillus species and 23 Neosartorya species. Four other Neosartorya species described previously were not available for this monograph, and consequently are relegated to the category of doubtful species.}, } @article {pmid18490943, year = {2007}, author = {Samson, RA and Varga, J and Witiak, SM and Geiser, DM}, title = {The species concept in Aspergillus: recommendations of an international panel.}, journal = {Studies in mycology}, volume = {59}, number = {}, pages = {71-73}, doi = {10.3114/sim.2007.59.09}, pmid = {18490943}, issn = {0166-0616}, } @article {pmid18490942, year = {2007}, author = {Rokas, A and Payne, G and Fedorova, ND and Baker, SE and Machida, M and Yu, J and Georgianna, DR and Dean, RA and Bhatnagar, D and Cleveland, TE and Wortman, JR and Maiti, R and Joardar, V and Amedeo, P and Denning, DW and Nierman, WC}, title = {What can comparative genomics tell us about species concepts in the genus Aspergillus?.}, journal = {Studies in mycology}, volume = {59}, number = {}, pages = {11-17}, pmid = {18490942}, issn = {0166-0616}, abstract = {Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.}, } @article {pmid18485741, year = {2009}, author = {Panksepp, J and Northoff, G}, title = {The trans-species core SELF: the emergence of active cultural and neuro-ecological agents through self-related processing within subcortical-cortical midline networks.}, journal = {Consciousness and cognition}, volume = {18}, number = {1}, pages = {193-215}, doi = {10.1016/j.concog.2008.03.002}, pmid = {18485741}, issn = {1090-2376}, mesh = {Affect/physiology ; Cerebral Cortex/*physiology ; Consciousness/physiology ; *Culture ; Humans ; Magnetic Resonance Imaging ; Nerve Net/*physiology ; *Self Concept ; }, abstract = {The nature of "the self" has been one of the central problems in philosophy and more recently in neuroscience. This raises various questions: (i) Can we attribute a self to animals? (ii) Do animals and humans share certain aspects of their core selves, yielding a trans-species concept of self? (iii) What are the neural processes that underlie a possible trans-species concept of self? (iv) What are the developmental aspects and do they result in various levels of self-representation? Drawing on recent literature from both human and animal research, we suggest a trans-species concept of self that is based upon what has been called a "core-self" which can be described by self-related processing (SRP) as a specific mode of interaction between organism and environment. When we refer to specific neural networks, we will here refer to the underlying system as the "core-SELF." The core-SELF provides primordial neural coordinates that represent organisms as living creatures-at the lowest level this elaborates interoceptive states along with raw emotional feelings (i.e., the intentions in action of a primordial core-SELF) while higher medial cortical levels facilitate affective-cognitive integration (yielding a fully-developed nomothetic core-self). Developmentally, SRP allows stimuli from the environment to be related and linked to organismic needs, signaled and processed within core-self structures within subcorical-cortical midline structures (SCMS) that provide the foundation for epigenetic emergence of ecologically framed, higher idiographic forms of selfhood across different individuals within a species. These functions ultimately operate as a coordinated network. We postulate that core SRP operates automatically, is deeply affective, and is developmentally and epigenetically connected to sensory-motor and higher cognitive abilities. This core-self is mediated by SCMS, embedded in visceral and instinctual representations of the body that are well integrated with basic attentional, emotional and motivational functions that are apparently shared between humans, non-human mammals, and perhaps in a proto-SELF form, other vertebrates. Such a trans-species concept of organismic coherence is thoroughly biological and affective at the lowest levels of a complex neural network, and culturally and ecologically molded at higher levels of neural processing. It allows organisms to selectively adapt to and integrate with physical and social environments. Such a psychobiologically universal, but environmentally diversified, concept may promote novel trans-species studies of the core-self across mammalian species.}, } @article {pmid18485204, year = {2008}, author = {DasSarma, P and DasSarma, S}, title = {On the origin of prokaryotic "species": the taxonomy of halophilic Archaea.}, journal = {Saline systems}, volume = {4}, number = {}, pages = {5}, pmid = {18485204}, issn = {1746-1448}, abstract = {The consistent use of the taxonomic system of binomial nomenclature (genus and species) was first popularized by Linnaeus nearly three-hundred years ago to classify mainly plants and animals. His main goal was to give labels that would ensure that biologists could agree on which organism was under investigation. One-hundred fifty years later, Darwin considered the term species as one of convenience and not essentially different from variety. In the modern era, exploration of the world's niches together with advances in genomics have expanded the number of named species to over 1.8 million, including many microorganisms. However, even this large number excludes over 90% of microorganisms that have yet to be cultured or classified. In naming new isolates in the microbial world, the challenge remains the lack of a universally held and evenly applied standard for a species. The definition of species based on the capacity to form fertile offspring is not applicable to microorganisms and 70% DNA-DNA hybridization appears rather crude in light of the many completed genome sequences. The popular phylogenetic marker, 16S rRNA, is tricky for classification since it does not provide multiple characteristics or phenotypes used classically for this purpose. Using most criteria, agreement may usually be found at the genus level, but species level distinctions are problematic. These observations lend credence to the proposal that the species concept is flawed when applied to prokaryotes. In order to address this topic, we have examined the taxonomy of extremely halophilic Archaea, where the order, family, and even a genus designation have become obsolete, and the naming and renaming of certain species has led to much confusion in the scientific community.}, } @article {pmid18478366, year = {2008}, author = {Gräser, Y and Scott, J and Summerbell, R}, title = {The new species concept in dermatophytes-a polyphasic approach.}, journal = {Mycopathologia}, volume = {166}, number = {5-6}, pages = {239-256}, pmid = {18478366}, issn = {0301-486X}, mesh = {Arthrodermataceae/*classification/genetics/physiology ; Dermatomycoses/microbiology ; Humans ; Mycological Typing Techniques/*methods ; Phylogeny ; Species Specificity ; }, abstract = {The dermatophytes are among the most frequently observed organisms in biomedicine, yet there has never been stability in the taxonomy, identification and naming of the approximately 25 pathogenic species involved. Since the identification of these species is often epidemiologically and ethically important, the difficulties in dermatophyte identification are a fruitful topic for modern molecular biological investigation, done in tandem with renewed investigation of phenotypic characters. Molecular phylogenetic analyses such as multilocus sequence typing have had to be tailored to accommodate differing the mechanisms of speciation that have produced the dermatophytes that are commonly seen today. Even so, some biotypes that were unambiguously considered species in the past, based on profound differences in morphology and pattern of infection, appear consistently not to be distinct species in modern molecular analyses. Most notable among these are the cosmopolitan bane of nails and feet, Trichophyton rubrum, and the endemic African agent of childhood tinea capitis, Trichophyton soudanense, which are effectively inseparable in all analyses. The molecular data require some reinterpretation of results seen in conventional phenotypic tests, but in most cases, phylogenetic insight is readily integrated with current laboratory testing procedures.}, } @article {pmid18478026, year = {2008}, author = {Wang, JY and Frasier, TR and Yang, SC and White, BN}, title = {Detecting recent speciation events: the case of the finless porpoise (genus Neophocaena).}, journal = {Heredity}, volume = {101}, number = {2}, pages = {145-155}, doi = {10.1038/hdy.2008.40}, pmid = {18478026}, issn = {1365-2540}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Flow ; Gene Frequency ; Microsatellite Repeats ; Phylogeny ; Porpoises/anatomy & histology/*classification/*genetics ; Taiwan ; }, abstract = {Recent speciation events provide important insights into the understanding and conservation of Earth's biodiversity, representing recent adaptations to a changing environment and an important source of future evolutionary potential. However, the most frequently applied criterion for molecular-based speciation investigations, that of reciprocal monophyly of mitochondrial sequences, overlooks recent speciation events where insufficient time has passed for fixed molecular differences to develop between putative species. Two morphologically distinguishable forms of finless porpoise (genus Neophocaena) exist in sympatry in the strait of Taiwan, however the taxonomic relationship of these different forms is controversial. To test the hypothesis that the two forms represent different species, a study was conducted based on morphological characters and microsatellite and mitochondrial markers. The data suggest that the two forms are highly differentiated in terms of both morphology and genetic characteristics, despite being sympatric, and therefore represent different species as defined by the biological species concept. Moreover, the two forms appear to have been reproductively isolated since sharing a common ancestor prior to the last major glaciation event approximately 18 000 years ago. However, this represents an insufficient amount of time for reciprocal monophyly to have developed, and thus previous studies based on this criterion have overlooked this speciation event and resulted in incorrect taxonomic classification of these forms.}, } @article {pmid18473264, year = {2008}, author = {Prata, C and Maraldi, T and Fiorentini, D and Zambonin, L and Hakim, G and Landi, L}, title = {Nox-generated ROS modulate glucose uptake in a leukaemic cell line.}, journal = {Free radical research}, volume = {42}, number = {5}, pages = {405-414}, doi = {10.1080/10715760802047344}, pmid = {18473264}, issn = {1029-2470}, mesh = {Antioxidants/metabolism ; Biological Transport ; Cell Line, Tumor ; *Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Leukemic ; Glucose/metabolism/*pharmacokinetics ; Glucose Transporter Type 1/metabolism ; Humans ; Leukemia/*therapy ; Membrane Glycoproteins/*metabolism ; NADPH Oxidase 2 ; NADPH Oxidase 4 ; NADPH Oxidases/*metabolism ; Phosphorylation ; Protein Isoforms ; Protein-Tyrosine Kinases/metabolism ; *Reactive Oxygen Species ; }, abstract = {The discovery of superoxide-generating enzymes homologues of phagocytic NAD(P)H oxidase, the Nox family, has led to the concept that reactive oxygen species (ROS) are 'intentionally' generated with biological functions in various cell types. In this study, by treating an acute leukaemic cell line with different antioxidants, ROS generation was shown to be crucially involved in the modulation of glucose transport (mediated by Glut1), which is frequently up-regulated in cancer cells. Then, this study tried to elucidate ROS source(s) and mechanisms by which ROS are involved in Glut1 activity regulation. Results prove that Nox2 and Nox4 are the candidates and that phosphorylation processes are important in the regulation of glucose uptake on which cancer cells rely. On the whole, data suggest that both Glut1 and Nox homologues may be considered new potential targets in the treatment of leukaemia.}, } @article {pmid18469471, year = {2008}, author = {Kompany-Zareh, M and Khoshkam, M}, title = {Application of chemometrics methods with kinetic constraints for estimation of rate constants of second order consecutive reactions.}, journal = {Analytical sciences : the international journal of the Japan Society for Analytical Chemistry}, volume = {24}, number = {5}, pages = {637-645}, doi = {10.2116/analsci.24.637}, pmid = {18469471}, issn = {0910-6340}, abstract = {To determine the rate constants for the second order consecutive reactions of the form U + V -(k1)--> W -(k2)--> P, a number of chemometrics and hard modeling-based methods are described. The absorption spectroscopic data from the reaction were utilized for performing the analysis. Concentrations and extinctions of components were comparable, and all of them were absorbing species. The number of steps in the reaction was less than the number of absorbing species, which resulted in a rank-deficient response matrix. This can cause difficulties for some of the methods described in the literature. The standard MATLAB functions were used for determining the solutions of the differential equations as well as for finding the optimal rate constants to describe the kinetic profiles. The available knowledge about the system determines the approaches described in this paper. The knowledge includes the spectra of reactants and products, the initial concentrations, and the exact kinetics. Some of this information is sometimes not available or is hard to estimate. Multiple linear regression for fitting the kinetic parameters to the obtained concentration profiles, rank augmentation using multiple batch runs, a mixed spectral approach which treats the reaction using a pseudo species concept, and principal components regression are the four groups of methods discussed in this study. In one of the simulated datasets the spectra are quite different, and in the other one the spectra of one reactant and of the product share a high degree of overlap. Instrumental noise, sampling error are the sources of error considered. Our aim was the investigation of the relative merits of each method.}, } @article {pmid18468701, year = {2008}, author = {Martinez, RC and Carvalho-Netto, EF and Amaral, VC and Nunes-de-Souza, RL and Canteras, NS}, title = {Investigation of the hypothalamic defensive system in the mouse.}, journal = {Behavioural brain research}, volume = {192}, number = {2}, pages = {185-190}, doi = {10.1016/j.bbr.2008.03.042}, pmid = {18468701}, issn = {0166-4328}, mesh = {Animals ; Anterior Hypothalamic Nucleus/metabolism/physiology ; Behavior, Animal/physiology ; Dorsomedial Hypothalamic Nucleus/metabolism/physiology ; Escape Reaction/*physiology ; Fear/physiology ; Freezing Reaction, Cataleptic/*physiology ; Hypothalamic Area, Lateral/metabolism/physiology ; Hypothalamus/*metabolism/physiology ; Immunohistochemistry ; Male ; Mice ; Neural Pathways/metabolism/physiology ; Paraventricular Hypothalamic Nucleus/metabolism/physiology ; Predatory Behavior/*physiology ; Preoptic Area/metabolism/physiology ; Proto-Oncogene Proteins c-fos/analysis/*metabolism ; Rats ; Rats, Long-Evans ; Species Specificity ; Ventromedial Hypothalamic Nucleus/metabolism/physiology ; }, abstract = {The hypothalamus plays especially important roles in various endocrine, autonomic, and behavioral responses that guarantee the survival of both the individual and the species. In the rat, a distinct hypothalamic defensive circuit has been defined as critical for integrating predatory threats, raising an important question as to whether this concept could be applied to other prey species. To start addressing this matter, in the present study, we investigated, in another prey species (the mouse), the pattern of hypothalamic Fos immunoreactivity in response to exposure to a predator (a rat, using the Rat Exposure Test). During rat exposure, mice remained concealed in the home chamber for a longer period of time and increased freezing and risk assessment activity. We were able to show that the mouse and the rat present a similar pattern of hypothalamic activation in response to a predator. Of particular note, similar to what has been described for the rat, we observed in the mouse that predator exposure induces a striking activation in the elements of the medial hypothalamic defensive system, namely, the anterior hypothalamic nucleus, the dorsomedial part of the ventromedial hypothalamic nucleus and the dorsal premammillary nucleus. Moreover, as described for the rat, predator-exposed mice also presented increased Fos levels in the autonomic and parvicellular parts of the paraventricular hypothalamic nucleus, lateral preoptic area and subfornical region of the lateral hypothalamic area. In conclusion, the present data give further support to the concept that a specific hypothalamic defensive circuit should be preserved across different prey species.}, } @article {pmid18464876, year = {1997}, author = {Ramser, J and Weising, K and Terauchi, R and Kahl, G and Lopez-Peralta, C and Terhalle, W}, title = {Molecular marker based taxonomy and phylogeny of Guinea yam (Dioscorea rotundata - D. cayenensis).}, journal = {Genome}, volume = {40}, number = {6}, pages = {903-915}, doi = {10.1139/g97-117}, pmid = {18464876}, issn = {0831-2796}, abstract = {Four different molecular techniques were used to assess relationships among 21 accessions of Guinea yam (Dioscorea rotundata and Dioscorea cayenensis) and 21 accessions belonging to seven putative progenitor species. Random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) analysis yielded 246 informative characters that were transformed into a matrix of pairwise distances and analyzed by neighbor joining or split decomposition. Both methods gave congruent results. Well-separated groups were formed that corresponded to their species designation. Dioscorea rotundata and D. cayenensis accessions were clearly separated from each other, supporting the concept that both are distinct species. Two morphological intermediates grouped together with D. rotundata. All investigated species fell into two main clusters, one comprising D. rotundata, D. cayenensis, Dioscorea abyssinica, Dioscorea liebrechtsiana, and Dioscorea praehensilis, the other comprising Dioscorea smilacifolia, Dioscorea minutiflora, Dioscorea burkilliana, and Dioscorea togoensis. The same grouping was also obtained by comparative sequence analysis of chloroplast DNA, which supports earlier studies of nuclear rDNA variation and chloroplast restriction fragment length polymorphisms. We also analyzed the same set of Dioscorea samples with the recently developed random amplified microsatellite polymorphism (RAMPO) technique. A series of diagnostic RAMPO bands was identified that clearly distinguished between D. rotundata and D. cayenensis. Some of these bands could also be traced back to the putative progenitors of both species. The evolutionary origin of Guinea yam is discussed in light of the present results.}, } @article {pmid18462953, year = {2008}, author = {Gamble, T and Berendzen, PB and Shaffer, HB and Starkey, DE and Simons, AM}, title = {Species limits and phylogeography of North American cricket frogs (Acris: Hylidae).}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {1}, pages = {112-125}, doi = {10.1016/j.ympev.2008.03.015}, pmid = {18462953}, issn = {1095-9513}, mesh = {Animals ; Cytochromes c/genetics ; *Genes, Mitochondrial ; Larva ; Liver/chemistry ; Muscle, Skeletal/chemistry ; Phylogeny ; Ranidae/*classification/*genetics/growth & development ; Tail/chemistry ; United States ; }, abstract = {Cricket frogs are widely distributed across the eastern United States and two species, the northern cricket frog (Acris crepitans) and the southern cricket frog (A. gryllus) are currently recognized. We generated a phylogenetic hypothesis for Acris using fragments of nuclear and mitochondrial genes in separate and combined phylogenetic analyses. We also used distance methods and fixation indices to evaluate species limits within the genus and the validity of currently recognized subspecies of A. crepitans. The distributions of existing A. crepitans subspecies, defined by morphology and call types, do not match the distributions of evolutionary lineages recovered using our genetic data. We discuss a scenario of call evolution to explain this disparity. We also recovered distinct phylogeographic groups within A. crepitans and A. gryllus that are congruent with other codistributed taxa. Under a lineage-based species concept, we recognize Acris blanchardi as a distinct species. The importance of this revised taxonomy is discussed in light of the dramatic declines in A. blanchardi across the northern and western portions of its range.}, } @article {pmid18461076, year = {2008}, author = {Achtman, M and Wagner, M}, title = {Microbial diversity and the genetic nature of microbial species.}, journal = {Nature reviews. Microbiology}, volume = {6}, number = {6}, pages = {431-440}, doi = {10.1038/nrmicro1872}, pmid = {18461076}, issn = {1740-1534}, mesh = {Archaea/*classification/*genetics ; Bacteria/*classification/*genetics/pathogenicity ; Ecosystem ; Environmental Microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genetic Variation ; Genetics, Microbial/*methods ; Models, Genetic ; Selection, Genetic ; }, abstract = {The earth contains a huge number of largely uncharacterized Bacteria and Archaea. Microbiologists are struggling to summarize their genetic diversity and classify them, which has resulted in heated debates on methods for defining species, mechanisms that lead to speciation and whether microbial species even exist. This Review proposes that decisions on the existence of species and methods to define them should be guided by a method-free species concept that is based on cohesive evolutionary forces. It summarizes current approaches to defining species and the problems of these approaches, and presents selected examples of the population genetic patterns at and below the species level.}, } @article {pmid18434207, year = {2008}, author = {Light, JE and Toups, MA and Reed, DL}, title = {What's in a name: the taxonomic status of human head and body lice.}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {3}, pages = {1203-1216}, doi = {10.1016/j.ympev.2008.03.014}, pmid = {18434207}, issn = {1055-7903}, mesh = {Animals ; Cell Nucleus/genetics ; Electron Transport Complex IV/genetics ; Gene Flow ; Genetic Variation ; Humans ; Likelihood Functions ; Nucleotides ; Pediculus/classification/genetics ; Phthiraptera/*classification/genetics ; Phylogeny ; Population Dynamics ; Software ; Time Factors ; }, abstract = {Human head lice (Anoplura: Pediculidae: Pediculus) are pandemic, parasitizing countless school children worldwide due to the evolution of insecticide resistance, and human body (clothing) lice are responsible for the deaths of millions as a result of vectoring several deadly bacterial pathogens. Despite the obvious impact these lice have had on their human hosts, it is unclear whether head and body lice represent two morphological forms of a single species or two distinct species. To assess the taxonomic status of head and body lice, we provide a synthesis of publicly available molecular data in GenBank, and we compare phylogenetic and population genetic methods using the most diverse geographic and molecular sampling presently available. Our analyses find reticulated networks, gene flow, and a lack of reciprocal monophyly, all of which indicate that head and body lice do not represent genetically distinct evolutionary units. Based on these findings, as well as inconsistencies of morphological, behavioral, and ecological variability between head and body lice, we contend that no known species concept would recognize these louse morphotypes as separate species. We recommend recognizing head and body lice as morphotypes of a single species, Pediculus humanus, until compelling new data and analyses (preferably analyses of fast evolving nuclear markers in a coalescent framework) indicate otherwise.}, } @article {pmid18421492, year = {2008}, author = {Marco, D}, title = {Metagenomics and the niche concept.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {127}, number = {3}, pages = {241-247}, pmid = {18421492}, issn = {1611-7530}, mesh = {Biodiversity ; Biological Evolution ; *Ecology/methods ; Environment ; Genetics, Microbial ; Genome ; *Genomics ; Hydrogen-Ion Concentration ; Models, Biological ; Models, Genetic ; Models, Theoretical ; Oxygen/chemistry ; Phenotype ; Plasmids/metabolism ; }, abstract = {The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space.}, } @article {pmid18406121, year = {2008}, author = {García-Blázquez, G and Göker, M and Voglmayr, H and Martín, MP and Tellería, MT and Oberwinkler, F}, title = {Phylogeny of Peronospora, parasitic on Fabaceae, based on ITS sequences.}, journal = {Mycological research}, volume = {112}, number = {Pt 5}, pages = {502-512}, doi = {10.1016/j.mycres.2007.10.007}, pmid = {18406121}, issn = {0953-7562}, mesh = {DNA, Fungal/genetics ; DNA, Ribosomal Spacer/*genetics ; Fabaceae/*microbiology ; Host-Pathogen Interactions ; Molecular Sequence Data ; Peronospora/*classification/cytology/genetics/isolation & purification ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Species concepts are a notoriously difficult taxonomic problem in plant-parasitic fungal-like organisms such as downy mildews (Peronosporomycetes, Peronosporales). This is particularly evident in the largest downy mildew genus, Peronospora, which contains a number of economically important pathogens. Here, we investigate relationships of Peronospora species infecting Fabaceae (angiosperms, Rosidae) originating from various collections from different species of host plants and from different European locations by molecular phylogenetic analysis of ITS sequences. Molecular trees were inferred with ML, MP and Bayesian methods and rooted with Pseudoperonospora. As in other downy mildew groups, molecular data mainly support the use of narrow species delimitations and host range as a taxonomic marker. Fabaceae parasites appear to be subdivided into a number of lineages displaying a considerable degree of host specialization with respect to host genera, as well as host subgenera or species. The number of repeats of a repetitive part of the ITS1 is, within limits, characteristic of subgroups within the cluster of Trifolium parasites. We reveal new hosts for Peronospora found on the Iberian Peninsula.}, } @article {pmid18346128, year = {2008}, author = {Mebert, K}, title = {Good species despite massive hybridization: genetic research on the contact zone between the watersnakes Nerodia sipedon and N. fasciata in the Carolinas, USA.}, journal = {Molecular ecology}, volume = {17}, number = {8}, pages = {1918-1929}, doi = {10.1111/j.1365-294X.2008.03725.x}, pmid = {18346128}, issn = {1365-294X}, mesh = {Animals ; Colubridae/*genetics ; DNA/chemistry/genetics ; Genetic Markers ; Genetic Variation ; Hybridization, Genetic/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Southeastern United States ; Species Specificity ; }, abstract = {Genomic markers generated with the amplified fragment length polymorphism method revealed extensive, panmictic-like hybridization along the narrow contact zone between the water snakes Nerodia sipedon and Nerodia fasciata in the Carolinas, USA. However, asymmetric distributions of diagnostic markers between both species and low frequencies of backcrossed hybrids with a high value of interspecific mixture infer selection against certain genotypes. This is consistent with a pronounced genetic and morphological preponderance of N. fasciata characters in the hybrid zone. Despite massive hybridization within the contact zone, the existence of nearly fixed genetic markers and the potential inferiority of certain hybrid genotypes support the species status of the two taxa and corroborate known, but nondiagnostic differences in morphology and ecology. This study stretches the applicability of species concepts to cases, where the genetic compatibility between two closely related species is very high, yet, they still evolve and persist as independent entities.}, } @article {pmid18328737, year = {2008}, author = {Downie, DA and Donaldson, JS and Oberprieler, RG}, title = {Molecular systematics and evolution in an African cycad-weevil interaction: Amorphocerini (Coleoptera: Curculionidae: Molytinae) weevils on Encephalartos.}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {1}, pages = {102-116}, doi = {10.1016/j.ympev.2008.01.023}, pmid = {18328737}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Coleoptera/*classification/genetics/physiology ; Cycadopsida/*physiology ; DNA/genetics ; DNA Primers ; *Phylogeny ; }, abstract = {Weevils in the tribe Amorphocerini have been implicated in pollination of Encephalartos species in southern Africa. The services they render these plants and the unique attributes of the cycad-weevil interaction make them important from both conservation and evolutionary standpoints. Oberprieler [Oberprieler, R.G., 1996. Systematics and evolution of the tribe Amorphocerini, with a review of the cycad weevils of the world. Ph.D. dissertation, University of the Free State, Bloemfontein, South Africa], using morphological characters, proposed a tentative hypothesis of relationships among the Amorphocerini which is tested here using DNA sequence data. Sequences from one mitochondrial and three nuclear genes were used to infer phylogenetic relationships, levels of sequence divergence, evolution of host associations, and patterns of speciation in this tribe. The results are reasonably consistent with the morphological hypothesis of relationships and species concepts, though important differences are observed, particularly in relationships among a Porthetes hispidus Boheman species group, which is indicated to have experienced recent divergences. In general, low levels of sequence divergence among species within two of the three genera indicate a recent radiation of this tribe onto African cycads, thus while cycad-insect interactions have often been considered ancient this may not be the case for some extant interactions. A complex pattern of host shifts onto both closely related and more distantly related hosts is suggested.}, } @article {pmid18328107, year = {2008}, author = {Tavares, ES and Baker, AJ}, title = {Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {81}, pmid = {18328107}, issn = {1471-2148}, mesh = {Animals ; *Biodiversity ; Birds/classification/*genetics ; *Computational Biology ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Library ; *Genes, Mitochondrial ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: DNA barcoding of life using a standardized COI sequence was proposed as a species identification system, and as a method for detecting putative new species. Previous tests in birds showed that individuals can be correctly assigned to species in ~94% of the cases and suggested a threshold of 10x mean intraspecific difference to detect potential new species. However, these tests were criticized because they were based on a single maternally inherited gene rather than multiple nuclear genes, did not compare phylogenetically identified sister species, and thus likely overestimated the efficacy of DNA barcodes in identifying species.

RESULTS: To test the efficacy of DNA barcodes we compared ~650 bp of COI in 60 sister-species pairs identified in multigene phylogenies from 10 orders of birds. In all pairs, individuals of each species were monophyletic in a neighbor-joining (NJ) tree, and each species possessed fixed mutational differences distinguishing them from their sister species. Consequently, individuals were correctly assigned to species using a statistical coalescent framework. A coalescent test of taxonomic distinctiveness based on chance occurrence of reciprocal monophyly in two lineages was verified in known sister species, and used to identify recently separated lineages that represent putative species. This approach avoids the use of a universal distance cutoff which is invalidated by variation in times to common ancestry of sister species and in rates of evolution.

CONCLUSION: Closely related sister species of birds can be identified reliably by barcodes of fixed diagnostic substitutions in COI sequences, verifying coalescent-based statistical tests of reciprocal monophyly for taxonomic distinctiveness. Contrary to recent criticisms, a single DNA barcode is a rapid way to discover monophyletic lineages within a metapopulation that might represent undiscovered cryptic species, as envisaged in the unified species concept. This identifies a smaller set of lineages that can also be tested independently for species status with multiple nuclear gene approaches and other phenotypic characters.}, } @article {pmid18314319, year = {2008}, author = {Wirtz, N and Printzen, C and Lumbsch, HT}, title = {The delimitation of Antarctic and bipolar species of neuropogonoid Usnea (Ascomycota, Lecanorales): a cohesion approach of species recognition for the Usnea perpusilla complex.}, journal = {Mycological research}, volume = {112}, number = {Pt 4}, pages = {472-484}, doi = {10.1016/j.mycres.2007.05.006}, pmid = {18314319}, issn = {0953-7562}, mesh = {Antarctic Regions ; Ascomycota ; DNA, Fungal/chemistry/genetics ; *Genetic Speciation ; *Phylogeny ; Usnea/*classification/cytology/*genetics ; }, abstract = {Species of the Neuropogon group in the lichen genus Usnea have their centre of distribution in polar regions of the Southern Hemisphere. Their morphological and chemical variability is poorly understood and several asexual taxa with uncertain relationships to fertile taxa occur in the group. The species concept is controversial. A phylogenetic analysis revealed three related complexes of mainly asexual lineages arranged around three fertile Usnea species: U. aurantiaco-atra, U. trachycarpa and U. perpusilla. In this study a dataset of 80 specimens was used to resolve species circumscriptions in the U. perpusilla complex. We used a phylogenetic and a haplotype network approach based on three gene fragments (ITS, IGS and RPB1) to detect distinct lineages. To support the hypothesis that these lineages represent different species, we tested for correlation of morphological and chemical characters with hierarchical nested haplotype groups, employing statistical tests of contingency tables and analysis of variance (ANOVA). This cohesion species recognition method detected three fertile U. perpusilla lineages. We could also delimit an undescribed fertile species with yellow apothecia and a new asexual species from the High Andes. Interestingly, there is an additional bipolar species, U. lambii, which was formerly confused with U. sphacelata. The fact that U. lambii shows a geographically disjunct distribution pattern, but the genetic distances among specimens are low, points to recent long-distance dispersal.}, } @article {pmid18313946, year = {2008}, author = {Reddy, S}, title = {Systematics and biogeography of the shrike-babblers (Pteruthius): species limits, molecular phylogenetics, and diversification patterns across southern Asia.}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {1}, pages = {54-72}, doi = {10.1016/j.ympev.2008.01.014}, pmid = {18313946}, issn = {1055-7903}, mesh = {Animals ; Asia ; Base Sequence ; Birds/*classification ; DNA Primers ; Geography ; *Phylogeny ; Species Specificity ; }, abstract = {Patterns of avian diversification in southern Asia are poorly understood due to the limited number of phylogenetic and biogeographic studies of endemic groups, mainly due to the dearth of recent tissue samples and a historical taxonomic bias underestimating avifaunal diversity. A systematic analysis of the endemic genus Pteruthius, the shrike-babblers, was undertaken in order to identify basal diagnosable taxa, analyze their phylogenetic relationships, and uncover patterns of diversification within southern Asia. Traditionally considered to be 5 species, a total of 19 distinct taxa of Pteruthius are diagnosable by fixed characters under the phylogenetic species concept-almost a four-fold increase in recognized diversity. Molecular phylogenetic analyses (85% of samples were from museum specimens) recovered a robust phylogeny that was largely congruent using parsimony, likelihood, and bayesian. Initial divergences in each major clade occurred in the early to mid-Pliocene, while the remaining majority of diversification events occurred in the Pleistocene. Within Pteruthius, timings of species divergences across similar geographic regions correspond to both single and multiple Earth history events, illustrating the complexities of continental diversification. A novel biogeographic pattern of species in peripheral areas (Java, W Himalayas, S Vietnam, Assam/Burma) diverging first from those in the core-mainland areas (E Himalayas, Yunnan, N Thailand, Indochina, Malay Peninsula) was uncovered.}, } @article {pmid18312319, year = {2008}, author = {Xie, X and Michel, AP and Schwarz, D and Rull, J and Velez, S and Forbes, AA and Aluja, M and Feder, JL}, title = {Radiation and divergence in the Rhagoletis pomonella species complex: inferences from DNA sequence data.}, journal = {Journal of evolutionary biology}, volume = {21}, number = {3}, pages = {900-913}, doi = {10.1111/j.1420-9101.2008.01507.x}, pmid = {18312319}, issn = {1420-9101}, mesh = {Animals ; Base Sequence ; Cloning, Molecular ; DNA/*genetics ; Demography ; *Genetic Variation ; Mexico ; Molecular Sequence Data ; Phylogeny ; Tephritidae/*genetics/physiology ; United States ; }, abstract = {Here, we investigate the evolutionary history and pattern of genetic divergence in the Rhagoletis pomonella (Diptera: Tephritidae) sibling species complex, a model for sympatric speciation via host plant shifting, using 11 anonymous nuclear genes and mtDNA. We report that DNA sequence results largely coincide with those of previous allozyme studies. Rhagoletis cornivora was basal in the complex, distinguished by fixed substitutions at all loci. Gene trees did not provide reciprocally monophyletic relationships among US populations of R. pomonella, R. mendax, R. zephyria and the undescribed flowering dogwood fly. However, private alleles were found for these taxa for certain loci. We discuss the implications of the results with respect to identifiable genetic signposts (stages) of speciation, the mosaic nature of genomic differentiation distinguishing formative species and a concept of speciation mode plurality involving a biogeographic contribution to sympatric speciation in the R. pomonella complex.}, } @article {pmid18285626, year = {2008}, author = {Litvin, DB}, title = {Ferroic classifications extended to ferrotoroidic crystals.}, journal = {Acta crystallographica. Section A, Foundations of crystallography}, volume = {64}, number = {Pt 2}, pages = {316-320}, doi = {10.1107/S0108767307068262}, pmid = {18285626}, issn = {0108-7673}, abstract = {Aizu's characterization of the 773 species of phase transitions by magnetization, polarization and strain is extended to include characterization by the recently observed toroidal moment. The resulting distinction quadruplet characterization is then used to classify the species into sub-ensembles, extending Schmid's concept of ensembles of species to include classification by toroidal moments. Tables are given of the distinction quadruplet characterization of each species and the species in each ensemble and sub-ensemble. The form of primary and secondary ferroic property tensors invariant under the 122 magnetic point groups have also been tabulated for use in determining the characterization of species and possible domain switching. In both cases, physical property tensors related to the toroidal moment are included.}, } @article {pmid18282592, year = {2008}, author = {Krivan, V and Cressman, R and Schneider, C}, title = {The ideal free distribution: a review and synthesis of the game-theoretic perspective.}, journal = {Theoretical population biology}, volume = {73}, number = {3}, pages = {403-425}, doi = {10.1016/j.tpb.2007.12.009}, pmid = {18282592}, issn = {1096-0325}, mesh = {Animals ; Biological Evolution ; *Game Theory ; Population Dynamics ; Predatory Behavior ; }, abstract = {The Ideal Free Distribution (IFD), introduced by Fretwell and Lucas in [Fretwell, D.S., Lucas, H.L., 1970. On territorial behavior and other factors influencing habitat distribution in birds. Acta Biotheoretica 19, 16-32] to predict how a single species will distribute itself among several patches, is often cited as an example of an evolutionarily stable strategy (ESS). By defining the strategies and payoffs for habitat selection, this article puts the IFD concept in a more general game-theoretic setting of the "habitat selection game". Within this game-theoretic framework, the article focuses on recent progress in the following directions: (1) studying evolutionarily stable dispersal rates and corresponding dispersal dynamics; (2) extending the concept when population numbers are not fixed but undergo population dynamics; (3) generalizing the IFD to multiple species. For a single species, the article briefly reviews existing results. It also develops a new perspective for Parker's matching principle, showing that this can be viewed as the IFD of the habitat selection game that models consumer behavior in several resource patches and analyzing complications involved when the model includes resource dynamics as well. For two species, the article first demonstrates that the connection between IFD and ESS is now more delicate by pointing out pitfalls that arise when applying several existing game-theoretic approaches to these habitat selection games. However, by providing a new detailed analysis of dispersal dynamics for predator-prey or competitive interactions in two habitats, it also pinpoints one approach that shows much promise in this general setting, the so-called "two-species ESS". The consequences of this concept are shown to be related to recent studies of population dynamics combined with individual dispersal and are explored for more species or more patches.}, } @article {pmid18279566, year = {2008}, author = {Dunn, JA and Thind, BB and Danks, C and Chambers, J}, title = {Rapid method for the detection of storage mites in cereals: feasibility of an ELISA based approach.}, journal = {Bulletin of entomological research}, volume = {98}, number = {2}, pages = {207-213}, doi = {10.1017/S0007485308005634}, pmid = {18279566}, issn = {0007-4853}, mesh = {Acaridae/*immunology ; Animals ; *Edible Grain ; Enzyme-Linked Immunosorbent Assay/*methods ; Feasibility Studies ; Food Handling/*methods ; Species Specificity ; }, abstract = {This paper describes the development of rapid immunodiagnostic tests for the detection of storage mite infestations in cereals and cereal products. The study's first phase (proof of concept) involved the production of a species-specific enzyme-linked immunoassay (ELISA) for the flour mite, Acarus siro (L.), a major pest of stored commodities. The specificity of this new assay was assessed against key stored product contaminants (13 species of mites of which three were predatory, five species of insects and five species of fungi) in the presence and absence of grain. The assay was species-specific (no cross-reactivity to other storage contaminants) and was unaffected by the presence of cereal antigens in the extract. In the study's second phase, species- and genera-specific ELISAs were developed for a range of key storage mite pests: the cosmopolitan food mite (Lepidoglyphus destructor), the grocers' itch mite (Glycyphagus domesticus), the grainstack mite (Tyrophagus longior), mites of the Tyrophagus and Glycyphagus generas, and all storage mites. All tests were demonstrably specific to target species or genera, with no cross-reactions observed to other storage pest contaminants or cereals. The final, validation phase, involved a comparative assessment of the species-specific A. siro and the genus-specific Tyrophagus ELISAs with the flotation technique using laboratory and field samples. Both ELISAs were quantitative (0-30 mites per 10 g wheat) and produced good comparative data with the flotation technique (A. siro r(2)=0.91, Tyrophagus spp. r(2)=0.99).}, } @article {pmid18248124, year = {2008}, author = {Bodily, KD and Katz, JS and Wright, AA}, title = {Matching-to-sample abstract-concept learning by pigeons.}, journal = {Journal of experimental psychology. Animal behavior processes}, volume = {34}, number = {1}, pages = {178-184}, doi = {10.1037/0097-7403.34.1.178}, pmid = {18248124}, issn = {0097-7403}, support = {MH-061798/MH/NIMH NIH HHS/United States ; MH-072616/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Cognition ; Columbidae ; *Learning ; Male ; *Semantics ; Transfer, Psychology ; }, abstract = {Abstract concepts--rules that transcend training stimuli--have been argued to be unique to some species. Pigeons, a focus of much concept-learning research, were tested for learning a matching-to-sample abstract concept. Five pigeons were trained with three cartoon stimuli. Pigeons pecked a sample 10 times and then chose which of two simultaneously presented comparison stimuli matched the sample. After acquisition, abstract-concept learning was tested by presenting novel cartoons on 12 out of 96 trials for 4 consecutive sessions. A cycle of doubling the training set followed by retraining and novel-testing was repeated eight times, increasing the set size from 3 to 768 items. Transfer performance improved from chance (i.e., no abstract-concept learning) to a level equivalent to baseline performance (>80%) and was similar to an equivalent function for same/different abstract-concept learning. Analyses assessed the possibility that item-specific choice strategies accounted for acquisition and transfer performance. These analyses converged to rule out item-specific strategies at all but the smallest set-sizes (3-24 items). Ruling out these possibilities adds to the evidence that pigeons learned the relational abstract concept of matching-to-sample.}, } @article {pmid18202871, year = {2005}, author = {Tattersall, I and Mowbray, K}, title = {Species and paleoanthropology.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {123}, number = {4}, pages = {371-379}, pmid = {18202871}, issn = {1431-7613}, abstract = {The biotic world is self-evidently "packaged" into units, of which the most basic is the species. It is necessary to develop an accurate understanding of what species are and how they are to be identified before we can proceed to more complex analyses of the evolutionary histories and relationships of extinct and extant taxa at all levels of the systematic hierarchy. In this article, we review the major species concepts current today among paleoanthropologists, and examine the limitations of their applicability to practical studies of extant and extinct faunas. The primary such limitation for paleoanthropologists is the fact that all major species definitions stress reproductive continuity (whether by exclusionary or inclusionary mechanisms), a quality that is inferential at best among forms known only as fossils (and, in many cases, in the extant fauna as well). The only reliable signal as to species status in the fossil record is morphology, yet speciation carries with it no specifiable quantity of morphological innovation. Some groups with autapomorphies are not species, and some species do not bear autapomorphies. How, then, are we to recognize species in the hominid and other fossil records? Noting that osteodental differences among congeneric primate species tend to be subtle, and that when consistent identifiable "morphs" can be found at least as many species are present, we recommend equating morphs based on several characters with species-realizing that only one or two distinctive characters may not make a morph. In this way, our views of the phylogenetic histories of higher taxa may be oversimplified, but their essential patterns will not be distorted.}, } @article {pmid18201051, year = {2007}, author = {Kosoff, RE and Chen, CY and Wooster, GA and Getchell, RG and Clifford, A and Craigmill, AL and Bowser, PR}, title = {Sulfadimethoxine and ormetoprim residues in three species of fish after oral dosing in feed.}, journal = {Journal of aquatic animal health}, volume = {19}, number = {2}, pages = {109-115}, doi = {10.1577/H06-038.1}, pmid = {18201051}, issn = {0899-7659}, mesh = {Animal Feed ; Animals ; Anti-Infective Agents/analysis/*pharmacokinetics ; Cichlids/*metabolism ; Drug Residues/*analysis/pharmacokinetics ; Fishes ; Flounder/*metabolism ; Perciformes/*metabolism ; Pyrimidines/analysis/pharmacokinetics ; Species Specificity ; Sulfadimethoxine/analysis/pharmacokinetics ; Temperature ; }, abstract = {Nile tilapia Oreochromis niloticus, summer flounder Paralichthys dentatus, and walleyes Sander vitreus were treated with Romet-30 (PHARMAQ AS, Oslo, Norway) via a medicated ration at 50 mg Romet-30 kg fish body weight(- 1) d(-1) for 10 d to compare the elimination kinetics of the test substance. This study was part of a larger effort to develop a species grouping concept for the labeling of therapeutic compounds for cultured fishes. The fish tests were conducted at the ideal water temperature for each species and at 5 degrees C lower than the ideal temperature except for summer flounder, which would not feed at the lower temperature of 15 degrees C. Test temperatures were 30 degrees C and 25 degrees C for Nile tilapia, 20 degrees C and 17 degrees C for summer flounder, and 25 degrees C and 20 degrees C for walleyes. Neither component of Romet-30 (sulfadimethoxine and ormetoprim) could be detected in samples of the edible portion of walleyes (muscle plus skin) collected at day 10 posttreatment or thereafter. In studies with summer flounder, only one fish had a detectable concentration of either component on day 21 or thereafter. Elimination of Romet-30 by Nile tilapia was extremely rapid. The limited number of Nile tilapia with detectable sulfadimethoxine or ormetoprim during the posttreatment period prevented the determination of elimination half-life or elimination in this species.}, } @article {pmid18173482, year = {2007}, author = {Beger, M and McKenna, SA and Possingham, HP}, title = {Effectiveness of surrogate taxa in the design of coral reef reserve systems in the Indo-Pacific.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {21}, number = {6}, pages = {1584-1593}, doi = {10.1111/j.1523-1739.2007.00795.x}, pmid = {18173482}, issn = {1523-1739}, mesh = {Animals ; *Anthozoa ; *Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; Fishes/physiology ; Indian Ocean ; Mollusca/physiology ; Pacific Ocean ; }, abstract = {Implementing systematically designed reserve systems is crucial to slowing the global decline of coral reef health and diversity. Yet, the paucity of spatial data for most coral reef taxa often requires conservation planners to design reserve systems based only on a subset of taxonomic groups as surrogates for all other taxa. In terrestrial systems the validity of surrogates for reserve design is established by testing for cross-taxon congruence (similarities in spatial patterns of species richness), but this concept has rarely been examined in the marine environment. We tested the suitability of taxa as conservation representation surrogates of coral reef species richness across the Indo-Pacific, based on species lists of fishes, corals, and mollusks from 167 sites. First, we tested the relevance of cross-taxon congruence patterns to predict these surrogacy patterns. We determined congruence between taxonomic groups by conducting a correlation analysis of dissimilarity values between pairs of sites. We then evaluated how well each taxonomic group represented the other groups in a marine reserve system selected by a greedy reserve-selection algorithm relative to reserve systems selected by chance. No taxonomic group we examined was a reliable surrogate for the other groups such that site selection based on that group always represented other taxa significantly better than random selection of sites. Sites selected based on hard corals represented the other taxonomic groups in a reserve system worse than randomly selected sites. Although we found high cross-taxon congruence between fishes and corals and between corals and mollusks, for some regions cross-taxon congruence was not always a reliable indicator of the ability of one taxonomic group to efficiently represent another in a reserve system. We concluded that in Indo-Pacific coral reef ecosystems one can only be sure that a target taxon is efficiently represented in a reserve system when data on that taxon are used to select a reserve system.}, } @article {pmid18171625, year = {2008}, author = {Pauls, SU and Graf, W and Haase, P and Lumbsch, HT and Waringer, J}, title = {Grazers, shredders and filtering carnivores--the evolution of feeding ecology in Drusinae (Trichoptera: Limnephilidae): insights from a molecular phylogeny.}, journal = {Molecular phylogenetics and evolution}, volume = {46}, number = {2}, pages = {776-791}, pmid = {18171625}, issn = {1055-7903}, support = {P 18073/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Evolution, Molecular ; Feeding Behavior ; Genes, Insect ; Insecta/anatomy & histology/*classification/genetics ; Larva/anatomy & histology/physiology ; *Phylogeny ; }, abstract = {We examined the phylogenetic relationships between species and genera within the caddisfly subfamily Drusinae (Trichoptera: Limnephilidae) using sequence data from two mitochondrial loci (cytochrome oxidase 1, large subunit rRNA) and one nuclear gene (wingless). Sequence data were analysed for 28 species from five genera from the subfamily. We analysed individual and combined data sets using a Bayesian Markov Chain Monte Carlo and a maximum parsimony approach and compared the performance of each partition for resolving phylogenetic relationships at this level. In terms of resolution and phylogenetic utility wingless outperformed the two mitochondrial gene partitions. Using both Shimodaira-Hasegawa and expected likelihood weights tests we tested several hypotheses of relationships previously inferred based on adult morphological characters. The data did not support the generic concept, or many previously proposed species groupings, based on adult morphology. In contrast, the molecular data correlated with the morphology and feeding ecology of larvae. Using Bayesian ancestral character state reconstructions we inferred the evolution of feeding ecology and relevant larval morphological characters. Our analyses showed that within the subfamily Drusinae two derived feeding types evolved. One of these--grazing epilithic algae--is otherwise unusual in the Limnephilidae and may have promoted the high degree of diversity in the Drusinae.}, } @article {pmid19831292, year = {2008}, author = {Jeune, B and Petersen, HC}, title = {[Buffon, the director of 'Jardin du Roi' in the 1700s].}, journal = {Dansk medicinhistorisk arbog}, volume = {36}, number = {}, pages = {57-96}, pmid = {19831292}, issn = {0084-9588}, mesh = {Academies and Institutes/*history/organization & administration ; Biological Evolution ; France ; Gardening/history ; History, 18th Century ; Natural History/*history ; Publications/history ; }, abstract = {Buffon and Linné were the two greatest naturalists of the 1700s. As they were both born in 1707, their 300 anniversaries were therefore celebrated in France and Sweden. At the celebration meeting at the University of Bourgogne in Dijon - The Buffon Legacy - September 3-6, 2007, we presented the following paper: "Buffon and the longevity of species". In the present paper the life and work of Buffon is introduced on the basis of recent literature, including Jacques Roger's famous biography. Among non-biologists Buffon has nearly been forgotten, even though in the 1700s he was considered to be at the same level as the most famous French thinkers of the Enlightenment - Montesquieu, Voltaire, Rousseau and Diderot. His largest contributions were the publication of his comprehensive "Histoire naturelle" and his long and significant leadership of "Jardin du Roi", which he built up to become one of the best scientific institutions of Europe. Buffon's scientific contributions wereas overshadowed by those of Linné, as it was his classification system, which became dominant all overn Europe. Buffon's student Lamarck and later Darwin contributed by pushing Buffon in oblivion of history, even though Darwin valued him highly. However, in recent decades Buffon is experiencing a renaissance in connection with the increasing interest in biological anthropology, biogeography, ethology, and ecology, as well as on account of his modern species concept.}, } @article {pmid18086221, year = {2008}, author = {Taylor, DL and McCormick, MK}, title = {Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas.}, journal = {The New phytologist}, volume = {177}, number = {4}, pages = {1020-1033}, doi = {10.1111/j.1469-8137.2007.02320.x}, pmid = {18086221}, issn = {0028-646X}, mesh = {Base Sequence ; Basidiomycota/*genetics ; DNA Primers/*genetics ; DNA, Fungal/*genetics ; DNA, Intergenic/*genetics ; Molecular Sequence Data ; Mycorrhizae/*genetics ; Orchidaceae/*microbiology ; Phylogeny ; }, abstract = {Despite advances owing to molecular approaches, several hurdles still obstruct the identification of fungi forming orchid mycorrhizas. The Tulasnellaceae exhibit accelerated evolution of the nuclear ribosomal operon, causing most standard primers to fail in polymerase chain reaction (PCR) trials. Insufficient sequences are available from well characterized isolates and fruitbodies. Lastly, taxon-specific PCR primers are needed in order to explore the ecology of the fungi outside of the orchid root. Here, progress in overcoming these hurdles is reported. Broad-spectrum basidiomycete internal transcribed spacer (ITS) primers that do not exclude most known Tulasnellaceae are presented. blast searches and empirical PCR tests support their wide utility within the Basidiomycota. Taxon-specific ITS primers are presented targeted to orchid-associated Tulasnella, and a core component of the Thelephora-Tomentella complex. The efficiency and selectivity of these primer sets are again supported by blast searches and empirical tests. Lastly, ITS DNA sequences are presented from several strains of Epulorhiza, Ceratorhiza, Ceratobasidium, Sistotrema, Thanatephorus and Tulasnella that were originally described in the landmark mycorrhizal studies of Currah and Warcup. Detailed phylogenetic analyses reveal some inconsistencies in species concepts in these taxonomically challenging resupinate basidiomycetes, but also help to place several sequences from environmental samples.}, } @article {pmid18083963, year = {2007}, author = {Zimmer, RK and Ferrer, RP}, title = {Neuroecology, chemical defense, and the keystone species concept.}, journal = {The Biological bulletin}, volume = {213}, number = {3}, pages = {208-225}, doi = {10.2307/25066641}, pmid = {18083963}, issn = {0006-3185}, mesh = {Animals ; Biodiversity ; *Ecosystem ; Poisons/toxicity ; Saxitoxin/*toxicity ; Sodium Channels/genetics ; Species Specificity ; Tetrodotoxin/*toxicity ; Venoms/metabolism/toxicity ; }, abstract = {Neuroecology unifies principles from diverse disciplines, scaling from biophysical properties of nerve and muscle cells to community-wide impacts of trophic interactions. Here, these principles are used as a common fabric, woven from threads of chemosensory physiology, behavior, and population and community ecology. The "keystone species" concept, for example, is seminal in ecological theory. It defines a species whose impacts on communities are far greater than would be predicted from its relative abundance and biomass. Similarly, neurotoxins could function in keystone roles. They are rare within natural habitats but exert strong effects on species interactions at multiple trophic levels. Effects of two guanidine alkaloids, tetrodotoxin (TTX) and saxitoxin (STX), coalesce neurobiological and ecological perspectives. These molecules compose some of the most potent natural poisons ever described, and they are introduced into communities by one, or only a few, host species. Functioning as voltage-gated sodium channel blockers for nerve and muscle cells, TTX and STX serve in chemical defense. When borrowed by resistant consumer species, however, they are used either in chemical defense against higher order predators or for chemical communication as chemosensory excitants. Cascading effects of the compounds profoundly impact community-wide attributes, including species compositions and rates of material exchange. Thus, a diverse array of physiological traits, expressed differentially across many species, renders TTX and STX fully functional as keystone molecules, with vast ecological consequences at multiple trophic levels.}, } @article {pmid18076327, year = {2007}, author = {Klein, J and Sato, A and Nikolaidis, N}, title = {MHC, TSP, and the origin of species: from immunogenetics to evolutionary genetics.}, journal = {Annual review of genetics}, volume = {41}, number = {}, pages = {281-304}, doi = {10.1146/annurev.genet.41.110306.130137}, pmid = {18076327}, issn = {0066-4197}, mesh = {Animals ; *Biological Evolution ; *Immunogenetics ; Major Histocompatibility Complex/*genetics/*immunology ; Species Specificity ; }, abstract = {The acronym Mhc, major histocompatibility complex, is customarily not allied with topics in evolutionary biology. Here, however, we attempt to demonstrate that the Mhc has much to offer to this discipline and intimate that evolutionary biologists who ignore its contributions miss out on a chance of applying a new approach to vexing questions. One aspect of the Mhc in particular affords a fresh look at the population processes that transform one species into another: the trans-species polymorphism, the passage of allelic lineages from ancestral to descendant species. We provide examples of using the Mhc polymorphism in estimating the size of the founding population of new species, and of analyzing the long-term population demographies of phylogenetic lineages. We then extend the concept of trans-species polymorphism to other genes, even those not evolving under balancing selection, and argue that the phenomenon is widespread between closely related species. On the example of the cichlid fishes of Lake Victoria, we demonstrate how the concept changes the interpretation of this so-called "species flock." We contend that the conclusions reached regarding the cichlid fishes apply also to other examples of adaptive radiation, for example that of Darwin's finches, and so provide new insights into the nature of speciation in general.}, } @article {pmid19430539, year = {2007}, author = {Xie, B and Luo, X and Zhao, C and Priest, CM and Chan, SY and O' Connor, PB and Kirschner, DA and Costello, CE}, title = {Molecular Characterization of Myelin Protein Zero in Xenopus laevis Peripheral Nerve: Equilibrium between Non-covalently Associated Dimer and Monomer.}, journal = {International journal of mass spectrometry}, volume = {268}, number = {2-3}, pages = {304-315}, pmid = {19430539}, issn = {1387-3806}, support = {P41 RR010888-11/RR/NCRR NIH HHS/United States ; P41 RR010888-09/RR/NCRR NIH HHS/United States ; P41 RR010888-10/RR/NCRR NIH HHS/United States ; S10 RR015942-01/RR/NCRR NIH HHS/United States ; P41 RR010888/RR/NCRR NIH HHS/United States ; P41 GM104603/GM/NIGMS NIH HHS/United States ; }, abstract = {Myelin protein zero (P0), a glycosylated single-pass transmembrane protein, is essential in the formation and maintenance of peripheral nervous system (PNS) compact myelin. P0 in Xenopus (xP0) exists primarily as a dimeric form that remains stable after various physical and chemical treatments. In exploring the nature of the interactions underlying the dimer stability, we found that xP0 dimer dissociated into monomer during continuous elution gel electrophoresis and conventional SDS-PAGE, indicating that the dimer is stabilized by non-covalent interactions. Furthermore, as some of the gel-purified monomer re-associated into dimer on SDS-PAGE gels, there is likely a dynamic equilibrium between xP0 dimer and monomer in vivo. Because the carbohydrate and fatty acyl moieties may be crucial for the adhesion role of P0, we used sensitive mass spectrometry approaches to elucidate the detailed N-glycosylation and S-acylation profiles of xP0. Asn92 was determined to be the single, fully-occupied glycosylation site of xP0, and a total of 12 glycans was detected that exhibited new structural features compared with those observed from P0 in other species: (1) the neutral glycans were composed mainly of high mannose and hybrid types; (2) five of twelve were acidic glycans, among which three were sialylated and the other two were sulfated; (3) none of the glycans had core fucosylation; and (4) no glucuronic acid, hence no HNK-1 epitope, was detected. The drastically different carbohydrate structures observed here support the concept of the species-specific variation in N-glycosylation of P0. Cys152 was found to be acylated with stearoyl (C18:0), whereas palmitoyl (C16:0) is the corresponding predominant fatty acyl group on P0 from higher vertebrates. We propose that the unique glycosylation and acylation patterns of Xenopus P0 may underlie its unusual dimerization behaviour. Our results should shed light on the understanding of the phylogenetic development of P0's adhesion role in PNS compact myelin.}, } @article {pmid18042407, year = {2008}, author = {Stuart, BL}, title = {The phylogenetic problem of Huia (Amphibia: Ranidae).}, journal = {Molecular phylogenetics and evolution}, volume = {46}, number = {1}, pages = {49-60}, doi = {10.1016/j.ympev.2007.09.016}, pmid = {18042407}, issn = {1055-7903}, mesh = {Animals ; Phylogeny ; Ranidae/anatomy & histology/*classification/genetics ; Sequence Analysis, DNA ; }, abstract = {A taxonomic consensus for the diverse and pan-global frog family Ranidae is lacking. A recently proposed classification of living amphibians [Frost, D.R., Grant, T., Faivovich, J., Bain, R. H., Haas, A., Haddad, C.F.B., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M., Wheeler, W.C., 2006. The amphibian tree of life. B. Am. Mus. Nat. Hist. 297, 1-370] included expansion of the Southeast Asian ranid frog genus Huia from seven to 47 species, but without having studied the type species of Huia. This study tested the monophyly of this concept of Huia by sampling the type species and putative members of Huia. Molecular phylogenetic analyses consistently recovered the type species H. cavitympanum as the sister taxon to other Bornean-endemic species in the genus Meristogenys, rendering all previously published concepts of Huia as polyphyletic. Members of Huia sensu [Frost, D.R., Grant, T., Faivovich, J., Bain, R. H., Haas, A., Haddad, C.F.B., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M., Wheeler, W.C., 2006. The amphibian tree of life. B. Am. Mus. Nat. Hist. 297, 1-370.] appear in four places within the family Ranidae. A clade containing the type species of Odorrana is phylogenetically unrelated to the type species of Huia, and Odorrana is removed from synonymy with Huia. These findings underscore the need to include relevant type species in phylogenetic studies before proposing sweeping taxonomic changes. The molecular phylogenetic analyses revealed a high degree of homoplasy in larval and adult morphology of Asian ranid frogs. Detailed studies are needed to identify morphological synapomorphies that unite members in these major clades of ranid frogs.}, } @article {pmid18027743, year = {2007}, author = {Schmitz, OJ}, title = {Predator diversity and trophic interactions.}, journal = {Ecology}, volume = {88}, number = {10}, pages = {2415-2426}, doi = {10.1890/06-0937.1}, pmid = {18027743}, issn = {0012-9658}, mesh = {Animals ; *Biodiversity ; *Ecosystem ; Food Chain ; Population Dynamics ; Predatory Behavior/*physiology ; Species Specificity ; }, abstract = {The recognition that predators play important roles in ecosystems has prompted research to resolve how combinations of predator species influence ecosystem functions. Interactions among predator species and their prey can lead to a host of linear and nonlinear effects. Understanding the conditions causing these effects is critical for assigning predator species to functional groups in ways that lead to predictive theory of predator diversity effects on trophic interactions. To this end, I provide a synthesis of experiments examining multiple-predator-species effects on mortality of single shared prey. I show how experimental design and experimental venue can determine the conclusion about the importance of predator diversity on trophic interactions. In addition, I link natural history insights on predator species habitat and hunting behavior with linear and nonlinear multiple-predator effects to derive a new concept of predator diversity effects on trophic interactions. This concept holds that the nature of predator diversity effects is contingent upon predator species hunting mode plus predator and prey species habitat domain (defined as the spatial extent to which a microhabitat is used by a species). This concept allows the classification of multiple-predator effects into four broad functional categories: substitutable, nonlinear due to predator species interference, nonlinear due to intraguild predation, and nonlinear due to predator species synergism. Experimental evidence so far provides ample and comparatively equal support for substitutable, interference, and intraguild effects, and equivocal support for nonlinear synergisms. The paper closes by discussing ways to further a research program aimed at using the building blocks presented here to understand predator functional diversity and trophic interactions in complex ecological systems.}, } @article {pmid18027281, year = {2007}, author = {De Queiroz, K}, title = {Species concepts and species delimitation.}, journal = {Systematic biology}, volume = {56}, number = {6}, pages = {879-886}, doi = {10.1080/10635150701701083}, pmid = {18027281}, issn = {1063-5157}, mesh = {*Biodiversity ; Biological Evolution ; *Classification ; Demography ; Models, Biological ; }, abstract = {The issue of species delimitation has long been confused with that of species conceptualization, leading to a half century of controversy concerning both the definition of the species category and methods for inferring the boundaries and numbers of species. Alternative species concepts agree in treating existence as a separately evolving metapopulation lineage as the primary defining property of the species category, but they disagree in adopting different properties acquired by lineages during the course of divergence (e.g., intrinsic reproductive isolation, diagnosability, monophyly) as secondary defining properties (secondary species criteria). A unified species concept can be achieved by treating existence as a separately evolving metapopulation lineage as the only necessary property of species and the former secondary species criteria as different lines of evidence (operational criteria) relevant to assessing lineage separation. This unified concept of species has several consequences for species delimitation, including the following: First, the issues of species conceptualization and species delimitation are clearly separated; the former secondary species criteria are no longer considered relevant to species conceptualization but only to species delimitation. Second, all of the properties formerly treated as secondary species criteria are relevant to species delimitation to the extent that they provide evidence of lineage separation. Third, the presence of any one of the properties (if appropriately interpreted) is evidence for the existence of a species, though more properties and thus more lines of evidence are associated with a higher degree of corroboration. Fourth, and perhaps most significantly, a unified species concept shifts emphasis away from the traditional species criteria, encouraging biologists to develop new methods of species delimitation that are not tied to those properties.}, } @article {pmid17978244, year = {2007}, author = {Brown, DR and Whitcomb, RF and Bradbury, JM}, title = {Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes).}, journal = {International journal of systematic and evolutionary microbiology}, volume = {57}, number = {Pt 11}, pages = {2703-2719}, pmid = {17978244}, issn = {1466-5026}, support = {R01 GM076584-01A1/GM/NIGMS NIH HHS/United States ; R15 HG002389-01A1/HG/NHGRI NIH HHS/United States ; 1R01GM076584-01A1/GM/NIGMS NIH HHS/United States ; R15 HG002389/HG/NHGRI NIH HHS/United States ; R01 GM076584/GM/NIGMS NIH HHS/United States ; 1R15HG02389-01A1/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacterial Typing Techniques/methods/*standards ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Genotype ; Nucleic Acid Hybridization/methods ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reference Standards ; Sequence Analysis, DNA/methods/standards ; Serology/methods/standards ; Species Specificity ; Tenericutes/*classification/genetics/physiology ; Terminology as Topic ; }, abstract = {Minimal standards for novel species of the class Mollicutes (trivial term, mollicutes), last published in 1995, require revision. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes proposes herein revised standards that reflect recent advances in molecular systematics and the species concept for prokaryotes. The mandatory requirements are: (i) deposition of the type strain into two recognized culture collections, preferably located in different countries; (ii) deposition of the 16S rRNA gene sequence into a public database, and a phylogenetic analysis of the relationships among the 16S rRNA gene sequences of the novel species and its neighbours; (iii) deposition of antiserum against the type strain into a recognized collection; (iv) demonstration, by using the combination of 16S rRNA gene sequence analyses, serological analyses and supplementary phenotypic data, that the type strain differs significantly from all previously named species; and (v) assignment to an order, a family and a genus in the class, with an appropriate specific epithet. The 16S rRNA gene sequence provides the primary basis for assignment to hierarchical rank, and may also constitute evidence of species novelty, but serological and supplementary phenotypic data must be presented to substantiate this. Serological methods have been documented to be congruent with DNA-DNA hybridization data and with 16S rRNA gene placements. The novel species must be tested serologically to the greatest extent that the investigators deem feasible against all neighbouring species whose 16S rRNA gene sequences show >0.94 similarity. The investigator is responsible for justifying which characters are most meaningful for assignment to the part of the mollicute phylogenetic tree in which a novel species is located, and for providing the means by which novel species can be identified by other investigators. The publication of the description should appear in a journal having wide circulation. If the journal is not the International Journal of Systematic and Evolutionary Microbiology, copies of the publication must be submitted to that journal so that the name may be considered for inclusion in a Validation List as required by the International Code of Bacteriological Nomenclature (the Bacteriological Code). Updated informal descriptions of the class Mollicutes and some of its constituent higher taxa are available as supplementary material in IJSEM Online.}, } @article {pmid17957712, year = {2008}, author = {Hofmann, RR and Streich, WJ and Fickel, J and Hummel, J and Clauss, M}, title = {Convergent evolution in feeding types: salivary gland mass differences in wild ruminant species.}, journal = {Journal of morphology}, volume = {269}, number = {2}, pages = {240-257}, doi = {10.1002/jmor.10580}, pmid = {17957712}, issn = {0362-2525}, mesh = {Adaptation, Biological ; Animals ; Biological Evolution ; Body Weight ; Cattle ; Diet ; Eating ; Phylogeny ; Ruminants/*anatomy & histology/*physiology ; Salivary Glands/*anatomy & histology/*physiology ; }, abstract = {In the ongoing debate about divergent evolutionary morphophysiological adaptations of grazing and browsing ruminants, the size of the salivary glands has received special attention. Here, we report the most comprehensive dataset on ruminant salivary glands so far, with data on the Glandula parotis (n=62 species), Gl. mandibularis (n=61), Gl. buccalis ventralis (n=44), and Gl. sublingualis (n=30). All four salivary gland complexes showed allometric scaling with body mass (BM); in all cases, the 95% confidence interval for the allometric exponent included 0.75 but did not include 1.0 (linearity); therefore, like other parameters linked to the process of food intake, salivary gland mass appears to be correlated to metabolic body weight (BM0.75), and comparisons of relative salivary gland mass between species should rather be made on the basis of BM0.75 than as a percentage of BM. In the subsequent analyses, the percentage of grass (%grass) in the natural diet was used to characterize the feeding type; the phylogenetic tree used for a controlled statistical evaluation was entirely based on mitochondrial DNA information. Regardless of phylogenetic control in the statistical treatment, there was, for all four gland complexes, a significant positive correlation of BM and gland mass, and a significant negative correlation between %grass in the natural diet and gland mass. If the Gl. parotis was analyzed either for cervid or for bovid species only, the negative correlation of gland mass and %grass was still significant in either case; an inspection of certain ruminant subfamilies, however, suggested that a convergent evolutionary adaptation can only be demonstrated if a sufficient variety of ruminant subfamilies are included in a dataset. The results support the concept that ruminant species that ingest more grass have smaller salivary glands, possibly indicating a reduced requirement for the production of salivary tannin-binding proteins.}, } @article {pmid17922703, year = {2007}, author = {Mitchell, SC and Cunjak, RA}, title = {Stream flow, salmon and beaver dams: roles in the structuring of stream fish communities within an anadromous salmon dominated stream.}, journal = {The Journal of animal ecology}, volume = {76}, number = {6}, pages = {1062-1074}, doi = {10.1111/j.1365-2656.2007.01286.x}, pmid = {17922703}, issn = {0021-8790}, mesh = {Animals ; *Biodiversity ; *Ecosystem ; Female ; Male ; New Brunswick ; Population Density ; Population Dynamics ; Rivers ; Rodentia ; Salmo salar/*physiology ; Trees ; *Water Movements ; }, abstract = {The current paradigm of fish community distribution is one of a downstream increase in species richness by addition, but this concept is based on a small number of streams from the mid-west and southern United States, which are dominated by cyprinids. Further, the measure of species richness traditionally used, without including evenness, may not be providing an accurate reflection of the fish community. We hypothesize that in streams dominated by anadromous salmonids, fish community diversity will be affected by the presence of the anadromous species, and therefore be influenced by those factors affecting the salmonid population. Catamaran Brook, New Brunswick, Canada, provides a long-term data set to evaluate fish community diversity upstream and downstream of an obstruction (North American beaver Castor canadensis dam complex), which affects distribution of Atlantic salmon Salmo salar. The Shannon Weiner diversity index and community evenness were calculated for sample sites distributed throughout the brook and over 15 years. Fish community diversity was greatest upstream of the beaver dams and in the absence of Atlantic salmon. The salmon appear to depress the evenness of the community but do not affect species richness. The community upstream of the beaver dams changes due to replacement of slimy sculpin Cottus cognatus by salmon, rather than addition, when access is provided. Within Catamaran Brook, location of beaver dams and autumn streamflow interact to govern adult Atlantic salmon spawner distribution, which then dictates juvenile production and effects on fish community. These communities in an anadromous Atlantic salmon dominated stream do not follow the species richness gradient pattern shown in cyprinid-dominated streams and an alternative model for stream fish community distribution in streams dominated by anadromous salmonids is presented. This alternative model suggests that community distribution may be a function of semipermeable obstructions, streamflow and the distribution of the anadromous species affecting resident stream fish species richness, evenness, biomass and production.}, } @article {pmid17893064, year = {2007}, author = {Müller-Wille, S}, title = {Collection and collation: theory and practice of Linnaean botany.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {38}, number = {3}, pages = {541-562}, doi = {10.1016/j.shpsc.2007.06.010}, pmid = {17893064}, issn = {1369-8486}, mesh = {*Botany ; Models, Theoretical ; Natural History ; *Species Specificity ; }, abstract = {Historians and philosophers of science have interpreted the taxonomic theory of Carl Linnaeus (1707-1778) as an 'essentialist', 'Aristotelian', or even 'scholastic' one. This interpretation is flatly contradicted by what Linnaeus himself had to say about taxonomy in Systema naturae (1735), Fundamenta botanica (1736) and Genera plantarum (1737). This paper straightens out some of the more basic misinterpretations by showing that: (1) Linnaeus's species concept took account of reproductive relations among organisms and was therefore not metaphysical, but biological; (2) Linnaeus did not favour classification by logical division, but criticized it for necessarily failing to represent what he called 'natural' genera; (3) Linnaeus's definitions of 'natural' genera and species were not essentialist, but descriptive and polytypic; (4) Linnaeus's method in establishing 'natural' definitions was not deductive, but consisted in an inductive, bottom-up procedure of comparing concrete specimens. The conclusion will discuss the fragmentary and provisional nature of Linnaeus's 'natural method'. I will argue in particular that Linnaeus opted for inductive strategies not on abstract epistemological grounds, but in order to confer stability and continuity to the explorative practices of contemporary natural history.}, } @article {pmid17879128, year = {2007}, author = {Burke, A}, title = {Recovery in naturally dynamic environments: a case study from the Sperrgebiet, southern African arid succulent karoo.}, journal = {Environmental management}, volume = {40}, number = {4}, pages = {635-648}, pmid = {17879128}, issn = {0364-152X}, mesh = {*Biodiversity ; Diamond ; *Environment ; Lichens ; Magnoliopsida ; *Mining ; Namibia ; }, abstract = {Little is known about the process of vegetation recovery and associated time frames in the Succulent Karoo Biome of southern Africa. This study investigated the recovery of vegetation on sites impacted by mining (different types of dumps and mined areas) in the arid succulent karoo. The main aim of this study was to determine the state of recovery, time frames, successional stages, and the influence of environmental factors on recovery of coastal dune and sand plain plant communities. For this purpose, vegetation was recorded on some 121 sites throughout a coastal strip of approximately 100 x 3 km in Namibia's restricted diamond area (Sperrgebiet). Using the species pool concept to derive vegetation reference sites and dominance-diversity curves, recovery of vegetation (measured in terms of species richness and cover) in these altered landscapes reached about 46% on the oldest, 51-year-old mine dumps. However, based on species richness, richness levels similar to the undisturbed reference sites were recorded after 30 years, following a logarithmic trend. Successional stages of natural recovery were indicated in this dynamic coastal environment and Cladoraphis cyperoides and Galenia fruticosa appear to be early successional species. Scaling up of studies to landscape level and developing a target community using the species pool concept are discussed as means to measure recovery in dynamic biological communities. On these altered, man-made landforms, the availability of seed may be the bottleneck to achieve vegetation cover comparable to undisturbed vegetation in the surrounding. Hence, restoration efforts should focus on this aspect.}, } @article {pmid17867856, year = {2007}, author = {Sumida, M and Kotaki, M and Islam, MM and Djong, TH and Igawa, T and Kondo, Y and Matsui, M and Anslem, de S and Khonsue, W and Nishioka, M}, title = {Evolutionary relationships and reproductive isolating mechanisms in the rice frog (Fejervarya limnocharis) species complex from Sri Lanka, Thailand, Taiwan and Japan, inferred from mtDNA gene sequences, allozymes, and crossing experiments.}, journal = {Zoological science}, volume = {24}, number = {6}, pages = {547-562}, doi = {10.2108/zsj.24.547}, pmid = {17867856}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Crosses, Genetic ; DNA, Mitochondrial/*chemistry/genetics ; Enzymes/*genetics ; Evolution, Molecular ; Female ; Gene Expression Regulation, Enzymologic ; *Genetic Variation ; Haplotypes ; Hybridization, Genetic ; Japan ; Male ; Phylogeny ; Ranidae/*classification/*genetics ; Reproduction ; Sequence Alignment/veterinary ; Species Specificity ; Sri Lanka ; Taiwan ; Thailand ; }, abstract = {The rice frog (Fejervarya limnocharis) species complex is widely distributed, from India to Japan, and most prevalently in Southeast Asia. Conspicuous morphological variation has been reported for this species complex throughout its distribution range. In the present study, we used mtDNA gene sequence and allozyme analyses to infer evolutionary affinities within this species complex using eight populations (Sri Lanka; Bangkok and Ranong in Thailand; Taiwan; and Hiroshima, Okinawa, Ishigaki and Iriomote in Japan). We also conducted crossing experiments among four populations from Japan, Thailand, and Sri Lanka in order to find out more about the reproductive isolating mechanisms that might exist among the East, Southeast, and South Asian populations of this species complex. The crossing experiments revealed that the Sri Lanka population is reproductively isolated from the Hiroshima, Bangkok, and Ranong populations by complete hybrid inviability, and that the Bangkok population may be reproductively isolated from the Hiroshima population by partial hybrid inviability. Thus, it is not unreasonable to regard the Sri Lanka population as a species separated from F. limnocharis. The mtDNA and allozyme data showed that the Ranong population is most closely related to the Bangkok population in nuclear genome, but more similar to the Okinawa and Taiwan populations in mtDNA genome. The present, preliminary survey may raise questions about the species status of these particular populations and also about the nature of the biological species concept.}, } @article {pmid17855791, year = {2007}, author = {Thalmann, U}, title = {Biodiversity, phylogeography, biogeography and conservation: lemurs as an example.}, journal = {Folia primatologica; international journal of primatology}, volume = {78}, number = {5-6}, pages = {420-443}, doi = {10.1159/000105153}, pmid = {17855791}, issn = {1421-9980}, mesh = {Adaptation, Physiological ; Animals ; *Biodiversity ; *Biological Evolution ; *Conservation of Natural Resources ; DNA, Mitochondrial/analysis ; Genetic Variation ; *Geography ; Lemur/genetics/*physiology ; Phylogeny ; Species Specificity ; }, abstract = {The lemurs of Madagascar represent a spectacular example of adaptive radiation among primates. Given the special setting under which they evolved (i.e. long isolation, geographical location, geological relief), they provide excellent models for study in many realms, and at different levels and scales, including diversity. At the same time, they occur in a 'hottest hot spot' region for biodiversity conservation. Although there is no single definition of biodiversity, the most commonly used units to measure biodiversity are species-species richness, species abundance and, for conservation purposes in particular, species endemism. However, what a species actually is or how, precisely, it should be defined are unresolved issues. Many species concepts have been proposed and several have been used in primatology in recent years. Nowadays, one of the more common approaches to measuring diversity, and eventually inferring species status, is to look at genetic diversity as reflected by mitochondrial DNA differences. Not enough attention has been paid, however, to the different levels at which genetic differences may occur. Lemurs provide instructive examples to highlight the questions involved in species recognition and definition. Using lemurs as examples, I will highlight the strengths and limitations of some analytical tools, including phylogeography and cladistic biogeography and, I will, in particular, emphasize the questions arising at the interface of scientific and conservation perceptions, both of which influence decisions in the field of biodiversity preservation.}, } @article {pmid17845444, year = {2007}, author = {Sampayo, EM and Franceschinis, L and Hoegh-Guldberg, O and Dove, S}, title = {Niche partitioning of closely related symbiotic dinoflagellates.}, journal = {Molecular ecology}, volume = {16}, number = {17}, pages = {3721-3733}, doi = {10.1111/j.1365-294X.2007.03403.x}, pmid = {17845444}, issn = {0962-1083}, mesh = {Animals ; Anthozoa/classification/genetics/*physiology ; Australia ; DNA, Ribosomal Spacer/chemistry ; Dinoflagellida/classification/genetics/*physiology ; *Ecosystem ; Multivariate Analysis ; Phylogeny ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Reef-building corals are fundamental to the most diverse marine ecosystems, yet a detailed understanding of the processes involved in the establishment, persistence and ecology of the coral-dinoflagellate association remains largely unknown. This study explores symbiont diversity in relation to habitat by employing a broad-scale sampling regime using ITS2 and denaturing gradient gel electrophoresis. Samples from Pocillopora damicornis, Stylophora pistillata and Seriatopora hystrix all harboured host-specific clade C symbiont types at Heron Island (Great Barrier Reef, Australia). While Ser. hystrix associated with a single symbiont profile along its entire depth distribution, both P. damicornis and Sty. pistillata associated with multiple symbiont profiles that showed a strong zonation with depth. It is shown that, with an increased sampling effort, previously identified 'rare' symbiont types within this group of host species are in fact environmental specialists. A multivariate approach was used to expand on the common distinction of symbionts by a single genetic identity. It shows merit in its capacity not only to include all the variability present within the marker region but also to reliably represent ecological diversification of symbionts. Furthermore, the cohesive species concept is explored to explain how niche partitioning may drive diversification of closely related symbiont lineages. This study provides thus evidence that closely related symbionts are ecologically distinct and fulfil their own niche within the ecosystem provided by the host and external environment.}, } @article {pmid17768627, year = {2007}, author = {Douhan, GW and Martin, DP and Rizzo, DM}, title = {Using the putative asexual fungus Cenococcum geophilum as a model to test how species concepts influence recombination analyses using sequence data from multiple loci.}, journal = {Current genetics}, volume = {52}, number = {5-6}, pages = {191-201}, pmid = {17768627}, issn = {0172-8083}, mesh = {Actins/genetics ; Ascomycota/classification/*genetics ; Base Sequence ; Genetic Markers ; Genetics, Population ; Mitosporic Fungi/classification/*genetics ; *Models, Genetic ; Phylogeny ; *Recombination, Genetic ; }, abstract = {Recent studies have found that three divergent lineages of the ectomycorrhizal fungus Cenococcum geophilum may co-occur within a single soil sample. To test how inference of population structure is affected by species concept, potential recombination in this putative asexual fungus was analyzed by sequencing 10 loci from 44 isolates from within one main lineage that is potentially sub-divisible into two phylogenetic species (A and B). Phylogenetic incongruence between these loci and recombination analyses using six different methods was consistent with recombination. However, most of the incongruence was caused by an apparently reciprocal recombination event between the actin locus and the other loci studied. Extreme divergence between the two types of actin loci suggests either an ancient recombination event or a more recent horizontal inheritance. We also found that random mating could not be rejected when A and B isolates were treated as members of a single species based on multilocus disequilibrium analyses, whereas random mating was rejected when all isolates were pooled. These results are significant and demonstrate that inferences of population structure can be confounded when isolates are pooled together based entirely on a morphological species concept.}, } @article {pmid17715057, year = {2007}, author = {Papke, RT and Zhaxybayeva, O and Feil, EJ and Sommerfeld, K and Muise, D and Doolittle, WF}, title = {Searching for species in haloarchaea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {35}, pages = {14092-14097}, pmid = {17715057}, issn = {0027-8424}, mesh = {Euryarchaeota/*classification/*genetics ; Fresh Water/microbiology ; Genes, Bacterial ; Genome, Archaeal ; Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic ; Seawater/microbiology ; Water Microbiology ; }, abstract = {Prokaryotic (bacterial and archaeal) species definitions and the biological concepts that underpin them entail clustering (cohesion) among individuals, in terms of genome content and gene sequence similarity. Homologous recombination can maintain gene sequence similarity within, while permitting divergence between, clusters and is thus the basis for recent efforts to apply the Biological Species Concept in prokaryote systematics and ecology. In this study, we examine isolates of the haloarchaeal genus Halorubrum from two adjacent ponds of different salinities at a Spanish saltern and a natural saline lake in Algeria by using multilocus sequence analysis. We show that, although clusters can be defined by concatenation of multiple marker sequences, barriers to exchange between them are leaky. We suggest that no nonarbitrary way to circumscribe "species" is likely to emerge for this group, or by extension, to apply generally across prokaryotes. Arbitrary criteria might have limited practical use, but still must be agreed upon by the community.}, } @article {pmid17677137, year = {2007}, author = {Viger, F and Barrat, A and Dall'Asta, L and Zhang, CH and Kolaczyk, ED}, title = {What is the real size of a sampled network? The case of the Internet.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {75}, number = {5 Pt 2}, pages = {056111}, doi = {10.1103/PhysRevE.75.056111}, pmid = {17677137}, issn = {1539-3755}, abstract = {Most data concerning the topology of complex networks are the result of mapping projects which bear intrinsic limitations and cannot give access to complete, unbiased datasets. A particularly interesting case is represented by the physical Internet. Router-level Internet mapping projects generally consist of sampling the network from a limited set of sources by using traceroute probes. This methodology, akin to the merging of spanning trees from the different sources to a set of destinations, leads necessarily to a partial, incomplete map of the Internet. The determination of the real Internet topology characteristics from such sampled maps is therefore, in part, a problem of statistical inference. In this paper we present a twofold contribution in order to address this problem. First, we argue that inference of some of the standard topological quantities is, in fact, a version of the so-called "species" problem in statistics, which is important in categorizing the problem and providing some indication of its inherent difficulties. Second, we tackle the issue of estimating arguably the most basic of network characteristics-its number of nodes-and propose two estimators for this quantity, based on subsampling principles. Numerical simulations, as well as an experiment based on probing the Internet, suggest the feasibility of accounting for measurement bias in reporting Internet topology characteristics.}, } @article {pmid17650475, year = {2007}, author = {Hart, MW and Sunday, J}, title = {Things fall apart: biological species form unconnected parsimony networks.}, journal = {Biology letters}, volume = {3}, number = {5}, pages = {509-512}, pmid = {17650475}, issn = {1744-9561}, mesh = {Animals ; Butterflies/*classification/genetics ; DNA, Mitochondrial/chemistry ; Haplotypes ; *Phylogeny ; Sequence Alignment ; Snails/*classification/genetics ; }, abstract = {The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.}, } @article {pmid17603112, year = {2007}, author = {Eppley, JM and Tyson, GW and Getz, WM and Banfield, JF}, title = {Genetic exchange across a species boundary in the archaeal genus ferroplasma.}, journal = {Genetics}, volume = {177}, number = {1}, pages = {407-416}, pmid = {17603112}, issn = {0016-6731}, mesh = {Genes, Bacterial ; *Genetic Speciation ; Genetic Variation ; Genetics, Population ; *Genome, Archaeal ; Genome, Bacterial ; In Situ Hybridization, Fluorescence ; *Recombination, Genetic ; Thermoplasmales/*classification/*genetics ; }, abstract = {Speciation as the result of barriers to genetic exchange is the foundation for the general biological species concept. However, the relevance of genetic exchange for defining microbial species is uncertain. In fact, the extent to which microbial populations comprise discrete clusters of evolutionarily related organisms is generally unclear. Metagenomic data from an acidophilic microbial community enabled a genomewide, comprehensive investigation of variation in individuals from two coexisting natural archaeal populations. Individuals are clustered into species-like groups in which cohesion appears to be maintained by homologous recombination. We quantified the dependence of recombination frequency on sequence similarity genomewide and found a decline in recombination with increasing evolutionary distance. Both inter- and intralineage recombination frequencies have a log-linear dependence on sequence divergence. In the declining phase of interspecies genetic exchange, recombination events cluster near the origin of replication and are localized by tRNAs and short regions of unusually high sequence similarity. The breakdown of genetic exchange with increasing sequence divergence could contribute to, or explain, the establishment and preservation of the observed population clusters in a manner consistent with the biological species concept.}, } @article {pmid17581782, year = {2007}, author = {Evans, KM and Wortley, AH and Mann, DG}, title = {An assessment of potential diatom "barcode" genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta).}, journal = {Protist}, volume = {158}, number = {3}, pages = {349-364}, doi = {10.1016/j.protis.2007.04.001}, pmid = {17581782}, issn = {1434-4610}, mesh = {Algal Proteins/genetics ; Cyclooxygenase 1/genetics ; DNA Primers ; DNA, Algal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer ; Diatoms/*classification/cytology/*genetics ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; RNA, Algal/genetics ; RNA, Ribosomal, 18S/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Due to limited morphological differentiation, diatoms can be very difficult to identify and cryptic speciation is widespread. There is a need for a narrower species concept if contentious issues such as diatom biodiversities and biogeographies are to be resolved. We assessed the effectiveness of several genes (cox1, rbcL, 18S and ITS rDNA) to distinguish cryptic species within the model 'morphospecies', Sellaphora pupula agg. This is the first time that the suitability of cox1 as an identification tool for diatoms has been assessed. A range of cox1 primers was tested on Sellaphora and various outgroup taxa. Sequences were obtained for 34 isolates belonging to 22 Sellaphora taxa and three others (Pinnularia, Eunotia and Tabularia). Intraspecific divergences ranged from 0 to 5bp (=0.8%) and interspecific levels were at least 18bp (=c. 3%). Cox1 divergence was usually much greater than rbcL divergence and always much more variable than 18S rDNA. ITS rDNA sequences were more variable than cox1, but well-known problems concerning intragenomic variability caution against its use in identification. More information and less sequencing effort mean that cox1 can be a very useful aid in diatom identification. The usefulness of cox1 for determining phylogenetic relationships among Sellaphora species was also assessed and compared to rbcL. Tree topologies were very similar, although support values were generally lower for cox1.}, } @article {pmid17578840, year = {2007}, author = {Pupo, E and Hardy, E}, title = {Isolation of smooth-type lipopolysaccharides to electrophoretic homogeneity.}, journal = {Electrophoresis}, volume = {28}, number = {14}, pages = {2351-2357}, doi = {10.1002/elps.200600744}, pmid = {17578840}, issn = {0173-0835}, mesh = {Electrophoresis, Polyacrylamide Gel/*methods ; Escherichia coli/*chemistry ; Lipopolysaccharides/chemistry/*isolation & purification ; }, abstract = {The high structural heterogeneity of smooth-type lipopolysaccharides (LPS) enormously complicates the isolation of their constituent molecular species. Proof of concept is given here on the feasibility of using preparative slab-PAGE to isolate highly homogeneous smooth-type LPS glycoforms. LPS species (from 3.6 to 14.2 kDa) from Escherichia coli K-235 were separated by preparative slab-PAGE and recovered by utilizing the combined on-gel LPS reverse staining, extrusion, and passive elution techniques. As a result, 15 electrophoretically pure LPS fractions were obtained. The LPS content in the recovered fractions ranged from 280 ng (intermediate mobility glycoforms) to 411 mug (highest mobility glycoforms). The quantities of LPS fractions were sufficient to allow quantitation of the Limulus amebocyte lysate (LAL) activities of these distinct-molecular-mass LPS species, in the range from (1.1 +/- 0.1)x10(3) to (8.7 +/- 0.3)x10(5) endotoxin units (EU)/mL, by standard LAL assay. We have thus definitively demonstrated that slab-PAGE may be a suitable platform to more selectively purify individual glycoform fractions from smooth-type LPS.}, } @article {pmid17551524, year = {2008}, author = {Ward, DM and Cohan, FM and Bhaya, D and Heidelberg, JF and Kühl, M and Grossman, A}, title = {Genomics, environmental genomics and the issue of microbial species.}, journal = {Heredity}, volume = {100}, number = {2}, pages = {207-219}, doi = {10.1038/sj.hdy.6801011}, pmid = {17551524}, issn = {1365-2540}, mesh = {Cyanobacteria/*classification/*genetics ; *Ecosystem ; Environment ; Genetics, Population ; *Genomics ; }, abstract = {A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function.}, } @article {pmid17550131, year = {2007}, author = {Martínez-Sánchez, G and Giuliani, A}, title = {Cellular redox status regulates hypoxia inducible factor-1 activity. Role in tumour development.}, journal = {Journal of experimental & clinical cancer research : CR}, volume = {26}, number = {1}, pages = {39-50}, pmid = {17550131}, issn = {0392-9078}, mesh = {Animals ; Antineoplastic Agents/pharmacology/therapeutic use ; Cell Hypoxia ; Cell Transformation, Neoplastic/drug effects/*metabolism ; Humans ; Hypoxia-Inducible Factor 1/antagonists & inhibitors/chemistry/*metabolism ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Models, Molecular ; Neoplasms/drug therapy/*metabolism/physiopathology ; Oxidation-Reduction ; *Oxidative Stress/drug effects ; Oxygen/metabolism ; Protein Conformation ; Reactive Oxygen Species/metabolism ; *Signal Transduction/drug effects ; }, abstract = {The transcription factor hypoxia-inducible factor-1 (HIF-1) regulates the expression of more than 100 genes involved in cellular adaptation and survival under hypoxic stress. Activation of HIF-1 is associated with numerous physiological and pathological processes that include tumorigenesis, vascular remodelling, inflammation, and hypoxia/ischemia-related tissue damage. Experimental data support the concept that modulation of Reactive Oxygen Species (ROS) levels have an important impact on the hypoxic response mediated by HIF-1 alpha. However, ROS generation, the exact kinetics and conditions of ROS production and their specific relevance to HIF-l alpha activation are issue still to be clarified. Clinical studies suggested that HIF-1 activation correlates directly with advanced disease stages and treatment resistance among cancer patients. Preclinical studies support the inhibition of HIF-1 as a major molecular target for anti-tumour drug discovery. Considerable effort is underway to identify therapeutically useful molecule HIF-1 inhibitors. Most of the compounds discovered to inhibit HIF-1 are natural products or synthetic compounds with structures that are based on natural product leads. Natural products have also served a vital role as molecular probes to elucidate the pathways that regulate HIF-1 activity. Many of the substances found to inhibit HIF-I are non-druggable compounds that are too cytotoxic to serve as drug leads. The application of high-throughput screening methods, complementary molecular-targeted assays, and structurally diverse chemical libraries hold promise for the discovery of therapeutically useful HIF-1 inhibitors.}, } @article {pmid17546075, year = {2007}, author = {Rex, M and Patzolt, K and Schulte, K and Zizka, G and Vásquez, R and Ibisch, PL and Weising, K}, title = {AFLP analysis of genetic relationships in the genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae).}, journal = {Genome}, volume = {50}, number = {1}, pages = {90-105}, doi = {10.1139/g06-141}, pmid = {17546075}, issn = {0831-2796}, mesh = {Bromeliaceae/*classification/*genetics ; Chromosome Banding ; Chromosomes, Plant/genetics ; DNA, Plant/genetics ; Geography ; Phylogeny ; Plant Leaves/anatomy & histology/genetics ; *Polymorphism, Genetic ; Random Amplified Polymorphic DNA Technique ; }, abstract = {The neotropical genus Fosterella L.B. Smith (Pitcairnioideae, Bromeliaceae) comprises about 30 species, with a centre of diversity in semiarid to humid habitats of the Andean slopes and valleys of Bolivia. Morphologic differentiation of species is difficult because of a paucity of diagnostic characters, and little is known about the infrageneric phylogeny. Here, we present the results of an amplified fragment length polymorphism (AFLP) analysis of 77 Fosterella specimens, covering 18 recognized species and 9 as-yet undescribed morphospecies. Eight primer combinations produced 310 bands, which were scored as presence/absence characters. Neighbour-joining tree reconstruction revealed 12 clusters (A-L) with various levels of support. Well-supported species groups were also recovered by a principal coordinates analysis. With few exceptions, morphologically defined species boundaries were confirmed by the molecular data. Phylogenetic relationships between species groups remained ambiguous, however, because of short internal branch lengths. The AFLP data were complemented by a survey of the leaf anatomy of 19 Fosterella species. Species concepts and assemblages are discussed in the context of molecular, morphologic, anatomic, ecologic, and biogeographic data. The data suggest that accidental long-distance dispersal and founder events have been important for Fosterella speciation.}, } @article {pmid17517633, year = {2007}, author = {Caputi, L and Andreakis, N and Mastrototaro, F and Cirino, P and Vassillo, M and Sordino, P}, title = {Cryptic speciation in a model invertebrate chordate.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {22}, pages = {9364-9369}, pmid = {17517633}, issn = {0027-8424}, support = {R24 GM075049/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ciona intestinalis/*classification/*genetics ; Female ; Male ; *Models, Biological ; Molecular Sequence Data ; *Phylogeny ; Species Specificity ; }, abstract = {We applied independent species concepts to clarify the phylogeographic structure of the ascidian Ciona intestinalis, a powerful model system in chordate biology and for comparative genomic studies. Intensive research with this marine invertebrate is based on the assumption that natural populations globally belong to a single species. Therefore, understanding the true taxonomic classification may have implications for experimental design and data management. Phylogenies inferred from mitochondrial and nuclear DNA markers accredit the existence of two cryptic species: C. intestinalis sp. A, genetically homogeneous, distributed in the Mediterranean, northeast Atlantic, and Pacific, and C. intestinalis sp. B, geographically structured and encountered in the North Atlantic. Species-level divergence is further entailed by cross-breeding estimates. C. intestinalis A and B from allopatric populations cross-fertilize, but hybrids remain infertile because of defective gametogenesis. Although anatomy illustrates an overall interspecific similarity lacking in diagnostic features, we provide consistent tools for in-field and in-laboratory species discrimination. Finding of two cryptic taxa in C. intestinalis raises interest in a new tunicate genome as a gateway to studies in speciation and ecological adaptation of chordates.}, } @article {pmid17502094, year = {2007}, author = {Cohan, FM and Perry, EB}, title = {A systematics for discovering the fundamental units of bacterial diversity.}, journal = {Current biology : CB}, volume = {17}, number = {10}, pages = {R373-86}, doi = {10.1016/j.cub.2007.03.032}, pmid = {17502094}, issn = {0960-9822}, mesh = {Bacteria/*classification/genetics ; *Biodiversity ; Biological Evolution ; Cluster Analysis ; Genetic Variation ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; }, abstract = {Bacterial systematists face unique challenges when trying to identify ecologically meaningful units of biological diversity. Whereas plant and animal systematists are guided by a theory-based concept of species, microbiologists have yet to agree upon a set of ecological and evolutionary properties that will serve to define a bacterial species. Advances in molecular techniques have given us a glimpse of the tremendous diversity present within the microbial world, but significant work remains to be done in order to understand the ecological and evolutionary dynamics that can account for the origin, maintenance, and distribution of that diversity. We have developed a conceptual framework that uses ecological and evolutionary theory to identify the DNA sequence clusters most likely corresponding to the fundamental units of bacterial diversity. Taking into account diverse models of bacterial evolution, we argue that bacterial systematics should seek to identify ecologically distinct groups with evidence of a history of coexistence, as based on interpretation of sequence clusters. This would establish a theory-based species unit that holds the dynamic properties broadly attributed to species outside of microbiology.}, } @article {pmid17479853, year = {2007}, author = {Denoël, M and Ficetola, GF}, title = {Landscape-level thresholds, and newt conservation.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {17}, number = {1}, pages = {302-309}, doi = {10.1890/1051-0761(2007)017[0302:ltanc]2.0.co;2}, pmid = {17479853}, issn = {1051-0761}, mesh = {Animals ; *Conservation of Natural Resources ; *Ecology ; Salamandridae ; }, abstract = {Ecological thresholds are defined as points or zones at which a rapid change occurs from one ecological condition to another. The existence of thresholds in species-habitat relationships has important implications for management, but the lack of concordance across studies and the wide range of methods used make generalizations difficult. We used two different statistical methods to test for the existence of thresholds for both individual species and the whole community, using three newt species as models. Based on a sample of 371 ponds, we found significant thresholds for both landscape configuration and composition. These were for the relationships between distance to forest and occurrence of Triturus alpestris and T. helveticus, and forest and crop cover and T. helveticus. Variability in the location of thresholds observed for the different species in this study caution against their use at the community level. Future studies should be based on the identification and assessment of thresholds for targeted species. Thresholds can be a useful concept from which tools may be developed to focus conservation effort for threatened species and their habitats.}, } @article {pmid17479849, year = {2007}, author = {Nicholson, E and Possingham, HP}, title = {Making conservation decisions under uncertainty for the persistence of multiple species.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {17}, number = {1}, pages = {251-265}, doi = {10.1890/1051-0761(2007)017[0251:mcduuf]2.0.co;2}, pmid = {17479849}, issn = {1051-0761}, mesh = {*Conservation of Natural Resources ; Species Specificity ; Uncertainty ; }, abstract = {Population models for multiple species provide one of the few means of assessing the impact of alternative management options on the persistence of biodiversity, but they are inevitably uncertain. Is it possible to use population models in multiple-species conservation planning given the associated uncertainties? We use information-gap decision theory to explore the impact of parameter uncertainty on the conservation decision when planning for the persistence of multiple species. An information-gap approach seeks robust outcomes that are most immune from error. We assess the impact of uncertainty in key model parameters for three species, whose extinction risks under four alternative management scenarios are estimated using a metapopulation model. Three methods are described for making conservation decisions across the species, taking into account uncertainty. We find that decisions based on single species are relatively robust to uncertainty in parameters, although the estimates of extinction risk increase rapidly with uncertainty. When identifying the best conservation decision for the persistence of all species, the methods that rely on the rankings of the management options by each species result in decisions that are similarly robust to uncertainty. Methods that depend on absolute values of extinction risk are sensitive to uncertainty, as small changes in extinction risk can alter the ranking of the alternative scenarios. We discover that it is possible to make robust conservation decisions even when the uncertainties of the multiple-species problem appear overwhelming. However, the decision most robust to uncertainty is likely to differ from the best decision when uncertainty is ignored, illustrating the importance of incorporating uncertainty into the decision-making process.}, } @article {pmid17475271, year = {2007}, author = {Leardi, R}, title = {Genetic algorithms in chemistry.}, journal = {Journal of chromatography. A}, volume = {1158}, number = {1-2}, pages = {226-233}, doi = {10.1016/j.chroma.2007.04.025}, pmid = {17475271}, issn = {0021-9673}, mesh = {*Algorithms ; *Chemistry Techniques, Analytical ; Mutation ; }, abstract = {Genetic algorithms (GAs) are a quite recent technique of optimization, whose basic concept is mimicking the evolution of a species, according to the Darwinian theory of the "survival of the fittest." The application of genetic algorithms to complex problems usually produces much better results than those obtained by the standard techniques. This paper explains in detail the different steps of the algorithm and the most relevant problems to be solved in order to obtain an efficient optimization tool.}, } @article {pmid17451719, year = {2007}, author = {Gibson, W}, title = {Resolution of the species problem in African trypanosomes.}, journal = {International journal for parasitology}, volume = {37}, number = {8-9}, pages = {829-838}, doi = {10.1016/j.ijpara.2007.03.002}, pmid = {17451719}, issn = {0020-7519}, mesh = {Animals ; Phylogeny ; Trypanosoma/*classification/*genetics ; Trypanosomiasis, African/*parasitology ; }, abstract = {There is a general assumption that eukaryote species are demarcated by morphological or genetic discontinuities. This stems from the idea that species are defined by the ability of individuals to mate and produce viable progeny. At the microscopic level, where organisms often proliferate more by asexual than sexual reproduction, this tidy classification system breaks down and species definition becomes messy and problematic. The dearth of morphological characters to distinguish microbial species has led to the widespread application of molecular methods for identification. As well as providing molecular markers for species identification, gene sequencing has generated the data for accurate estimation of relatedness between different populations of microbes. This has led to recognition of conflicts between current taxonomic designations and phylogenetic placement. In the case of microbial pathogens, the extent to which taxonomy has been driven by utilitarian rather than biological considerations has been made explicit by molecular phylogenetic analysis. These issues are discussed with reference to the taxonomy of the African trypanosomes, where pathogenicity, host range and distribution have been influential in the designation of species and subspecies. Effectively, the taxonomic units recognised are those that are meaningful in terms of human or animal disease. The underlying genetic differences separating the currently recognised trypanosome taxa are not consistent, ranging from genome-wide divergence to presence/absence of a single gene. Nevertheless, if even a minor genetic difference reflects adaptation to a particular parasitic niche, for example, in Trypanosoma brucei rhodesiense, the presence of a single gene conferring the ability to infect humans, then it can prove useful as an identification tag for the taxon occupying that niche. Thus, the species problem can be resolved by bringing together considerations of utility, genetic difference and adaptation.}, } @article {pmid17395791, year = {2007}, author = {Beeson, TD and Mastracchio, A and Hong, JB and Ashton, K and Macmillan, DW}, title = {Enantioselective organocatalysis using SOMO activation.}, journal = {Science (New York, N.Y.)}, volume = {316}, number = {5824}, pages = {582-585}, pmid = {17395791}, issn = {1095-9203}, support = {R01 GM078201/GM/NIGMS NIH HHS/United States ; R01 GM078201-01-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Aldehydes/*chemistry ; Amines/chemistry ; *Catalysis ; Cyclization ; Halogens/chemistry ; Molecular Structure ; Organic Chemicals/*chemistry ; Oxidation-Reduction ; *Stereoisomerism ; }, abstract = {The asymmetric α-addition of relatively nonpolar hydrocarbon substrates, such as allyl and aryl groups, to aldehydes and ketones remains a largely unsolved problem in organic synthesis, despite the wide potential utility of direct routes to such products. We reasoned that well-established chiral amine catalysis, which activates aldehydes toward electrophile addition by enamine formation, could be expanded to this important reaction class by applying a single-electron oxidant to create a transient radical species from the enamine. We demonstrated the concept of singly occupied molecular orbital (SOMO) activation with a highly selective α-allylation of aldehydes, and we here present preliminary results for enantioselective heteroarylations and cyclization/halogenation cascades.}, } @article {pmid17391407, year = {2007}, author = {Valbuena-Carabaña, M and González-Martínez, SC and Hardy, OJ and Gil, L}, title = {Fine-scale spatial genetic structure in mixed oak stands with different levels of hybridization.}, journal = {Molecular ecology}, volume = {16}, number = {6}, pages = {1207-1219}, doi = {10.1111/j.1365-294X.2007.03231.x}, pmid = {17391407}, issn = {0962-1083}, mesh = {Gene Flow/genetics ; *Genetics, Population ; *Hybridization, Genetic ; Microsatellite Repeats/genetics ; Plant Leaves/anatomy & histology ; Polymerase Chain Reaction ; Population Density ; Principal Component Analysis ; Quercus/anatomy & histology/*genetics ; Spain ; Species Specificity ; }, abstract = {Oaks are model species for the study of natural introgressive hybridization. High interfertility among oak taxa might result in collective evolution, through transpecific spread of advantageous alleles, challenging the standard concept of species. Nine highly polymorphic microsatellite (nuSSR) loci were analysed in three mixed oak populations of Quercus pyrenaica and Quercus petraea (Montejo, Somosierra and Robregordo) with different density and hybridization rates. Both leaf morphology and molecular markers were used to assess individual admixture rates. Insights about the relative effect of density and hybridization rates on fine-scale spatial genetic structure (SGS) were obtained from autocorrelograms and Sp statistics. Differences in SGS among populations were higher than between species. These differences cannot be attributed solely to census densities but also relate to other factors, such as the spatial configuration of the population. Hybridization was an important factor shaping within-population spatial genetic structure, and an interspecific component of SGS was found in Somosierra. Indirect estimates of historical gene flow in Montejo were compared with actual values of gene dispersal assessed by parentage analysis in a former study. Similar values were found for current and historical gene flow in both species, which might reflect demographical stability.}, } @article {pmid17381161, year = {2007}, author = {Fan, HJ and Knez, M and Scholz, R and Hesse, D and Nielsch, K and Zacharias, M and Gösele, U}, title = {Influence of surface diffusion on the formation of hollow nanostructures induced by the Kirkendall effect: the basic concept.}, journal = {Nano letters}, volume = {7}, number = {4}, pages = {993-997}, doi = {10.1021/nl070026p}, pmid = {17381161}, issn = {1530-6984}, mesh = {Aluminum Oxide/*chemistry ; Computer Simulation ; Crystallization/*methods ; Diffusion ; Macromolecular Substances/chemistry ; Materials Testing ; *Models, Chemical ; *Models, Molecular ; Molecular Conformation ; Nanostructures/*chemistry/*ultrastructure ; Nanotechnology/methods ; Particle Size ; Surface Properties ; Zinc Oxide/*chemistry ; }, abstract = {The Kirkendall effect has been widely applied for fabrication of nanoscale hollow structures, which involves an unbalanced counterdiffusion through a reaction interface. Conventional treatment of this process only considers the bulk diffusion of growth species and vacancies. In this letter, a conceptual extension is proposed: the development of the hollow interior undergoes two main stages. The initial stage is the generation of small Kirkendall voids intersecting the compound interface via a bulk diffusion process; the second stage is dominated by surface diffusion of the core material (viz., the fast-diffusing species) along the pore surface. This concept applies to spherical as well as cylindrical nanometer and microscale structures, and even to macroscopic bilayers. As supporting evidence, we show the results of a spinel-forming solid-state reaction of core-shell nanowires, as well as of a planar bilayer of ZnO-Al2O3 to illustrate the influence of surface diffusion on the morphology evolution.}, } @article {pmid17375335, year = {2007}, author = {Mouillot, D and Mason, NW and Wilson, JB}, title = {Is the abundance of species determined by their functional traits? A new method with a test using plant communities.}, journal = {Oecologia}, volume = {152}, number = {4}, pages = {729-737}, pmid = {17375335}, issn = {0029-8549}, mesh = {*Ecosystem ; *Models, Biological ; New Zealand ; Plants/*metabolism ; }, abstract = {The relation between functional traits and abundance of species has the potential to provide evidence on the mechanisms that structure local ecological communities. The niche-limitation/limiting-similarity hypothesis, derived from MacArthur and Levins' original concept, predicts that species that are similar to others in terms of functional traits will suffer greater competition and hence be less abundant. On the other hand, the environment-filtering/habitat-optimum hypothesis predicts that groups of species with functional traits that are close to the optimum for that environment, and are therefore similar to other species, will be more abundant. We propose a new niche-assembly model for predicting the relative abundance of species in communities from their functional traits, which can detect the patterns that would be expected from either of these hypotheses. The model was fitted to eight plant communities sampled in the Lake Ohau district of New Zealand. For seven of the sites, the patterns could not be distinguished from that expected under a null model. However, in one site there was highly significant departure from the null model in the direction expected from the niche-limitation hypothesis. The site was probably the most productive of those examined. It is possible that competition for light rather than belowground resources, or faster recovery from disturbance, allowed greater predictability. Surprisingly, the predictability was seen when just the presences of a species' neighbours in trait space were taken into account, but not when the potential effects of those neighbours were weighted by their abundance. For three of the four model types, the effects of species on each other were consistently negative: a significant trend. These results contradict the various neutral models of ecological communities.}, } @article {pmid17375184, year = {2007}, author = {Isaac, NJ and Turvey, ST and Collen, B and Waterman, C and Baillie, JE}, title = {Mammals on the EDGE: conservation priorities based on threat and phylogeny.}, journal = {PloS one}, volume = {2}, number = {3}, pages = {e296}, pmid = {17375184}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; *Conservation of Natural Resources ; Endangered Species/*statistics & numerical data ; *Extinction, Biological ; Mammals/classification/*physiology ; Species Specificity ; Time ; }, abstract = {Conservation priority setting based on phylogenetic diversity has frequently been proposed but rarely implemented. Here, we define a simple index that measures the contribution made by different species to phylogenetic diversity and show how the index might contribute towards species-based conservation priorities. We describe procedures to control for missing species, incomplete phylogenetic resolution and uncertainty in node ages that make it possible to apply the method in poorly known clades. We also show that the index is independent of clade size in phylogenies of more than 100 species, indicating that scores from unrelated taxonomic groups are likely to be comparable. Similar scores are returned under two different species concepts, suggesting that the index is robust to taxonomic changes. The approach is applied to a near-complete species-level phylogeny of the Mammalia to generate a global priority list incorporating both phylogenetic diversity and extinction risk. The 100 highest-ranking species represent a high proportion of total mammalian diversity and include many species not usually recognised as conservation priorities. Many species that are both evolutionarily distinct and globally endangered (EDGE species) do not benefit from existing conservation projects or protected areas. The results suggest that global conservation priorities may have to be reassessed in order to prevent a disproportionately large amount of mammalian evolutionary history becoming extinct in the near future.}, } @article {pmid17357395, year = {2004}, author = {Retana-Salazar, AP and Retana-Salazar, S}, title = {[Towards a simple logic in the determination of biological groups: the species and supraspecific groups].}, journal = {Revista de biologia tropical}, volume = {52}, number = {1}, pages = {19-26}, pmid = {17357395}, issn = {0034-7744}, mesh = {Animal Population Groups/*classification ; Animals ; *Biological Evolution ; Models, Biological ; Species Specificity ; }, abstract = {In this paper we discuss about the utility of the species concept as real definition, particularly the Mayr concept. We propose a method for the logical separation of taxa based in the statements of the logical mathematics and the application of the sets theory to the concepts in systematic. We attempt to provide an objective methodology for the interpretation of natural groups in biology including the species as a basic group in evolution. We introduce the concept of the hypothetical ancestor as a mathematical possibility derived from the use of matrix calculations for non square matrix.}, } @article {pmid17346235, year = {2007}, author = {Zhang, Z and Tang, YR}, title = {Genome-wide analysis of enzyme structure-function combination across three domains of life.}, journal = {Protein and peptide letters}, volume = {14}, number = {3}, pages = {291-297}, doi = {10.2174/092986607780090775}, pmid = {17346235}, issn = {0929-8665}, mesh = {Animals ; Archaea/*enzymology/genetics ; Bacteria/*enzymology/genetics ; *Chromosome Mapping ; Databases, Genetic ; Enzymes/*chemistry/*genetics/*physiology ; Eukaryotic Cells/*enzymology ; Evolution, Molecular ; Genome ; Humans ; Mice ; Sequence Analysis, DNA ; *Structure-Activity Relationship ; }, abstract = {To investigate diverse enzyme structure-function combination (SFC) types in different species, 34 different genome sequences were annotated using the protein catalytic domain database SCOPEC (http://www.enzome.com/enzome/), in which both the structure and function for each entry are known. Annotated enzymes with catalytic domains from the same SCOP superfamily are considered to have an identical structure. Annotated enzymes sharing the identical three-digit EC number are considered to have the same enzymatic function. Results reveal that the different SFC types for enzymes identified in archaea, bacteria and eukaryota are 137, 300 and 313, respectively. About 80% of the SFCs identified in archaea can be consistently found in bacteria and eukaryota species, whereas 28% and 35% combination types in bacteria and eukaryota respectively are unique to their corresponding groups. The number of functions per structure and the number of structures per function for the annotated sequences were measured in different species. Furthermore, a new concept was proposed to represent enzymatic structures as a functional similarity network. Thus, the current study will be helpful to enhance the global view on the evolution of enzymatic structure and function.}, } @article {pmid17324817, year = {2007}, author = {LaPorte, J}, title = {In defense of species.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {38}, number = {1}, pages = {255-269}, doi = {10.1016/j.shpsc.2006.12.013}, pmid = {17324817}, issn = {1369-8486}, mesh = {Animals ; Biodiversity ; Biological Evolution ; *Classification/methods ; Conservation of Natural Resources ; Extinction, Biological ; Humans ; *Phylogeny ; Species Specificity ; Tigers/classification ; }, abstract = {In this paper, I address the charge that the category species should be abandoned in biological work. The widespread appeal to species in scientific discourse provides a presumption in favor of the category's usefulness, but a defeasible presumption. Widely acknowledged troubles attend species: these troubles might render the concept unusable by showing that 'species' is equivocal or meaningless or in some similar way fatally flawed. Further, there might be better alternatives to species. I argue that the presumption in favor of species is not defeated on these scores. Troubles attending species, which arise on account of contextual variation attending the use of 'species', do not indicate that the concept is unusable. And alternatives to the use of 'species', which have been proposed in connection with rank-free systematics and in connection with conservation efforts, fail to provide a proper replacement for species.}, } @article {pmid17319954, year = {2007}, author = {Mallet, J and Beltrán, M and Neukirchen, W and Linares, M}, title = {Natural hybridization in heliconiine butterflies: the species boundary as a continuum.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {28}, pmid = {17319954}, issn = {1471-2148}, mesh = {Animals ; Butterflies/classification/*genetics ; DNA, Mitochondrial/genetics ; Genetic Markers ; *Genetic Speciation ; Genetics, Population ; *Hybridization, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: To understand speciation and the maintenance of taxa as separate entities, we need information about natural hybridization and gene flow among species.

RESULTS: Interspecific hybrids occur regularly in Heliconius and Eueides (Lepidoptera: Nymphalidae) in the wild: 26-29% of the species of Heliconiina are involved, depending on species concept employed. Hybridization is, however, rare on a per-individual basis. For one well-studied case of species hybridizing in parapatric contact (Heliconius erato and H. himera), phenotypically detectable hybrids form around 10% of the population, but for species in sympatry hybrids usually form less than 0.05% of individuals. There is a roughly exponential decline with genetic distance in the numbers of natural hybrids in collections, both between and within species, suggesting a simple "exponential failure law" of compatibility as found in some prokaryotes.

CONCLUSION: Hybridization between species of Heliconius appears to be a natural phenomenon; there is no evidence that it has been enhanced by recent human habitat disturbance. In some well-studied cases, backcrossing occurs in the field and fertile backcrosses have been verified in insectaries, which indicates that introgression is likely, and recent molecular work shows that alleles at some but not all loci are exchanged between pairs of sympatric, hybridizing species. Molecular clock dating suggests that gene exchange may continue for more than 3 million years after speciation. In addition, one species, H. heurippa, appears to have formed as a result of hybrid speciation. Introgression may often contribute to adaptive evolution as well as sometimes to speciation itself, via hybrid speciation. Geographic races and species that coexist in sympatry therefore form part of a continuum in terms of hybridization rates or probability of gene flow. This finding concurs with the view that processes leading to speciation are continuous, rather than sudden, and that they are the same as those operating within species, rather than requiring special punctuated effects or complete allopatry. Although not qualitatively distinct from geographic races, nor "real" in terms of phylogenetic species concepts or the biological species concept, hybridizing species of Heliconius are stably distinct in sympatry, and remain useful groups for predicting morphological, ecological, behavioural and genetic characteristics.}, } @article {pmid17301281, year = {2007}, author = {Conville, PS and Witebsky, FG}, title = {Analysis of multiple differing copies of the 16S rRNA gene in five clinical isolates and three type strains of Nocardia species and implications for species assignment.}, journal = {Journal of clinical microbiology}, volume = {45}, number = {4}, pages = {1146-1151}, pmid = {17301281}, issn = {0095-1137}, support = {//Intramural NIH HHS/United States ; }, mesh = {Base Sequence ; DNA, Bacterial/chemistry/*genetics ; DNA, Ribosomal/chemistry/*genetics ; Gene Dosage ; Humans ; Molecular Sequence Data ; Nocardia/*classification/*genetics ; Nocardia Infections/microbiology ; Nucleic Acid Hybridization ; Point Mutation ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Five clinical isolates of Nocardia that showed ambiguous bases within the variable region of the 16S rRNA gene sequence were evaluated for the presence of multiple copies of this gene. The type strains of three Nocardia species, Nocardia concava, Nocardia ignorata, and Nocardia yamanashiensis, which also showed ambiguous bases in the variable region, were also examined. Cloning experiments using an amplified region of the 16S rRNA that contains the variable region showed that each isolate possessed 16S rRNA genes with at least two different sequences. In addition, hybridization studies using a 16S rRNA gene-specific probe and extracted genomic DNA of the patient isolates and of the type strain of N. ignorata showed that each isolate possessed at least three copies of the gene. These multiple differing copies of the 16S rRNA gene and the results of DNA-DNA hybridization studies indicate problems of species definition and identification for such isolates. A broader species concept than that currently in vogue may be required to accommodate such organisms.}, } @article {pmid17300983, year = {2007}, author = {Morgante, M and De Paoli, E and Radovic, S}, title = {Transposable elements and the plant pan-genomes.}, journal = {Current opinion in plant biology}, volume = {10}, number = {2}, pages = {149-155}, doi = {10.1016/j.pbi.2007.02.001}, pmid = {17300983}, issn = {1369-5266}, mesh = {Base Composition/genetics ; DNA Transposable Elements/*genetics ; Genetic Variation ; Genome, Plant/*genetics ; Models, Genetic ; }, abstract = {The comparative sequencing of several grass genomes has revealed that transposable elements are largely responsible for extensive variation in both intergenic and local genic content, not only between closely related species but also among individuals within a species. These observations indicate that a single genome sequence might not reflect the entire genomic complement of a species, and prompted us to introduce the concept of the plant pan-genome, which includes core genomic features that are common to all individuals and a dispensable genome composed of partially shared and/or non-shared DNA sequence elements. Uncovering the intriguing nature of the dispensable genome, namely its composition, origin and function, represents a step forward towards an understanding of the processes that generate genetic diversity and phenotypic variation. The developing view of transcriptional regulation as a complex and modular system, in which long-range interactions and the involvement of transposable elements are frequently observed, lends support to the possibility of an important functional role for the dispensable genome and could make it less dispensable than previously thought.}, } @article {pmid17298371, year = {2007}, author = {Sikorski, J and Nevo, E}, title = {Patterns of thermal adaptation of Bacillus simplex to the microclimatically contrasting slopes of 'Evolution Canyons' I and II, Israel.}, journal = {Environmental microbiology}, volume = {9}, number = {3}, pages = {716-726}, doi = {10.1111/j.1462-2920.2006.01193.x}, pmid = {17298371}, issn = {1462-2912}, mesh = {*Adaptation, Physiological ; Bacillus/*genetics/*growth & development/isolation & purification/physiology ; *Biological Evolution ; *Climate ; Ecosystem ; Europe ; Heat-Shock Response ; Hot Temperature ; Israel ; *Soil Microbiology ; Species Specificity ; *Temperature ; }, abstract = {Identification of selective forces that drive evolution and speciation of bacteria in natural habitats is a central issue in bacterial ecology and evolution. Exploring the adaptive evolution of Bacillus simplex at 'Evolution Canyons' I and II, Israel, we report here on the impact of high heat stress on the speciation progress of individual evolutionary lineages. These canyons represent similar ecological replicates, separated by 40 km, in which the orientation of the sun yields a strong sun-exposed and hot 'African' south-facing slope (SFS) versus a rather cooler and mesic-lush 'European' north-facing slope (NFS) within a distance of only 50-100 m at the bottom and 400 m at the top. Among 131 strains studied, in Luria-Bertani broth, 'African' strains grow better than 'European' strains at a stressful high temperature (43.25 degrees C). The results suggest that adaptation to the hotter and more stressful SFS is continuously ongoing. The patterns of heat adaptation override the phylogenetic history of individual lineages. A positive correlation of growth rates at 43.25 degrees C and 20 degrees C, more markedly among 'African' strains, reflects probably the broader temperature range on the SFS. Summarizing, the hot temperature stress on the 'African' slope is a major environmental force driving the twin evolutionary processes of adaptation and speciation of B. simplex at 'Evolution Canyon'. Finally, we discuss the data in light of current controversies on species concepts.}, } @article {pmid17298360, year = {2007}, author = {Boenigk, J and Jost, S and Stoeck, T and Garstecki, T}, title = {Differential thermal adaptation of clonal strains of a protist morphospecies originating from different climatic zones.}, journal = {Environmental microbiology}, volume = {9}, number = {3}, pages = {593-602}, doi = {10.1111/j.1462-2920.2006.01175.x}, pmid = {17298360}, issn = {1462-2912}, support = {P 18767/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Adaptation, Physiological ; Chrysophyta/*classification/genetics/growth & development/*physiology ; *Climate ; *Ecosystem ; Fresh Water/microbiology ; Molecular Sequence Data ; Seawater/microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; *Temperature ; }, abstract = {Eco-physiological variation and local adaptation are key issues in microbial ecology. Here, we investigated the thermal adaptation of 19 strains of the same Spumella morphospecies (Chrysophyceae, Heterokonta). In order to test for local adaptation and the existence of specific ecotypes we analysed growth rates of these strains, which originated from different climate regions. We applied temperature-adaptation as an eco-physiological marker and analysed growth rates of the different Spumella strains at temperatures between 0 degrees C and 35 degrees C. The temperatures allowing for maximal growth of strains from temperate and warm climatic zones ranged between 19.9 degrees C and 33.4 degrees C. Phylogenetically, most of these 'warm'-adapted strains fall into two different previously defined 18S rDNA Spumella clusters, one of them consisting of mostly soil organisms and the other one being a freshwater cluster. As a rule, the 'warm'-adapted strains of the soil cluster grew slower than the 'warm'-adapted isolates within the freshwater cluster. This difference most probably reflect different strategies, i.e. the formation of cysts at the expense of lower growth rates in soil organisms. In contrast, as expected, all isolates from Antarctica were cold-adapted and grew already around melting point of freshwater. Surprisingly, optimum temperature for these strains was between 11.8 degrees C and 17.7 degrees C and maximum temperature tolerated was between 14.6 degrees C and 23.5 degrees C. Our data indicate that despite the relatively high optimal temperature of most Antarctic strains, they may have a relative advantage below 5-10 degrees C only. Based on the thermal adaptation of the flagellate strains the Antarctic strains were clearly separated from the other investigated strains. This may indicate a limited dispersal of flagellates to and from Antarctica. Even if the latter assumption needs support from more data, we argue that the high levels of eco-physiological and molecular microdiversity indicate that the current species concepts do not sufficiently reflect protist eco-physiological differentiation.}, } @article {pmid17289408, year = {2007}, author = {Grünig, CR and Brunner, PC and Duò, A and Sieber, TN}, title = {Suitability of methods for species recognition in the Phialocephala fortinii-Acephala applanata species complex using DNA analysis.}, journal = {Fungal genetics and biology : FG & B}, volume = {44}, number = {8}, pages = {773-788}, doi = {10.1016/j.fgb.2006.12.008}, pmid = {17289408}, issn = {1087-1845}, mesh = {Ascomycota/*classification/genetics ; Cluster Analysis ; DNA, Fungal/chemistry/*genetics ; Fungal Proteins/genetics ; Genetics, Population ; Molecular Sequence Data ; Mycology/*methods ; Peptide Elongation Factor 1/genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Tubulin/genetics ; }, abstract = {Sequence data of two coding and three non-coding loci were used to study the taxonomic identity within and relatedness among seven previously defined cryptic species (CSP) of Phialocephala fortinii and Acephala applanata using two approaches of species recognition. Identification of taxonomic groups corresponding to CSP was ambiguous in some cases when applying solely the genealogical concordance phylogenetic species recognition (GCPSR) concept. The definition of groups corresponding to CSP using GCPSR was complicated due to shared sequence haplotypes between CSP, unresolved CSP for several loci, and possible introgression. GCPSR in conjunction with a population genetic approach improved resolution significantly and the CSP status could be confirmed for all seven CSP of P. fortinii s.l. The most critical step in both analyses was the definition of groups. The combination of several classes of markers differing in resolution helped to define species boundaries.}, } @article {pmid17265850, year = {2006}, author = {Imam, I and Labisch, A}, title = {Species sanitation of malaria in the Netherlands East Indies (1913-1942)--an example of applied medical history?.}, journal = {Medizinhistorisches Journal}, volume = {41}, number = {3-4}, pages = {291-313}, pmid = {17265850}, issn = {0025-8431}, mesh = {Animals ; *Anopheles ; History, 20th Century ; Humans ; Indonesia ; Malaria/*history ; Mosquito Control/*history ; World Health Organization/*history ; }, abstract = {To the World Health Organization malaria remains "one of the world's most important public health concerns". During the post-eradication era of the 1980s there was no clear answer to the following question: what kind of intervention could be effective against malaria in the 'roll-back malaria' programme? In this situation there were also calls for an 'applied history of medicine', since the anti-malaria programmes during the pre-eradication era might help overcome the crisis of finding an appropriate way to fight malaria. At this point the concept of species sanitation was considered. Developed in the 1920s in the former Netherlands East Indies the thrust of this concept is that anopheles, as obligatory vectors of malaria, have species-specific breeding sites; when these sites are sanitised, malaria is deprived of its ecological preconditions. This double question - the history of species sanitation and the possibility of an applied history of medicine - is the starting point of this paper. The results of the historical analysis are that in terms of the biological, technical, economical, social and political conditions, species sanitation remains limited to a few locally specified exceptions. The attempt to find answers in history demonstrates that an evaluation of historical anti-malaria measures can be helpful in determining the fundamental elements of a given situation necessary for an effective malaria control programme.}, } @article {pmid17255503, year = {2007}, author = {Fraser, C and Hanage, WP and Spratt, BG}, title = {Recombination and the nature of bacterial speciation.}, journal = {Science (New York, N.Y.)}, volume = {315}, number = {5811}, pages = {476-480}, pmid = {17255503}, issn = {1095-9203}, support = {030662//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Computer Simulation ; *Genetic Speciation ; Genetic Variation ; Models, Genetic ; *Recombination, Genetic ; Streptococcus/genetics ; }, abstract = {Genetic surveys reveal the diversity of bacteria and lead to the questioning of species concepts used to categorize bacteria. One difficulty in defining bacterial species arises from the high rates of recombination that results in the transfer of DNA between relatively distantly related bacteria. Barriers to this process, which could be used to define species naturally, are not apparent. Here, we review conceptual models of bacterial speciation and describe our computer simulations of speciation. Our findings suggest that the rate of recombination and its relation to genetic divergence have a strong influence on outcomes. We propose that a distinction be made between clonal divergence and sexual speciation. Hence, to make sense of bacterial diversity, we need data not only from genetic surveys but also from experimental determination of selection pressures and recombination rates and from theoretical models.}, } @article {pmid17237078, year = {2007}, author = {Górecki, P and Tiuryn, J}, title = {Inferring phylogeny from whole genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {23}, number = {2}, pages = {e116-22}, doi = {10.1093/bioinformatics/btl296}, pmid = {17237078}, issn = {1367-4811}, mesh = {*Algorithms ; Chromosome Mapping/*methods ; Conserved Sequence ; *Evolution, Molecular ; Genome, Fungal/*genetics ; *Phylogeny ; Proteome/*genetics ; Sequence Alignment/methods ; Sequence Analysis, Protein/*methods ; }, abstract = {MOTIVATION: Inferring species phylogenies with a history of gene losses and duplications is a challenging and an important task in computational biology. This problem can be solved by duplication-loss models in which the primary step is to reconcile a rooted gene tree with a rooted species tree. Most modern methods of phylogenetic reconstruction (from sequences) produce unrooted gene trees. This limitation leads to the problem of transforming unrooted gene tree into a rooted tree, and then reconciling rooted trees. The main questions are 'What about biological interpretation of choosing rooting?', 'Can we find efficiently the optimal rootings?', 'Is the optimal rooting unique?'.

RESULTS: In this paper we present a model of reconciling unrooted gene tree with a rooted species tree, which is based on a concept of choosing rooting which has minimal reconciliation cost. Our analysis leads to the surprising property that all the minimal rootings have identical distributions of gene duplications and gene losses in the species tree. It implies, in our opinion, that the concept of an optimal rooting is very robust, and thus biologically meaningful. Also, it has nice computational properties. We present a linear time and space algorithm for computing optimal rooting(s). This algorithm was used in two different ways to reconstruct the optimal species phylogeny of five known yeast genomes from approximately 4700 gene trees. Moreover, we determined locations (history) of all gene duplications and gene losses in the final species tree. It is interesting to notice that the top five species trees are the same for both methods.

AVAILABILITY: Software and documentation are freely available from http://bioputer.mimuw.edu.pl/~gorecki/urec}, } @article {pmid17220447, year = {2007}, author = {Goris, J and Konstantinidis, KT and Klappenbach, JA and Coenye, T and Vandamme, P and Tiedje, JM}, title = {DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {57}, number = {Pt 1}, pages = {81-91}, doi = {10.1099/ijs.0.64483-0}, pmid = {17220447}, issn = {1466-5026}, mesh = {*Bacterial Typing Techniques ; DNA, Bacterial/analysis/genetics ; Genome, Bacterial/*genetics ; Gram-Negative Bacteria/classification/genetics ; Gram-Positive Bacteria/classification/genetics ; Nucleic Acid Hybridization/*methods ; *Sequence Analysis, DNA ; }, abstract = {DNA-DNA hybridization (DDH) values have been used by bacterial taxonomists since the 1960s to determine relatedness between strains and are still the most important criterion in the delineation of bacterial species. Since the extent of hybridization between a pair of strains is ultimately governed by their respective genomic sequences, we examined the quantitative relationship between DDH values and genome sequence-derived parameters, such as the average nucleotide identity (ANI) of common genes and the percentage of conserved DNA. A total of 124 DDH values were determined for 28 strains for which genome sequences were available. The strains belong to six important and diverse groups of bacteria for which the intra-group 16S rRNA gene sequence identity was greater than 94 %. The results revealed a close relationship between DDH values and ANI and between DNA-DNA hybridization and the percentage of conserved DNA for each pair of strains. The recommended cut-off point of 70 % DDH for species delineation corresponded to 95 % ANI and 69 % conserved DNA. When the analysis was restricted to the protein-coding portion of the genome, 70 % DDH corresponded to 85 % conserved genes for a pair of strains. These results reveal extensive gene diversity within the current concept of "species". Examination of reciprocal values indicated that the level of experimental error associated with the DDH method is too high to reveal the subtle differences in genome size among the strains sampled. It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available.}, } @article {pmid17197201, year = {2007}, author = {Frøslev, TG and Jeppesen, TS and Laessøe, T and Kjøller, R}, title = {Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe.}, journal = {Molecular phylogenetics and evolution}, volume = {44}, number = {1}, pages = {217-227}, doi = {10.1016/j.ympev.2006.11.013}, pmid = {17197201}, issn = {1055-7903}, mesh = {Agaricales/classification/*genetics ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/drug effects ; Europe ; *Genetic Speciation ; Molecular Sequence Data ; *Phylogeny ; RNA Polymerase II/genetics ; Sequence Analysis, DNA ; }, abstract = {Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to different taxonomic schools. Here, we evaluated species delimitation within this taxonomically difficult group of species and estimated their phylogenetic relationships. Species were delimited by phylogenetic inference and by comparison of ITS sequence data in combination with morphological characters. A total of 421 ITS sequences were analyzed, including data from 53 type specimens. The phylogenetic relationships of the identified species were estimated by analyzing ITS data in combination with sequence data from the two largest subunits of RNA polymerase II (RPB1 and RPB2). Seventy-nine species were identified, which are believed to constitute the bulk of the diversity of this group in Europe. The delimitation of species based on ITS sequences is more consistent with a conservative morphological species concept for most groups. ITS sequence data from 30 of the 53 types were identical to other taxa, and most of these can be readily treated as synonyms. This emphasizes the importance of critical analysis of collections before describing new taxa. The phylogenetic separation of species was, in general, unambiguous and there is considerable potential for using ITS sequence data as a barcode for the group. A high level of homoplasy and phenotypic plasticity was observed for morphological and ecological characters. Whereas most species and several minor lineages can be recognized by morphological and ecological character states, these same states are poor indicators at higher levels.}, } @article {pmid20228966, year = {2007}, author = {Katz, JS and Wright, AA and Bodily, KD}, title = {Issues in the Comparative Cognition of Abstract-Concept Learning.}, journal = {Comparative cognition & behavior reviews}, volume = {2}, number = {}, pages = {79-92}, pmid = {20228966}, issn = {1911-4745}, support = {R01 MH061798/MH/NIMH NIH HHS/United States ; R01 MH072616/MH/NIMH NIH HHS/United States ; R01 MH072616-02/MH/NIMH NIH HHS/United States ; }, abstract = {-concept learning, including same/different and matching-to-sample concept learning, provides the basis for many other forms of "higher" cognition. The issue of which species can learn abstract concepts and the extent to which abstract-concept learning is expressed across species is discussed. Definitive answers to this issue are argued to depend on the subjects' learning strategy (e.g., a relational-learning strategy) and the particular procedures used to test for abstract-concept learning. Some critical procedures that we have identified are: How to present the items to-be-compared (e.g., in pairs), a high criterion for claiming abstract-concept learning (e.g., transfer performance equivalent to baseline performance), and systematic manipulation of the training set (e.g., increases in the number of rule exemplars when transfer is less than baseline performance). The research covered in this article on the recent advancements in abstract-concept learning show this basic ability in higher-order cognitive processing is common to many animal species and that "uniqueness" may be limited more to how quickly new abstract concepts are learned rather than to the ability itself.}, } @article {pmid19924266, year = {2007}, author = {Bradley, RD and Durish, ND and Rogers, DS and Miller, JR and Engstrom, MD and Kilpatrick, CW}, title = {TOWARD A MOLECULAR PHYLOGENY FOR PEROMYSCUS: EVIDENCE FROM MITOCHONDRIAL CYTOCHROME-b SEQUENCES.}, journal = {Journal of mammalogy}, volume = {88}, number = {5}, pages = {1146-1159}, pmid = {19924266}, issn = {0022-2372}, support = {R01 AI041435/AI/NIAID NIH HHS/United States ; R01 AI041435-08/AI/NIAID NIH HHS/United States ; }, abstract = {One hundred DNA sequences from the mitochondrial cytochrome-b gene of 44 species of deer mice (Peromyscus (sensu stricto), 1 of Habromys, 1 of Isthmomys, 2 of Megadontomys, and the monotypic genera Neotomodon, Osgoodomys, and Podomys were used to develop a molecular phylogeny for Peromyscus. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were conducted to evaluate alternative hypotheses concerning taxonomic arrangements (sensu stricto versus sensu lato) of the genus. In all analyses, monophyletic clades were obtained that corresponded to species groups proposed by previous authors; however, relationships among species groups generally were poorly resolved. The concept of the genus Peromyscus based on molecular data differed significantly from the most current taxonomic arrangement. Maximum-likelihood and Bayesian trees depicted strong support for a clade placing Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys within Peromyscus. If Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are regarded as genera, then several species groups within Peromyscus (sensu stricto) should be elevated to generic rank. Isthmomys was associated with the genus Reithrodontomys; in turn this clade was sister to Baiomys, indicating a distant relationship of Isthmomys to Peromyscus. A formal taxonomic revision awaits synthesis of additional sequence data from nuclear markers together with inclusion of available allozymic and karyotypic data.}, } @article {pmid17181793, year = {2006}, author = {Haig, SM and Beever, EA and Chambers, SM and Draheim, HM and Dugger, BD and Dunham, S and Elliott-Smith, E and Fontaine, JB and Kesler, DC and Knaus, BJ and Lopes, IF and Loschl, P and Mullins, TD and Sheffield, LM}, title = {Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {20}, number = {6}, pages = {1584-1594}, doi = {10.1111/j.1523-1739.2006.00530.x}, pmid = {17181793}, issn = {0888-8892}, mesh = {Animals ; *Classification ; Conservation of Natural Resources/*legislation & jurisprudence/methods ; *Ecosystem ; Extinction, Biological ; Government Regulation ; Phylogeny ; Species Specificity ; United States ; }, abstract = {The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.}, } @article {pmid17173970, year = {2007}, author = {Fourie, F and Reinecke, SA and Reinecke, AJ}, title = {The determination of earthworm species sensitivity differences to cadmium genotoxicity using the comet assay.}, journal = {Ecotoxicology and environmental safety}, volume = {67}, number = {3}, pages = {361-368}, doi = {10.1016/j.ecoenv.2006.10.005}, pmid = {17173970}, issn = {0147-6513}, mesh = {Animals ; Cadmium/*toxicity ; Comet Assay/instrumentation/*methods ; *DNA Damage ; Environmental Monitoring ; Oligochaeta/classification/*drug effects/physiology ; Risk Assessment ; Soil Pollutants/*toxicity ; Species Specificity ; }, abstract = {The concept of species sensitivity differences is important in ecotoxicology and environmental risk assessment, but testing usually focuses on lethality of toxicants. The effects on the suborganismal level are mostly ignored; therefore, the present study assessed a biomarker of genotoxicity (the alkaline comet assay) to compare species sensitivities. Five earthworm species (Amynthas diffringens, Aporrectodea caliginosa, Dendrodrilus rubidus, Eisenia fetida and Microchaetus benhami) were exposed for 48 h to sublethal concentrations of cadmium sulphate in reconstituted soil water and DNA integrity was evaluated with the parameter Tail DNA %. Significant amounts of DNA damage were detected in three (A. caliginosa, D. rubidus and E. fetida) species. E. fetida exhibited the highest level of DNA damage, although D. rubidus showed the highest increase (3-fold) in DNA damage from the control. All exposed earthworms accumulated Cd, although body loads did not correspond with DNA damage levels; most of the Cd was probably sequestrated and rendered harmless.}, } @article {pmid17163148, year = {2006}, author = {Riapis, LA}, title = {[Concept of a bacterial species and the evolution of the prokaryotic genome].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {6}, pages = {97-101}, pmid = {17163148}, issn = {0372-9311}, mesh = {Bacteria/*classification/*genetics/pathogenicity ; Bacterial Infections/*microbiology ; Evolution, Molecular ; *Genome, Bacterial ; Humans ; Recombination, Genetic ; Species Specificity ; Virulence/genetics ; }, abstract = {The present concepts of evolution and species delineation in prokaryotes are considered. Recently a considerable extension of knowledge on the processes of microevolution of medically significant bacteria was noted alongside with the importance of horizontal and lateral transfer of genes. The phylophenetic concept of species was considered in detail. The inclusion of the ecological criterion into a phylophenetic concept of a species is supposed to facilitate the development of more adequate notion on the evolution of bacteria, the improvement of species delineation in prokaryotes, their classification and nomenclature.}, } @article {pmid17161018, year = {2006}, author = {Bobbert, M}, title = {Ethical questions concerning research on human embryos, embryonic stem cells and chimeras.}, journal = {Biotechnology journal}, volume = {1}, number = {12}, pages = {1352-1369}, doi = {10.1002/biot.200600179}, pmid = {17161018}, issn = {1860-7314}, mesh = {Cloning, Organism/*ethics ; Embryo Disposition/*ethics ; *Embryonic Stem Cells ; Germany ; Humans ; Reproductive Techniques, Assisted/*ethics ; Research Embryo Creation/*ethics ; Stem Cell Transplantation/*ethics ; }, abstract = {Research using human embryos and embryonic stem cells is viewed as important for various reasons. Apart from questions concerning legal regulations, numerous ethical objections are raised pertaining to the use of surplus embryos from reproductive medicine as well as the creation of embryos and stem cells through cloning. In the hopes of avoiding ethical problems, alternatives have been proposed including the extraction of egg cells from "dead" embryos derived from in vitro fertilization procedures, the extraction of pluripotent stem cells from blastocysts, technologies such as "altered nuclear transfer" (ANT) and "oocyte-assisted reprogramming" (ANT-OAR) as well as parthenogenesis. Initial ethical assessments show that certain questions pertaining to such strategies have remained unanswered. Furthermore, with the help of new or more differentiated biotechnological procedures, it is possible to create chimeras and hybrids in which human and non-human cells are combined. Human-animal chimeras, in which gametes or embryonic tissue have been mixed with embryonic or adult stem cells, demonstrate a different "quality" and "degree of penetration" from those produced in previous experiments. Not only does this have consequences regarding questions of patentability, this situation also raises fundamental questions concerning the human being's self image, the concept of person, identity and species and the moral rights and duties that are connected with such concepts. There is a need for legal regulation, on the national as well as the international level.}, } @article {pmid17140099, year = {2006}, author = {Sansonetti, P}, title = {[How to define the species barrier to pathogen transmission?].}, journal = {Bulletin de l'Academie nationale de medecine}, volume = {190}, number = {3}, pages = {611-22; discussion 623, 625-7}, pmid = {17140099}, issn = {0001-4079}, mesh = {Animals ; Birds ; Carrier State ; Communicable Diseases, Emerging/genetics/immunology/microbiology/*transmission ; Disease Models, Animal ; Disease Reservoirs ; Disease Vectors ; Ducks ; Humans ; Influenza in Birds/transmission ; Influenza, Human/transmission ; Mice ; Mice, Transgenic ; Mutation ; Phenotype ; Recombination, Genetic ; Species Specificity ; Virus Diseases/genetics/immunology/transmission ; Zoonoses/etiology/microbiology/*transmission ; }, abstract = {A given microbial pathogen usually targets a restricted number of animal species. Some pathogens can be transmitted to humans from another animal species, either directly (rabies, brucellosis, etc.) or through a vector (Lyme's disease, West Nile fever, etc.). Few infectious agents with animal reservoirs infect humans, and even fewer are capable of human-human transmission. This is attributed to the "species barrier", a simplistic concept that in fact involves a series of conditions for successful inter-species transmission. These include access to an infectable surface, multiplication on that surface, colonisation, invasion, multiplication inside the new host, and resistance to innate and adaptive immune mechanisms. Each of these steps requires a specific ligand-receptor interaction. The full series of events must be "reprogrammed" for efficient implantation in a new host. These changes occur through mutations or genetic exchanges. Direct human-to-human transmission often requires additional adaptive modifications.}, } @article {pmid21672808, year = {2006}, author = {Lutton, B and Callard, I}, title = {Evolution of reproductive-immune interactions.}, journal = {Integrative and comparative biology}, volume = {46}, number = {6}, pages = {1060-1071}, doi = {10.1093/icb/icl050}, pmid = {21672808}, issn = {1540-7063}, abstract = {The comparative approach in biological sciences has provided valuable insights into the role of different organ systems in adaptation and evolution, and seeks to establish unifying themes. This approach also plays a key role in identifying model species and systems for the study of specific questions and problems. Further, by applying the concept of homology, information about nonmammalian species may be used either to directly understand mammalian/human regulatory processes, or to formulate hypotheses for direct testing. Individual physiological systems function in a milieu provided by the integrated activities of all of the systems to adapt, adjust and sustain the organism in its environment. The overlapping interfaces between the different physiological systems provide fertile ground for new insights and to enhance our knowledge. These interdisciplinary areas are of great importance if we are to understand the full complexity of organismal function. Of particular interest are the interactions between the reproductive system and the immune system. The reproductive system is unique in that its primary role is to assure the continuity of the species, while the immune system provides internal protection and thus facilitates continued health and survival. The modus operandi of these 2 morphologically diffuse systems involves widely distributed chemical signals in response to environmental input, and both systems must interact for the normal functioning of each. While the major focus of reproductive-immune research has historically been with mammals, and has provided substantial insight into the interactions between these physiological systems, comparative studies offer unique perspectives. Further, dysregulation of normal physiological interactions between the reproductive and immune systems can lead to disorders and diseases effecting one system or the other. Thus, comparative studies of these interactions may shed some light upon the evolutionary mechanisms involved in such cases.}, } @article {pmid17135463, year = {2006}, author = {Rubinoff, D and Cameron, S and Will, K}, title = {A genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification.}, journal = {The Journal of heredity}, volume = {97}, number = {6}, pages = {581-594}, doi = {10.1093/jhered/esl036}, pmid = {17135463}, issn = {0022-1503}, mesh = {Animals ; *Biodiversity ; Classification/*methods ; DNA, Mitochondrial/*chemistry ; Evolution, Molecular ; Genome ; Phylogeny ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {Approximately 600-bp sequences of mitochondrial DNA (mtDNA) have been designated as "DNA barcodes" and have become one of the most contentious and animated issues in the application of genetic information to global biodiversity assessment and species identification. Advocates of DNA barcodes have received extensive attention and promotion in many popular and refereed scientific publications. However, we suggest that the utility of barcodes is suspect and vulnerable to technical challenges that are particularly pertinent to mtDNA. We review the natural history of mtDNA and discuss problems for barcoding which are particularly associated with mtDNA and inheritance, including reduced effective population size, maternal inheritance, recombination, inconsistent mutation rate, heteroplasmy, and compounding evolutionary processes. The aforementioned could significantly limit the application and utility of mtDNA barcoding efforts. Furthermore, global use of barcodes will require application and acceptance of a barcode-based species concept that has not been evaluated in the context of the extensive literature concerning species designation. Implementation of mtDNA barcodes in spite of technical and practical shortcomings we discuss may degrade the longstanding synthesis of genetic and organism-based research and will not advance studies ranging from genomic evolution to biodiversity assessment.}, } @article {pmid17132047, year = {2006}, author = {Courchamp, F and Angulo, E and Rivalan, P and Hall, RJ and Signoret, L and Bull, L and Meinard, Y}, title = {Rarity value and species extinction: the anthropogenic Allee effect.}, journal = {PLoS biology}, volume = {4}, number = {12}, pages = {e415}, pmid = {17132047}, issn = {1545-7885}, mesh = {Animals ; Animals, Domestic ; Biodiversity ; Empirical Research ; *Extinction, Biological ; Humans ; Medicine, Traditional ; *Models, Theoretical ; }, abstract = {Standard economic theory predicts that exploitation alone is unlikely to result in species extinction because of the escalating costs of finding the last individuals of a declining species. We argue that the human predisposition to place exaggerated value on rarity fuels disproportionate exploitation of rare species, rendering them even rarer and thus more desirable, ultimately leading them into an extinction vortex. Here we present a simple mathematical model and various empirical examples to show how the value attributed to rarity in some human activities could precipitate the extinction of rare species-a concept that we term the anthropogenic Allee effect. The alarming finding that human perception of rarity can precipitate species extinction has serious implications for the conservation of species that are rare or that may become so, be they charismatic and emblematic or simply likely to become fashionable for certain activities.}, } @article {pmid17120882, year = {2006}, author = {Wolbring, G}, title = {Three challenges to the Ottawa Spirit of Health promotion, trends in global health, and disabled people.}, journal = {Canadian journal of public health = Revue canadienne de sante publique}, volume = {97}, number = {5}, pages = {405-408}, pmid = {17120882}, issn = {0008-4263}, mesh = {Canada ; *Disabled Persons ; Health Promotion/*organization & administration/trends ; *Human Rights ; Humans ; *Public Health ; }, abstract = {Health promotion according to the 1986 Ottawa Charter of the first global health promotion conference "is the process of enabling people to increase control over, and to improve, their health. To reach a state of complete physical, mental and social well-being, an individual or group must be able to identify and to realize aspirations, to satisfy needs, and to change or cope with the environment". In this commentary, I explore three powerful challenges to the spirit of the Ottawa Charter and to global health. The first challenge is the departure from the WHO definition of health; the second challenge relates to the appearance of the transhumanist/enhancement model of health which includes human performance enhancement beyond species-typical boundaries as part of the concept of health. The third challenge consists of the limited involvement and understanding of disabled people with their different models of 'disability/impairment' (medical, social, transhumanist/enhancement) in the discourse of global health and health promotion. Not dealing with these challenges impairs the ability of health promotion to deal with global health problems, the 'health' needs of marginalized groups--in particular, disabled people--and the Millennium Development Goals.}, } @article {pmid17081107, year = {2006}, author = {Schieke, SM and Finkel, T}, title = {Mitochondrial signaling, TOR, and life span.}, journal = {Biological chemistry}, volume = {387}, number = {10-11}, pages = {1357-1361}, doi = {10.1515/BC.2006.170}, pmid = {17081107}, issn = {1431-6730}, mesh = {Aging/physiology ; Animals ; Humans ; Life Expectancy ; Mitochondria/*metabolism ; Protein Kinases/*metabolism ; *Signal Transduction ; TOR Serine-Threonine Kinases ; }, abstract = {Growing evidence supports the concept that mitochondrial metabolism and reactive oxygen species (ROS) play a major role in aging and determination of an organism's life span. Cellular signaling pathways regulating mitochondrial activity, and hence the generation of ROS and retrograde signaling events originating in mitochondria, have recently moved into the spotlight in aging research. Involvement of the energy-sensing TOR pathway in both mitochondrial signaling and determination of life span has been shown in several studies. This brief review summarizes the recent progress on how mitochondrial signaling might contribute to the aging process with a particular emphasis on TOR signaling from invertebrates to humans.}, } @article {pmid17064284, year = {2006}, author = {Dei-Cas, E and Chabé, M and Moukhlis, R and Durand-Joly, I and Aliouat, el M and Stringer, JR and Cushion, M and Noël, C and de Hoog, GS and Guillot, J and Viscogliosi, E}, title = {Pneumocystis oryctolagi sp. nov., an uncultured fungus causing pneumonia in rabbits at weaning: review of current knowledge, and description of a new taxon on genotypic, phylogenetic and phenotypic bases.}, journal = {FEMS microbiology reviews}, volume = {30}, number = {6}, pages = {853-871}, doi = {10.1111/j.1574-6976.2006.00037.x}, pmid = {17064284}, issn = {0168-6445}, mesh = {Animals ; Animals, Wild/microbiology ; France ; Fungal Proteins/genetics ; Genes, Fungal ; Lung/microbiology ; Microscopy, Electron ; Molecular Sequence Data ; Phylogeny ; Pneumocystis/*classification/genetics/isolation & purification/pathogenicity/ultrastructure ; Pneumonia, Pneumocystis/microbiology/*veterinary ; Rabbits/microbiology ; Species Specificity ; }, abstract = {The genus Pneumocystis comprises noncultivable, highly diversified fungal pathogens dwelling in the lungs of mammals. The genus includes numerous host-species-specific species that are able to induce severe pneumonitis, especially in severely immunocompromised hosts. Pneumocystis organisms attach specifically to type-1 epithelial alveolar cells, showing a high level of subtle and efficient adaptation to the alveolar microenvironment. Pneumocystis species show little difference at the light microscopy level but DNA sequences of Pneumocystis from humans, other primates, rodents, rabbits, insectivores and other mammals present a host-species-related marked divergence. Consistently, selective infectivity could be proven by cross-infection experiments. Furthermore, phylogeny among primate Pneumocystis species was correlated with the phylogeny of their hosts. This observation suggested that cophylogeny could explain both the current distribution of pathogens in their hosts and the speciation. Thus, molecular, ultrastructural and biological differences among organisms from different mammals strengthen the view of multiple species existing within the genus Pneumocystis. The following species were subsequently described: Pneumocystis jirovecii in humans, Pneumocystis carinii and Pneumocystis wakefieldiae in rats, and Pneumocystis murina in mice. The present work focuses on Pneumocystis oryctolagi sp. nov. from Old-World rabbits. This new species has been described on the basis of both biological and phylogenetic species concepts.}, } @article {pmid17062414, year = {2006}, author = {Fenchel, T and Finlay, BJ}, title = {The diversity of microbes: resurgence of the phenotype.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {361}, number = {1475}, pages = {1965-1973}, pmid = {17062414}, issn = {0962-8436}, mesh = {Bacteria/*classification/*cytology/genetics ; *Biodiversity ; Classification/*methods ; Geography ; *Phenotype ; *Phylogeny ; Species Specificity ; }, abstract = {The introduction of molecular genetic methods has caused confusion about the nature of microbial species. Environmental DNA extraction has indicated the existence of a vast diversity of genotypes, but how this relates to functional and phenotypic diversity has not been sufficiently explored. It has been implied that genetic distance per se correlates with phenotypic differentiation and thus reflects subtle (but undiscovered) adaptive fine-tuning to the environment, and that microbes may show biogeographic patterns at the genetic level. Here, we argue that no theoretically based species concept exists; species represent only the basic unit in the taxonomic hierarchy. The significance of naming species is that it organizes biological information. The reason why microbial species collectively represent large genetic differences is owing to huge absolute population sizes, absence of allopatric speciation and low extinction rates. Microbial phenotypes are, therefore, ancient in terms of the geological time-scale and have been maintained through stabilizing selection. These problems are discussed with special reference to eukaryotic micro-organisms.}, } @article {pmid17062410, year = {2006}, author = {Gevers, D and Dawyndt, P and Vandamme, P and Willems, A and Vancanneyt, M and Swings, J and De Vos, P}, title = {Stepping stones towards a new prokaryotic taxonomy.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {361}, number = {1475}, pages = {1911-1916}, pmid = {17062410}, issn = {0962-8436}, mesh = {Archaea/*classification ; Bacteria/*classification ; Classification/*methods ; *Phylogeny ; }, abstract = {Technological developments provide new insights into prokaryotic evolution and diversity and provoke a continuous need to update taxonomy and revise classification schemes. Our present species concept and definition are being challenged by the growing amount of whole genomic information, which should allow improvements in the natural species definition. The continuous quest for an objective and stable method for sorting strains into coherent homogeneous groups is inherent to prokaryotic systematics and nomenclature. Morphological, biochemical, physiological, phenotypic and chemotaxonomic criteria have been complemented by molecular data and pragmatic, purpose built, species definitions are being replaced by more natural ones based on evolutionary insights. It is imperative to give due consideration to both fundamental and applied aspects of future species concepts and definitions. The present paper discusses the present practice in prokaryotic taxonomy of how this system developed and how it may evolve in the future.}, } @article {pmid17062409, year = {2006}, author = {Staley, JT}, title = {The bacterial species dilemma and the genomic-phylogenetic species concept.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {361}, number = {1475}, pages = {1899-1909}, pmid = {17062409}, issn = {0962-8436}, mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Classification/*methods ; *Genetic Speciation ; Genetic Techniques ; *Phylogeny ; Species Specificity ; }, abstract = {The number of species of Bacteria and Archaea (ca 5000) is surprisingly small considering their early evolution, genetic diversity and residence in all ecosystems. The bacterial species definition accounts in part for the small number of named species. The primary procedures required to identify new species of Bacteria and Archaea are DNA-DNA hybridization and phenotypic characterization. Recently, 16S rRNA gene sequencing and phylogenetic analysis have been applied to bacterial taxonomy. Although 16S phylogeny is arguably excellent for classification of Bacteria and Archaea from the Domain level down to the family or genus, it lacks resolution below that level. Newer approaches, including multilocus sequence analysis, and genome sequence and microarray analyses, promise to provide necessary information to better understand bacterial speciation. Indeed, recent data using these approaches, while meagre, support the view that speciation processes may occur at the subspecies level within ecological niches (ecovars) and owing to biogeography (geovars). A major dilemma for bacterial taxonomists is how to incorporate this new information into the present hierarchical system for classification of Bacteria and Archaea without causing undesirable confusion and contention. This author proposes the genomic-phylogenetic species concept (GPSC) for the taxonomy of prokaryotes. The aim is twofold. First, the GPSC would provide a conceptual and testable framework for bacterial taxonomy. Second, the GPSC would replace the burdensome requirement for DNA hybridization presently needed to describe new species. Furthermore, the GPSC is consistent with the present treatment at higher taxonomic levels.}, } @article {pmid17061380, year = {2006}, author = {Myskja, BK}, title = {The moral difference between intragenic and transgenic modification of plants.}, journal = {Journal of agricultural & environmental ethics}, volume = {19}, number = {3}, pages = {225-238}, doi = {10.1007/s10806-005-6164-0}, pmid = {17061380}, issn = {1187-7863}, mesh = {Community Participation ; Crops, Agricultural ; Food Supply ; Food, Genetically Modified ; Genetic Engineering/*classification/*ethics/*methods ; Organisms, Genetically Modified/genetics ; Plants/*classification/*genetics ; Plants, Genetically Modified/*classification/*genetics ; *Public Opinion ; Risk Assessment ; *Species Specificity ; Uncertainty ; Wedge Argument ; }, abstract = {Public policy on the development and use of genetically modified organisms (GMOs) has mainly been concerned with defining proper strategies of risk management. However, surveys and focus group interviews show that although lay people are concerned with risks, they also emphasize that genetic modification is ethically questionable in itself. Many people feel that this technology "tampers with nature" in an unacceptable manner. This is often identified as an objection to the crossing of species borders in producing transgenic organisms. Most scientists reject these opinions as based on insufficient knowledge about biotechnology, the concept of species, and nature in general. Some recent projects of genetic modification aim to accommodate the above mentioned concerns by altering the expression of endogenous genes rather than introducing genes from other species. There can be good scientific reasons for this approach, in addition to strategic reasons related to greater public acceptability. But are there also moral reasons for choosing intragenic rather than transgenic modification? I suggest three interrelated moral reasons for giving priority to intragenic modification. First, we should respect the opinions of lay people even when their view is contrary to scientific consensus; they express an alternative world-view, not scientific ignorance. Second, staying within species borders by strengthening endogenous traits reduces the risks and scientific uncertainty. Third, we should show respect for nature as a complex system of laws and interconnections that we cannot fully control. The main moral reason for intragenic modification, in our view, is the need to respect the "otherness" of nature.}, } @article {pmid17040683, year = {1998}, author = {de Meeûs, T and Michalakis, Y and Renaud, F}, title = {Santa rosalia revisited: or why are there so many kinds of parasites in ;the garden of earthly delights'?.}, journal = {Parasitology today (Personal ed.)}, volume = {14}, number = {1}, pages = {10-13}, doi = {10.1016/s0169-4758(97)01163-0}, pmid = {17040683}, issn = {0169-4758}, abstract = {As is the case for free-living species, a very large number of parasitic species are not described adequately by the biological species concept. Furthermore, Thierry de Meeûs, Yannis Michalakis and François Renaud argue that because hosts represent a highly heterogeneous and changing environment as well as a breeding site, favouring the association of host-adaptation and host-choice genes, sympatric speciation may occur frequently in parasitic organisms. Therefore, parasites appear to be ideal biological models for the study of ecological specialization and speciation. Beyond the relevance of such considerations in fundamental science, the study of the origin and evolution of parasite diversity has important implications for more applied fields such as epidemiology and diagnosis.}, } @article {pmid17034624, year = {2006}, author = {Tani, N and Yoshimaru, H and Kawahara, T and Hoshi, Y and Nobushima, F and Yasui, T}, title = {Determination of the genetic structure of remnant Morus boninensis Koidz. trees to establish a conservation program on the Bonin Islands, Japan.}, journal = {BMC ecology}, volume = {6}, number = {}, pages = {14}, pmid = {17034624}, issn = {1472-6785}, mesh = {*Conservation of Natural Resources ; DNA, Plant/*genetics ; *Genetic Variation ; Japan ; Microsatellite Repeats/genetics ; Morus/*genetics ; }, abstract = {BACKGROUND: Morus boninensis, is an endemic plant of the Bonin (Ogasawara) Islands of Japan and is categorized as "critically endangered" in the Japanese red data book. However, little information is available about its ecological, evolutionary and genetic status, despite the urgent need for guidelines for the conservation of the species. Therefore, we adopted Moritz's MU concept, based on the species' current genetic structure, to define management units and to select mother tree candidates for seed orchards.

RESULTS: Nearly all individuals of the species were genotyped on the basis of seven microsatellite markers. Genetic diversity levels in putative natural populations were higher than in putative man-made populations with the exception of those on Otouto-jima Island. This is because a limited number of maternal trees are likely to have been used for seed collection to establish the man-made populations. A model-based clustering analysis clearly distinguished individuals into nine clusters, with a large difference in genetic composition between the population on Otouto-jima Island, the putative natural populations and the putative man-made populations. The Otouto-jima population appeared to be genetically differentiated from the others; a finding that was also supported by pairwise FST and RST analysis. Although multiple clusters were detected in the putative man-made populations, the pattern of genetic diversity was monotonous in comparison to the natural populations.

CONCLUSION: The genotyping by microsatellite markers revealed strong genetic structures. Typically, artificial propagation of this species has ignored the genetic structure, relying only on seeds from Otouto-jima for replanting on other islands, because of a problem with inter-specific hybridization on Chichi-jima and Haha-jima Islands. However, this study demonstrates that we should be taking into consideration the genetic structure of the species when designing a propagation program for the conservation of this species.}, } @article {pmid17020593, year = {2006}, author = {Doolittle, WF and Papke, RT}, title = {Genomics and the bacterial species problem.}, journal = {Genome biology}, volume = {7}, number = {9}, pages = {116}, pmid = {17020593}, issn = {1474-760X}, mesh = {Bacteria/classification/*genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Bacterial ; Genomics ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Whether or not bacteria have species is a perennially vexatious question. Given what we now know about variation among bacterial genomes, we argue that there is no intrinsic reason why the processes driving diversification and adaptation must produce groups of individuals sufficiently coherent in their genetic and phenotypic properties to merit the designation 'species'--although sometimes they might.}, } @article {pmid17002756, year = {2006}, author = {Vucetich, JA and Nelson, MP and Phillips, MK}, title = {The normative dimension and legal meaning of endangered and recovery in the U.S. Endangered Species Act.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {20}, number = {5}, pages = {1383-1390}, doi = {10.1111/j.1523-1739.2006.00493.x}, pmid = {17002756}, issn = {0888-8892}, mesh = {Conservation of Natural Resources/*legislation & jurisprudence ; *Ecosystem ; *Government Regulation ; Population Dynamics ; Public Policy ; *Terminology as Topic ; United States ; }, abstract = {The ethical, legal, and social significance of the U.S. Endangered Species Act of 1973 (ESA) is widely appreciated. Much of the significance of the act arises from the legal definitions that the act provides for the terms threatened species and endangered species. The meanings of these terms are important because they give legal meaning to the concept of a recovered species. Unfortunately, the meanings of these terms are often misapprehended and rarely subjected to formal analysis. We analyzed the legal meaning of recovered species and illustrate key points with details from "recovery" efforts for the gray wolf (Canis lupus). We focused on interpreting the phrase "significant portion of its range," which is part of the legal definition of endangered species. We argue that recovery and endangerment entail a fundamentally normative dimension (i.e., specifying conditions of endangerment) and a fundamentally scientific dimension (i.e., determining whether a species meets the conditions of endangerment). Specifying conditions for endangerment is largely normative because it judges risks of extinction to be either acceptable or unacceptable. Like many other laws that specify what is unacceptable, the ESA largely specifies the conditions that constitute unacceptable extinction risk. The ESA specifies unacceptable risks of extinction by defining endangered species in terms of the portion of a species' range over which a species is "in danger of extinction." Our analysis indicated that (1) legal recovery entails much more than the scientific notion of population viability, (2) most efforts to recover endangered species are grossly inadequate, and (3) many unlisted species meet the legal definition of an endangered or threatened species.}, } @article {pmid16997582, year = {2007}, author = {Hillis, DM}, title = {Constraints in naming parts of the Tree of Life.}, journal = {Molecular phylogenetics and evolution}, volume = {42}, number = {2}, pages = {331-338}, doi = {10.1016/j.ympev.2006.08.001}, pmid = {16997582}, issn = {1055-7903}, mesh = {Amphibians/*classification/genetics ; Animals ; Classification/*methods ; *Phylogeny ; Reproducibility of Results ; *Terminology as Topic ; }, abstract = {There are now overlapping codes of nomenclature that govern some of the same names of biological taxa. The International Code of Zoological Nomenclature (ICZN) uses the non-evolutionary concept of a "type species" to fix the names of animal taxa to particular ranks in the nomenclatural hierarchy. The PhyloCode, in contrast, uses phylogenetic definitions for supraspecific taxa at any hierarchical level within the Tree of Life (without associating the names to particular ranks), but does not deal with the names of species. Thus, biologists who develop classifications of animals need to use both systems of nomenclature, or else operate without formal rules for the names of some taxa (either species or many monophyletic groups). In addition, the ICZN does not permit the unique naming of many taxa that are considered to be between the ranks of genus and species. Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] provided recommendations for the classification of New World true frogs that utilized the ICZN to provide names for species, and the PhyloCode to provide names for supraspecific taxa. Nonetheless, they created new taxon names that followed both sets of rules, to avoid conflicting classifications. They also recommended that established names for both species and clades be used whenever possible, to stabilize the names of both species and clades under either set of rules, and to avoid conflicting nomenclatures. Dubois [Dubois, A., 2006. Naming taxa from cladograms: a cautionary tale. Mol. Phylogenet. Evol., 42, 317-330] objected to these principles, and argued that the names provided by Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] are unavailable under the ICZN, and that the two nomenclatural systems are incompatible. Here, I argue that he is incorrect in these assertions, and present arguments for retaining the established names of New World true frogs, which are largely compatible under both sets of nomenclatural rules.}, } @article {pmid16983567, year = {2006}, author = {Kovács, GM and Jakucs, E}, title = {Morphological and molecular comparison of white truffle ectomycorrhizae.}, journal = {Mycorrhiza}, volume = {16}, number = {8}, pages = {567-574}, pmid = {16983567}, issn = {0940-6360}, mesh = {Basidiomycota/*cytology/*genetics ; Mycorrhizae/*cytology/*genetics ; Phylogeny ; Populus/microbiology ; }, abstract = {In the present study, white truffle ectomycorrhizae (EM) collected in deciduous forests (Populus, Quercus, and Fagus) from Hungary were characterized by morphological-anatomical and molecular methods. Our investigations suggest that the EM of white truffles (e.g., Tuber rapaeodorum, Tuber puberulum, Tuber rufum) are common and abundant members of the forest communities in the area. The ITS sequences of 14 EM specimens and 46 additional fruitbody sequences from the GenBank were clustered into four main groups in phylogenetic analyses. In the ITS-1 region, a characteristic indel pattern was found, which supports the clades. Although our analyses indicate definite genetic distance between the groups of the phylogenetic tree, these clades do not correspond to the traditional taxons identified by fruitbody characteristics. Comparison of the ectomycorrhizae shows that neither is mycorrhizal anatomy a good tool to separate the groups, because the characters (like the epidermoid or angular mantle structure, cell wall thickness, the sape and size of cystidia) are too variable and overlap between the clades. The interspecific similarity, observed both in ectomycorrhizal and fruitbody characters, strengthen the sensu lato morpho-species concept of this group. Our study, which combines comprehensive molecular and anatomical approach to characterize and identify ectomycorrhizae of white truffles from natural samples, stress out the need of the taxonomical revision of this group.}, } @article {pmid16951060, year = {2006}, author = {Liti, G and Barton, DB and Louis, EJ}, title = {Sequence diversity, reproductive isolation and species concepts in Saccharomyces.}, journal = {Genetics}, volume = {174}, number = {2}, pages = {839-850}, pmid = {16951060}, issn = {0016-6731}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {*Base Sequence ; Cell Division/genetics ; DNA, Fungal/*analysis/isolation & purification ; *Genetic Speciation ; *Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Reproduction, Asexual/*genetics ; Saccharomyces/*genetics/growth & development/physiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Using the biological species definition, yeasts of the genus Saccharomyces sensu stricto comprise six species and one natural hybrid. Previous work has shown that reproductive isolation between the species is due primarily to sequence divergence acted upon by the mismatch repair system and not due to major gene differences or chromosomal rearrangements. Sequence divergence through mismatch repair has also been shown to cause partial reproductive isolation among populations within a species. We have surveyed sequence variation in populations of Saccharomyces sensu stricto yeasts and measured meiotic sterility in hybrids. This allows us to determine the divergence necessary to produce the reproductive isolation seen among species. Rather than a sharp transition from fertility to sterility, which may have been expected, we find a smooth monotonic relationship between diversity and reproductive isolation, even as far as the well-accepted designations of S. paradoxus and S. cerevisiae as distinct species. Furthermore, we show that one species of Saccharomyces--S. cariocanus--differs from a population of S. paradoxus by four translocations, but not by sequence. There is molecular evidence of recent introgression from S. cerevisiae into the European population of S. paradoxus, supporting the idea that in nature the boundary between these species is fuzzy.}, } @article {pmid16947112, year = {2006}, author = {Kikuzawa, K and Lechowicz, MJ}, title = {Toward synthesis of relationships among leaf longevity, instantaneous photosynthetic rate, lifetime leaf carbon gain, and the gross primary production of forests.}, journal = {The American naturalist}, volume = {168}, number = {3}, pages = {373-383}, doi = {10.1086/506954}, pmid = {16947112}, issn = {1537-5323}, mesh = {Carbon/*metabolism ; *Ecosystem ; Photosynthesis/*physiology ; Plant Leaves/*metabolism ; Species Specificity ; Time Factors ; Trees/*physiology ; }, abstract = {The assimilation of carbon by plant communities (gross primary production [GPP]) is a central concern in plant ecology as well as for our understanding of global climate change. As an alternative to traditional methods involving destructive harvests or time-consuming measurements, we present a simple, general model for GPP as the product of the lifetime carbon gain by a single leaf, the daily leaf production rate, and the length of the favorable period for photosynthesis. To test the model, we estimated leaf lifetime carbon gain for 26 species using the concept of mean labor time for leaves (the part of each day the leaf functions to full capacity), average potential photosynthetic capacity over the leaf lifetime, and functional leaf longevity (leaf longevity discounted for periods within a year wholly unfavorable for photosynthesis). We found that the lifetime carbon gain of leaves was rather constant across species. Moreover, when foliar biomass was regressed against functional leaf longevity, aseasonal and seasonal forests fell on a single line, suggesting that the leaf production rate during favorable periods is not substantially different among forests in the world. The gross production of forest ecosystems then can be predicted to a first approximation simply by the annual duration of the period favorable for photosynthetic activity in any given region.}, } @article {pmid16937653, year = {2006}, author = {Cognato, AI}, title = {Standard percent DNA sequence difference for insects does not predict species boundaries.}, journal = {Journal of economic entomology}, volume = {99}, number = {4}, pages = {1037-1045}, doi = {10.1603/0022-0493-99.4.1037}, pmid = {16937653}, issn = {0022-0493}, mesh = {Animals ; *Genetic Speciation ; Insecta/*genetics ; }, abstract = {Diagnosis and assessment of species boundaries of economically important insects are often problematic because of limited morphological and/or biological characters. DNA data can help to identify and revise species. Nonoverlapping intra- and interspecific sequence divergences are often used as evidence for species. Thus, the establishment of a standardized percent nucleotide divergence to predict species boundaries would aid in cases where species status is suspect. However, given variation in nucleotide mutation rates and species concepts, association between a standard percent sequence divergence and species is questionable. This review surveys the percent DNA sequence difference found between sister-species of economically important insects, to assess whether a standard divergence associates with all taxa. Sixty-two comparisons of intra- and interspecific pairwise DNA differences were made for mitochondrial and nuclear loci spanning families of Isoptera, Phthiraptera, Hemiptera, Coleoptera, Lepidoptera, Diptera, and Hymenoptera. Intra- and interspecific sequence divergences varied widely among insects, 0.04-26.0 and 1.0-30.7%, respectively. The ranges of intra- and interspecific sequence divergences overlapped in 28 of 62 comparisons. This implies that a standardized percent sequence divergence would fail to correctly diagnose species for 45% of the cases. Common occurrence of nonmonophyly among closely related species probably explains this observation. Nonmonophyly and overlap of intra- and interspecific divergences were significantly associated. The reviewed studies suggest that a standard percent sequence divergence does not predict species boundaries among economically important insects. DNA data can help best to predict species boundaries via its inclusion in nonphenetic phylogenetic analysis and subsequent systematic expert scrutiny.}, } @article {pmid16934965, year = {2006}, author = {Högnabba, F}, title = {Molecular phylogeny of the genus Stereocaulon (Stereocaulaceae, lichenized ascomycetes).}, journal = {Mycological research}, volume = {110}, number = {Pt 9}, pages = {1080-1092}, doi = {10.1016/j.mycres.2006.04.013}, pmid = {16934965}, issn = {0953-7562}, mesh = {Ascomycota/*classification/genetics ; DNA, Fungal/analysis/isolation & purification ; DNA, Ribosomal Spacer/analysis ; Evolution, Molecular ; Lichens/*microbiology ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; Tubulin/genetics ; }, abstract = {In the present study phylogenetic relationships of the genus Stereocaulon (lichenized ascomycetes) were examined using DNA sequences from the ITS1-5.8 S-ITS2 rDNA gene cluster and from the protein-coding beta-tubulin gene. In addition to the fruticose species traditionally classified in Stereocaulon, representatives of the crustose species that have recently been transferred to the genus were included. Muhria, a monotypic genus that is morphologically similar to Stereocaulon, differing only in apothecia ontogeny, was also incorporated. The analyses included 101 specimens from the ingroup representing 49 taxa. Sequences from both DNA regions were analysed simultaneously using direct optimization under the parsimony optimality criterion. The results support the inclusion of the crustose species and Muhria in Stereocaulon, while the current infrageneric classification is not supported. As Muhria is securely nested within Stereocaulon the new combination Stereocaulon urceolatum comb. nov. (syn. Muhria urceolata) is made. Further, species concepts need to be re-examined, as some species do not appear as monophyletic entities in the phylogeny.}, } @article {pmid16932983, year = {2007}, author = {Hassani-Mehraban, A and Saaijer, J and Peters, D and Goldbach, R and Kormelink, R}, title = {Molecular and biological comparison of two Tomato yellow ring virus (TYRV) isolates: challenging the Tospovirus species concept.}, journal = {Archives of virology}, volume = {152}, number = {1}, pages = {85-96}, doi = {10.1007/s00705-006-0827-7}, pmid = {16932983}, issn = {0304-8608}, mesh = {Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; Iran ; Lycopersicon esculentum/virology ; Molecular Sequence Data ; Nucleocapsid Proteins/genetics ; Phylogeny ; Plant Diseases/virology ; RNA, Viral/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Solanum tuberosum/virology ; Soybeans/virology ; Species Specificity ; Tospovirus/classification/*genetics/*isolation & purification ; }, abstract = {Two strains of Tomato yellow ring virus (TYRV, genus Tospovirus), one from tomato (referred to as TYRV-t) and the other from soybean and potato (denoted TYRV-s), collected from different geographical regions in Iran, were compared. Their genomic S RNA segments differed in size by 55 nucleotides. Comparison of the S RNA intergenic regions revealed the absence of a stretch of 115 nucleotides within the S RNA segment of TYRV-s and, conversely, of 56 nts in that of TYRV-t, apparently a stable genetic difference as it was also found in another isolate of TYRV-s collected from potato. Sequence comparison of the N protein ORFs revealed an identity of 92% between the N proteins of both strains, and the observed strong cross-reaction of TYRV-s in DAS-ELISA with a polyclonal antiserum directed against the TYRV-t N protein confirmed this high identity. Host range analysis revealed several differences, e.g. TYRV-s, but not TYRV-t, being able to systemically infect Nicotiana species, and TYRV-s being localised in tomato. The observed molecular and biological differences of both viruses call into question the currently used criteria for Tospovirus species demarcation.}, } @article {pmid16922219, year = {2006}, author = {Rubinoff, D}, title = {Utility of mitochondrial DNA barcodes in species conservation.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {20}, number = {4}, pages = {1026-1033}, doi = {10.1111/j.1523-1739.2006.00372.x}, pmid = {16922219}, issn = {0888-8892}, mesh = {Biodiversity ; Conservation of Natural Resources/*methods ; DNA, Mitochondrial/*classification ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; *Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Molecular tools are a standard part of many conservation studies and can be informative at many different levels of analysis, although there are inherent limitations and strengths of different genes or parts of genes to inform specific questions. Animal DNA barcodes, 600- to 800-base-pair segments of the mitochondrial gene cytochrome oxidase I, have been proposed as a means to quantify global biodiversity. Although mitochondrial (mt) DNA has a long history of use at the species level, recent analyses suggest that the use of a single gene, particularly mitochondrial, is unlikely to yield data that are balanced, universally acceptable, or sufficient in taxonomic scope to recognize many species lineages. Mitochondrial and nuclear genomes have different patterns of evolution and modes of inheritance, which can result in very different assessments of biodiversity. The ramifications of choosing a particular definition of species (species concept) need to be carefully considered because current efforts have designated DNA barcodes as the universal species concept without demonstrating its superiority over preexisting concepts. The results of such a barcoding paradigm may include a failure to recognize significant portions of biodiversity or nuclear/mitochondrial mixed lineages and could spuriously focus conservation resources on populations with relatively minor mtDNA divergence. DNA barcodes are most likely to provide potentially useful information for groups that are already well studied, and such taxa do not constitute the majority of biodiversity or those in most need of research attention. DNA barcode-length sequences are an important source of data but, when used alone or out of context, may offer only a fraction of the information needed to characterize species while taking resources from broader studies that could produce information essential to robust and informed conservation decisions.}, } @article {pmid16917524, year = {2006}, author = {Murali, TS and Suryanarayanan, TS and Geeta, R}, title = {Endophytic Phomopsis species: host range and implications for diversity estimates.}, journal = {Canadian journal of microbiology}, volume = {52}, number = {7}, pages = {673-680}, doi = {10.1139/w06-020}, pmid = {16917524}, issn = {0008-4166}, mesh = {Ascomycota/classification/*genetics/isolation & purification/*physiology ; Biodiversity ; Ecosystem ; India ; Lamiaceae/microbiology ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/*microbiology ; Trees/microbiology ; }, abstract = {Foliar endophyte assemblages of teak trees growing in dry deciduous and moist deciduous forests of Nilgiri Biosphere Reserve were compared. A species of Phomopsis dominated the endophyte assemblages of teak, irrespective of the location of the host trees. Internal transcribed spacer sequence analysis of 11 different Phomopsis isolates (ten from teak and one from Cassia fistula) showed that they fall into two groups, which are separated by a relatively long branch that is strongly supported. The results showed that this fungus is not host restricted and that it continues to survive as a saprotroph in teak leaf, possibly by exploiting senescent leaves as well as the litter. Although the endophyte assemblage of a teak tree growing about 500 km from the forests was also dominated by a Phomopsis sp., it separated into a different group based on internal transcribed spacer sequence analysis. Our results with an endophytic Phomopsis sp. reinforce the earlier conclusions reached by others for pathogenic Phomopsis sp., i.e., that this fungus is not host specific, and the species concept of Phomopsis needs to be redefined.}, } @article {pmid16911222, year = {2006}, author = {Witt, JD and Threloff, DL and Hebert, PD}, title = {DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation.}, journal = {Molecular ecology}, volume = {15}, number = {10}, pages = {3073-3082}, doi = {10.1111/j.1365-294X.2006.02999.x}, pmid = {16911222}, issn = {0962-1083}, mesh = {Amphipoda/*genetics ; Animals ; California ; *Conservation of Natural Resources ; *Genetic Variation ; Geography ; Likelihood Functions ; Nevada ; Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {DNA barcoding has revealed unrecognized species in several animal groups. In this study we have employed DNA barcoding to examine Hyalella, a taxonomically difficult genus of amphipod crustaceans, from sites in the southern Great Basin of California and Nevada, USA. We assessed the extent of species diversity using a species screening threshold (SST) set at 10 times the average intrapopulation cytochrome c oxidase subunit I (COI) haplotype divergence. Despite the fact that this threshold approach is more conservative in delineating provisional species than the phylogenetic species concept, our analyses revealed extraordinary levels of cryptic diversity and endemism. The SST discriminated two provisional species within Hyalella sandra, and 33 provisional species within Hyalella azteca. COI nucleotide divergences among these provisional species ranged from 4.4% to 29.9%. These results have important implications for the conservation of life in desert springs - habitats that are threatened as a result of groundwater over-exploitation.}, } @article {pmid16906737, year = {2006}, author = {Potyrailo, RA and Morris, WG and Leach, AM and Sivavec, TM and Wisnudel, MB and Boyette, S}, title = {Analog signal acquisition from computer optical disk drives for quantitative chemical sensing.}, journal = {Analytical chemistry}, volume = {78}, number = {16}, pages = {5893-5899}, doi = {10.1021/ac060684e}, pmid = {16906737}, issn = {0003-2700}, mesh = {Biosensing Techniques/*instrumentation/methods ; Calcium/analysis ; Compact Disks ; *Optical Storage Devices ; }, abstract = {Optoelectronic consumer products that are widely employed in the office and home attract attention for optical sensor applications due to (1) their cost advantage over analytical instruments produced only in small quantities, (2) robustness in operation due to the detailed manufacturability improvements, and (3) ease of operation. We demonstrate here a new approach for quantitative chemical/biochemical sensing when analog signals are acquired from conventional optical disk drives, and these signals are used for quantitative detection of optical changes of sensor films deposited on conventional CD and DVD optical disks. Because we do not alter manufacturing process of optical disks, any disk can be employed for deposition and readout of sensor films. The optical disk drives also perform their original function of reading and writing digital content to optical media because no optical modifications are introduced to obtain the analog signal. Such a sensor platform is quite universal and can be applied for chemical and biological quantitative detection, as well as for monitoring of changes of physical properties of regions deposited onto a CD or DVD (e.g., during combinatorial screening of materials). As a model example, we demonstrate the concept using chemical detection of ionic species such as Ca2+ in liquids (e.g., blood, urine, or water). Colorimetric calcium-sensitive sensor films were deposited onto a DVD, exposed to water with different concentrations of Ca2+, and quantified in the optical disk drive. The developed lab-on-DVD system demonstrated a 5 ppm detection limit of Ca2+ determinations, similar or slightly better than that achieved using a conventional fiber-optic portable spectrometer. This detection limit corresponded to a 0.023 absorbance unit resolution, as determined by the measurement of the same colorimetric films with a portable spectrometer. Determinations of Ca2+ unknowns using the lab-on-DVD system demonstrated +/-5 ppm accuracy and 2-5% relative standard deviation precision in predicting 100 ppm Ca2+.}, } @article {pmid21642183, year = {2006}, author = {Zomlefer, WB and Whitten, WM and Williams, NH and Judd, WS}, title = {Infrageneric phylogeny of Schoenocaulon (Liliales: Melanthiaceae) with clarification of cryptic species based on ITS sequence data and geographical distribution.}, journal = {American journal of botany}, volume = {93}, number = {8}, pages = {1178-1192}, doi = {10.3732/ajb.93.8.1178}, pmid = {21642183}, issn = {0002-9122}, abstract = {As currently defined, the 24 species of Schoenocaulon occur in three disjunct areas: north central Florida (one species, S. dubium), southern Peru (portion of the range of S. officinale), and the region from southeastern New Mexico-Texas south to Venezuela; the 20 species endemic to Mexico are geographically restricted. Species delimitations, often based on tepal morphology, have been problematic. Our analyses of ITS sequence data for all 27 species and infraspecific taxa support recognition of two new species and recircumscription and placement of elements of the polyphyletic S. ghiesbreghtii and S. mortonii complexes. For taxa with adequate sampling, our data also indicate 11-12 cladospecies and 3-6 metaspecies according to the apomorphic species concept. The resolved phylogeny, correlated with geography and morphology, allows insight into biogeographical diversification and the evolution of some unusual morphological characters within the genus, such as nectary differentiation and tepal margin type.}, } @article {pmid19890476, year = {2006}, author = {Baker, RJ and Bradley, RD}, title = {SPECIATION IN MAMMALS AND THE GENETIC SPECIES CONCEPT.}, journal = {Journal of mammalogy}, volume = {87}, number = {4}, pages = {643-662}, pmid = {19890476}, issn = {0022-2372}, support = {R01 AI041435/AI/NIAID NIH HHS/United States ; R01 AI041435-08/AI/NIAID NIH HHS/United States ; }, abstract = {We define a genetic species as a group of genetically compatible interbreeding natural populations that is genetically isolated from other such groups. This focus on genetic isolation rather than reproductive isolation distinguishes the Genetic Species Concept from the Biological Species Concept. Recognition of species that are genetically isolated (but not reproductively isolated) results in an enhanced understanding of biodiversity and the nature of speciation as well as speciation-based issues and evolution of mammals. We review criteria and methods for recognizing species of mammals and explore a theoretical scenario, the Bateson-Dobzhansky-Muller (BDM) model, for understanding and predicting genetic diversity and speciation in mammals. If the BDM model is operating in mammals, then genetically defined phylogroups would be predicted to occur within species defined by morphology, and phylogroups experiencing stabilizing selection will evolve genetic isolation without concomitant morphological diversification. Such species will be undetectable using classical skin and skull morphology (Morphological Species Concept). Using cytochrome-b data from sister species of mammals recognized by classical morphological studies, we estimated the number of phylogroups that exist within mammalian species and hypothesize that there will be >2,000 currently unrecognized species of mammals. Such an underestimation significantly affects conclusions on the nature of speciation in mammals, barriers associated with evolution of genetic isolation, estimates of biodiversity, design of conservation initiatives, zoonoses, and so on. A paradigm shift relative to this and other speciation-based issues will be needed. Data that will be effective in detecting these "morphologically cryptic genetic species" are genetic, especially DNA-sequence data. Application of the Genetic Species Concept uses genetic data from mitochondrial and nuclear genomes to identify species and species boundaries, the extent to which the integrity of the gene pool is protected, nature of hybridization (if present), and introgression. Genetic data are unique in understanding species because the use of genetic data 1) can quantify genetic divergence from different aspects of the genome (mitochondrial and nuclear genes, protein coding genes, regulatory genes, mobile DNA, microsatellites, chromosomal rearrangements, heterochromatin, etc.); 2) can provide divergence values that increase with time, providing an estimate of time since divergence; 3) can provide a population genetics perspective; 4) is less subject to convergence and parallelism relative to other sets of characters; 5) can identify monophyly, sister taxa, and presence or absence of introgression; and 6) can accurately identify hybrid individuals (kinship and source of hybrid individuals, F(1)s, backcrosses, direction of hybridization, and in concert with other data identify which hybrids are sterile or fertile). The proposed definition of the Genetic Species Concept is more compatible with a description of biodiversity of mammals than is "reproductively isolated species." Genetic profiles of mammalian species will result in a genetic description of species and mammalian diversity, and such studies are being accelerated by technological advances that reduce cost and increase speed and efficiency of generating genetic data. We propose that this genetic revolution remain museum- and voucher specimen-based and that new names are based on a holotype (including associated tissues) deposited in an accredited museum.}, } @article {pmid16871802, year = {2006}, author = {Naumova, ES and Gazdiev, DO and Naumov, GI}, title = {[Heterogeneity of the yeasts Zygowilliopsis californica: Z. californica var. dimennae comb. nov., stat. nov. and Z. californica var. fukushimae comb. nov., stat. nov].}, journal = {Mikrobiologiia}, volume = {75}, number = {3}, pages = {358-363}, pmid = {16871802}, issn = {0026-3656}, mesh = {Asia ; Australasia ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer ; Europe ; North America ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Fungal/genetics ; RNA, Ribosomal, 5.8S/genetics ; Soil Microbiology ; Species Specificity ; Yeasts/*classification/genetics ; }, abstract = {A significant heterogeneity of the species Zygowilliopsis californica was revealed using RFLP-analysis of the PCR-amplified rDNA fragment spanning the 5.8S rRNA gene and the internal transcribed spacers ITS1 and ITS2. Phylogenetic analysis of the nucleotide sequences of ITS1 and ITS2 rDNA differentiated three varieties: Z. californica var. californica, Z. californica var. dimennae, and Z. californica var. fukushimae. The most variable was the ITS 2 region, where 7-26 nucleotide substitutions were revealed. The varieties formed semisterile hybrids with meiotic segregation of control markers. The limits of the phylogenetic species concept are discussed.}, } @article {pmid16859013, year = {2004}, author = {Niewiadomska, T and Pojmańska, T}, title = {[A concept of parasite species at the times of molecular studies].}, journal = {Wiadomosci parazytologiczne}, volume = {50}, number = {2}, pages = {109-115}, pmid = {16859013}, issn = {0043-5163}, mesh = {Animals ; Base Sequence ; Echinococcus/*classification/*genetics ; Evolution, Molecular ; Genotype ; Molecular Sequence Data ; *Phylogeny ; Species Specificity ; Taenia/*classification/*genetics ; Trichinella/*classification/*genetics ; }, abstract = {The problem of species recognition in relation to parasite organisms is discussed, based on literature data. Taking into account that over 20 species concepts have hitherto been formulated, the choice of characters, which should define a species differs from author to author. Lately the differences in some gene fragments are regarded as one of most important feature for species differentiation. On this basis some lineages, genotypes or strains have been differentiated within some species, but in most cases the respective authors did not decide to elevate these units to the species level. The present paper focuses on the studies on species representing three genera (Taenia, Echinococcus, Trichinella) as they show, especially the complex studies on the species within the genus Trichinella, how big material is necessary to formulate any proper conclusion and, on the other hand, that the differences in the DNA sequences cannot be the only characters defining species; some other features (morphological, biological, behavioral) should not be considered redundant.}, } @article {pmid16815046, year = {2006}, author = {Suatoni, E and Vicario, S and Rice, S and Snell, T and Caccone, A}, title = {An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis.}, journal = {Molecular phylogenetics and evolution}, volume = {41}, number = {1}, pages = {86-98}, doi = {10.1016/j.ympev.2006.04.025}, pmid = {16815046}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; DNA, Ribosomal Spacer ; Electron Transport Complex IV/genetics ; Female ; Geography ; Male ; Molecular Sequence Data ; *Phylogeny ; Reproduction, Asexual ; Rotifera/anatomy & histology/genetics/*physiology ; Sexual Behavior, Animal ; Zygote ; }, abstract = {Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.}, } @article {pmid16800306, year = {2006}, author = {Réblová, M}, title = {Molecular systematics of Ceratostomella sensu lato and morphologically similar fungi.}, journal = {Mycologia}, volume = {98}, number = {1}, pages = {68-93}, doi = {10.1080/15572536.2006.11832714}, pmid = {16800306}, issn = {0027-5514}, mesh = {Ascomycota/*classification/cytology/*genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Microscopy ; Molecular Sequence Data ; Mycelium/growth & development ; Photomicrography ; Phylogeny ; Sequence Analysis, DNA ; Spores, Fungal/cytology ; }, abstract = {The systematic position and phylogenetic relationships of Ceratostomella sensu lato and phenotypically similar fungi using comparative morphological and culture studies and phylogenetic analyses of the nuclear large- and small-subunit ribosomal DNA were explored. In the light of inferred phylogenies and morphological data the genus Ceratostomella is redescribed, the generic concept is emended and four species are accepted (viz. C. cuspidata, C. pyrenaica, C. rhynchophora and C. rostrata). A new genus Xylomelasma is introduced and delimited from Ceratostomella, with two new species described (viz. X. novaezelandiae and X. sordida). In culture species of both Ceratostomella and Xylomelasma produced sterile mycelium. The genus Lentomitella with a phaeoisaria-like anamorph formed in vitro is reinstated to encompass taxa formerly attributed to the broadly perceived Ceratostomella with three accepted species (viz. L. cirrhosa, L. crinigera and L. tomentosa). Lentomitella and Ceratostomella are clearly distinguishable by the morphology of asci, ascospores and centrum. Lentomitella is compared to phenotypically similar Ceratosphaeria, which formed a harpophora-like anamorph in vitro. In the present phylogenies Ceratostomella, Ceratosphaeria, Lentomitella and Xylomelasma are shown as clearly separate genera belonging to three different groups of perithecial ascomycetes. Ceratostomella, Lentomitella and Xylomelasma reside within a large unsupported clade consisting of members the Ophiostomatales, the freshwater Annulatascaceae and a group of nonstromatic, terrestrial taxa. Ceratosphaeria is well supported within the Magnaporthaceae. The systematic value of morphological characters of ascospores, paraphyses, asci, centrum and conidiogenesis in segregating taxa from Ceratostomella sensu lato and their relatives is discussed.}, } @article {pmid16769557, year = {2006}, author = {Reydon, TA}, title = {Generalizations and kinds in natural science: the case of species.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {37}, number = {2}, pages = {230-255}, doi = {10.1016/j.shpsc.2006.03.003}, pmid = {16769557}, issn = {1369-8486}, mesh = {Homeostasis ; Humans ; *Metaphysics ; *Natural Science Disciplines ; *Phylogeny ; Species Specificity ; Terminology as Topic ; }, abstract = {Species in biology are traditionally perceived as kinds of organisms about which explanatory and predictive generalizations can be made, and biologists commonly use species in this manner. This perception of species is, however, in stark contrast with the currently accepted view that species are not kinds or classes at all, but individuals. In this paper I investigate the conditions under which the two views of species might be held simultaneously. Specifically, I ask whether upon acceptance of an ontology of species as diachronic segments of the tree of life (this is one version of the species as individuals ontology) species can perform the epistemic role of kinds of organisms to which explanatory and predictive generalizations apply. I show that, for species-level segments of the tree of life, several requirements have to be met before the performance of this epistemic role is possible, and I argue that these requirements can be met by defining species according to the Composite Species Concept proposed by Kornet and McAllister in the 1990s.}, } @article {pmid16762447, year = {2006}, author = {Hey, J}, title = {On the failure of modern species concepts.}, journal = {Trends in ecology & evolution}, volume = {21}, number = {8}, pages = {447-450}, doi = {10.1016/j.tree.2006.05.011}, pmid = {16762447}, issn = {0169-5347}, mesh = {Animals ; Biological Evolution ; *Species Specificity ; }, abstract = {The modern age of species concepts began in 1942, when Ernst Mayr gave concept names to several different approaches to species identification. A long list of species concepts then followed, as well as a complex literature on their merits, motivations and uses. Some of these complexities arose as a consequence of the semantic shift that Mayr introduced, in which procedures for identifying species were elevated to concepts. Much of the debate in recent decades over concepts, and over pluralism versus monism, can be seen as an unnecessary consequence of treating species identification criteria as if they were more fundamental concepts. Recently, biologists have begun to recognize both the shortcomings of a lexicon of multiple species concepts and a common evolutionary idea that underlies them.}, } @article {pmid16758297, year = {2006}, author = {Bartoli, P and Gibson, DI and Bray, RA}, title = {Prosorhynchoides gracilescens (Rudolphi, 1819) (Digenea: Bucephalidae) from Lophius piscatorius L. is a species complex: a redescription of this species (sensu stricto) from the western Mediterranean and the description of P. borealis n. sp. from the northern North-East Atlantic.}, journal = {Systematic parasitology}, volume = {63}, number = {3}, pages = {203-221}, pmid = {16758297}, issn = {0165-5752}, mesh = {Animals ; Europe ; Female ; Fish Diseases/*parasitology ; Fishes/*parasitology ; France ; Intestines/parasitology ; Male ; Mediterranean Sea ; Oceans and Seas ; Species Specificity ; Trematoda/anatomy & histology/*classification ; Trematode Infections/parasitology/*veterinary ; }, abstract = {The bucephalid digenean Prosorhynchoides gracilescens (Rudolphi, 1819) is a common intestinal parasite of the angler fish Lophius piscatorius in European marine waters. Detailed studies of new material collected off the coasts of both Marseilles and Corsica in the western Mediterranean, and comparison with museum material from the northern North-East Atlantic, indicated that the accepted concept of this species comprises two distinct taxa. The Mediterranean form occurs in relatively small numbers and has small eggs, a large rhynchus and a vitelline distribution that finishes well short of the rhynchus, whereas the NE Atlantic form, which comprises the majority of records, occurs often in large numbers, has larger eggs, a relatively smaller rhynchus and a vitelline distribution that tends to reach the rhynchus. Since the type-material is from the Mediterranean and resembles the Mediterranean form, there was little option but to consider the latter as P. gracilescens (sensu stricto) and to describe the NE Atlantic form as a new species, for which the name P. borealis n. sp. is coined to reflect its northerly distribution. Both species are described and figured in detail, and a table and illustration of the diagnostic features are presented. In addition, some discussion is included on the distribution of these two species and whether P. gracilescens (s. str.) might be a relict species, and on non-European records of P. gracilescens (sensu lato).}, } @article {pmid16758295, year = {2006}, author = {Reich, S and Magallanes, J and Dawidowski, L and Gómez, D and Groselj, N and Zupan, J}, title = {An analysis of secondary pollutants in Buenos Aires City.}, journal = {Environmental monitoring and assessment}, volume = {119}, number = {1-3}, pages = {441-457}, pmid = {16758295}, issn = {0167-6369}, mesh = {Air Pollutants/*analysis ; Air Pollution/*analysis/prevention & control ; Argentina ; Carbon Monoxide/analysis ; Environmental Monitoring/*methods ; Nitrogen Dioxide/analysis ; Ozone/analysis ; Sulfur Dioxide/analysis ; Vehicle Emissions/analysis ; }, abstract = {Air pollutant concentrations from a monitoring campaign in Buenos Aires City, Argentina, are used to investigate the relationships between ambient levels of ozone (O3), nitric oxide (NO) and nitrogen dioxide (NO2) as a function of NO(x) (= NO + NO2). This campaign undertaken by the electricity sector was aimed at elucidating the apportionment of thermal power plants to air quality deterioration. Concentrations of carbon monoxide (CO) and sulphur dioxide (SO2) were also registered. Photo stationary state (PSS) of the NO, NO2, O3 and peroxy radicals species has been analysed. The 'oxidant' level concept has been introduced, OX (= O3 + NO2), which varies with the level of NO(x). It is shown that this level is made up of NO(x)-independent and NO(x)-dependent contributions. The former is a regional contribution that equates the background O3 level, whereas the latter is a local contribution that correlates with the level of primary pollution. Furthermore, the anticorrelation between NO2 and O3 levels, which is a characteristic of the atmospheric photo stationary cycle has been verified. The analysis of the concentration of the primary pollutants CO and NO strongly suggests that the vehicle traffic is the principal source of them. Levels of continuous measurements of SO2 for Buenos Aires City are reported in this work as a complement of previously published results.}, } @article {pmid16756105, year = {2006}, author = {Pavlinov, IIa}, title = {[Classical and non-classical taxonomy: where does the boundary pass?].}, journal = {Zhurnal obshchei biologii}, volume = {67}, number = {2}, pages = {83-106}, pmid = {16756105}, issn = {0044-4596}, mesh = {*Biodiversity ; *Biological Evolution ; Species Specificity ; }, abstract = {Rise of non-classical science during XX century had certain influence upon development of biological taxonomy. Scientific pluralism (especially normative naturalism of Laudan), contrary to positivist and early post-positivist treatments, made taxonomy acknowledged scientific discipline of its own right. The present state of some schools of taxonomy makes it possible to consider them as a part of non-classical science and constituting the non-classical taxonomy. The latter is characterized by the following most important features. Ontological substantiation of both classificatory approaches and particular classifications is requested which invalidates such formal approaches as nominalistic and phenetic (numerical) schools. This substantiation takes a form of content-wise background preferably causal models which include certain axioms and presumptions about taxonomic diversity being studied, together with its causes, and thus define initial conditions of classificatory procedures. From this viewoint, phylogenetic classificatory approach is the most developed part of non-classical taxonomy. The entire taxonomic diversity is structured into several aspects of different levels of generality, each being outlined by a particular consideration aspect. The latter makes personal knowledge constituting an irremovable part of any scientific statement about taxonomic diversity, thus opposition of "objectively" and "subjectively" elaborated classifications becomes vague. Interrelation of various species concepts corresponding to its different consideration aspects is described by uncertainty relation principle. Classificatory algorithms are to be compatible with the conditions of a background model to ensure particular classifications obtained by their means are interpretable within the same model: this is provided by the correspondence principle. Classification is considered as a taxonomic hypothesis, i.e. a conjectural judgement about structure of particular fragment of taxonomic diversity considered within given consideration aspect; wich is to be forwarded and tested according to certain rules. Recognition of different aspects of taxonomic diversity makes it "legal" to elaborate several classifications of equal status, each reflecting a particular aspect of a fixed fragment of that diversity. This viewpoint makes classical ideas of the "ultimate" Natural (whatever might be its definition) or the best reference systems futile. In general, any pretension of an approach to be "the best" in reflecting taxonomic divesrity is contr-productive. Instead, elaboration of particular spectra of complementary classifications becomes the main task of non-classical taxonomy which describes in sum the entire taxonomic diversity. So, not opposition but correct mutual interpretation of such classifications and uniting them into the comprehensive picture of taxonomic diversity become focal points of non-classical taxonomy.}, } @article {pmid16740182, year = {2006}, author = {Martinsen, ES and Paperna, I and Schall, JJ}, title = {Morphological versus molecular identification of avian Haemosporidia: an exploration of three species concepts.}, journal = {Parasitology}, volume = {133}, number = {Pt 3}, pages = {279-288}, doi = {10.1017/S0031182006000424}, pmid = {16740182}, issn = {0031-1820}, mesh = {Animal Migration ; Animals ; Bird Diseases/*parasitology ; Birds ; Cytochromes b/*genetics ; DNA Primers/chemistry ; Haemosporida/*classification/genetics/isolation & purification/*ultrastructure ; Israel ; Molecular Sequence Data ; Parasitemia/parasitology/veterinary ; Phylogeny ; Protozoan Infections, Animal/*parasitology ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {More than 200 species of avian Haemosporidia (genera Plasmodium, Haemoproteus, and Leucocytozoon) have been described based primarily on morphological characters seen in blood smears. Recent molecular studies, however, suggest that such methods may mask a substantial cryptic diversity of avian haemosporidians. We surveyed the haemosporidians of birds sampled at 1 site in Israel. Parasites were identified to species based on morphology, and a segment of the parasite's cytochrome b gene was sequenced. We compared 3 species concepts: morphological, genetic, and phylogenetic. Fifteen morphological species were present. Morphological species that occurred once within our dataset were associated with a unique gene sequence, displayed large genetic divergence from other morphological species, and were not contained within clades of morphological species that occurred more than once. With only 1 exception, morphological species that were identified from multiple bird hosts presented identical sequences for all infections, or differed by few synonymous substitutions, and were monophyletic for all phylogenetic analyses. Only the morphological species Haemoproteus belopolskyi did not follow this trend, falling instead into at least 2 genetically distant clades. Thus, except for H. belopolskyi, parasites identified to species by morphology were supported by both the genetic and phylogenetic species concepts.}, } @article {pmid16716289, year = {2007}, author = {Basu, N and Scheuhammer, AM and Bursian, SJ and Elliott, J and Rouvinen-Watt, K and Chan, HM}, title = {Mink as a sentinel species in environmental health.}, journal = {Environmental research}, volume = {103}, number = {1}, pages = {130-144}, doi = {10.1016/j.envres.2006.04.005}, pmid = {16716289}, issn = {0013-9351}, mesh = {Animals ; Environmental Health ; Environmental Monitoring/*methods ; Environmental Pollutants/metabolism/toxicity ; Hydrocarbons, Chlorinated/metabolism/toxicity ; Mercury/metabolism/toxicity ; *Mink ; }, abstract = {The concept of "sentinel species" is important in the environmental health sciences because sentinel species can provide integrated and relevant information on the types, amounts, availability, and effects of environmental contaminants. Here we discuss the use of mink (Mustela vison) as a sentinel organism by reviewing the pertinent literature from exposure- and effects-based studies. The review focuses on mercury (Hg) and polychlorinated biphenyls (PCBs), as they are persistent, ubiquitous, and bioaccumulative contaminants of concern to both humans and wildlife. Mink are widely distributed, abundant, and regularly trapped in temperate, aquatic ecosystems, and this makes them an excellent model to address issues in environmental pollution on both temporal and spatial scales. As a high-trophic-level, piscivorous mammal, mink can bioaccumulate appreciable concentrations of certain pollutants and have been shown to be sensitive to their toxic effects. The husbandry and life history of mink are well understood, and this has permitted controlled dosing experiments to be conducted using animals reared in captivity. These manipulative studies have yielded important quantitative information on exposure-response relationships and benchmarks of adverse health effects, and have also allowed the cellular mechanisms underlying toxic effects to be explored. Furthermore, the data accrued from the laboratory continue to validate observations made in the field. Research derived from mink can bridge and integrate multiple disciplines, and the information collected from this species has allowed environmental health scientists to better understand and characterize pollution effects on ecosystems.}, } @article {pmid16713373, year = {2007}, author = {Van Regenmortel, MH}, title = {Virus species and virus identification: past and current controversies.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {7}, number = {1}, pages = {133-144}, doi = {10.1016/j.meegid.2006.04.002}, pmid = {16713373}, issn = {1567-1348}, mesh = {Classification/methods ; Terminology as Topic ; Virology/*trends ; Viruses/*classification ; }, abstract = {The basic concepts used in virus classification are analyzed. A clear distinction is drawn between viruses that are real, concrete objects studied by virologists and virus species that are man-made taxonomic constructions that exist only in the mind. Classical views regarding the nature of biological species are reviewed and the concept of species used in virology is explained. The use of pair-wise sequence comparisons between the members of a virus family for delineating species and genera is reviewed. The difference between the process of virus identification using one or a few diagnostic properties and the process of creating virus taxa using a combination of many properties is emphasized. The names of virus species in current use are discussed as well as a binomial system that may be introduced in the future.}, } @article {pmid16702098, year = {2006}, author = {Gräser, Y and De Hoog, S and Summerbell, RC}, title = {Dermatophytes: recognizing species of clonal fungi.}, journal = {Medical mycology}, volume = {44}, number = {3}, pages = {199-209}, doi = {10.1080/13693780600606810}, pmid = {16702098}, issn = {1369-3786}, mesh = {Arthrodermataceae/*classification/cytology/genetics ; Genotype ; Phylogeny ; }, abstract = {Now that molecular data have forever changed our perspective on the anthropophilic and zoophilic dermatophyte species, the concepts of these species needs re-evaluation. In this paper, main concepts (morphological, biological (BSC), phylogenetic and genealogical concordance phylogenetic species recognition (GCPSR)) are compared. While in geophilic dermatophytes the application of the BSC works well for species distinction and is supported by molecular data, it is not applicable for the anthropophilic and zoophilic dermatophytes where the majority of species reproduce purely asexually. Also, the application of GCPSR (an operational method to define the limits of species using molecular, multi-locus data) is problematic. GCPSR can be applied in recombining fungi even when recombination is infrequent and fungi lack phenotypic sexuality. In truly clonal fungi, however, no incongruities in multi-locus data are found, and thus separation of species may be difficult. In fungi this problem is currently taken to be non-existent, since clonality is supposed to lead to extinction. In the medically relevant, host-associated dermatophytes, however, is reason to suggest that clonal dermatophyte lineages are able to maintain ongoing populations and to follow independent evolutionary trajectories. We distinguish seasonal, short-lived and long-lived clonal species. The final goal of a species concept, in the dermatophytes as well as in other fungi, is to provide a taxonomic system that reflects the evolution of the fungal species so that the underlying biological trends elucidated in this way may be brought forward to help to guide the clinician in applying optimal therapy and prophylaxis. The application of the different species concepts may have an enormous impact on the nomenclature of dermatophytes, directly affecting the quality of communications with care providers.}, } @article {pmid16701459, year = {2006}, author = {Rubinoff, D and Cameron, S and Will, K}, title = {Are plant DNA barcodes a search for the Holy Grail?.}, journal = {Trends in ecology & evolution}, volume = {21}, number = {1}, pages = {1-2}, doi = {10.1016/j.tree.2005.10.019}, pmid = {16701459}, issn = {0169-5347}, mesh = {Biodiversity ; *Classification ; Evolution, Molecular ; Gene Amplification ; *Genome ; Inheritance Patterns ; Phylogeny ; Plants/*classification/*genetics ; *Sequence Analysis, DNA ; }, abstract = {In a recent study, Kress et al. compared two plant genomes to seek out plant DNA barcodes. Two promising markers balanced the variability that is needed to distinguish species with conserved primer regions that enable universal amplification. Although this study is the most rigorous effort to date, problems from earlier barcoding efforts, such as the use of non-evolutionary species concepts and differential sorting of genes and species, could reemerge. Single-gene barcoding might not be universally effective owing to inherent inaccuracies. Kress et al. suggest the use of multiple genes, reflecting an integrated approach that is likely to be the best answer to identifying species quickly and accurately.}, } @article {pmid16701333, year = {2005}, author = {Knapp, S and Lughadha, EN and Paton, A}, title = {Taxonomic inflation, species concepts and global species lists.}, journal = {Trends in ecology & evolution}, volume = {20}, number = {1}, pages = {7-8; author reply 8-9}, doi = {10.1016/j.tree.2004.11.001}, pmid = {16701333}, issn = {0169-5347}, } @article {pmid16701332, year = {2005}, author = {James Harris, D and Froufe, E}, title = {Taxonomic inflation: species concept or historical geopolitical bias?.}, journal = {Trends in ecology & evolution}, volume = {20}, number = {1}, pages = {6-7; author reply 8-9}, doi = {10.1016/j.tree.2004.11.004}, pmid = {16701332}, issn = {0169-5347}, } @article {pmid16701308, year = {2004}, author = {Isaac, NJ and Mallet, J and Mace, GM}, title = {Taxonomic inflation: its influence on macroecology and conservation.}, journal = {Trends in ecology & evolution}, volume = {19}, number = {9}, pages = {464-469}, doi = {10.1016/j.tree.2004.06.004}, pmid = {16701308}, issn = {0169-5347}, abstract = {Species numbers are increasing rapidly. This is due mostly to taxonomic inflation, where known subspecies are raised to species as a result in a change in species concept, rather than to new discoveries. Yet macroecologists and conservation biologists depend heavily on species lists, treating them as accurate and stable measures of biodiversity. Deciding on a standardized, universal species list might ameliorate the mismatch between taxonomy and the uses to which it is put. However, taxonomic uncertainty is ultimately due to the evolutionary nature of species, and is unlikely to be solved completely by standardization. For the moment, at least, users must acknowledge the limitations of taxonomic species and avoid unrealistic expectations of species lists.}, } @article {pmid16696653, year = {2006}, author = {Kwon-Chung, KJ and Varma, A}, title = {Do major species concepts support one, two or more species within Cryptococcus neoformans?.}, journal = {FEMS yeast research}, volume = {6}, number = {4}, pages = {574-587}, doi = {10.1111/j.1567-1364.2006.00088.x}, pmid = {16696653}, issn = {1567-1356}, support = {//Intramural NIH HHS/United States ; }, mesh = {Cryptococcus neoformans/*classification/genetics ; Genotype ; Humans ; Phenotype ; Phylogeny ; Serotyping ; Species Specificity ; }, abstract = {Cryptococcus neoformans, the agent of cryptococcosis, had been considered a homogeneous species until 1949 when the existence of four serotypes was revealed based on the antigenic properties of its polysaccharide capsule. Such heterogeneity of the species, however, remained obscure until the two morphologically distinct teleomorphs of C. neoformans were discovered during the mid 1970s. The teleomorph Filobasidiella neoformans was found to be produced by strains of serotype A and D, and Filobasidiella bacillispora was found to be produced by strains of serotype B and C. Ensuing studies revealed numerous differences between the anamorphs of the two Filobasidiella species with regard to their ecology, epidemiology, pathobiology, biochemistry and genetics. At present, the etiologic agent of cryptococcosis is classified into two species, C. neoformans (serotypes A and D) and Cryptococcus gattii (serotypes B and C). Intraspecific genetic diversity has also been revealed as more genotyping methods have been applied for each serotype. As a result, the number of scientifically valid species within C. neoformans has become a controversial issue because of the differing opinions among taxonomists as to the appropriate definition of a species. There are three major species concepts that govern classification of organisms: phenetic (morphologic, phenotypic), biologic (interbreeding) and cladistic (evolutionary, phylogenetic). Classification of the two C. neoformans species has been based on the phenetic as well as the biologic species concept, which is also supported by the cladistic species concept. In this paper, we review and attest to the validity of the current two-species system in light of the three major species concepts.}, } @article {pmid16629308, year = {2006}, author = {Toledo, R and Carpena, I and Espert, A and Sotillo, J and Muñoz-Antoli, C and Esteban, JG}, title = {A quantitative approach to the experimental transmission success of Echinostoma friedi (Trematoda: Echinostomatidae) in rats.}, journal = {The Journal of parasitology}, volume = {92}, number = {1}, pages = {16-20}, doi = {10.1645/GE-574R1.1}, pmid = {16629308}, issn = {0022-3395}, mesh = {Animals ; Cricetinae ; Echinostoma/*physiology ; Echinostomiasis/transmission/*veterinary ; Evaluation Studies as Topic ; Lymnaea/*parasitology ; Male ; Mesocricetus/parasitology ; Ovum/growth & development ; Parasite Egg Count/veterinary ; Rats/*parasitology ; Rats, Wistar ; Rodent Diseases/parasitology/*transmission ; Time Factors ; }, abstract = {Using a range of parameters, the ability of rats (Rattus norvegicus) to successfully transmit Echinostoma friedi to the next host was examined under experimental conditions. The concept of Experimental Transmission Success (TM), defined as the number of hosts that become successfully infected after exposure to a number of infective stages produced by a previous host per unit of inoculation at which this latter host was exposed, was introduced. Using data for the egg output and miracidium hatching and infectivity, the TM permits us to estimate the ability of a particular definitive host species to successfully transmit a parasite species. This concept may be also useful to compare the transmission fitness of a parasite in different definitive host species. Moreover, variations of the Experimental Transmission Success over the course of the infection were calculated by the use of the Weekly Experimental Transmission Success (TMW). Overall, considering the complete duration of the experiment, the TM of E. friedi using rats as definitive hosts was 0.68 infected snails/metacercaria. However, positive values of the TMW were only obtained from 2 to 4 wk post-infection, with a maximum during the third wk post-infection. When comparing the TM values of E. friedi in rats with those calculated in hamsters on the basis of previously published data, E. friedi appears to be more appropriate to move through this portion of its life cycle when using hamsters (Mesocricetus auratus) as the final host than rats.}, } @article {pmid16621333, year = {2006}, author = {Wright, AA and Katz, JS}, title = {Mechanisms of same/different concept learning in primates and avians.}, journal = {Behavioural processes}, volume = {72}, number = {3}, pages = {234-254}, doi = {10.1016/j.beproc.2006.03.009}, pmid = {16621333}, issn = {0376-6357}, support = {MH-61798/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Cebus ; Columbidae ; *Concept Formation ; *Discrimination Learning ; *Generalization, Psychological ; Macaca mulatta ; *Pattern Recognition, Visual ; Species Specificity ; *Transfer, Psychology ; }, abstract = {Mechanisms of same/different concept learning by rhesus monkeys, capuchin monkeys, and pigeons were studied in terms of how these species learned the task (e.g., item-specific learning versus relational learning) and how rapidly they learned the abstract concept, as the training set size was doubled. They had similar displays, training stimuli, test stimuli, and contingencies. The monkey species learned the abstract concept at similar rates and more rapidly than pigeons, thus showing a quantitative difference across species. All species eventually showed full concept learning (novel-stimulus transfer equivalent to baseline: 128-item set size for monkeys; 256-item set for pigeons), thus showing a qualitative similarity across species. Issues of stimulus regularity/symmetry, generalization from item pairs, and familiarity processing were not considered to be major factors in the final performances, converging on the conclusion that these species were increasingly controlled by the sample-test relationship (i.e., relational processing) leading to full abstract-concept learning.}, } @article {pmid16571578, year = {2004}, author = {Crow, TJ}, title = {Auditory hallucinations as primary disorders of syntax: an evolutionary theory of the origins of language.}, journal = {Cognitive neuropsychiatry}, volume = {9}, number = {1-2}, pages = {125-145}, doi = {10.1080/13546800344000192}, pmid = {16571578}, issn = {1354-6805}, abstract = {A theory of the evolutionary origins of language is built around: (1) the notion that language is a sapiens-specific capacity that arose in the speciation event that separated modern Homo sapiens from a prior hominid species, and (2) Broca's concept of asymmetry (subsequently recognised as a "torque" from right frontal to left occipital cortices) as the defining characteristic of the human brain. The four chambers of human association cortex thus created allow the separation of "thought" from the speech output and "meaning" from the speech input, these abstractions representing the associations in the nondominant hemisphere of the motor and sensory phonological representations in the dominant hemisphere. The nuclear symptoms of schizophrenia are conceived as manifestations of the breakdown of the boundaries between these four compartments, and as indicating the necessity of the separation of motor and sensory speech engrams as the basis for the speaker-hearer distinction. They further illustrate a requirement for a "deictic core" to the cerebral organisation of language as Mueller and Buehler proposed. In this sense the nuclear symptoms are disorders of the syntax of universal grammar.}, } @article {pmid16570614, year = {2006}, author = {Fishtik, I}, title = {Thermodynamic stability relations in redox systems.}, journal = {Environmental science & technology}, volume = {40}, number = {6}, pages = {1902-1910}, doi = {10.1021/es051749i}, pmid = {16570614}, issn = {0013-936X}, mesh = {*Algorithms ; Chemistry, Physical/*methods ; *Computer Graphics ; *Data Interpretation, Statistical ; Electrochemistry ; Oxidation-Reduction ; Thermodynamics ; }, abstract = {Graphical stability relations in redox systems known as Pourbaix diagrams are analyzed employing the concept of overall stability of chemical species in multiple chemical reaction systems recently developed by us (Fishtik, I. J. Phys. Chem. B 2005, 109, 3851). The overall stability approach provides a simple and systematic algorithm for generating thermodynamically and stoichiometrically consistent Pourbaix diagrams that are referred to as overall Pourbaix diagrams. The conditions under which the conventional Pourbaix diagrams coincide with the overall Pourbaix diagrams are also discussed.}, } @article {pmid16422301, year = {2005}, author = {Rodrigues, AG and Araujo, R and Pina-Vaz, C}, title = {Human albumin promotes germination, hyphal growth and antifungal resistance by Aspergillus fumigatus.}, journal = {Medical mycology}, volume = {43}, number = {8}, pages = {711-717}, doi = {10.1080/13693780500129814}, pmid = {16422301}, issn = {1369-3786}, mesh = {Amphotericin B/pharmacology ; Antifungal Agents/*pharmacology ; Aspergillus flavus/growth & development ; Aspergillus fumigatus/drug effects/*growth & development ; Aspergillus niger/growth & development ; *Drug Resistance, Fungal ; Growth Substances/*pharmacology ; Hyphae/*growth & development ; Itraconazole/pharmacology ; Microbial Sensitivity Tests ; Pyrimidines/pharmacology ; Serum Albumin/*pharmacology ; Triazoles/pharmacology ; Voriconazole ; }, abstract = {Invasive aspergillosis is one of the most common deep-seated fungal infections among patients with an impaired immune system. Albumin is a serum protein commonly administered to critical patients. Our objective was to evaluate the in vitro effect of human albumin upon germination and hyphal growth of Aspergillus species, especially the most pathogenic, Aspergillus fumigatus, as well as its influence on antifungal drug activity. Human albumin induced, at normal serum concentrations (2-4%), a significant promotion of conidial germination by A. fumigatus, but not by Aspergillus flavus and Aspergillus niger. However, mycelium growth following germination was enhanced in all Aspergillus species. Minimal inhibitory concentrations (MIC) of all strains tested to amphotericin B and itraconazole increased in the presence of physiological concentrations of human albumin. Voriconazole activity was not, however, significantly affected by the presence of the protein. Conidial germination represents a crucial initial step in the progression to invasive disease, involving metabolic pathways that may differ considerably among Aspergillus species. Our results support the concept that human albumin may promote a faster onset and enhanced dissemination of invasive aspergillosis.}, } @article {pmid16417126, year = {2006}, author = {Vighi, M and Finizio, A and Villa, S}, title = {The evolution of the Environmental Quality concept: from the US EPA Red Book to the European Water Framework Directive.}, journal = {Environmental science and pollution research international}, volume = {13}, number = {1}, pages = {9-14}, doi = {10.1065/espr2006.01.003}, pmid = {16417126}, issn = {0944-1344}, mesh = {Animals ; Conservation of Natural Resources/*legislation & jurisprudence ; Ecology ; Environmental Pollution/*prevention & control ; Europe ; *Fresh Water ; Government Regulation ; Humans ; *Seawater ; United States ; United States Environmental Protection Agency ; }, abstract = {BACKGROUND: Water Quality Criteria were firstly defined in the 1970s by the EPA in the USA and the EIFAC in Europe, recognizing the need for protecting water quality in order to allow the use of water resources by man. In the 1990s, the European Commission emphasized the importance of safeguarding structure and function of biologic communities. These approaches were chemically-based. The European Water Framework Directive (WFD) substantially changes the concept of Water Quality, by assuming that a water body needs to be protected as an environmental good and not as a resource to be exploited. In this frame, the biological-ecological quality assumes a prevailing role.

MAIN FEATURES: The Water Quality concept introduced by the WFD is a challenge for environmental sciences. Reference conditions should be defined for different typologies of water bodies and for different European ecoregions. Suitable indicators should be developed in order to quantify ecological status and to define what a 'good' ecological status is. Procedures should be developed for correlating the deviation from a good ecological to the effects of multiple stressors on function and structure of the ecosystem. The protection of biodiversity becomes a key objective. In this frame, the traditional procedures for ecotoxicological risk assessment, mainly based on laboratory testing, should be overcome by more site-specific approaches, taking into account the characteristics and the homeostatic capabilities of natural communities. In the paper an overview of the present knowledge and of the new trends in ecotoxicology to get these objectives will be given. A procedure is suggested based on the concept of Species Sensitivity Distribution (SSD).

The need for more site-specific and ecologically-oriented approaches in ecotoxicology is strongly recommended. The development of new tools for implementing the concept of 'Stress Ecology' has been recently proposed by van Straalen (2003). In the same time, more 'cological realism' is needed in practically applicable procedures for regulatory purposes.}, } @article {pmid16406705, year = {2006}, author = {Tibayrenc, M}, title = {The species concept in parasites and other pathogens: a pragmatic approach?.}, journal = {Trends in parasitology}, volume = {22}, number = {2}, pages = {66-70}, doi = {10.1016/j.pt.2005.12.010}, pmid = {16406705}, issn = {1471-4922}, mesh = {Animals ; Biological Evolution ; Host-Parasite Interactions ; Humans ; Parasites/*classification ; Phenotype ; Philosophy ; Phylogeny ; Species Specificity ; *Terminology as Topic ; }, abstract = {Although the problem of speciation is a puzzle for evolutionists, species are not mere fantasies. In many cases, it is possible to identify evolutionary entities that deserve to be attributed the name 'species' and that are relevant to medical researchers and decision makers. All approaches to the problem of speciation in pathogens are specific cases of four main concepts (or combinations thereof): biological, phylogenetic, phenetic and phenotypic. Modern genetic concepts and technologies help to juggle these concepts.}, } @article {pmid16396551, year = {2005}, author = {Korff, BM and Troppmann, U and Kompa, KL and de Vivie-Riedle, R}, title = {Manganese pentacarbonyl bromide as candidate for a molecular qubit system operated in the infrared regime.}, journal = {The Journal of chemical physics}, volume = {123}, number = {24}, pages = {244509}, doi = {10.1063/1.2141615}, pmid = {16396551}, issn = {0021-9606}, abstract = {Our concept for a quantum computational system is based on qubits encoded in vibrational normal modes of polyatomic molecules. The quantum gates are implemented by shaped femtosecond laser pulses. We adopt this concept to the new species manganese pentacarbonyl bromide [MnBr(CO)5] and show that it is a promising candidate in the mid-infrared (IR) frequency range to connect theory and experiment. As direct reference for the ab initio calculations we evaluated experimentally the absorption bands of MnBr(CO)5 in the mid-IR as well as the related transition dipole moments. The two-dimensional potential-energy surface spanned by the two strongest IR active modes and the dipole vector surfaces are calculated with density-functional theory. The vibrational eigenstates representing the qubit system are determined. Laser pulses are optimized by multitarget optimal control theory to form a set of global quantum gates: NOT, CNOT, Pi, and Hadamard. For all of them simply structured pulses with low pulse energies around 1 microJ could be obtained. Exemplarily for the CNOT gate we investigated the possible transfer to experimental shaping, based on the mask function for pulse shaping in the frequency regime as well as decomposition into a train of subpulses.}, } @article {pmid16389960, year = {2005}, author = {Rehner, SA and Buckley, E}, title = {A Beauveria phylogeny inferred from nuclear ITS and EF1-alpha sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs.}, journal = {Mycologia}, volume = {97}, number = {1}, pages = {84-98}, doi = {10.3852/mycologia.97.1.84}, pmid = {16389960}, issn = {0027-5514}, mesh = {Animals ; Cordyceps/classification/genetics ; DNA, Fungal/analysis ; DNA, Ribosomal Spacer/analysis/*genetics ; Hypocreales/*classification/genetics ; Insecta/classification/microbiology ; Molecular Sequence Data ; Mycological Typing Techniques ; Peptide Elongation Factor 1/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Beauveria is a globally distributed genus of soil-borne entomopathogenic hyphomycetes of interest as a model system for the study of entomopathogenesis and the biological control of pest insects. Species recognition in Beauveria is difficult due to a lack of taxonomically informative morphology. This has impeded assessment of species diversity in this genus and investigation of their natural history. A gene-genealogical approach was used to investigate molecular phylogenetic diversity of Beauveria and several presumptively related Cordyceps species. Analyses were based on nuclear ribosomal internal transcribed spacer (ITS) and elongation factor 1-alpha (EF1-alpha) sequences for 86 exemplar isolates from diverse geographic origins, habitats and insect hosts. Phylogenetic trees were inferred using maximum parsimony and Bayesian likelihood methods. Six well supported clades within Beauveria, provisionally designated A-F, were resolved in the EF1-alpha and combined gene phylogenies. Beauveria bassiana, a ubiquitous species that is characterized morphologically by globose to subglobose conidia, was determined to be non-monophyletic and consists of two unrelated lineages, clades A and C. Clade A is globally distributed and includes the Asian teleomorph Cordyceps staphylinidaecola and its probable synonym C. bassiana. All isolates contained in Clade C are anamorphic and originate from Europe and North America. Clade B includes isolates of B. brongniartii, a Eurasian species complex characterized by ellipsoidal conidia. Clade D includes B. caledonica and B. vermiconia, which produce cylindrical and comma-shaped conidia, respectively. Clade E, from Asia, includes Beauveria anamorphs and a Cordyceps teleomorph that both produce ellipsoidal conidia. Clade F, the basal branch in the Beauveria phylogeny includes the South American species B. amorpha, which produces cylindrical conidia. Lineage diversity detected within clades A, B and C suggests that prevailing morphological species concepts underestimate species diversity within these groups. Continental endemism of lineages in B. bassiana s.l. (clades A and C) indicates that isolation by distance has been an important factor in the evolutionary diversification of these clades. Permutation tests indicate that host association is essentially random in both B. bassiana s.l. clades A and C, supporting past assumptions that this species is not host specific. In contrast, isolates in clades B and D occurred primarily on coleopteran hosts, although sampling in these clades was insufficient to assess host affliation at lower taxonomic ranks. The phylogenetic placement of Cordyceps staphylinidaecola/bassiana, and C. scarabaeicola within Beauveria corroborates prior reports of these anamorph-teleomorph connections. These results establish a phylogenetic framework for further taxonomic, phylogenetic and comparative biological investigations of Beauveria and their corresponding Cordyceps teleomorphs.}, } @article {pmid16387882, year = {2006}, author = {Kalinowski, ST and Taper, ML and Metz, AM}, title = {How are humans related to other primates? A guided inquiry laboratory for undergraduate students.}, journal = {Genetics}, volume = {172}, number = {3}, pages = {1379-1383}, pmid = {16387882}, issn = {0016-6731}, mesh = {Animals ; *Curriculum ; Genetics/*education/organization & administration/standards ; Humans ; *Phylogeny ; Primates/*genetics ; }, abstract = {Understanding that phylogenies depict the evolutionary history of species is a critical concept for undergraduate biology students. We present an inquiry-based laboratory exercise exploring this concept in the context of the human phylogeny. This activity reinforces several important biological concepts and skills. Bolstered concepts include that evolution is descent with modification, that evolution is a genetic process, and that humans are closely related to apes. In terms of thinking skills, the lab gives students practice with hypothetical-deductive thinking, quantifying patterns from complex data, and evaluating evidence.}, } @article {pmid19455206, year = {2007}, author = {Faith, DP and Baker, AM}, title = {Phylogenetic diversity (PD) and biodiversity conservation: some bioinformatics challenges.}, journal = {Evolutionary bioinformatics online}, volume = {2}, number = {}, pages = {121-128}, pmid = {19455206}, issn = {1176-9343}, abstract = {Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, "PD", has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a). While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, "cryptic", taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based "species" designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.}, } @article {pmid16365305, year = {2005}, author = {Silander, OK and Weinreich, DM and Wright, KM and O'Keefe, KJ and Rang, CU and Turner, PE and Chao, L}, title = {Widespread genetic exchange among terrestrial bacteriophages.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {52}, pages = {19009-19014}, pmid = {16365305}, issn = {0027-8424}, support = {F32 GM020736/GM/NIGMS NIH HHS/United States ; GM207636/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*genetics ; Cystoviridae/genetics ; Genetic Variation ; Genome, Viral ; Linkage Disequilibrium ; Models, Genetic ; Molecular Sequence Data ; Mutation ; Phylogeny ; Polymerase Chain Reaction ; RNA/genetics ; RNA, Double-Stranded/chemistry ; Recombination, Genetic ; Sequence Analysis, DNA ; Species Specificity ; Viruses/genetics ; }, abstract = {Bacteriophages are the most numerous entities in the biosphere. Despite this numerical dominance, the genetic structure of bacteriophage populations is poorly understood. Here, we present a biogeography study involving 25 previously undescribed bacteriophages from the Cystoviridae clade, a group characterized by a dsRNA genome divided into three segments. Previous laboratory manipulation has shown that, when multiple Cystoviruses infect a single host cell, they undergo (i) rare intrasegment recombination events and (ii) frequent genetic reassortment between segments. Analyzing linkage disequilibrium (LD) within segments, we find no significant evidence of intrasegment recombination in wild populations, consistent with (i). An extensive analysis of LD between segments supports frequent reassortment, on a time scale similar to the genomic mutation rate. The absence of LD within this group of phages is consistent with expectations for a completely sexual population, despite the fact that some segments have >50% nucleotide divergence at 4-fold degenerate sites. This extraordinary rate of genetic exchange between highly unrelated individuals is unprecedented in any taxa. We discuss our results in light of the biological species concept applied to viruses.}, } @article {pmid16332336, year = {2005}, author = {Cordeiro, LM and Reis, RA and Cruz, LM and Stocker-Wörgötter, E and MartinGrube, and Iacomini, M}, title = {Molecular studies of photobionts of selected lichens from the coastal vegetation of Brazil.}, journal = {FEMS microbiology ecology}, volume = {54}, number = {3}, pages = {381-390}, doi = {10.1016/j.femsec.2005.05.003}, pmid = {16332336}, issn = {0168-6496}, mesh = {Base Sequence ; Bayes Theorem ; Brazil ; Chlorophyta/classification/*cytology/*genetics ; DNA, Ribosomal Spacer/genetics ; Lichens/classification/*cytology/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {A light microscopic and molecular analysis of photobionts in Ramalina and Cladonia from coastal habitats of Brazil is presented. A Bayesian phylogenetic analysis of ITS rDNA sequences suggests a Trebouxia lineage which is preferentially tropical in geographic distribution. This highly diverse clade also includes the morphological similar species Trebouxia higginsiae and galapagensis. Within the predominantly tropical clade of Trebouxia we distinguish several subclades, three of which are represented in our samples of Ramalina species. Since sexuality has not been recognized in coccal lichenised photobionts until recently, we cannot apply a biological species concept, but when compared with the sequence diversity between known species we conclude that several new species need to be described in this clade. The mutually exclusive presence of other Trebouxia lineages in temperate samples of Ramalina suggests an evolution towards higher selectivity in this genus. A strictly tropical lineage is not conspicuous in the photobionts of the genus Asterochloris sampled from Cladonia so far.}, } @article {pmid16322518, year = {2006}, author = {Nesbø, CL and Dlutek, M and Doolittle, WF}, title = {Recombination in Thermotoga: implications for species concepts and biogeography.}, journal = {Genetics}, volume = {172}, number = {2}, pages = {759-769}, pmid = {16322518}, issn = {0016-6731}, mesh = {Base Sequence ; *Genes, Bacterial ; Genetic Speciation ; Genomics ; Genotype ; Likelihood Functions ; Molecular Sequence Data ; Multigene Family ; Phenotype ; Phylogeny ; *Recombination, Genetic ; Sequence Alignment ; Species Specificity ; Thermotoga maritima/*genetics/isolation & purification/physiology ; Thermotoga neapolitana/*genetics/isolation & purification/physiology ; *Water Microbiology ; }, abstract = {Here we characterize regions of the genomes of eight members of the hyperthermophilic genus Thermotoga. These bacteria differ from each other physiologically and by 3-20% in gene content and occupy physically distinct environments in widely disparate regions of the globe. Among the four different lineages (represented by nine different strains) that we compare, no two are closer than 96% in the average sequences of their genes. By most accepted recent definitions these are different "ecotypes" and different "species." And yet we find compelling evidence for recombination between them. We suggest that no single prokaryotic species concept can accommodate such uncoupling of ecotypic and genetic aspects of cohesion and diversity, and that without a single concept, the question of whether or not prokaryotic species might in general be cosmopolitan cannot be sensibly addressed. We can, however, recast biogeographical questions in terms of the distribution of genes and their alleles.}, } @article {pmid16299765, year = {2005}, author = {de Queiroz, K}, title = {Different species problems and their resolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {27}, number = {12}, pages = {1263-1269}, doi = {10.1002/bies.20325}, pmid = {16299765}, issn = {0265-9247}, mesh = {Animals ; *Biological Evolution ; *Models, Biological ; Species Specificity ; }, abstract = {At least three different issues are commonly referred to by the term "the species problem": one concerns the necessary properties of species, a second the processes responsible for the existence of species, and a third methods for inferring species limits. Solutions have recently been proposed to the first two problems, which are conceptual in nature (the third is methodological). The first equates species with metapopulation lineages and proposes that existence as a separately evolving metapopulation lineage be considered the only necessary property of species. The second views the species category as a cluster concept and proposes that no single process or set of processes be considered necessary for the existence of species. Although these two solutions have been portrayed as being in conflict, they are, in fact, highly compatible. Moreover, the proposals in question clarify the problem concerning methods for inferring the limits of species, which has for a long time been confused with the problem concerning the necessary properties of species. Together these proposals provide the opportunity for biology to move beyond debates about the definition of the species category and focus on estimating the boundaries and numbers of species as well as studying the diverse processes involved in their origin and persistence.}, } @article {pmid16293236, year = {2005}, author = {Doctor, BP and Saxena, A}, title = {Bioscavengers for the protection of humans against organophosphate toxicity.}, journal = {Chemico-biological interactions}, volume = {157-158}, number = {}, pages = {167-171}, doi = {10.1016/j.cbi.2005.10.024}, pmid = {16293236}, issn = {0009-2797}, mesh = {Animals ; Antidotes ; Butyrylcholinesterase/metabolism/*pharmacology ; Cattle ; Guinea Pigs ; Horses ; Humans ; Macaca fascicularis ; Macaca mulatta ; Mice ; Organophosphorus Compounds/*antagonists & inhibitors/*toxicity ; }, abstract = {Current antidotes for organophosphorus compounds (OP) poisoning consist of a combination of pretreatment with carbamates (pyridostigmine bromide), to protect acetylcholinesterase (AChE) from irreversible inhibition by OP compounds, and post-exposure therapy with anti-cholinergic drugs (atropine sulfate) to counteract the effects of excess acetylcholine and oximes (e.g., 2-PAM chloride) to reactivate OP-inhibited AChE. These antidotes are effective in preventing lethality from OP poisoning, but they do not prevent post-exposure incapacitation, convulsions, seizures, performance decrements, or in many cases permanent brain damage. These symptoms are commonly observed in experimental animals and are likely to occur in humans. The problems intrinsic to these antidotes stimulated attempts to develop a single protective drug, itself devoid of pharmacological effects, which would provide protection against the lethality of OP compounds and prevent post-exposure incapacitation. One approach is the use of enzymes such as cholinesterases (ChEs), beta-esterases in general, as single pretreatment drugs to sequester highly toxic OP anti-ChEs before they reach their physiological targets. This approach turns the irreversible nature of the OP: ChE interaction from disadvantage to an advantage; instead of focusing on OP as an anti-ChE, one can use ChE as an anti-OP. Using this approach, it was shown that administration of fetal bovine serum AChE (FBSAChE) or equine serum butyrylcholinesterase (EqBChE) or human serum BChE (HuBChE) protected the animals from multiple LD50s of a variety of highly toxic OPs without any toxic effects or performance decrements. The bioscavengers that have been explored to date for the detoxification of OPs fall into three categories: (A) those that can catalytically hydrolyze OPs and thus render them non-toxic, such as OP hydrolase and OP anhydrase; (B) those that stoichiometrically bind to OPs, that is, 1 mol of enzyme neutralizes one or 2 mol of OP inactivating both, such as ChEs and related enzymes; and (C) and those generally termed as "pseudo catalytic", e.g., a combination of ChE and an oxime pre-treatment such that the catalytic activity of OP-inhibited ChE can rapidly and continuously be restored in the presence of an oxime. Since the biochemical mechanism underlying prophylaxis by exogenous esterases such as ChEs is established and tested in several animal species, including non-human primates, this concept should allow a reliable extrapolation of results from animal experiments to human application. Having being extensively investigated by several groups, plasma derived HuBChE is judged to be the most suitable bioscavenger for its advancement for human use. The program is being developed at the present time for conducting a safety clinical trial in human volunteers. Several other candidate bioscavengers will follow; e.g., recombinant HuBChE expressed in the milk of transgenic goats, pseudo catalytic scavenger(s), e.g., a combination of ChE and oxime, and possibly PON 1 as a catalytic scavenger in the future.}, } @article {pmid16270327, year = {2006}, author = {Starosta, V and Griese, M}, title = {Protein oxidation by chronic pulmonary diseases in children.}, journal = {Pediatric pulmonology}, volume = {41}, number = {1}, pages = {67-73}, doi = {10.1002/ppul.20289}, pmid = {16270327}, issn = {8755-6863}, mesh = {Adolescent ; Blotting, Western ; Bronchoalveolar Lavage Fluid/*chemistry/cytology ; Case-Control Studies ; Child ; Child, Preschool ; Chronic Disease ; Electrophoresis, Gel, Two-Dimensional ; Female ; Humans ; Infant ; Leukocyte Count ; Male ; Neutrophils/cytology ; Oxidation-Reduction ; Oxidative Stress ; Pneumonia/*metabolism ; Protein Carbonylation/physiology ; Proteins/*metabolism ; Regression Analysis ; }, abstract = {The oxidation of proteins may play an important role in the pathogenesis of chronic inflammatory lung diseases, and may contribute to lung damage. However, the extent of oxidation and the distribution among proteins are not known for most pediatric lung diseases. In this work, protein oxidation was assessed as protein carbonyls. Bronchoalveolar lavages (BAL) from children with chronic lung diseases were investigated by dot-blot assay for content and for pattern of distribution of oxidized proteins by two-dimensional (2D) electrophoresis and Western blotting. Significantly higher levels of protein oxidation than in healthy controls were determined in groups of patients with interstitial lung disease, gastro-esophageal reflux disease, and pulmonary alveolar proteinosis. The proteins most sensitive to oxidation were serum albumin, surfactant protein A, and alpha1-antitrypsin. Our data show increased oxidative stress in lungs of children with chronic pulmonary diseases, with significant interindividual variations. The extent of protein oxidation was proportional to the count of neutrophilic granulocytes in BAL fluid. These findings strongly support the concept that an abundance of reactive oxygen species produced during neutrophilic inflammation may be a deleterious factor, leading to pulmonary damage in these patients.}, } @article {pmid16268170, year = {2005}, author = {De Zwart, D and Posthuma, L}, title = {Complex mixture toxicity for single and multiple species: proposed methodologies.}, journal = {Environmental toxicology and chemistry}, volume = {24}, number = {10}, pages = {2665-2676}, doi = {10.1897/04-639r.1}, pmid = {16268170}, issn = {0730-7268}, mesh = {Animals ; Biodiversity ; Drug Interactions ; Ecology ; Environmental Pollutants/*toxicity ; *Hazardous Waste ; Risk Assessment/methods ; Toxicity Tests ; }, abstract = {Methods for the assessment of ecological risks associated with exposure to defined mixtures of toxicants are reviewed and formalized for single-species toxicity. Depending on the modes of action of toxicants in a mixture, these methods apply either the model for concentration additivity (CA) or the model for response additivity (RA). For complex mixtures, the present paper advocates the use of a new, two-step, mixed-model approach as a logical extension of model selection: Mixture toxicity for individual modes of action is evaluated with the CA model, and the toxicities of different modes of action are combined using the RA model. Using comparable mixture toxicity strategies in combination with the concept of species-sensitivity distributions, we develop a method to address and predict the risk for direct effects on the composition of species assemblages and biodiversity. The data needed for modeling can be obtained from existing databases, and lack of data can, in part, be addressed by the use of toxicity patterns in those databases. Both single- and multiple-species methods of mixture risk prediction are useful for risk management, because they allow ranking of polluted sites and affected species as well as identification of the most hazardous contaminants, at least in a comparative way. Validation of the proposed methods is feasible but currently limited because of a lack of appropriate data.}, } @article {pmid16214960, year = {2002}, author = {Clark, SF}, title = {The biochemistry of antioxidants revisited.}, journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition}, volume = {17}, number = {1}, pages = {5-17}, doi = {10.1177/011542650201700105}, pmid = {16214960}, issn = {0884-5336}, abstract = {Biochemical relationships between oxidative stress, antioxidant nutrients, and chronic diseases are complicated and often conflicting. Basic research supports the concept that reactive oxygen species precipitate changes that result in oxidative damage to lipid, protein, and DNA biomolecules. Oxidative stress is implicated in the development of cancer, cardiovascular disease, diabetes, sepsis, various eye diseases, and neurologic conditions. Supplementation with antioxidant nutrients seems plausible to counter the effects of oxidative stress, but the preferred mode of delivery for these nutrients may be through the patient's diet rather than as supplements to the diet. In fact, evidence supporting consumption of at least 5 servings of fruits and vegetables continues to grow. To better understand the role of antioxidant nutrients in disease promotion or prevention, this review will discuss basic nutritional biochemistry relating to oxidative stress and antioxidant defense systems, followed by a discussion of the metabolism (vitamins E, C, A) and interrelationships of select antioxidant nutrients.}, } @article {pmid16210546, year = {2005}, author = {Miller, AA and Drummond, GR and Schmidt, HH and Sobey, CG}, title = {NADPH oxidase activity and function are profoundly greater in cerebral versus systemic arteries.}, journal = {Circulation research}, volume = {97}, number = {10}, pages = {1055-1062}, doi = {10.1161/01.RES.0000189301.10217.87}, pmid = {16210546}, issn = {1524-4571}, mesh = {Angiotensin II/pharmacology ; Animals ; Arteries/*enzymology ; Cerebral Arteries/*enzymology ; Hydrogen Peroxide/pharmacology ; Male ; NADP/pharmacology ; NADPH Oxidase 4 ; NADPH Oxidases/blood/genetics/*physiology ; Nitroprusside/pharmacology ; RNA, Messenger/analysis ; Rats ; Rats, Sprague-Dawley ; Reactive Oxygen Species/metabolism ; Superoxides/metabolism ; Vasoconstriction/drug effects ; Vasodilation/drug effects ; }, abstract = {Recent studies suggest that the superoxide generating enzyme NADPH oxidase may play a functional role in regulating cerebral vascular tone. We tested whether the activity, function, and expression of NADPH oxidase differs between rat cerebral and systemic arteries. Superoxide production by basilar (BA), middle cerebral (MCA), carotid (CA), renal (RA), and mesenteric (MA) arteries and aorta (AO) was measured using lucigenin-enhanced chemiluminescence. Superoxide production from NADPH oxidase was localized and semiquantified using dihydroethidium. Vascular functional responses were assessed in a myograph or organ bath. Vascular Nox4 protein expression was measured using Western blotting. Superoxide production (basal or in response to NADPH or angiotensin II) in the intracranial arteries, BA, and MCA was 10- to 100-fold greater than in AO, CA, RA, or MA. Similar results were found using either intact vessels or arterial homogenates, and were associated with 10-fold greater expression of Nox4 in the BA versus AO, CA, and MA. Superoxide production was attenuated by the NADPH oxidase inhibitors, diphenyleneiodonium, apocynin, and gp91ds-tat. NADPH and H2O2 were strong relaxing stimuli in the BA, where the H2O2 scavenger catalase, as well as apocynin, attenuated these relaxations and also augmented contractions to angiotensin II. NADPH oxidase activity is markedly higher in intracranial versus systemic arteries, in association with higher Nox4 expression. In cerebral arteries, endogenous H2O2 derived from NADPH oxidase activation appears to cause relaxation and is able to offset angiotensin II-induced constriction. These data are consistent with the concept that NADPH oxidase-derived reactive oxygen species modulate cerebral vascular tone under physiological conditions.}, } @article {pmid16197965, year = {2005}, author = {Giangrande, A and Licciano, M and Musco, L}, title = {Polychaetes as environmental indicators revisited.}, journal = {Marine pollution bulletin}, volume = {50}, number = {11}, pages = {1153-1162}, doi = {10.1016/j.marpolbul.2005.08.003}, pmid = {16197965}, issn = {0025-326X}, mesh = {Animals ; Conservation of Natural Resources/*methods ; Ecology/*methods ; *Environment ; Environmental Monitoring/*methods ; Environmental Pollution/*analysis ; Mediterranean Sea ; Polychaeta/*growth & development ; Species Specificity ; }, abstract = {The utilization of polychaetes in descriptive ecology is reviewed in the light of recent research especially concerning the biota hard bottom environments. Polychaetes, often linked in the past to the concept of opportunistic species able to proliferate after an increase in organic matter, have played an important role especially with regard to impacted soft-bottom habitats. Increased knowledge of the group, suggests that not only opportunistic species can be utilised as indicators, so that these organisms can be disengaged from the old concept of opportunistic taxa. Moreover, recent researches conducted on this group allowed demonstrating as surrogacy is not always applicable. Among polychaetes inhabiting hard bottom environment, the analysis of family Syllidae appears particularly promising. Studied conducted in our laboratory demonstrated as syllid species decrease in abundance or completely disappear under varying sources of negative impact. The distribution of species also appeared indicative in underlying effects of marine protected areas (MPA) functioning, or in describing different climatic areas within biogeographical sectors. It is obvious that good results can only be obtained on the basis of good taxonomic resolution. We suggested that, in monitoring studies, operational time could be optimized not only by working at a higher-level on the whole invertebrate data set, but by also selecting a particularly indicative group and working at fine level.}, } @article {pmid16168944, year = {2005}, author = {Godreuil, S and Cohan, F and Shah, H and Tibayrenc, M}, title = {Which species concept for pathogenic bacteria? An E-Debate.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {5}, number = {4}, pages = {375-387}, doi = {10.1016/j.meegid.2004.03.004}, pmid = {16168944}, issn = {1567-1348}, mesh = {Animals ; Bacteria/*classification/*genetics ; *Biological Evolution ; Concept Formation ; Humans ; Models, Theoretical ; Molecular Diagnostic Techniques ; Recombination, Genetic ; }, } @article {pmid16166214, year = {2005}, author = {Scharf, JG and Unterman, TG and Kietzmann, T}, title = {Oxygen-dependent modulation of insulin-like growth factor binding protein biosynthesis in primary cultures of rat hepatocytes.}, journal = {Endocrinology}, volume = {146}, number = {12}, pages = {5433-5443}, doi = {10.1210/en.2005-0948}, pmid = {16166214}, issn = {0013-7227}, mesh = {Animals ; Base Sequence ; Cell Hypoxia/physiology ; Cells, Cultured ; Deferoxamine/pharmacology ; Hepatocytes/drug effects/*metabolism ; Hydrogen Peroxide/pharmacology ; Insulin-Like Growth Factor Binding Protein 1/*biosynthesis/genetics/metabolism ; Insulin-Like Growth Factor Binding Protein 4/biosynthesis/genetics/metabolism ; Isoenzymes/pharmacology ; Male ; Oxidants/pharmacology ; Oxygen/blood/*metabolism ; Procollagen-Proline Dioxygenase/pharmacology ; Promoter Regions, Genetic ; RNA, Messenger/biosynthesis/metabolism ; Rats ; Rats, Wistar ; Siderophores/pharmacology ; Time Factors ; Veins ; }, abstract = {Higher levels of IGF-binding protein 1 (IGFBP-1) mRNA are expressed in the less aerobic perivenous zone of the liver. Because gradients in oxygen tension (pO(2)) may contribute to zonated gene expression, the influence of arterial and venous pO(2) on IGFBP-1 biosynthesis was studied in primary cultures of rat hepatocytes. Maximal IGFBP-1 mRNA and protein levels were observed under venous pO(2), whereas less than 30% of maximal levels were observed under arterial pO(2). In contrast, the expression of IGFBP-4 was greatest under arterial pO(2), indicating that this effect of hypoxia on IGFBP-1 gene expression is specific. The response to hypoxia appears to involve reactive oxygen species, because treatment with H(2)O(2) results in a dose-dependent decrease of IGFBP-1 mRNA levels under venous pO(2), whereas IGFBP-1 mRNA expression under arterial pO(2) was not affected. Inhibition of the hypoxia-dependent IGFBP-1 mRNA induction by actinomycin D indicates that this effect is mediated at the level of gene transcription, and inhibition of IGFBP-1 mRNA by the iron chelator desferrioxamine under both venous and arterial pO(2) suggested the involvement of hypoxia-inducible transcription factors (HIF). Transfection experiments demonstrated that especially HIF-3alpha and HIF-2alpha, and to a lesser extent HIF-1alpha, contribute to the induction of IGFBP-1 mRNA expression in isolated hepatocytes, whereas experiments with vectors for the HIF prolyl hydroxylases (PHD) indicated a major role of PHD-2 in destabilization of HIFs, attenuating the induction of IGFBP-1 under venous pO(2). Reporter gene studies indicate that hypoxia stimulates IGFBP-1 expression through a putative HIF response element located approximately 250 bp upstream from the transcription initiation site. Together, these results support the concept that iron, radical oxygen species, and the HIF-2 and -3 as well as the PHD pathways play important roles in mediating effects of hypoxia on IGFBP-1 gene expression in the liver.}, } @article {pmid16138101, year = {2005}, author = {Gevers, D and Cohan, FM and Lawrence, JG and Spratt, BG and Coenye, T and Feil, EJ and Stackebrandt, E and Van de Peer, Y and Vandamme, P and Thompson, FL and Swings, J}, title = {Opinion: Re-evaluating prokaryotic species.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {9}, pages = {733-739}, doi = {10.1038/nrmicro1236}, pmid = {16138101}, issn = {1740-1526}, mesh = {Bacteria/classification/*genetics ; DNA, Bacterial/genetics ; Models, Genetic ; Phylogeny ; }, abstract = {There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we review the classical approaches to prokaryotic species definition and discuss the current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics. We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters.}, } @article {pmid16126664, year = {2005}, author = {Balakrishnan, R}, title = {Species concepts, species boundaries and species identification: a view from the tropics.}, journal = {Systematic biology}, volume = {54}, number = {4}, pages = {689-693}, doi = {10.1080/10635150590950308}, pmid = {16126664}, issn = {1063-5157}, mesh = {Classification/*methods ; Conservation of Natural Resources/methods ; Phylogeny ; Species Specificity ; *Terminology as Topic ; }, } @article {pmid16125442, year = {2005}, author = {Ward, N and Fraser, CM}, title = {How genomics has affected the concept of microbiology.}, journal = {Current opinion in microbiology}, volume = {8}, number = {5}, pages = {564-571}, doi = {10.1016/j.mib.2005.08.011}, pmid = {16125442}, issn = {1369-5274}, mesh = {Eukaryotic Cells ; Genome, Archaeal ; Genome, Bacterial ; Genome, Viral ; *Genomics/trends ; *Microbiology/trends ; Prokaryotic Cells ; }, abstract = {Genomics influences multiple areas of microbiology, and thus affects key microbiological concepts. Recent reports that describe the large genome and unusual coding capacity of mimivirus, the minimized fungal genomes that contain elements of bacterial metabolism, and the 'signature' eukaryotic proteins in bacteria are introducing grey shades into the black-and-white distinctions between microbial domains. The concept of the 'universal' minimal genome is being challenged, and the ability of minimal genomes to support cellular complexity is under investigation. There have been intriguing insights into microbe-microbe relationships, for example conflict mediation in competing bacteriophages that rapidly evolve survival mechanisms when cooperation is experimentally enforced. Genomics has given birth to metagenomics, but has also stimulated the development of improved cultivation techniques. Lastly, the taxonomic potential of genomics is emerging, as studies of multiple strains allow us to revise and refine the bacterial species concept as well as the idea of a static genome.}, } @article {pmid16120262, year = {2005}, author = {Reydon, TA}, title = {On the nature of the species problem and the four meanings of 'species'.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {36}, number = {1}, pages = {135-158}, doi = {10.1016/j.shpsc.2004.12.004}, pmid = {16120262}, issn = {1369-8486}, mesh = {*Biological Evolution ; Cultural Diversity ; Humans ; Individuation ; *Knowledge ; *Philosophy ; *Selection, Genetic ; *Species Specificity ; }, abstract = {Present-day thought on the notion of species is troubled by a mistaken understanding of the nature of the issue: while the species problem is commonly understood as concerning the epistemology and ontology of one single scientific concept, I argue that in fact there are multiple distinct concepts at stake. An approach to the species problem is presented that interprets the term 'species' as the placeholder for four distinct scientific concepts, each having its own role in biological theory, and an explanation is given of the concepts involved. To illustrate how these concepts are commonly conflated, two widely accepted ideas on species are criticized: species individualism and species pluralism. I argue that by failing to distinguish between the four concepts and their particular roles in contemporary biological theory, these ideas stand in the way of a final resolution of the species problem.}, } @article {pmid16048136, year = {2005}, author = {Koch, TA and Ekelund, F}, title = {Strains of the heterotrophic flagellate Bodo designis from different environments vary considerably with respect to salinity preference and SSU rRNA gene composition.}, journal = {Protist}, volume = {156}, number = {1}, pages = {97-112}, doi = {10.1016/j.protis.2004.12.001}, pmid = {16048136}, issn = {1434-4610}, mesh = {Animals ; Bayes Theorem ; DNA, Protozoan/genetics ; Genetic Variation ; Kinetoplastida/*classification/genetics/growth & development ; RNA, Ribosomal/*analysis/genetics ; Sequence Analysis, DNA ; Sodium Chloride ; }, abstract = {The morpho species Bodo designis is widespread and abundant globally in highly contrasting terrestrial and aquatic ecosystems. Whether the forms of Bodo designis from contrasting environments are conspecific, i.e. largely genetically identical, or whether they merely share the external morphology is presently not known. We examined the ability of different strains of Bodo designis isolated from different environments at different geographical sites to survive and grow at a salinity range of 0.5-45%. The Bodo designis strains from marine, freshwater, and terrestrial environments showed a different ability to cope with altered physiological conditions. Most of the tested strains were only able to tolerate a small salinity range, whereas others were able to withstand all tested salinity levels. We further examined the phylogenetic relationship between the different strains by sequencing the small subunit (SSU) rRNA gene. The resulting phylogenetic analyses suggest a huge genetic variation within Bodo designis, and also imply that Dimastigella and Rhyncomonas are developed inside Bodo designis. If the biological species concept is used, the genetic differences as well as the physiological barriers between the different strains of Bodo designis, would suggest that they should be assigned to different species.}, } @article {pmid16040990, year = {2005}, author = {Voza, T and Vigário, AM and Belnoue, E and Grüner, AC and Deschemin, JC and Kayibanda, M and Delmas, F and Janse, CJ and Franke-Fayard, B and Waters, AP and Landau, I and Snounou, G and Rénia, L}, title = {Species-specific inhibition of cerebral malaria in mice coinfected with Plasmodium spp.}, journal = {Infection and immunity}, volume = {73}, number = {8}, pages = {4777-4786}, pmid = {16040990}, issn = {0019-9567}, mesh = {Animals ; Blood/parasitology ; CD8-Positive T-Lymphocytes/immunology ; Flow Cytometry ; Genes, Reporter ; Malaria, Cerebral/*immunology/physiopathology ; Mice ; Plasmodium/*immunology ; Species Specificity ; Time Factors ; }, abstract = {Recent epidemiological observations suggest that clinical evolution of Plasmodium falciparum infections might be influenced by the concurrent presence of another Plasmodium species, and such mixed-species infections are now known to occur frequently in residents of most areas of endemicity. We used mice infected with P. berghei ANKA (PbA), a model for cerebral malaria (CM), to investigate the influence of experimental mixed-species infections on the expression of this pathology. Remarkably, the development of CM was completely inhibited by the simultaneous presence of P. yoelii yoelii but not that of P. vinckei or another line of P. berghei. In the protected coinfected mice, the accumulation of CD8(+) T cells in the brain vasculature, a pivotal step in CM pathogenesis, was found to be abolished. Protection from CM was further found to be associated with species-specific suppression of PbA multiplication. These observations establish the concept of mixed Plasmodium species infections as potential modulators of pathology and open novel avenues to investigate mechanisms implicated in the pathogenesis of malaria.}, } @article {pmid16036611, year = {2005}, author = {Colavitti, R and Finkel, T}, title = {Reactive oxygen species as mediators of cellular senescence.}, journal = {IUBMB life}, volume = {57}, number = {4-5}, pages = {277-281}, doi = {10.1080/15216540500091890}, pmid = {16036611}, issn = {1521-6543}, mesh = {Animals ; Cellular Senescence ; Free Radicals ; Humans ; MAP Kinase Signaling System ; Models, Biological ; Oxidants/pharmacology ; Oxidative Stress ; Oxygen/metabolism ; *Reactive Oxygen Species ; Signal Transduction ; Telomerase/metabolism ; Transcription, Genetic ; }, abstract = {Aging has often been viewed as a random process arising from the accumulation of both genetic and epigenetic changes. Increasingly, the notion that aging is a stochastic process is being supplanted by the concept that maximum lifespan of an organism is tightly regulated. This knowledge has led to a growing overlap between classical signal transduction paradigms and the biology of aging. We review certain specific examples where these seemingly disparate disciplines intersect. In particular, we review the concept that intracellular reactive oxygen species function as signalling molecules and that oxidants play a central role as mediators of cellular senescence.}, } @article {pmid16011763, year = {2005}, author = {Herbert, RA and Ranchou-Peyruse, A and Duran, R and Guyoneaud, R and Schwabe, S}, title = {Characterization of purple sulfur bacteria from the South Andros Black Hole cave system: highlights taxonomic problems for ecological studies among the genera Allochromatium and Thiocapsa.}, journal = {Environmental microbiology}, volume = {7}, number = {8}, pages = {1260-1268}, doi = {10.1111/j.1462-2920.2005.00815.x}, pmid = {16011763}, issn = {1462-2912}, mesh = {Bahamas ; Base Composition ; Chromatiaceae/*classification/genetics/physiology ; DNA, Bacterial/analysis ; DNA, Ribosomal/analysis ; Genes, rRNA ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Photosynthesis ; Pigments, Biological/metabolism ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Thiocapsa/*classification/genetics/physiology ; }, abstract = {A dense 1 m thick layer of phototrophic purple sulfur bacteria is present at the pycnocline (17.8 m depth) in the meromictic South Andros Black Hole cave system (Bahamas). Two purple sulfur bacteria present in samples collected from this layer have been identified as belonging to the family Chromatiaceae. One isolate (BH-1), pink coloured, is non-motile, non-gas vacuolated, 2-3 microm in diameter and surrounded by a capsule. The other isolates (BH-2 and BH-2.4), reddish-brown coloured, are small celled (4 microm x 2 microm), motile by means of a single polar flagellum. In both isolates (BH-1 and BH-2), the intracellular photosynthetic membranes are of the vesicular type and bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series are present. Both isolates grow well in the presence of sulfide and carbon dioxide in the light. During photoautotrophic growth sulfur globules are stored intracellularly as intermediate oxidation products. According to the 16S rRNA gene sequence data the isolates belong to the genera Thiocapsa and Allochromatium. However, at the species level a number of inconsistencies exist between the phenotypic and phylogenetic data, highlighting taxonomic problems within these genera. These inconsistencies may have implications for microbiologists studying the ecology of anoxygenic phototrophs. For ecologists studying the functioning of an ecosystem it may not be particularly important to know whether a specific isolate belongs to one species or another. However, if one wants to study the role of different populations within a particular functional group then the species concept is important. This study demonstrates that further work is still required on the taxonomy of purple sulfur bacteria in order that microbial ecologists are able to accurately identify a population/species isolated from hitherto undescribed aquatic ecosystems.}, } @article {pmid15937797, year = {2005}, author = {Hunt, G and Roy, K and Jablonski, D}, title = {Species-level heritability reaffirmed: a comment on "on the heritability of geographic range sizes".}, journal = {The American naturalist}, volume = {166}, number = {1}, pages = {129-35; discussion 136-43}, doi = {10.1086/430722}, pmid = {15937797}, issn = {1537-5323}, mesh = {Animals ; Biological Evolution ; Birds/*genetics/*physiology ; *Ecosystem ; Fossils ; Gastropoda/*genetics/*physiology ; *Models, Biological ; Population Dynamics ; Species Specificity ; }, abstract = {For many current issues in macroevolution and macroecology, it is important to know to what degree the attributes of species are shared among closely related lineages, a concept sometimes referred to as species-level heritability. Recently, Webb and Gaston proposed a new method for analyzing the heritability of geographic range size and concluded that range size is not heritable in Cretaceous gastropods (data from Jablonski) and modern birds (their data). Here we show that Webb and Gaston's method is flawed in that it implicitly assumes that range sizes are uniformly distributed. When range size distributions show their characteristic strong right skew, Webb and Gaston's method spuriously tends to find that range sizes of closely related pairs of species are more dissimilar than the random expectation. A reanalysis of Jablonski's data finds range size to be robustly and strongly heritable in Cretaceous gastropods and less strongly but still significantly heritable in present-day birds.}, } @article {pmid15926573, year = {2005}, author = {Hendriks, AJ and Traas, TP and Huijbregts, MA}, title = {Critical body residues linked to octanol-water partitioning, organism composition, and LC50 QSARs: meta-analysis and model.}, journal = {Environmental science & technology}, volume = {39}, number = {9}, pages = {3226-3236}, doi = {10.1021/es048442o}, pmid = {15926573}, issn = {0013-936X}, mesh = {Animals ; Body Burden ; Calibration ; Lethal Dose 50 ; *Models, Theoretical ; Octanols/chemistry ; Quantitative Structure-Activity Relationship ; Risk Assessment ; Solubility ; Tissue Distribution ; Water/chemistry ; Water Pollutants/*pharmacokinetics/*toxicity ; }, abstract = {To protect thousands of species from thousands of chemicals released in the environment, various risk assessment tools have been developed. Here, we link quantitative structure-activity relationships (QSARs) for response concentrations in water (LC50) to critical concentrations in organisms (C50) by a model for accumulation in lipid or non-lipid phases versus water Kpw. The model indicates that affinity for neutral body components such as storage fat yields steep Kpw-Kow relationships, whereas slopes for accumulation in polar phases such as proteins are gentle. This pattern is confirmed by LC50 QSARs for different modes of action, such as neutral versus polar narcotics and organochlorine versus organophosphor insecticides. LC50 QSARs were all between 0.00002 and 0.2Kow(-1). After calibrating the model with the intercepts and, for the first time also, with the slopes of the LC50 QSARs, critical concentrations in organisms C50 are calculated and compared to an independent validation data set. About 60% of the variability in lethal body burdens C50 is explained by the model. Explanations for differences between estimated and measured levels for 11 modes of action are discussed. In particular, relationships between the critical concentrations in organisms C50 and chemical (Kow) or species (lipid content) characteristics are specified and tested. The analysis combines different models proposed before and provides a substantial extension of the data set in comparison to previous work. Moreover, the concept is applied to species (e.g., plants, lean animals) and substances (e.g., specific modes of action) that were scarcely studied quantitatively so far.}, } @article {pmid15880621, year = {2005}, author = {Perera, MR and Vanstone, VA and Jones, MG}, title = {A novel approach to identify plant parasitic nematodes using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.}, journal = {Rapid communications in mass spectrometry : RCM}, volume = {19}, number = {11}, pages = {1454-1460}, doi = {10.1002/rcm.1943}, pmid = {15880621}, issn = {0951-4198}, mesh = {Animals ; Australia ; Crops, Agricultural/parasitology ; Nematoda/*chemistry/*isolation & purification/ultrastructure ; Plants/*parasitology ; Species Specificity ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; }, abstract = {Plant parasitic nematodes are difficult to identify because different species are morphologically similar, and this makes their control more difficult. The aim of this work was to develop a rapid, simple method to identify plant parasitic nematodes, based on analysis of protein profiles of nematodes generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). Two methods have been used: grinding and direct analysis of intact nematodes. Both methods were standardised using the nematode Anguina tritici (wheat seed-gall nematode) as a model. Development of the approach involved optimisation of experimental parameters to generate reproducible diagnostic protein profiles for plant parasitic nematodes. With alpha-cyano-4-hydroxycinnamic acid (CHCA) as the matrix, the most effective solvent extraction was with 90% acetone. With sinapinic acid (SA) as matrix, 90% ethanol was most effective. When intact nematodes were analysed directly by mixing with the matrix solution, 40 min extraction with CHCA matrix solution generated the best protein profiles. The standardised methods were applied to analyse the seed-gall nematodes A. tritici and A. funesta and to the root-knot nematode, Meloidogyne javanica, which infects many horticultural crops. Typical protein profiles and diagnostic peaks were identified for these nematode species and for mixtures of Anguina species. The results provide 'proof-of-concept' that these nematode species can be identified by protein profiling using MALDI-TOFMS. This new approach could be extended to identify other plant and non-plant parasitic nematodes.}, } @article {pmid15871043, year = {2005}, author = {Schmitt, S and Hentschel, U and Zea, S and Dandekar, T and Wolf, M}, title = {ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae).}, journal = {Journal of molecular evolution}, volume = {60}, number = {3}, pages = {327-336}, pmid = {15871043}, issn = {0022-2844}, mesh = {Animals ; Base Pairing/*genetics ; Base Sequence ; DNA Primers ; DNA, Ribosomal Spacer/*genetics ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Oceans and Seas ; *Phylogeny ; Porifera/classification/*genetics ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {18S ribosomal DNA and internal transcribed spacer 2 (ITS-2) full-length sequences, each of which was sequenced three times, were used to construct phylogenetic trees with alignments based on secondary structures, in order to elucidate genealogical relationships within the Aplysinidae (Verongida). The first poriferan ITS-2 secondary structures are reported. Altogether 11 Aplysina sponges and 3 additional sponges (Verongula gigantea, Aiolochroia crassa, Smenospongia aurea) from tropical and subtropical oceans were analyzed. Based on these molecular studies, S. aurea, which is currently affiliated with the Dictyoceratida, should be reclassified to the Verongida. Aplysina appears as monophyletic. A soft form of Aplysina lacunosa was separated from other Aplysina and stands at a basal position in both 18S and ITS-2 trees. Based on ITS-2 sequence information, the Aplysina sponges could be distinguished into a single Caribbean-Eastern Pacific cluster and a Mediterranean cluster. The species concept for Aplysina sponges as well as a phylogenetic history with a possibly Tethyan origin is discussed.}, } @article {pmid15869886, year = {2005}, author = {Fu, J and Weadick, CJ and Zeng, X and Wang, Y and Liu, Z and Zheng, Y and Li, C and Hu, Y}, title = {Phylogeographic analysis of the Bufo gargarizans species complex: a revisit.}, journal = {Molecular phylogenetics and evolution}, volume = {37}, number = {1}, pages = {202-213}, doi = {10.1016/j.ympev.2005.03.023}, pmid = {15869886}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Bufonidae/*classification/genetics ; DNA, Mitochondrial ; Electrophoresis ; Evolution, Molecular ; Gene Frequency ; Genetic Variation ; *Genetics, Population ; Geography ; Isoenzymes ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Using mtDNA sequencing and allozyme electrophoresis data, we tested the "vicariance followed by dispersal" hypothesis of the Bufo gargarizans species group and re-evaluated the species status in the general lineages species concept. A phylogenetic analysis suggested that dispersal, instead of vicariance, dominated the history of the species group. There was a general trend of west to east dispersal, while some lineages from the east subsequently returned to the west. The secondary admixture of those previously allopatric lineages produced substantial levels of sympatric genetic diversity, often as high as 7.0% pairwise difference within populations. The phylogenetic hypothesis does not support the current two species designation. Neither B. andrewsi nor B. gargarizans represents an independent evolutionary lineage, and monophyletic groups did not correspond to geographically discrete groups. Allozyme data also failed to reveal any fixed allelic difference among the populations. Therefore, we recommend regarding the complex as a single species, Bufo gargarizans, without subspecies division.}, } @article {pmid15851679, year = {2005}, author = {West-Eberhard, MJ}, title = {Developmental plasticity and the origin of species differences.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102 Suppl 1}, number = {Suppl 1}, pages = {6543-6549}, pmid = {15851679}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; Environment ; Recombination, Genetic/genetics ; Reproduction/genetics/physiology ; Species Specificity ; }, abstract = {Speciation is the origin of reproductive isolation and divergence between populations, according to the "biological species concept" of Mayr. Studies of reproductive isolation have dominated research on speciation, leaving the origin of species differences relatively poorly understood. Here, I argue that the origin of species differences, and of novel phenotypes in general, involves the reorganization of ancestral phenotypes (developmental recombination) followed by the genetic accommodation of change. Because selection acts on phenotypes, not directly on genotypes or genes, novel traits can originate by environmental induction as well as mutation, then undergo selection and genetic accommodation fueled by standing genetic variation or by subsequent mutation and genetic recombination. Insofar as phenotypic novelties arise from adaptive developmental plasticity, they are not "random" variants, because their initial form reflects adaptive responses with an evolutionary history, even though they are initiated by mutations or novel environmental factors that are random with respect to (future) adaptation. Change in trait frequency involves genetic accommodation of the threshold or liability for expression of a novel trait, a process that follows rather than directs phenotypic change. Contrary to common belief, environmentally initiated novelties may have greater evolutionary potential than mutationally induced ones. Thus, genes are probably more often followers than leaders in evolutionary change. Species differences can originate before reproductive isolation and contribute to the process of speciation itself. Therefore, the genetics of speciation can profit from studies of changes in gene expression as well as changes in gene frequency and genetic isolation.}, } @article {pmid15851674, year = {2005}, author = {de Queiroz, K}, title = {Ernst Mayr and the modern concept of species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102 Suppl 1}, number = {Suppl 1}, pages = {6600-6607}, pmid = {15851674}, issn = {0027-8424}, mesh = {Animals ; Biological Evolution ; Classification/*methods ; *Models, Biological ; Species Specificity ; }, abstract = {Ernst Mayr played a central role in the establishment of the general concept of species as metapopulation lineages, and he is the author of one of the most popular of the numerous alternative definitions of the species category. Reconciliation of incompatible species definitions and the development of a unified species concept require rejecting the interpretation of various contingent properties of metapopulation lineages, including intrinsic reproductive isolation in Mayr's definition, as necessary properties of species. On the other hand, the general concept of species as metapopulation lineages advocated by Mayr forms the foundation of this reconciliation, which follows from a corollary of that concept also advocated by Mayr: the proposition that the species is a fundamental category of biological organization. Although the general metapopulation lineage species concept and Mayr's popular species definition are commonly confused under the name "the biological species concept," they are more or less clearly distinguished in Mayr's early writings on the subject. Virtually all modern concepts and definitions of the species category, not only those that require intrinsic reproductive isolation, are to be considered biological according to the criterion proposed by Mayr. Definitions of the species category that identify a particular contingent property of metapopulation lineages (including intrinsic reproductive isolation) as a necessary property of species reduce the number of metapopulation lineages that are to be recognized taxonomically as species, but they cause conflicts among alternative species definitions and compromise the status of the species as a basic category of biological organization.}, } @article {pmid15851673, year = {2005}, author = {Ochman, H and Lerat, E and Daubin, V}, title = {Examining bacterial species under the specter of gene transfer and exchange.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102 Suppl 1}, number = {Suppl 1}, pages = {6595-6599}, pmid = {15851673}, issn = {0027-8424}, support = {R01 GM056120/GM/NIGMS NIH HHS/United States ; GM56120/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Bacterial ; Phylogeny ; }, abstract = {Even in lieu of a dependable species concept for asexual organisms, the classification of bacteria into discrete taxonomic units is considered to be obstructed by the potential for lateral gene transfer (LGT) among lineages at virtually all phylogenetic levels. In most bacterial genomes, large proportions of genes are introduced by LGT, as indicated by their compositional features and/or phylogenetic distributions, and there is also clear evidence of LGT between very distantly related organisms. By adopting a whole-genome approach, which examined the history of every gene in numerous bacterial genomes, we show that LGT does not hamper phylogenetic reconstruction at many of the shallower taxonomic levels. Despite the high levels of gene acquisition, the only taxonomic group for which appreciable amounts of homologous recombination were detected was within bacterial species. Taken as a whole, the results derived from the analysis of complete gene inventories support several of the current means to recognize and define bacterial species.}, } @article {pmid15826295, year = {2005}, author = {Grossherr, M and Sedemund-Adib, B and Klotz, KF}, title = {[Indication for antimycotic therapy for tracheobronchial candidosis under artificial ventilation].}, journal = {Mycoses}, volume = {48 Suppl 1}, number = {}, pages = {89-93}, doi = {10.1111/j.1439-0507.2005.01114.x}, pmid = {15826295}, issn = {0933-7407}, mesh = {Antifungal Agents/therapeutic use ; Bronchial Diseases/diagnosis/drug therapy/microbiology ; Candida/isolation & purification ; Candidiasis/diagnosis/*drug therapy/microbiology ; Humans ; Intensive Care Units ; Respiration, Artificial ; Tracheal Diseases/diagnosis/drug therapy/microbiology ; Ventilators, Mechanical ; }, abstract = {Tracheobronchial candidosis is an impetuous complication in intensive care medicine. This article presents a concept to compare diagnostic procedure, Candida species and resistant species of different intensive care units with each other. This concept should encourage bench marking between similar intensive care units. The report and retrospective analysis of the intensive care course offer the opportunity to reflect own decisions and to adjust them to the current therapy strategies. Both procedures should improve the antimycotic therapy for intensive care units and should avoid the occurrence of resistant species. Candida species are often detected in the respiratory system of ventilated patients in intensive care, but this alone is no indication for antimycotic therapy. A strict retention is recommended, but this retention is diminished by an unclear infection, critical situation of the patient in the case of multiple organ failure, additional infection and long term ventilation. A therapy strategy for individual situations should be established and a close diagnostic procedure should be performed. A positive blood culture or detection of Candida species in two or more diagnostic materials indicate an early antimycotic therapy.}, } @article {pmid15816917, year = {2005}, author = {Kuenen, JG}, title = {Crystal ball. The roots of the "species" concept must be quantified.}, journal = {Environmental microbiology}, volume = {7}, number = {4}, pages = {476-477}, doi = {10.1111/j.1462-2920.2005.803_6.x}, pmid = {15816917}, issn = {1462-2912}, mesh = {*Adaptation, Biological ; Adaptation, Physiological ; Biodegradation, Environmental ; Biodiversity ; *Biological Evolution ; *Bioreactors ; Industrial Waste ; Organic Chemicals/*metabolism ; Waste Disposal, Fluid/*methods ; Water Microbiology ; }, } @article {pmid15808739, year = {2005}, author = {Coenye, T and Gevers, D and Van de Peer, Y and Vandamme, P and Swings, J}, title = {Towards a prokaryotic genomic taxonomy.}, journal = {FEMS microbiology reviews}, volume = {29}, number = {2}, pages = {147-167}, doi = {10.1016/j.femsre.2004.11.004}, pmid = {15808739}, issn = {0168-6445}, mesh = {Bacteria/*classification/*genetics ; Bacterial Typing Techniques ; *Evolution, Molecular ; *Genome, Bacterial ; *Genomics ; Oligonucleotide Array Sequence Analysis ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {One of the most interesting developments in the field of modern-day microbiology is the ever increasing number of whole-genome sequences that is publicly available. There is an increasing interest in the use of these genome sequences to assess evolutionary relationships among microbial taxa, as it is anticipated that much additional taxonomic information can be extracted from these sequences. In a first part of the present review, mechanisms that are responsible for the evolution of genomes will be discussed. Subsequently, we will give an overview of approaches that are presently available to assess the taxonomic relationships between prokaryotic species based on complete genome sequences, followed by a brief discussion of the potential implications of these novel approaches for bacterial taxonomy in general and our thinking about the bacterial species concept in particular.}, } @article {pmid15764555, year = {2004}, author = {Johnson, J and Dowling, T and Belk, M}, title = {Neglected taxonomy of rare desert fishes: congruent evidence for two species of leatherside chub.}, journal = {Systematic biology}, volume = {53}, number = {6}, pages = {841-855}, doi = {10.1080/10635150490522557}, pmid = {15764555}, issn = {1063-5157}, mesh = {Animals ; Biological Evolution ; *Classification ; Conservation of Natural Resources ; Cyprinidae/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Desert Climate ; *Genetic Markers ; North America ; }, abstract = {Conservation biologists rely heavily on taxonomy to set the scope for biological monitoring and recovery planning of rare or threatened species. Yet, taxonomic boundaries are seldom evaluated as falsifiable hypotheses that can be statistically tested. Here, we examine species boundaries in leatherside chub (Teleostei, Cyprinidae), an imperiled desert fish native to the Bonneville Basin and upper Snake River drainages of western North America. Recent molecular data hint that this fish could be composed of two distinct taxa that are geographically separated into northern and southern species. To formally test this hypothesis, we evaluated leatherside chub using several different categories of species concepts, including criteria dependent on phylogenetic, morphological, and ecological data. We found that leatherside chub is composed of two reciprocally monophyletic clades (candidate species) characterized by numerous fixed genetic differences for both mitochondrial and nuclear DNA markers; mtDNA sequence divergence between the two clades approached 8%. The candidate species also showed significant differences in cranial shape, revealed by morphometric analysis. Finally, controlled growth and foraging experiments using representative populations from each clade show that candidate species appear to be locally adapted to the thermal environments where they now occur. Combined, these three lines of evidence support the hypothesis that leatherside chub is composed of two species. Moreover, all lines of evidence place these two species within the genusLepidomeda, a group consisting of three additional species of endangered spinedace fishes, and one extinct species, all native to the Colorado River system. Hence, we elevate the two clades of leatherside chub to distinct species status (Lepidomeda copeiin the north andL. aliciaein the south), and argue that each warrants independent conservation and recovery action.}, } @article {pmid15755924, year = {2005}, author = {Balajee, SA and Gribskov, JL and Hanley, E and Nickle, D and Marr, KA}, title = {Aspergillus lentulus sp. nov., a new sibling species of A. fumigatus.}, journal = {Eukaryotic cell}, volume = {4}, number = {3}, pages = {625-632}, pmid = {15755924}, issn = {1535-9778}, support = {R21 AI055928/AI/NIAID NIH HHS/United States ; R21 AI 55928/AI/NIAID NIH HHS/United States ; }, mesh = {*Aspergillus/classification/genetics/metabolism/ultrastructure ; *Aspergillus fumigatus/classification/genetics/metabolism/ultrastructure ; DNA, Fungal ; Drug Resistance, Multiple, Fungal ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {In a prior study, we identified seven clinical isolates of an Aspergillus sp. that were slow to sporulate in multiple media and demonstrated decreased in vitro susceptibilities to multiple antifungals, including amphotericin B, itraconazole, voriconazole, and caspofungin. These isolates were initially considered to be variants of Aspergillus fumigatus because of differences in mitochondrial cytochrome b sequences and unique randomly amplified polymorphic DNA PCR patterns (S. A. Balajee, M. Weaver, A. Imhof, J. Gribskov, and K. A. Marr, Antimicrob. Agents Chemother. 48: 1197-1203, 2004). The present study was performed to clarify the taxonomic status of these organisms by phylogenetic analyses based on multilocus sequence typing of five genes (the beta-tubulin gene, the rodlet A gene, the salt-responsive gene, the mitochondrial cytochrome b gene, and the internal transcribed spacer regions). Results revealed that four of the seven variant isolates clustered together in a clade very distant from A. fumigatus and distinct from other members of the A. fumigatus group. This new clade, consisting of four members, was monophyletic with strong bootstrap support when the protein-encoding regions were analyzed, indicating a new species status under the phylogenetic species concept. Phenotype studies revealed that the variant isolate has smaller conidial heads with diminutive vesicles compared to A. fumigatus and is not able to survive at 48 degrees C. Our findings suggest the presence of a previously unrecognized, potentially drug-resistant Aspergillus species that we designate A. lentulus.}, } @article {pmid15752428, year = {2005}, author = {Hanage, WP and Fraser, C and Spratt, BG}, title = {Fuzzy species among recombinogenic bacteria.}, journal = {BMC biology}, volume = {3}, number = {}, pages = {6}, pmid = {15752428}, issn = {1741-7007}, mesh = {Cluster Analysis ; *Fuzzy Logic ; Neisseria/*classification/*genetics ; Quantitative Trait Loci/genetics ; *Recombination, Genetic ; Species Specificity ; }, abstract = {BACKGROUND: It is a matter of ongoing debate whether a universal species concept is possible for bacteria. Indeed, it is not clear whether closely related isolates of bacteria typically form discrete genotypic clusters that can be assigned as species. The most challenging test of whether species can be clearly delineated is provided by analysis of large populations of closely-related, highly recombinogenic, bacteria that colonise the same body site. We have used concatenated sequences of seven house-keeping loci from 770 strains of 11 named Neisseria species, and phylogenetic trees, to investigate whether genotypic clusters can be resolved among these recombinogenic bacteria and, if so, the extent to which they correspond to named species.

RESULTS: Alleles at individual loci were widely distributed among the named species but this distorting effect of recombination was largely buffered by using concatenated sequences, which resolved clusters corresponding to the three species most numerous in the sample, N. meningitidis, N. lactamica and N. gonorrhoeae. A few isolates arose from the branch that separated N. meningitidis from N. lactamica leading us to describe these species as 'fuzzy'.

CONCLUSION: A multilocus approach using large samples of closely related isolates delineates species even in the highly recombinogenic human Neisseria where individual loci are inadequate for the task. This approach should be applied by taxonomists to large samples of other groups of closely-related bacteria, and especially to those where species delineation has historically been difficult, to determine whether genotypic clusters can be delineated, and to guide the definition of species.}, } @article {pmid15743226, year = {2005}, author = {Jones, NC and Field, D and Ziesel, JP and Field, TA}, title = {Virtual state scattering with cold electrons: para-xylene and para-difluorobenzene.}, journal = {The Journal of chemical physics}, volume = {122}, number = {7}, pages = {074301}, doi = {10.1063/1.1850457}, pmid = {15743226}, issn = {0021-9606}, abstract = {The scattering of electrons with kinetic energies down to a few meV by para-xylene and para-difluorobenzene has been observed experimentally with an electron beam energy resolution of 0.95 to 1.5 meV (full width half maximum). At low electron energies the collisions can be considered as cold scattering events because the de Broglie wavelength of the electron is considerably larger than the target dimensions. The scattering cross sections measured rise rapidly at low energy due to virtual state scattering. The nature of this scattering process is discussed using s- and p-wave phase shifts derived from the experimental data. Scattering lengths are derived of, respectively, -9.5+/-0.5 and -8.0+/-0.5 a.u. for para-xylene and para-difluorobenzene. The virtual state effect is interpreted in terms of nuclear diabatic and partially adiabatic models, involving the electronic and vibronic symmetries of the unoccupied orbitals in the target species. The concept of direct and indirect virtual state scattering is introduced, through which the present species, in common with carbon dioxide and benzene, scatter through an indirect virtual state process, whereas other species, such as perfluorobenzene, scatter through a direct process.}, } @article {pmid15736861, year = {2005}, author = {Hendrichs, M and Begerow, D and Bauer, R and Oberwinkler, F}, title = {The genus Anthracoidea (Basidiomycota, Ustilaginales): a molecular phylogenetic approach using LSU rDNA sequences.}, journal = {Mycological research}, volume = {109}, number = {Pt 1}, pages = {31-40}, doi = {10.1017/s0953756204001686}, pmid = {15736861}, issn = {0953-7562}, mesh = {Bayes Theorem ; DNA, Fungal/analysis ; DNA, Ribosomal/analysis ; Evolution, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Ustilaginales/*classification/*genetics/growth & development ; Ustilago/classification/genetics ; }, abstract = {The phylogenetic relationship of 52 specimens representing 30 species of Anthracoidea (Ustilaginales) was investigated by molecular analyses using sequence data from the large subunit (LSU) of nuclear rDNA. Phylogenetic trees were inferred with neighbour-joining (NJ), maximum parsimony (MP), and Bayesian Markov chain Monte Carlo (MCMC) methods. The results are discussed with respect to the species concept and the subdivision of the genus into subgenera and sections. Collections from different hosts and localities were compared. Our analyses can neither support nor significantly reject the hypothesis of the bipartition of the genus Anthracoidea. Thus, the representatives of the subgenus Proceres appeared in the NJ analysis as a moderately supported monophylum, whereas MCMC analysis revealed a polyphyletic topology for this group. Paraphyly of the subgenus Anthracoidea was supported by all methods used. Sections Echinosporae and Leiosporae were each represented by two species in our analyses which grouped together with high support. Section Anthracoidea should be restricted to a highly supported group with extremely irregular to angular teliospore shape. However, these three sections do not cover the whole diversity of the subgenus Anthracoidea. Molecular data largely supported the traditional circumscription of species, and species delimitations are discussed.}, } @article {pmid21652432, year = {2005}, author = {Muellner, AN and Samuel, R and Chase, MW and Pannell, CM and Greger, H}, title = {Aglaia (Meliaceae): an evaluation of taxonomic concepts based on DNA data and secondary metabolites.}, journal = {American journal of botany}, volume = {92}, number = {3}, pages = {534-543}, doi = {10.3732/ajb.92.3.534}, pmid = {21652432}, issn = {0002-9122}, abstract = {We performed maximum parsimony and Bayesian analyses (nuclear ITS rDNA, plastid rps16 intron) to estimate phylogenetic relationships within Aglaia (over 100 species in Southeast Asia, the Pacific, and Australia) and its relations among Aglaieae (Meliaceae). Based on 67 accessions of Aglaieae, three taxa of Guareae, and two taxa of Melieae (outgroup), this study provides the first assessment of the current circumscription of Aglaieae, Aglaia, and its sections and to a more limited extent of species concepts in Aglaia. DNA data are compared to recently collected data on chemical profiles. Our analyses indicate (1) the monophyly of Aglaieae; (2) the polyphyly of Aphanamixis; (3) the paraphyly of Aglaia; (4) the existence of at least three entities with respect to Aglaia: (a) the core group of Aglaia section Amoora (dehiscent fruits) with close relationships to Lansium and Reinwardtiodendron, (b) a group comprising morphological intermediates between the two sections, and (c) the core group of Aglaia section Aglaia (indehiscent fruits). Macro- and micromolecular data indicate that complex species are more heterogeneous, i.e., probably containing more than one taxon each, than taxonomically isolated species. A third section in Aglaia is recognized to accommodate A. lawii, A. teysmanniana, and A. beccarii.}, } @article {pmid15719989, year = {2005}, author = {Schmitt-Jansen, M and Altenburger, R}, title = {Predicting and observing responses of algal communities to photosystem II-herbicide exposure using pollution-induced community tolerance and species-sensitivity distributions.}, journal = {Environmental toxicology and chemistry}, volume = {24}, number = {2}, pages = {304-312}, doi = {10.1897/03-647.1}, pmid = {15719989}, issn = {0730-7268}, mesh = {Atrazine/*toxicity ; Biomass ; Dose-Response Relationship, Drug ; Eukaryota/*drug effects/metabolism ; Herbicides/*toxicity ; Lethal Dose 50 ; Photosystem II Protein Complex/*drug effects/metabolism ; Population Dynamics ; Predictive Value of Tests ; Risk Assessment ; Species Specificity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Various test strategies are in use in ecotoxicology to assess the potential risks of toxicants on aquatic communities. The species-sensitivity distribution concept (SSD) works by arranging single-species laboratory test data in a cumulative frequency distribution. The pollution-induced community tolerance concept (PICT) uses observable community responses by measuring increases in community tolerance caused by the replacement of sensitive species after exposure. The aim of this study was to compare these two concepts in assessing the effects of three herbicides. Atrazine, prometryn, and isoproturon were found to increase community tolerance by a factor up to six. Atrazine increased community tolerance only at higher test concentrations (0.125 mg L(-1)). Species-sensitivity distributions correspond well to community responses: The median effective concentrations (EC50s) of untreated periphyton communities tested covered 55 to 65% of affected species represented in the SSD. The sensitivities of tolerant algal communities shifted to the right end of the SSDs. In the microcosm experiments, higher test concentrations affected biomass, species numbers, and community structure. Community tolerance could not be induced any further, suggesting that these concentrations represent a maximum of functional redundancy of a functional group. At higher concentrations, even the least-sensitive species are affected. These results can be interpreted as a confirmation of the SSD concept by observed algal community responses, when applied to photosystem II (PSII)-inhibiting herbicides.}, } @article {pmid15706059, year = {2004}, author = {Prata, C and Maraldi, T and Zambonin, L and Fiorentini, D and Hakim, G and Landi, L}, title = {ROS production and Glut1 activity in two human megakaryocytic cell lines.}, journal = {BioFactors (Oxford, England)}, volume = {20}, number = {4}, pages = {223-233}, doi = {10.1002/biof.5520200406}, pmid = {15706059}, issn = {0951-6433}, mesh = {Biological Transport ; Cell Line ; Cell Survival ; Cytokines/pharmacology ; Deoxyglucose/pharmacokinetics ; Glucose/metabolism ; Glucose Transporter Type 1 ; Growth Substances/pharmacology ; Humans ; Kinetics ; Megakaryocytes/cytology/*metabolism ; Monosaccharide Transport Proteins/*metabolism ; Reactive Oxygen Species/*metabolism ; }, abstract = {Reactive oxygen species (ROS) has been increasingly recognised as intracellular messengers in signal transduction following receptor activation by a variety of bioactive peptides including growth factors, cytokines and hormones. In this study ROS production and glucose transport activity were evaluated in the growth factor dependent M07e cells and in B1647 cells, not requiring additional hematopoietic cytokines for growth: the aim was to investigate whether ROS could be involved in the regulation of Glut1-mediated glucose uptake in both cell lines. The effect of the synthetic superoxide and hydrogen peroxide scavenger EUK-134 on DOG uptake activity and intracellular ROS formation supports the concept of reactive oxygen species as signalling molecules. In order to investigate ROS generation sources, diphenyleneiodonium, an inhibitor of flavoprotein centres and apocynin, an inhibitor of NAD(P)H oxidase, were used: they inhibit both ROS production and glucose uptake activation. All these data support the hypothesis that ROS can contribute to the regulation of glucose transport, not only in M07e cells but also in B1647 cells; we could speculate that one possible source of ROS, linked somehow with Glut1 activity, can be a NAD(P)H oxidase similar to that one present in phagocytic cells.}, } @article {pmid15679948, year = {2004}, author = {Johnston, M and Zakharov, A and Papaiconomou, C and Salmasi, G and Armstrong, D}, title = {Evidence of connections between cerebrospinal fluid and nasal lymphatic vessels in humans, non-human primates and other mammalian species.}, journal = {Cerebrospinal fluid research}, volume = {1}, number = {1}, pages = {2}, pmid = {15679948}, issn = {1743-8454}, abstract = {BACKGROUND: The parenchyma of the brain does not contain lymphatics. Consequently, it has been assumed that arachnoid projections into the cranial venous system are responsible for cerebrospinal fluid (CSF) absorption. However, recent quantitative and qualitative evidence in sheep suggest that nasal lymphatics have the major role in CSF transport. Nonetheless, the applicability of this concept to other species, especially to humans has never been clarified. The purpose of this study was to compare the CSF and nasal lymph associations in human and non-human primates with those observed in other mammalian species. METHODS: Studies were performed in sheep, pigs, rabbits, rats, mice, monkeys and humans. Immediately after sacrifice (or up to 7 hours after death in humans), yellow Microfil was injected into the CSF compartment. The heads were cut in a sagittal plane. RESULTS: In the seven species examined, Microfil was observed primarily in the subarachnoid space around the olfactory bulbs and cribriform plate. The contrast agent followed the olfactory nerves and entered extensive lymphatic networks in the submucosa associated with the olfactory and respiratory epithelium. This is the first direct evidence of the association between the CSF and nasal lymph compartments in humans. CONCLUSIONS: The fact that the pattern of Microfil distribution was similar in all species tested, suggested that CSF absorption into nasal lymphatics is a characteristic feature of all mammals including humans. It is tempting to speculate that some disorders of the CSF system (hydrocephalus and idiopathic intracranial hypertension for example) may relate either directly or indirectly to a lymphatic CSF absorption deficit.}, } @article {pmid15633245, year = {2005}, author = {Druzhinina, I and Kubicek, CP}, title = {Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters?.}, journal = {Journal of Zhejiang University. Science. B}, volume = {6}, number = {2}, pages = {100-112}, pmid = {15633245}, issn = {1673-1581}, mesh = {Chromosome Mapping/*methods ; Conserved Sequence ; Evolution, Molecular ; *Genome, Fungal ; Hypocrea/*classification/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Sequence Homology, Nucleic Acid ; Species Specificity ; Trichoderma/*classification/*genetics ; }, abstract = {Trichoderma/Hypocrea is a genus of soil-borne or wood-decaying fungi containing members important to mankind as producers of industrial enzymes and biocontrol agents against plant pathogens, but also as opportunistic pathogens of immunocompromised humans. Species identification, while essential in view of the controversial properties of taxa of this genus, has been problematic by traditional methods. Here we will present a critical survey of the various identification methods in use. In addition, we will present an update on the taxonomy and phylogeny of the 88 taxa (which occur as 14 holomorphs, 49 teleomorphs and 25 anamorphs in nature) of Trichoderma/Hypocrea that have been confirmed by a combination of morphological, physiological and genetic approaches.}, } @article {pmid15626750, year = {2005}, author = {Bruysters, M and Jongejan, A and Gillard, M and van de Manakker, F and Bakker, RA and Chatelain, P and Leurs, R}, title = {Pharmacological differences between human and guinea pig histamine H1 receptors: Asn84 (2.61) as key residue within an additional binding pocket in the H1 receptor.}, journal = {Molecular pharmacology}, volume = {67}, number = {4}, pages = {1045-1052}, doi = {10.1124/mol.104.008847}, pmid = {15626750}, issn = {0026-895X}, mesh = {Animals ; Binding Sites ; COS Cells ; Guinea Pigs ; Histamine Agonists/*metabolism ; Histamine H1 Antagonists/*metabolism ; Humans ; Models, Molecular ; Mutagenesis, Site-Directed ; Pyrilamine/metabolism ; Receptors, Histamine H1/chemistry/*metabolism ; Species Specificity ; Structure-Activity Relationship ; }, abstract = {We tested several histamine H(1) receptor (H(1)R) and antagonists for their differences in agonists binding affinities between human and guinea pig H(1)Rs transiently expressed in African green monkey kidney (COS-7) cells. Especially, the bivalent agonist histaprodifen-histamine dimer (HP-HA) shows a higher affinity for guinea pig than for human H(1)Rs. Based on the structure of HP-HA, we have further identified VUF 4669 [7-(3-(4-(hydroxydiphenylmethyl)piperidin-1-yl)propoxy)-4-oxochroman-2-carboxylic acid] as a guinea pig-preferring H(1)R antagonist, demonstrating that the concept of species selectivity is not limited to agonists. To delineate the molecular mechanisms behind the observed species selectivity, we have created mutant human H(1)Rs in which amino acids were individually replaced by their guinea pig H(1)R counterparts. Residue Asn(84) (2.61) in transmembrane domain (TM) 2 seemed to act as a selectivity switch in the H(1)R. Molecular modeling and site-directed mutagenesis studies suggest that Asn(84) interacts with the conserved Tyr(458) (7.43) in TM7. Our data provide the first evidence that for some H(1)R ligands, the binding pocket is not only limited to TMs 3, 4, 5, and 6 but also comprises an additional pocket formed by TMs 2 and 7.}, } @article {pmid15614555, year = {2005}, author = {Gyllenberg, M and Meszéna, G}, title = {On the impossibility of coexistence of infinitely many strategies.}, journal = {Journal of mathematical biology}, volume = {50}, number = {2}, pages = {133-160}, pmid = {15614555}, issn = {0303-6812}, mesh = {Competitive Behavior ; *Ecosystem ; *Models, Biological ; *Population Dynamics ; }, abstract = {We investigate the possibility of coexistence of pure, inherited strategies belonging to a large set of potential strategies. We prove that under biologically relevant conditions every model allowing for coexistence of infinitely many strategies is structurally unstable. In particular, this is the case when the "interaction operator" which determines how the growth rate of a strategy depends on the strategy distribution of the population is compact. The interaction operator is not assumed to be linear. We investigate a Lotka-Volterra competition model with a linear interaction operator of convolution type separately because the convolution operator is not compact. For this model, we exclude the possibility of robust coexistence supported on the whole real line, or even on a set containing a limit point. Moreover, we exclude coexistence of an infinite set of equidistant strategies when the total population size is finite. On the other hand, for infinite populations it is possible to have robust coexistence in this case. These results are in line with the ecological concept of "limiting similarity" of coexisting species. We conclude that the mathematical structure of the ecological coexistence problem itself dictates the discreteness of the species.}, } @article {pmid15607177, year = {2005}, author = {Novotny, V and Bartosová, A and O'Reilly, N and Ehlinger, T}, title = {Unlocking the relationship of biotic integrity of impaired waters to anthropogenic stresses.}, journal = {Water research}, volume = {39}, number = {1}, pages = {184-198}, doi = {10.1016/j.watres.2004.09.002}, pmid = {15607177}, issn = {0043-1354}, mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources ; Fishes ; Food Chain ; Greenhouse Effect ; Invertebrates ; *Models, Theoretical ; Risk Assessment ; Rivers ; Urbanization ; Water Pollution, Chemical/*prevention & control ; }, abstract = {The Clean Water Act expressed its goals in terms of restoring and preserving the physical, chemical and biological integrity of the Nation's waters. Integrity has been defined as the ability of the water body's ecological system to support and maintain a balanced integrated, adaptive community of organisms comparable to that of a natural biota of the region. Several indices of biotic integrity (IBIs) have been developed to measure quantitatively the biotic composition and, hence, the integrity. Integrity can be impaired by discharges of pollutants from point and nonpoint sources and by other pollution-related to watershed/landscape and channel stresses, including channel and riparian zone modifications and habitat impairment. Various models that link the stressors to the biotic assessment endpoints, i.e., the IBIs, have been presented and discussed. Simple models that link IBIs directly to single or multiple surrogate stressors such as percent imperviousness are inadequate because they may not represent a true cause-effect proximate relationship. Furthermore, some surrogate landscape parameters are irreversible and the relationships cannot be used for development of plans for restoration of the water body integrity. A concept of a layered hierarchical model that will link the watershed, landscape and stream morphology pollution stressors to the biotic assessment endpoints (IBIs) is described. The key groups of structural components of the model are: IBIs and their metrics in the top layer, chemical water and sediment risks and a habitat quality index in the layer below, in-stream concentrations in water and sediments and channel/habitat impairment parameters in the third layer, and watershed/landscaper pollution generating stressors, land use change rates, and hydrology in the lowest layer of stressors. A modified and expanded Maximum Species Richness concept is developed and used to reveal quantitatively the functional relationships between the top two layers of the structural components and parameters of the model.}, } @article {pmid15598633, year = {2005}, author = {Mackie, AS and Oliver, PG and Darbyshire, T and Mortimer, K}, title = {Shallow marine benthic invertebrates of the Seychelles Plateau: high diversity in a tropical oligotrophic environment.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {363}, number = {1826}, pages = {203-228}, doi = {10.1098/rsta.2004.1488}, pmid = {15598633}, issn = {1364-503X}, mesh = {Animals ; *Biodiversity ; Cluster Analysis ; Indian Ocean ; Indian Ocean Islands ; Mollusca/classification/*growth & development ; Polychaeta/classification/*growth & development ; }, abstract = {Soft sedimentary biotopes are extensive in the shallow Western Indian Ocean, especially on the Seychelles Plateau and Mascarene Ridge, yet pro rata compared with coral reefs the research effort devoted to them has been minimal. In this study we examine the benthic mollusc and polychaete worm assemblages of the shallow waters (11-62 m) around Mahe, in the Seychelles, and make direct comparisons with the temperate Irish Sea area and subtropical waters of Hong Kong, China (using identical methodology). Two assemblages were recognized, characterized by depth and sediment type. Of these, assemblage A (in shallow carbonate sands) was the most diverse, with diversity and richness measures exceeding those from the Irish Sea or Hong Kong. Hong Kong generally had the poorest fauna. Considering the Bivalvia alone, estimates of taxonomic distinctness showed this to be least for Seychelles assemblage A. The degree of conformity of the results to the concept of the latitudinal gradient in species richness and the possible underlying causes are discussed. Comparisons with other data suggest that the Seychelles support a benthic fauna at least as diverse as any other described from the tropics. A tentative examination of total bivalve species richness suggests a total of 400-500 for the Seychelles. This is in keeping with other Indian Ocean localities, but higher than known figures for continental east Africa. The findings of this paper support the case for widespread ecological and taxonomic studies of the Western Indian Ocean benthic invertebrates.}, } @article {pmid15597872, year = {2004}, author = {De Schamphelaere, KA and Janssen, CR}, title = {Bioavailability and chronic toxicity of zinc to juvenile rainbow trout (Oncorhynchus mykiss): comparison with other fish species and development of a biotic ligand model.}, journal = {Environmental science & technology}, volume = {38}, number = {23}, pages = {6201-6209}, doi = {10.1021/es049720m}, pmid = {15597872}, issn = {0013-936X}, mesh = {Animals ; Biological Availability ; Cations ; Daphnia/metabolism ; Fishes/metabolism ; Ligands ; Metals/metabolism/toxicity ; Models, Biological ; Oncorhynchus mykiss/*metabolism ; Predictive Value of Tests ; Risk Assessment ; Species Specificity ; Toxicity Tests ; Water Pollutants/pharmacokinetics/*toxicity ; Zinc/pharmacokinetics/*toxicity ; }, abstract = {In this study, the effects of modifying Ca (0.2-4 mM), Mg (0.05-3 mM), Na (0.75-5 mM), and pH (5.5-7.5) on the chronic toxicity of zinc to juvenile rainbow trout (Oncorhynchus mykiss) were investigated using standard 30-d assays in which survival and growth were monitored. Survival was observed to be a more sensitive end point than growth, and mortality mainly occurred during the initial stages of the exposure. This suggested that the mode of action of zinc toxicity was mainly of an acute nature. A review and analysis of existing literature demonstrated similar results for most other fish species investigated. Overall, up to a 30-fold variation of zinc toxicity was observed, as indicated by no observed effect concentrations varying between 32.7 and 974 microg of Zn L(-1). Increased concentrations of Ca2+, Mg2+, Na+, and H+ (within the tested ranges) resulted in a reduction of chronic zinc toxicity by a factor of 12, 3, >2, and 2, respectively. This suggests the major importance of Ca competing with zinc and protecting against zinc toxicity, which seems to be a ubiquitous concept in fish species (and probably also invertebrate). On the basis of the toxicity data obtained, a chronic biotic ligand model (BLM) was developed that takes into account both chemical speciation of zinc and competition between zinc and the above-mentioned cations. The developed model was able to predict chronic effect concentrations with an error of less than a factor of 2 in most cases. Hence, it was concluded that the chronic Zn BLM can reduce toxicity variability due to bioavailability to a considerable extent and that the BLM can become an important tool in criteria setting and risk assessment practice of zinc and zinc substances.}, } @article {pmid15591111, year = {2004}, author = {Taylor, BW and Irwin, RE}, title = {Linking economic activities to the distribution of exotic plants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {51}, pages = {17725-17730}, pmid = {15591111}, issn = {0027-8424}, mesh = {*Ecosystem ; *Models, Economic ; *Plant Development ; Population Dynamics ; }, abstract = {The human enterprise is flooding Earth's ecosystems with exotic species. Human population size is often correlated with species introductions, whereas more proximate mechanisms, such as economic activities, are frequently overlooked. Here we present a hypothesis that links ecology and economics to provide a causal framework for the distribution of exotic plants in the United States. We test two competing hypotheses (the population-only and population-economic models) using a national data set of exotic plants, employing a statistical framework to simultaneously model direct and indirect effects of human population and ecological and economic variables. The population-only model included direct effects of human population and ecological factors as predictors of exotics. In contrast, the population-economic model included the direct effects of economic and ecological factors and the indirect effects of human population as predictors of exotics. The explicit addition of economic activity in the population-economic model provided a better explanation for the distribution of exotics than did the population-only model. The population-economic model explained 75% of the variation in the number of exotic plants in the 50 states and provided a good description of the observed number of exotic plants in the Canadian provinces and in other nations in 85% of the cases. A specific economic activity, real estate gross state product, had the strongest positive effect on the number of exotics. The strong influence of economics on exotics demonstrates that economics matter for resolving the exotic-species problem because the underlying causes, and some of the solutions, may lie in human-economic behaviors.}, } @article {pmid15590291, year = {2005}, author = {Wang, K and Xu, JJ and Sun, DC and Wei, H and Xia, XH}, title = {Selective glucose detection based on the concept of electrochemical depletion of electroactive species in diffusion layer.}, journal = {Biosensors & bioelectronics}, volume = {20}, number = {7}, pages = {1366-1372}, doi = {10.1016/j.bios.2004.05.009}, pmid = {15590291}, issn = {0956-5663}, mesh = {*Biosensing Techniques ; Electrodes ; Glucose/*analysis ; Microscopy, Electron, Scanning ; }, abstract = {A glucose detection approach based on the concept of electrochemical depletion of electroactive species in diffusion layer was established, using scanning electrochemical microscopy (SECM). By controlling the glucose oxidase (GOD) modified electrode (substrate electrode) at a proper potential of electrochemical oxidation of interfering electroactive species, i.e., ascorbic acid (AA), an interference-free microcircumstance was formed in the diffusion layer of the substrate electrode. Consequently, we could successfully sense hydrogen peroxide generated from an enzymatic reaction by locating a Pt ultramicroelectrode (UME) (tip electrode, 5 microm in radius) into the diffusion layer of the substrate electrode. Properties of this interference-removing approach based on electrochemical depletion were systematically investigated. Results showed that the interference-removing efficiency was significantly determined by the tip-substrate distance and substrate potential. When the tip-substrate distance was 11 microm (2.2 times of the tip electrode radius) and the substrate potential was 0.5 V, nearly 90% of AA (0.5 mM) could be depleted within 30s without consumption of H2O2. Under these conditions, 0.1 mM AA showed no influence on the detection of 0.5 mM glucose. The linear range of glucose detection is 0.01-1 mM with a detection limit (DL) of 0.005 mM (correlation coefficient is 0.9948). This research will open a new way for developing selective micro-biosensors.}, } @article {pmid15579380, year = {2005}, author = {Vinuesa, P and Silva, C and Werner, D and Martínez-Romero, E}, title = {Population genetics and phylogenetic inference in bacterial molecular systematics: the roles of migration and recombination in Bradyrhizobium species cohesion and delineation.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {29-54}, doi = {10.1016/j.ympev.2004.08.020}, pmid = {15579380}, issn = {1055-7903}, mesh = {Base Sequence ; Bradyrhizobium/classification/*genetics ; DNA Fingerprinting ; Evolution, Molecular ; Fabaceae/microbiology ; *Genetics, Population ; Likelihood Functions ; Oxidoreductases/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Rec A Recombinases/genetics ; *Recombination, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {A combination of population genetics and phylogenetic inference methods was used to delineate Bradyrhizobium species and to uncover the evolutionary forces acting at the population-species interface of this bacterial genus. Maximum-likelihood gene trees for atpD, glnII, recA, and nifH loci were estimated for diverse strains from all but one of the named Bradyrhizobium species, and three unnamed "genospecies," including photosynthetic isolates. Topological congruence and split decomposition analyses of the three housekeeping loci are consistent with a model of frequent homologous recombination within but not across lineages, whereas strong evidence was found for the consistent lateral gene transfer across lineages of the symbiotic (auxiliary) nifH locus, which grouped strains according to their hosts and not by their species assignation. A well resolved Bayesian species phylogeny was estimated from partially congruent glnII+recA sequences, which is highly consistent with the actual taxonomic scheme of the genus. Population-level analyses of isolates from endemic Canarian genistoid legumes based on REP-PCR genomic fingerprints, allozyme and DNA polymorphism analyses revealed a non-clonal and slightly epidemic population structure for B. canariense isolates of Canarian and Moroccan origin, uncovered recombination and migration as significant evolutionary forces providing the species with internal cohesiveness, and demonstrated its significant genetic differentiation from B. japonicum, its sister species, despite their sympatry and partially overlapped ecological niches. This finding provides strong evidence for the existence of well delineated species in the bacterial world. The results and approaches used herein are discussed in the context of bacterial species concepts and the evolutionary ecology of (brady)rhizobia.}, } @article {pmid15566544, year = {2004}, author = {Astuti, R and Solomon, GE and Carey, S}, title = {Constraints on conceptual development: a case study of the acquisition of folkbiological and folksociological knowledge in Madagascar.}, journal = {Monographs of the Society for Research in Child Development}, volume = {69}, number = {3}, pages = {1-135, vii-viii; discussion 136-61}, doi = {10.1111/j.0037-976X.2004.00296.x}, pmid = {15566544}, issn = {0037-976X}, mesh = {Adult ; Child ; *Child Development ; *Concept Formation ; Cross-Cultural Comparison ; *Cultural Evolution ; *Culture ; Ethnopsychology ; Family ; Humans ; Judgment ; Madagascar ; United States ; }, abstract = {How different are the concepts held by children who grow up in a North American middle class neighborhood and by children who grow up in a rural Malagasy fishing village? By probing Malagasy children's and adults' conceptual representations of human and animal kind, biological inheritance, innate potential and family relations, the studies presented in this Monograph address current debates about the acquisition and the nature of concepts in the domains of folkbiology and folksociology. Cross-cultural and developmental studies of this kind bear on the hypothesis that conceptual development in these domains is supported and constrained by innate conceptual content. If so, one would expect cross-cultural universality in the relevant adult concepts and their early emergence in childhood regardless of widely different input conditions. We chose to conduct these studies among the Vezo of Madagascar because the ethnographic literature has attributed to them folkbiological and folksociological theories that are radically different, even in commensurable, with those of North American adults. Vezo therefore provide a challenging test for the innate conceptual constraints hypothesis.Four studies probed aspects of biological and sociological reasoning of Vezo children, adolescents and adults through a number of adoption scenarios. Despite ethnographic reports to the contrary, we found cross-cultural convergence in adult concepts of biological inheritance, but the pattern of development of this concept differed greatly from that seen in North America. Moreover, in agreement with the ethnographic literature, we found that Vezo adults have constructed a distinctive theory of social group identity. However, we found that children's reasoning in this domain is under the influence of endogenous constraints that are overturned in the course of development. Finally, we found cross-cultural convergence in adults' concept of species kind, as well as evidence for the early emergence of this concept. In light of these findings, we discuss the nature of the constraints on children's conceptual representations, the developmental process through which the adults' concepts are constructed, and relations between Vezotheories of folkbiology and folksociology.}, } @article {pmid15560865, year = {2004}, author = {Morgan, K and Millar, RP}, title = {Evolution of GnRH ligand precursors and GnRH receptors in protochordate and vertebrate species.}, journal = {General and comparative endocrinology}, volume = {139}, number = {3}, pages = {191-197}, doi = {10.1016/j.ygcen.2004.09.015}, pmid = {15560865}, issn = {0016-6480}, mesh = {Animals ; Chordata, Nonvertebrate/*metabolism ; *Evolution, Molecular ; Gonadotropin-Releasing Hormone/*metabolism ; Ligands ; Protein Precursors/metabolism ; Receptors, LHRH/*metabolism ; Vertebrates/*metabolism ; }, abstract = {Primary structure relationships between GnRH precursors or GnRH receptors have received significant attention recently due to rapid DNA sequence determination of gene fragments and cDNAs from diverse species. Concepts concerning the evolutionary history of the GnRH system and its function in mammals, including humans, are likely to be modified as more complete sequence information becomes available. Current evidence suggests occurrence of fewer GnRH ligand and GnRH receptor genes in mammals compared to protochordates, fish and amphibians. Whilst several sequence-related GnRH decapeptide precursors and 2 or 3 separate GnRH receptors are encoded within the genomes of protochordates, fish and amphibians, only two types of GnRH (GnRH-I and GnRH-II) and two GnRH receptors occur in mammals. In addition, fish and mammalian genomes both retain inactive remnants of GnRH ligand or GnRH receptor genes. The number of distinct GnRH receptor genes in teleosts (at least five complete genes in pufferfish and three in zebrafish) partly reflects whole genome duplication during the evolution of this order of animals. Three GnRH receptor genes occur in certain frog species, consistent with the occurrence of up to three types of prepro-GnRH in amphibians. In contrast, only one functional GnRH receptor gene (the type I GnRH receptor) has been identified in humans and chimpanzees and a gene encoding a second receptor, homologous to a functional monkey receptor (the type II GnRH receptor), is either partially or completely silenced in a range of mammalian species (human, chimpanzee, sheep, cow, rat, and mouse). Further work is required to determine the significance of species-specific differences in the GnRH system to reproductive biology. For instance, recent data show that even species as closely related as humans and chimpanzees exhibit important organisational changes in the genes comprising the GnRH system.}, } @article {pmid15535070, year = {2004}, author = {Trouillas, FP and Gubler, WD}, title = {Identification and characterization of Eutypa leptoplaca, a new pathogen of grapevine in Northern California.}, journal = {Mycological research}, volume = {108}, number = {Pt 10}, pages = {1195-1204}, doi = {10.1017/s0953756204000863}, pmid = {15535070}, issn = {0953-7562}, mesh = {Ascomycota/genetics/*growth & development/ultrastructure ; Base Sequence ; Biological Assay ; California ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/*microbiology ; Polymerase Chain Reaction ; Sequence Alignment ; Spores, Fungal/genetics/growth & development/ultrastructure ; *Vitis ; }, abstract = {Although Eutypa lata is the main agent of Eutypa dieback of grapevine, another species of Eutypa has been isolated from diseased grapevines in Northern California. Stromata of this recently discovered Eutypa were also collected from Acer macrophyllum, A. negundo, and Fraxinus latifolia in the vicinity of vineyards, and appeared commonly on Umbellularia californica in some mixed-evergreen forests of Napa and Sonoma counties. This second species of Eutypa was distinguished from E. lata because of the sulcate ostiole of the perithecium and smaller ascospores. A morphological comparison with type specimens revealed identical features between the Californian isolates and E. leptoplaca sensu Rappaz (1987). This identification was confirmed through phylogenetic analyses of Eutypa spp. based on the complete sequence of the internal transcribed spacer (ITS) of the rDNA and partial sequence of the beta-tubulin gene. These analyses also separated collections of E. maura, E. sparsa, E. lejoplaca, E. tetragona, E. leptoplaca and E. lata, confirming the previously proposed species concepts. The pathogenicity of E. leptoplaca on grapevine was established using isolates collected from Vitis vinifera, U. californica, and A. macrophyllum. The importance of E. leptoplaca in relation to Eutypa dieback and its role as a necrotrophic pathogen are discussed.}, } @article {pmid15523849, year = {2004}, author = {Bogdanov, AS}, title = {[Allozyme variation of the pygmy wood mouse Sylvaemus uralensis (Rodentia, Muridae) and estimation of the divergence of its chromosome forms].}, journal = {Genetika}, volume = {40}, number = {8}, pages = {1099-1112}, pmid = {15523849}, issn = {0016-6758}, mesh = {Animals ; *Chromosomes ; Enzymes/*genetics ; *Genetic Variation ; Mice ; Muridae/*genetics ; Species Specificity ; }, abstract = {The genetic divergence between the eastern European, southern European, and Asian chromosome forms of the pygmy wood mouse Sylvaemus uralensis, whose karyotypes differ from one another in the amount of pericentromeric heterochromatin, has been reevaluated using allozyme analysis. In general, Asian S. uralensis living in eastern Kazakhstan, eastern Turkmenistan (the Kugitang Ridge), and Uzbekistan are more monomorphic than European populations of this species. However, the allozyme differences between all chromosome forms of the pygmy wood mouse is comparable with the interpopulation differences within each form and are an order of magnitude smaller than those between "good" species of the genus Sylvaemus. Thus, the chromosome forms of S. uralensis cannot be considered to be separate species. The concept of races as large population groups that have not diverged enough to regard them as species but differ from one another in some genetic characters is used to describe the differentiation of S. uralensis forms more adequately. The currently available evidence suggests the existence of two S. uralensis races, the Asian and the European ones, and two chromosome forms (eastern and western) of the European race. The possible historical factors that have determined the formation of the races of the pygmy wood mouse are considered. According to the most plausible hypothesis, the shift and fragmentation of the broad-leaved forest zone during the most recent glacial period (late Pleistocene) were the crucial factors of the formation of these races, because they resulted in a prolonged isolation of the European and Asian population groups of S. uralensis from each other.}, } @article {pmid15506013, year = {2004}, author = {Weiss, M and Selosse, MA and Rexer, KH and Urban, A and Oberwinkler, F}, title = {Sebacinales: a hitherto overlooked cosm of heterobasidiomycetes with a broad mycorrhizal potential.}, journal = {Mycological research}, volume = {108}, number = {Pt 9}, pages = {1003-1010}, doi = {10.1017/s0953756204000772}, pmid = {15506013}, issn = {0953-7562}, mesh = {Basidiomycota/*classification/*genetics ; DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Mycorrhizae/*classification/*genetics ; Phylogeny ; Symbiosis ; }, abstract = {Within the basidiomycetes, the vast majority of known mycorrhizal species are homobasidiomycetes. It was therefore surprising when molecular and ultrastructural studies revealed a broad diversity of mycorrhizal associations involving members of the heterobasidiomycetous Sebacinaceae, fungi which, due to their inconspicuous basidiomes, have been often overlooked. To investigate the phylogenetic position of the Sebacinaceae within the basidiomycetes and to infer phylogenetic relationships within the Sebacinaceae, we made molecular phylogenetic analyses based on nuclear rDNA. We present a well-resolved phylogeny of the main lineages of basidiomycetes which suggests that the Sebacinaceae is the most basal group with known mycorrhizal members. Since more basal taxa of basidiomycetes consist of predominantly mycoparasitic and phytoparasitic fungi, it seems possible that a mycorrhizal life strategy, which was transformed into a saprotrophic strategy several times convergently, is an apomorphic character for the Hymenomycetidae. Mycorrhizal taxa of Sebacinaceae, including mycobionts of ectomycorrhizas, orchid mycorrhizas, ericoid mycorrhizas, and jungermannioid mycorrhizas, are distributed over two subgroups. One group contains species with macroscopically visible basidiomes, whereas members of the other group probably lack basidiomes. Sebacina appears to be polyphyletic; current species concepts in Sebacinaceae are questionable. Sebacina vermifera sensu Warcup & Talbot consists of a broad complex of species possibly including mycobionts of jungermannioid and ericoid mycorrhizas. This wide spectrum of mycorrhizal types in one fungal family is unique. Extrapolating from the known rDNA sequences in Sebacinaceae, it is evident that there is a cosm of mycorrhizal biodiversity yet to be discovered in this group. Taxonomically, we recognise the Sebacinaceae as constituting a new order, the Sebacinales.}, } @article {pmid15499502, year = {2004}, author = {Hose, GC and Van den Brink, PJ}, title = {Confirming the species-sensitivity distribution concept for endosulfan using laboratory, mesocosm, and field data.}, journal = {Archives of environmental contamination and toxicology}, volume = {47}, number = {4}, pages = {511-520}, doi = {10.1007/s00244-003-3212-5}, pmid = {15499502}, issn = {0090-4341}, mesh = {Animals ; Arthropods ; Australia ; Endosulfan/*toxicity ; *Hydrocarbons, Chlorinated ; Insecticides/*toxicity ; Lethal Dose 50 ; *Models, Theoretical ; Reference Values ; }, abstract = {In Australia, water-quality trigger values for toxicants are derived using protective concentration values based on species-sensitivity distribution (SSD) curves. SSD curves are generally derived from laboratory data with an emphasis on using local or site-specific data. In this study, Australian and non-Australian laboratory-species based SSD curves were compared and the concept of species protection confirmed by comparison of laboratory-based SSD curves with local mesocosm experiments and field monitoring data. Acute LC50 data for the organochlorine pesticide endosulfan were used for these comparisons; SSD curves were fitted using the Burr type III distribution. SSD curves indicated that the sensitivities of Australian fish and arthropods were not significantly different from those of corresponding non-Australian taxa. Arthropod taxa in the mesocosm were less sensitive than taxa in laboratory tests, which suggests that laboratory-generated single-species data may be used to predict concentrations protective of semifield (mesocosm) systems. SSDs based on laboratory data were also protective of field populations.}, } @article {pmid15459879, year = {2004}, author = {Cressman, R and Krivan, V and Garay, J}, title = {Ideal free distributions, evolutionary games, and population dynamics in multiple-species environments.}, journal = {The American naturalist}, volume = {164}, number = {4}, pages = {473-489}, doi = {10.1086/423827}, pmid = {15459879}, issn = {1537-5323}, mesh = {Animal Migration ; Animals ; *Behavior, Animal ; Competitive Behavior ; *Ecosystem ; *Game Theory ; Population Dynamics ; Predatory Behavior ; }, abstract = {In this article, we develop population game theory, a theory that combines the dynamics of animal behavior with population dynamics. In particular, we study interaction and distribution of two species in a two-patch environment assuming that individuals behave adaptively (i.e., they maximize Darwinian fitness). Either the two species are competing for resources or they are in a predator-prey relationship. Using some recent advances in evolutionary game theory, we extend the classical ideal free distribution (IFD) concept for single species to two interacting species. We study population dynamical consequences of two-species IFD by comparing two systems: one where individuals cannot migrate between habitats and one where migration is possible. For single species, predator-prey interactions, and competing species, we show that these two types of behavior lead to the same population equilibria and corresponding species spatial distributions, provided interspecific competition is patch independent. However, if differences between patches are such that competition is patch dependent, then our predictions strongly depend on whether animals can migrate or not. In particular, we show that when species are settled at their equilibrium population densities in both habitats in the environment where migration between habitats is blocked, then the corresponding species spatial distribution need not be an IFD. Thus, when species are given the opportunity to migrate, they will redistribute to reach an IFD (e.g., under which the two species can completely segregate), and this redistribution will also influence species population equilibrial densities. Alternatively, we also show that when two species are distributed according to the IFD, the corresponding population equilibrium can be unstable.}, } @article {pmid15385504, year = {2004}, author = {Atochina, EN and Beck, JM and Preston, AM and Haczku, A and Tomer, Y and Scanlon, ST and Fusaro, T and Casey, J and Hawgood, S and Gow, AJ and Beers, MF}, title = {Enhanced lung injury and delayed clearance of Pneumocystis carinii in surfactant protein A-deficient mice: attenuation of cytokine responses and reactive oxygen-nitrogen species.}, journal = {Infection and immunity}, volume = {72}, number = {10}, pages = {6002-6011}, pmid = {15385504}, issn = {0019-9567}, support = {R01 HL 64520/HL/NHLBI NIH HHS/United States ; HL-58047/HL/NHLBI NIH HHS/United States ; R01 HL064520/HL/NHLBI NIH HHS/United States ; R01 59823//PHS HHS/United States ; R01 HL058047/HL/NHLBI NIH HHS/United States ; R01 HL 59867/HL/NHLBI NIH HHS/United States ; P01 HL024075/HL/NHLBI NIH HHS/United States ; HL-24075/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bronchoalveolar Lavage Fluid/chemistry ; Cytokines/*metabolism ; Humans ; Inflammation/complications/metabolism/microbiology/pathology ; Lung/metabolism/*microbiology/*pathology ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Nitric Oxide/metabolism ; Pneumocystis Infections/immunology/metabolism/microbiology/pathology ; Pneumocystis carinii/*physiology ; Pulmonary Surfactant-Associated Protein A/*deficiency/genetics ; Pulmonary Surfactant-Associated Protein D/metabolism ; Reactive Nitrogen Species/*metabolism ; *Reactive Oxygen Species/*metabolism ; Tyrosine/*analogs & derivatives/metabolism ; }, abstract = {Surfactant protein A (SP-A), a member of the collectin family, selectively binds to Pneumocystis carinii and mediates interactions between pathogen and host alveolar macrophages in vitro. To test the hypothesis that mice lacking SP-A have delayed clearance of Pneumocystis organisms and enhanced lung injury, wild-type C57BL/6 (WT) and SP-A-deficient mice (SP-A(-/-)) with or without selective CD4(+)-T-cell depletion were intratracheally inoculated with Pneumocystis organisms. Four weeks later, CD4-depleted SP-A-deficient mice had developed a more severe Pneumocystis infection than CD4-depleted WT (P. carinii pneumonia [PCP] scores of 3 versus 2, respectively). Whereas all non-CD4-depleted WT mice were free of PCP, intact SP-A(-/-) mice also had evidence of increased organism burden. Pneumocystis infection in SP-A-deficient mice was associated histologically with enhanced peribronchial and/or perivascular cellularity (score of 4 versus 2, SP-A(-/-) versus C57BL/6 mice, respectively) and a corresponding increase in bronchoalveolar lavage (BAL) cell counts. Increases in SP-D content, gamma interferon, interleukin-4, interleukin-5, and tumor necrosis factor alpha in BAL fluid occurred but were attenuated in PCP-infected SP-A(-/-) mice compared to WT mice. There were increases in total BAL NO levels in both infected groups, but nitrite levels were higher in SP-A(-/-) mice, indicating a reduction in production of higher oxides of nitrogen that was also reflected in lower levels of 3-nitrotyrosine staining in the SP-A(-/-) group. We conclude that despite increases in inflammatory cells, SP-A-deficient mice infected with P. carinii exhibit an enhanced susceptibility to the organism and attenuated production of proinflammatory cytokines and reactive oxygen-nitrogen species. These data support the concept that SP-A is a local effector molecule in the lung host defense against P. carinii in vivo.}, } @article {pmid15378046, year = {2004}, author = {Fang, FC}, title = {Antimicrobial reactive oxygen and nitrogen species: concepts and controversies.}, journal = {Nature reviews. Microbiology}, volume = {2}, number = {10}, pages = {820-832}, doi = {10.1038/nrmicro1004}, pmid = {15378046}, issn = {1740-1526}, mesh = {Cytokines/biosynthesis ; Granulomatous Disease, Chronic/metabolism/microbiology ; Humans ; Immunity, Innate ; Nitric Oxide Synthase/genetics/metabolism ; Nitric Oxide Synthase Type II ; Phagocytes/immunology/*metabolism/*microbiology ; Polymorphism, Genetic ; Reactive Nitrogen Species/*metabolism ; Reactive Oxygen Species/*metabolism ; }, abstract = {Phagocyte-derived reactive oxygen and nitrogen species are of crucial importance for host resistance to microbial pathogens. Decades of research have provided a detailed understanding of the regulation, generation and actions of these molecular mediators, as well as their roles in resisting infection. However, differences of opinion remain with regard to their host specificity, cell biology, sources and interactions with one another or with myeloperoxidase and granule proteases. More than a century after Metchnikoff first described phagocytosis, and more than four decades after the discovery of the burst of oxygen consumption that is associated with microbial killing, the seemingly elementary question of how phagocytes inhibit, kill and degrade microorganisms remains controversial. This review updates the reader on these concepts and the topical questions in the field.}, } @article {pmid15353563, year = {2004}, author = {Thompson, FL and Iida, T and Swings, J}, title = {Biodiversity of vibrios.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {68}, number = {3}, pages = {403-31, table of contents}, pmid = {15353563}, issn = {1092-2172}, mesh = {Animals ; Bacterial Typing Techniques ; Bacteriology/history ; *Biodiversity ; Cholera/history ; History, 19th Century ; History, 20th Century ; Humans ; Phylogeny ; Vibrio/*classification/genetics/*growth & development/pathogenicity ; Vibrio Infections/*microbiology ; *Water Microbiology ; }, abstract = {Vibrios are ubiquitous and abundant in the aquatic environment. A high abundance of vibrios is also detected in tissues and/or organs of various marine algae and animals, e.g., abalones, bivalves, corals, fish, shrimp, sponges, squid, and zooplankton. Vibrios harbour a wealth of diverse genomes as revealed by different genomic techniques including amplified fragment length polymorphism, multilocus sequence typing, repetetive extragenic palindrome PCR, ribotyping, and whole-genome sequencing. The 74 species of this group are distributed among four different families, i.e., Enterovibrionaceae, Photobacteriaceae, Salinivibrionaceae, and Vibrionaceae. Two new genera, i.e., Enterovibrio norvegicus and Grimontia hollisae, and 20 novel species, i.e., Enterovibrio coralii, Photobacterium eurosenbergii, V. brasiliensis, V. chagasii, V. coralliillyticus, V. crassostreae, V. fortis, V. gallicus, V. hepatarius, V. hispanicus, V. kanaloaei, V. neonatus, V. neptunius, V. pomeroyi, V. pacinii, V. rotiferianus, V. superstes, V. tasmaniensis, V. ezurae, and V. xuii, have been described in the last few years. Comparative genome analyses have already revealed a variety of genomic events, including mutations, chromosomal rearrangements, loss of genes by decay or deletion, and gene acquisitions through duplication or horizontal transfer (e.g., in the acquisition of bacteriophages, pathogenicity islands, and super-integrons), that are probably important driving forces in the evolution and speciation of vibrios. Whole-genome sequencing and comparative genomics through the application of, e.g., microarrays will facilitate the investigation of the gene repertoire at the species level. Based on such new genomic information, the taxonomy and the species concept for vibrios will be reviewed in the next years.}, } @article {pmid15353123, year = {2004}, author = {Murphy, CR}, title = {Uterine receptivity and the plasma membrane transformation.}, journal = {Cell research}, volume = {14}, number = {4}, pages = {259-267}, doi = {10.1038/sj.cr.7290227}, pmid = {15353123}, issn = {1001-0602}, mesh = {Animals ; Cell Membrane/*physiology/ultrastructure ; Cell Surface Extensions/physiology/ultrastructure ; Endometrium/*physiology/ultrastructure ; Epithelial Cells/*physiology/ultrastructure ; Female ; Humans ; Membrane Proteins/metabolism ; Placenta/physiology/ultrastructure ; Placentation/*physiology ; Pregnancy ; Rodentia/anatomy & histology/physiology ; Species Specificity ; }, abstract = {This review begins with a brief commentary on the diversity of placentation mechanisms, and then goes on to examine the extensive alterations which occur in the plasma membrane of uterine epithelial cells during early pregnancy across species. Ultrastructural, biochemical and more general morphological data reveal that strikingly common phenomena occur in this plasma membrane during early pregnancy despite the diversity of placental types--from epitheliochorial to hemochorial, which ultimately form in different species. To encapsulate the concept that common morphological and molecular alterations occur across species, that they are found basolaterally as well as apically, and that moreover they are an ongoing process during much of early pregnancy, not just an event at the time attachment, the term 'plasma membrane transformation' is suggested which also emphasises that alterations in this plasma membrane during early pregnancy are key to uterine receptivity.}, } @article {pmid21148927, year = {2004}, author = {Paulus, B and Gadek, P and Hyde, K}, title = {Phylogenetic and morphological assessment of five new species of Thozetella from an Australian rainforest.}, journal = {Mycologia}, volume = {96}, number = {5}, pages = {1074-1087}, pmid = {21148927}, issn = {0027-5514}, abstract = {During an investigation of saprobic microfungi in leaf litter from an Australian rainforest, five new species of Thozetella, namely T. acerosa, T. boonjiensis, T. falcata, T. gigantea and T. queenslandica, were identified and these are described and illustrated here. The morphology of specimens derived from cultures grown under different conditions and from natural substrata was compared. DNA sequence data of ITS regions within nuclear rDNA confirmed the morphological species concept and indicated that Thozetella species are anamorphs of the ascomycete genus Chaetosphaeria.}, } @article {pmid15282579, year = {2004}, author = {Mallet, J}, title = {Species problem solved 100 years ago.}, journal = {Nature}, volume = {430}, number = {6999}, pages = {503}, doi = {10.1038/430503b}, pmid = {15282579}, issn = {1476-4687}, mesh = {Animals ; *Biological Evolution ; Butterflies/classification/physiology ; *Classification ; Entomology/history ; Female ; History, 19th Century ; History, 20th Century ; Male ; Reproduction/physiology ; Species Specificity ; }, } @article {pmid15270087, year = {2004}, author = {Karvonen, A and Valtonen, ET}, title = {Helminth assemblages of whitefish (Coregonus lavaretus) in interconnected lakes: similarity as a function of species specific parasites and geographical separation.}, journal = {The Journal of parasitology}, volume = {90}, number = {3}, pages = {471-476}, doi = {10.1645/GE-3099}, pmid = {15270087}, issn = {0022-3395}, mesh = {Animals ; Finland/epidemiology ; Fish Diseases/epidemiology/*parasitology ; *Fresh Water ; Helminthiasis, Animal/epidemiology/*parasitology ; Helminths/*classification/physiology ; Regression Analysis ; Salmonidae/*parasitology ; Species Specificity ; }, abstract = {This article examined the composition of parasite assemblages of whitefish (Coregonus lavaretus) in 8 interconnected lakes in northeastern Finland and evaluated the role of coregonid specific parasites and the geographical distance between populations in determining the similarity of the assemblages. Parasite assemblages were compared using the Jaccard qualitative similarity index and a quantitative similarity index and by incorporating the allogenic-autogenic species concept and the effects of 2 corresponding measures of geographical distance between the lakes. The majority of the parasite species found (10 of 14) were specific to salmonids. Similarity of assemblages of autogenic parasites between the lakes was negatively correlated with geographical distance. The dominance of 2 parasite species, the whitefish specialist Ichthyocotylurus erraticus and the generalist Ergasilus sieboldi, was also demonstrated. We concluded that the high proportion of widespread parasite species specific to coregonids is an important determinant of similarity in these assemblages. However, ecological factors were likely to contribute to qualitative (presence of species) and quantitative (difference in abundances) differences between lakes, in the case of autogenic parasites, their importance increasing with geographical separation.}, } @article {pmid15266388, year = {2004}, author = {Wiens, JJ}, title = {What is speciation and how should we study it?.}, journal = {The American naturalist}, volume = {163}, number = {6}, pages = {914-923}, doi = {10.1086/386552}, pmid = {15266388}, issn = {1537-5323}, mesh = {Animals ; *Biological Evolution ; Classification ; Conservation of Natural Resources ; Ecology ; Geography ; Species Specificity ; *Terminology as Topic ; }, abstract = {To understand speciation, we first need to know what species are. Yet debates over species concepts have seemed endless, with little obvious relevance to the study of speciation. Recently, there has been progress in resolving these debates, favoring a lineage-based, evolutionary species concept. This progress calls for reconsideration of the study of speciation. Traditional speciation research based on the biological species concept has led to great advances in understanding how nonallopatric speciation occurs and how species diverge and remain separate from each other. However, this research has neglected the question of how new species arise in the first place for the most common geographic mode (allopatric). A new and very different research program is needed to understand the ecological and evolutionary processes that split an ancestral species into new allopatric lineages. This research program will connect speciation to many other fundamental questions in evolutionary biology, ecology, biogeography, and conservation biology.}, } @article {pmid15262937, year = {2004}, author = {Ward, TJ and Gorski, L and Borucki, MK and Mandrell, RE and Hutchins, J and Pupedis, K}, title = {Intraspecific phylogeny and lineage group identification based on the prfA virulence gene cluster of Listeria monocytogenes.}, journal = {Journal of bacteriology}, volume = {186}, number = {15}, pages = {4994-5002}, pmid = {15262937}, issn = {0021-9193}, mesh = {Animals ; Bacterial Proteins/*genetics ; *Evolution, Molecular ; Food Microbiology ; Humans ; Listeria monocytogenes/*classification/genetics/*pathogenicity ; Listeriosis/microbiology ; Molecular Sequence Data ; *Multigene Family ; Peptide Termination Factors ; *Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA ; Serotyping ; Trans-Activators/*genetics ; Virulence ; }, abstract = {Listeria monocytogenes is a serious food-borne pathogen that can cause invasive disease in humans and other animals and has been the leading cause of food recalls due to microbiological concerns in recent years. In order to test hypotheses regarding L. monocytogenes lineage composition, evolution, ecology, and taxonomy, a robust intraspecific phylogeny was developed based on prfA virulence gene cluster sequences from 113 L. monocytogenes isolates. The results of the multigene phylogenetic analyses confirm that L. monocytogenes comprises at least three evolutionary lineages, demonstrate that lineages most frequently (lineage 1) and least frequently (lineage 3) associated with human listeriosis are sister-groups, and reveal for the first time that the human epidemic associated serotype 4b is prevalent among strains from lineage 1 and lineage 3. In addition, a PCR-based test for lineage identification was developed and used in a survey of food products demonstrating that the low frequency of association between lineage 3 isolates and human listeriosis cases likely reflects rarity of exposure and not reduced virulence for humans as has been previously suggested. However, prevalence data do suggest lineage 3 isolates may be better adapted to the animal production environment than the food-processing environment. Finally, analyses of haplotype diversity indicate that lineage 1 has experienced a purge of genetic variation that was not observed in the other lineages, suggesting that the three L. monocytogenes lineages may represent distinct species within the framework of the cohesion species concept.}, } @article {pmid15253350, year = {2004}, author = {Forey, PL and Fortey, RA and Kenrick, P and Smith, AB}, title = {Taxonomy and fossils: a critical appraisal.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {359}, number = {1444}, pages = {639-653}, pmid = {15253350}, issn = {0962-8436}, mesh = {*Anatomy, Comparative ; *Biodiversity ; Classification/*methods ; Computational Biology/*methods ; *Fossils ; Internet ; *Phylogeny ; Species Specificity ; Terminology as Topic ; Time Factors ; }, abstract = {Many compendia at the species, genus and family levels document the fossil record, but these are not standardized, nor usually critical in content, and few are available on the World Wide Web. The sampling of the available record is good for organisms with fossilizable parts, but preservational constraints on the entire morphology, life history and geographical distribution lead to difficulties in recognizing and naming species. We recommend abandoning some of the palaeontological species concepts such as chronospecies and stratospecies, and we advocate species recognition based on unique combinations of characters. The compilation of species lists is extremely time consuming, and given the inherent problems we suggest that compilation of generic lists is a more achievable goal because genera are recognized by definitive morphological characters. In calculating taxon duration, care must be taken to distinguish between mono-, para- and polyphyletic groups, the first being the only reliable unit for use in calculating diversity curves. We support the inclusion of fossils into classifications based on Recent organisms, but we recognize some of the problems this may pose for standard Linnaean classifications. Web-based taxonomy is the way forward, having the advantages of speed and currency of information dissemination, universal access with links to primary literature and increasingly sophisticated imagery. These advantages over conventional outlets will only be realized with careful Web design and a commitment to maintenance.}, } @article {pmid15253347, year = {2004}, author = {Finlay, BJ}, title = {Protist taxonomy: an ecological perspective.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {359}, number = {1444}, pages = {599-610}, pmid = {15253347}, issn = {0962-8436}, mesh = {Animals ; Classification/*methods ; *Ecosystem ; *Environment ; Eukaryota/*genetics/physiology/*ultrastructure ; Species Specificity ; }, abstract = {This is an exploration of contemporary protist taxonomy within an ecological perspective. As it currently stands, the 'morphospecies' does not accommodate the information that might support a truly ecological species concept for the protists. But the 'morphospecies' is merely a first step in erecting a taxonomy of the protists, and it is expected to become more meaningful in the light of genetic, physiological and ecological research in the near future. One possible way forward lies in the recognition that sexual and asexual protists may all be subject to forces of cohesion that result in (DNA) sequence-similarity clusters. A starting point would then be the detection of 'ecotypes'--where genotypic and phenotypic clusters correspond; but for that we need better information regarding the extent of clonality in protists, and better characterization of ecological niches and their boundaries. There is some progress with respect to the latter. Using the example of a community of ciliated protozoa living in the stratified water column of a freshwater pond, it is shown to be possible to gauge the potential of protists to partition their local environment into ecological niches. Around 40 morphospecies can coexist in the superimposed water layers, which presumably represent different ecological niches, but we have yet to discover if these are discrete or continuously variable. It is a myth that taxonomic problems are more severe for protists than for animals and plants. Most of the fundamental problems associated with species concepts (e.g. asexuals, sibling species, phenotypic variation) are distributed across biota in general. The recent history of the status of Pfiesteria provides a model example of an integrated approach to solving what are essentially taxonomic problems.}, } @article {pmid15244853, year = {2004}, author = {Frean, MR and Abraham, ER}, title = {Adaptation and enslavement in endosymbiont-host associations.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {69}, number = {5 Pt 1}, pages = {051913}, doi = {10.1103/PhysRevE.69.051913}, pmid = {15244853}, issn = {1539-3755}, mesh = {Animals ; Biological Evolution ; Ecology ; Evolution, Molecular ; Models, Biological ; Models, Statistical ; *Symbiosis ; Time Factors ; }, abstract = {The evolutionary persistence of symbiotic associations is a puzzle. Adaptation should eliminate cooperative traits if it is possible to enjoy the advantages of cooperation without reciprocating-a facet of cooperation known in game theory as the Prisoner's Dilemma. Despite this barrier, symbioses are widespread and may have been necessary for the evolution of complex life. The discovery of strategies such as tit-for-tat has been presented as a general solution to the problem of cooperation. However, this only holds for within-species cooperation, where a single strategy will come to dominate the population. In a symbiotic association each species may have a different strategy, and the theoretical analysis of the single-species problem is no guide to the outcome. We present basic analysis of two-species cooperation and show that a species with a fast adaptation rate is enslaved by a slowly evolving one. Paradoxically, the rapidly evolving species becomes highly cooperative, whereas the slowly evolving one gives little in return. This helps understand the occurrence of endosymbioses where the host benefits, but the symbionts appear to gain little from the association.}, } @article {pmid15237227, year = {2004}, author = {Hauffe, HC and Panithanarak, T and Dallas, JF and Piálek, J and Gündüz, I and Searle, JB}, title = {The tobacco mouse and its relatives: a "tail" of coat colors, chromosomes, hybridization and speciation.}, journal = {Cytogenetic and genome research}, volume = {105}, number = {2-4}, pages = {395-405}, doi = {10.1159/000078212}, pmid = {15237227}, issn = {1424-859X}, mesh = {Animals ; Chromosomes ; Genetic Variation ; Hair Color/genetics ; *Hybridization, Genetic ; Italy ; Mice/classification/*genetics ; Switzerland ; }, abstract = {The article reviews over 30 years' study of the chromosomal variation of the western house mice (Mus musculus domesticus) from the neighboring valleys of Poschiavo and Valtellina on the Swiss-Italian border. This is done in the context of the social and political history of this area, on the grounds that mice, as commensals, are influenced by human history. The chromosomal study of mice in this area was initiated because their unusual black coat color led a 19th century naturalist to describe the "tobacco mice" from Val Poschiavo as a separate species (Mus poschiavinus). The special coloration of the Val Poschiavo mice is matched by their chromosomes: they have 26 chromosomes instead of the usual 40. The Val Poschiavo mice are not a separate species according to the Biological Species Concept; instead they constitute a chromosome race (the "Poschiavo", POS) that is related to other races with reduced chromosome numbers that occur in N Italy (of which only those races in Val Poschiavo and Upper Valtellina have black coats). A phylogenetic analysis of mitochondrial DNA sequences suggests that the lineage of chromosome races found in N Italy was not formed during an extreme population bottleneck, although such bottlenecks have apparently occurred during the origin of individual races and certainly have influenced single populations. In one small, isolated population in Valtellina (Migiondo), two chromosome races (the POS and the "Upper Valtellina", UV, 2n = 24) became reproductively isolated from each other. In another small population (Sernio) bottlenecking led to fixation of a hybrid form with the UV karyotype and coat color, but with allozyme and microsatellite alleles characteristic of mice with the standard 40-chromosome karyotype. Two of the chromosome races in Valtellina (the UV and the "Mid Valtellina", MV, 2n = 24) also appear to be the product of hybridization. The dynamic history and patchy distribution of the house mouse chromosome races in Val Poschiavo and Valtellina in part reflects extinction-recolonization events; the formation of the UV and MV races and the introduction of the pale brown Standard race mice are believed to reflect such events. Dynamism in the chromosomal constitution of single populations is also evident from 25 years of data on the population in Migiondo. Due to change in agricultural practices, house mice in Valtellina and Val Poschiavo are becoming rarer, which is likely to have further impacts on the distribution and characteristics of the chromosome races in this area.}, } @article {pmid15232950, year = {2004}, author = {Agapow, PM and Bininda-Emonds, OR and Crandall, KA and Gittleman, JL and Mace, GM and Marshall, JC and Purvis, A}, title = {The impact of species concept on biodiversity studies.}, journal = {The Quarterly review of biology}, volume = {79}, number = {2}, pages = {161-179}, doi = {10.1086/383542}, pmid = {15232950}, issn = {0033-5770}, mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources ; Humans ; Models, Biological ; *Phylogeny ; *Species Specificity ; }, abstract = {Species are defined using a variety of different operational techniques. While discussion of the various methodologies has previously been restricted mostly to taxonomists, the demarcation of species is also crucial for conservation biology. Unfortunately, different methods of diagnosing species can arrive at different entities. Most prominently, it is widely thought that use of a phylogenetic species concept may lead to recognition of a far greater number of much less inclusive units. As a result, studies of the same group of organisms can produce not only different species identities but also different species range and number of individuals. To assess the impact of different definitions on conservation issues, we collected instances from the literature where a group of organisms was categorized both under phylogenetic and nonphylogenetic concepts. Our results show a marked difference, with surveys based on a phylogenetic species concept showing more species (48%) and an associated decrease in population size and range. We discuss the serious consequences of this trend for conservation, including an apparent change in the number of endangered species, potential political fallout, and the difficulty of deciding what should be conserved.}, } @article {pmid15230330, year = {2004}, author = {Duboudin, C and Ciffroy, P and Magaud, H}, title = {Acute-to-chronic species sensitivity distribution extrapolation.}, journal = {Environmental toxicology and chemistry}, volume = {23}, number = {7}, pages = {1774-1785}, pmid = {15230330}, issn = {0730-7268}, mesh = {Analysis of Variance ; Animals ; Biotransformation ; Data Interpretation, Statistical ; Environmental Pollutants/analysis/*toxicity ; Invertebrates ; Mercury/metabolism/toxicity ; *Models, Biological ; Predictive Value of Tests ; *Risk Assessment ; Sensitivity and Specificity ; Species Specificity ; Vertebrates ; }, abstract = {Seeking to make greater use of available data for risk assessment of substances, we constructed, for the situation in which chronic data are limited or even nonexistent but acute data are relatively large, an acute to chronic transformation (ACT) methodology based on the concept of species sensitivity distributions (SSDs). This ACT methodology uses a comparison of acute and chronic SSDs, separately for vertebrate data (with 22 substances) and for invertebrate data (with 15 substances). Rather than comparing an acute toxicity value with a chronic value, as when calculating an acute to chronic ratio (ACR), samples of acute and chronic data corresponding to the same category of species were compared. Starting from a sample of acute data, the ACT methodology showed relationships that enable the creation of a sample of predicted chronic values. This sample can then be used to calculate a predicted chronic hazardous concentration potentially affecting 5% of species (HC5%), just as with a sample of real chronic toxicity values. This ACT approach was tested on 11 substances. For each substance, the real chronic HC5% and the predicted chronic HC5% were calculated and compared. The ratio between chronic HC5% and ACT HC5% was, on average, 1.6 and did not exceed 4.4 for the 11 substances studied.}, } @article {pmid21148893, year = {2004}, author = {Enjalbert, F and Cassanas, G and Rapior, S and Renault, C and Chaumont, JP}, title = {Amatoxins in wood-rotting Galerina marginata.}, journal = {Mycologia}, volume = {96}, number = {4}, pages = {720-729}, doi = {10.1080/15572536.2005.11832920}, pmid = {21148893}, issn = {0027-5514}, abstract = {Amatoxins, bicyclic octapeptide derivatives responsible for severe hepatic failure, are present in several Basidiomycota species belonging to four genera, i.e. Amanita, Conocybe, Galerina and Lepiota. DNA studies for G. autumnalis, G. marginata, G. oregonensis, G. unicolor and G. venenata (section Naucoriopsis) determined that these species are the same, supporting the concept of Galerina marginata complex. These mostly lignicolous species are designated as white-rot fungi having a broad host range and capable of degrading both hardwoods and softwoods. Twenty-seven G. marginata basidiomes taken from different sites and hosts (three sets) as well as 17 A. phalloides specimens (three sets) were collected in French locations. The 44 basidiomes were examined for amatoxins and phallotoxins using high-performance liquid chromatography. Toxinological data for the wood-rotting G. marginata and the ectomycorrhizal A. phalloides species were compared and statistically analyzed. The acidic and neutral phallotoxins were not detected in any G. marginata specimen, whereas the acidic (β-Ama) and neutral (α-Ama and γ-Ama) amanitins were found in all basidiomes from either Angiosperms or Gymnosperms hosts. The G. marginata amatoxin content varied from 78.17 to 243.61 μg.mg(-1) of fresh weight and was elevated significantly in one set out of three. The amanitin amounts from certain Galerina specimens were higher than those from some A. phalloides basidiomes. Relationship between the amanitin distribution and the chemical composition of substrate was underlined and statistically validated for the white-rot G. marginata. Changes in nutritional components from decayed host due to enzymatic systems and genetic factors as well as environmental conditions seem to play a determinant role in the amanitin profile. Variability noticed in the amanitin distribution for the white-rot G. marginata basidiomes was not observed for the ectomycorrhizal A. phalloides specimens.}, } @article {pmid15209283, year = {2004}, author = {Peterson, SW}, title = {Multilocus DNA sequence analysis shows that Penicillium biourgeianum is a distinct species closely related to P. brevicompactum and P. olsonii.}, journal = {Mycological research}, volume = {108}, number = {Pt 4}, pages = {434-440}, doi = {10.1017/s0953756204009761}, pmid = {15209283}, issn = {0953-7562}, mesh = {Base Sequence ; Calmodulin/chemistry/genetics ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Penicillium/classification/*genetics/ultrastructure ; Peptide Elongation Factor 1/chemistry/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 28S/chemistry/genetics ; Sequence Alignment ; }, abstract = {Penicillium brevicompactum and other isolates with the compact, complex conidiogenous apparatus typical of the species were sequenced in one ribosomal and two protein coding regions. The aligned DNA sequences were analyzed by maximum parsimony and the data from different loci were tested for compatibility using the partition homogeneity test. Analysis of each of the three loci revealed three clades corresponding to P. brevicompactum, P. olsonii and P. biourgeianum. Using the phylogenetic species concept and the genetic isolation of the clades, P. hagemi, P. patrismei, P. stoloniferum, and P. griseobrunneum are all synonyms of P. brevicompactum. P. volgaense is a synonym of Penicillium olsonii, while P. biourgeianum is a distinct species closely related to P. brevicompactum and P. olsonii. Phenotypic distinctions between the species are mostly based on colony characteristics such as colour. P. bialowiezenze, often treated as a synonym of P. brevicompactum, is most closely related to P. polonicum.}, } @article {pmid21653452, year = {2004}, author = {Hillig, KW and Mahlberg, PG}, title = {A chemotaxonomic analysis of cannabinoid variation in Cannabis (Cannabaceae).}, journal = {American journal of botany}, volume = {91}, number = {6}, pages = {966-975}, doi = {10.3732/ajb.91.6.966}, pmid = {21653452}, issn = {0002-9122}, abstract = {Cannabinoids are important chemotaxonomic markers unique to Cannabis. Previous studies show that a plant's dry-weight ratio of Δ(9)-tetrahydrocannabinol (THC) to cannabidiol (CBD) can be assigned to one of three chemotypes and that alleles B(D) and B(T) encode alloenzymes that catalyze the conversion of cannabigerol to CBD and THC, respectively. In the present study, the frequencies of B(D) and B(T) in sample populations of 157 Cannabis accessions were determined from CBD and THC banding patterns, visualized by starch gel electrophoresis. Gas chromatography was used to quantify cannabinoid levels in 96 of the same accessions. The data were interpreted with respect to previous analyses of genetic and morphological variation in the same germplasm collection. Two biotypes (infraspecific taxa of unassigned rank) of C. sativa and four biotypes of C. indica were recognized. Mean THC levels and the frequency of B(T) were significantly higher in C. indica than C. sativa. The proportion of high THC/CBD chemotype plants in most accessions assigned to C. sativa was <25% and in most accessions assigned to C. indica was >25%. Plants with relatively high levels of tetrahydrocannabivarin (THCV) and/or cannabidivarin (CBDV) were common only in C. indica. This study supports a two-species concept of Cannabis.}, } @article {pmid21653451, year = {2004}, author = {Henderson, AJ}, title = {A multivariate analysis of Hyospathe (Palmae).}, journal = {American journal of botany}, volume = {91}, number = {6}, pages = {953-965}, doi = {10.3732/ajb.91.6.953}, pmid = {21653451}, issn = {0002-9122}, abstract = {Previous systematic treatments of the neotropical palm genus Hyospathe have recognized from two to 18 species. An explicit, quantitative, repeatable sequence of operations for delimiting and testing groups of specimens and applying species concepts is carried out. Multivariate statistical analysis of morphological data is used to delimit and test groups of specimens. Cluster analysis is used to distinguish between characters and traits. Analysis of qualitative and quantitative characters reveals six groups of specimens, and the Phylogenetic Species Concept is applied to these groups. Two species, H. peruviana Henderson and H. frontinensis Henderson, are described as new. One of the specimen groups is large and widespread, and six geographically separate subgroups can be recognized within it. These subgroups can be distinguished by one or more significantly different quantitative characters. A Phylogenetic Subspecies Concept is applied to these subgroups. Three subspecies, H. elegans subsp. costaricensis Henderson, H. elegans subsp. sanblasensis Henderson, and H. elegans subsp. tacarcunensis Henderson are described as new, and two new combinations are made: H. elegans subsp. sodiroi (Dammer ex Burret) Henderson and H. elegans subsp. concinna (H. E. Moore) Henderson. One subspecies occurring in the Amazon region is complex morphologically and is not resolved by the methods used here.}, } @article {pmid15120396, year = {2004}, author = {Guillot, J and Demanche, C and Norris, K and Wildschutte, H and Wanert, F and Berthelemy, M and Tataine, S and Dei-Cas, E and Chermette, R}, title = {Phylogenetic relationships among Pneumocystis from Asian macaques inferred from mitochondrial rRNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {3}, pages = {988-996}, doi = {10.1016/j.ympev.2003.10.022}, pmid = {15120396}, issn = {1055-7903}, mesh = {Animals ; Cloning, Molecular ; DNA/genetics ; Genetic Variation ; Macaca/*microbiology ; Phylogeny ; Pneumocystis/*genetics ; RNA/*genetics ; RNA, Mitochondrial ; Species Specificity ; }, abstract = {The presence of Pneumocystis organisms was detected by nested-PCR at mitochondrial large subunit (mtLSU) rRNA gene in 23 respiratory samples from Asian macaques representing two species: Macaca mulatta and M. fascicularis. A very high level of sequence heterogeneity was detected with 18 original sequence types. Two genetic groups of Pneumocystis could be distinguished from the samples. Within each group, the extent of genetic divergence was low (2.5+/-1.4% in group 1 and 2.3+/-1.7% in group 2). Genetic divergences were systematically higher when macaque-derived sequence types were compared with Pneumocystis mtLSU sequences from other primate species (from 5.3+/-2.7% to 19.3+/-3.0%). The two macaque-derived groups may be considered as distinct Pneumocystis species. Surprisingly, these Pneumocystis species were recovered from both M. mulatta and M. fascicularis suggesting that host-species restriction may not systematically occur in the genus Pneumocystis. Alternatively, these observations question about the species concept in macaques.}, } @article {pmid21148880, year = {2004}, author = {Alves, A and Correia, A and Luque, J and Phillips, A}, title = {Botryosphaeria corticola, sp. nov. on Quercus species, with notes and description of Botryosphaeria stevensii and its anamorph, Diplodia mutila.}, journal = {Mycologia}, volume = {96}, number = {3}, pages = {598-613}, pmid = {21148880}, issn = {0027-5514}, abstract = {Botr yosphaeria stevensii frequently has been associated with dieback and canker diseases of oak, mainly in the western Mediterranean area but more rarely in other regions. The species concept of B. stevensii has been unclear, and it is possible that some collections were identified incorrectly. A collection of fungal strains isolated from diseased oak trees and initially identified as B. stevensii was characterized on the basis of morphology and ITS nucleotide sequences. Morphology was compared with the type specimens of Physalospora mutila (= B. stevensii) and its anamorph, Diplodia mutila. It was concluded that the isolates from oak differed from B. stevensii in having larger ascospores and conidia as well as different spore shapes and represented an as yet undescribed species, which is described here as B. corticola. Moreover, ITS sequence data separated B. corticola from all other known species of Botryosphaeria. Amended descriptions of B. stevensii and its anamorph are provided to differentiate B. stevensii from B. corticola and to clarify some of the earlier taxonomic uncertainties.}, } @article {pmid15079826, year = {2004}, author = {Lukin, O and Godt, A and Vögtle, F}, title = {Residual topological isomerism of intertwined molecules.}, journal = {Chemistry (Weinheim an der Bergstrasse, Germany)}, volume = {10}, number = {8}, pages = {1878-1883}, doi = {10.1002/chem.200305203}, pmid = {15079826}, issn = {0947-6539}, abstract = {The growing number of molecular assemblies with unusual geometry and topology requires from time to time a revision of certain aspects of stereochemistry. The present paper analyzes several representatives of intertwined molecules that have bridges connecting their loops. In spite of the experimentally proven chirality, these species lack elements of both classical and topological chirality. Due to the relationship of these types of molecules to the well-recognized topologically nontrivial compounds, such as catenanes and knots, we propose the term "residual topology" illustrated by a simple scheme of excessive or missing bridges that could be excluded or included, respectively, in molecular graphs of these species to render them topologically nontrivial. This concept paper represents, therefore, an update on the currently applied nomenclature.}, } @article {pmid15068264, year = {2004}, author = {Caron, DA and Countway, PD and Brown, MV}, title = {The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools.}, journal = {The Journal of eukaryotic microbiology}, volume = {51}, number = {1}, pages = {38-48}, doi = {10.1111/j.1550-7408.2004.tb00159.x}, pmid = {15068264}, issn = {1066-5234}, mesh = {Animals ; DNA Primers ; DNA, Protozoan/genetics ; Ecosystem ; Eukaryota/*genetics/immunology ; Genetic Variation ; Molecular Biology/methods ; }, abstract = {Modern genetic and immunological techniques have become important tools for assessing protistan species diversity for both the identification and quantification of specific taxa in natural microbial communities. Although these methods are still gaining use among ecologists, the new approaches have already had a significant impact on our understanding of protistan diversity and biogeography. For example, genetic studies of environmental samples have uncovered many protistan phylotypes that do not match the DNA sequences of any cultured organisms, and whose morphological identities are unknown at the present time. Additionally, rapid and sensitive methods for detecting and enumerating taxa of special importance (e.g. bloom-forming algae, parasitic protists) have enabled much more detailed distributional and experimental studies than have been possible using traditional methods. Nevertheless, while the application of molecular approaches has advanced some aspects of aquatic protistan ecology, significant issues still thwart the widespread adoption of these approaches. These issues include the highly technical nature of some of the molecular methods, the reconciliation of morphology-based and sequence-based species identifications, and the species concept itself.}, } @article {pmid15062786, year = {2004}, author = {Ravaoarimanana, IB and Tiedemann, R and Montagnon, D and Rumpler, Y}, title = {Molecular and cytogenetic evidence for cryptic speciation within a rare endemic Malagasy lemur, the Northern Sportive Lemur (Lepilemur septentrionalis).}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {2}, pages = {440-448}, doi = {10.1016/j.ympev.2003.08.020}, pmid = {15062786}, issn = {1055-7903}, mesh = {Animals ; Cytochromes b/genetics ; Cytogenetic Analysis ; DNA, Mitochondrial/*genetics ; Geography ; Haplotypes/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Strepsirhini/*classification/genetics ; }, abstract = {Evolutionary relationships of different populations of the threatened malagasy lemur Lepilemur septentrionalis were assessed by sequence analysis of mitochondrial DNA (D-loop region and partial Cyt b gene). One hundred and fifty nine samples were collected from five main different localities in the northern part of Madagascar. We applied the phylogenetic species concept based on fixed diagnostic differences to determine the status of different geographical populations. No nucleotide site diagnoses Ankarana from Andrafiamena or Analamera. However, numerous fixed differences separate Sahafary from all other populations. These results were corroborated by phylogenetic trees. As previous cytogenetic studies, our molecular data suggest that two cryptic species of Lepilemur occur in the extreme north of Madagascar. This speciation is probably caused by chromosomal rearrangements in at least one of the evolutionary lineages. Our study comprises another striking example of how molecular genetic assay can detect phylogenetic discontinuities that are not reflected in traditional morphologically based taxonomies. Our study indicates that the Sahafary population is a hitherto undescribed endangered endemic species which urgently needs conservation efforts.}, } @article {pmid15054802, year = {2004}, author = {Pröckl, SS and Kleist, W and Gruber, MA and Köhler, K}, title = {In situ generation of highly active dissolved palladium species from solid catalysts-a concept for the activation of aryl chlorides in the Heck reaction.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {43}, number = {14}, pages = {1881-1882}, doi = {10.1002/anie.200353473}, pmid = {15054802}, issn = {1433-7851}, } @article {pmid15031899, year = {2003}, author = {Wu, Z and Wu, W and Gao, J and Zhang, S}, title = {[Analysis of urban forest landscape pattern in Hefei].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {14}, number = {12}, pages = {2117-2122}, pmid = {15031899}, issn = {1001-9332}, mesh = {China ; *Ecology ; Geographic Information Systems ; Trees/*growth & development ; Urbanization ; }, abstract = {Based on the theory and methodology of landscape ecology, the landscape pattern of the study area (17.6 km2) in the downtown of Hefei was analyzed by using the techniques of RS, GPS and GIS. The object was to provide a comprehensive method to study urban forest structure and its function in environmental improvement. The results showed that there were 5 major landscape elements, i.e., building and hard pavement surface, water, road, urban forest, and general green land in the area. The landscape matrix was building and pavement surface, occupied 73.13% of total land. Road was the typical corridor element in the city and occupied 6.89%. Green land occupied 11.44%, in which, urban forest patch occupied 9.18%. There were 408 urban forest patches, with an area of 161.16 hm2. The average area of the patch was 0.396 hm2, and the maximum area was 12 hm2. 48% of urban forest patch was identified as small scale patches with < 500 m2 of area, and only 8.6% of them was larger than 1 hm2. The number of general green land patch was 255, with an area of 39.74 hm2, which accounted for 2.26% of land area, and its average and maximum area was 0.1558 hm2 and 3.86 hm2, respectively. There were 147 water patches, with an area of 149.93 hm2, and occupied 8.54% of land, and the average and maximum area of the patch was 1.02 hm2 and 16 hm2, respectively. In the study area, both of the Shannon-Weiner landscape diversity index and evenness were low, only 0.928 and 0.576, respectively. In addition, the dominance of urban forest patch and general green land was 0.39 showing that the two landscape elements had a certain influence on the environment of the study area. The concept of interior habitat for forest was introduced in this paper, which was employed to make a scale class system of urban forest patch. The threshold area with interior habitat for urban forest patch was 9800 m2, and there was 31.69 hm2 of interior habitat of urban forest in total, which occupied 19.7% of the total area of urban forest patch. This situation was not favorable for providing more habitats to support species diversity. It's suggested that the concept of interior habitat could be employed to identify urban forest patch, and a scale system of small scale patch of urban forest-middle patch-large patch-extra large patch was build in the paper. Based on this system, the ratio of different scales of urban forest patch in the study area should be 2:2:2:3. The authors also suggested that larger pieces (1.5-3.0 hm2) of urban forest patch should be built, and more urban forests should be established in the northeastern part of the city in the future.}, } @article {pmid19434958, year = {2004}, author = {Schwabe, CW}, title = {Keynote address: the calculus of disease-importance of an integrating mindset.}, journal = {Preventive veterinary medicine}, volume = {62}, number = {3}, pages = {193-205}, pmid = {19434958}, issn = {0167-5877}, mesh = {Animals ; *Cooperative Behavior ; Education, Veterinary ; Epidemiology ; Humans ; Interdepartmental Relations ; *Interprofessional Relations ; *Medicine ; Research ; *Veterinary Medicine ; }, abstract = {"The concept of One Medicine integrates the diverse relationships between humans and other animal species. Success in applying this concept requires more than the left-brain activities of categorizing and differentiating items and events. Success requires that we also allow ourselves-encourage ourselves-to use the right-brain activities of synthesis and creativity. If we find success in One Medicine, we shall have enhanced our positive influence on activities beyond what we typically consider"Veterinary Medicine"; we will have benefited the production of food and other agricultural products, the maintenance of environmental quality, and promoted humane values in society.}, } @article {pmid15012382, year = {1999}, author = {Thompson, SN}, title = {Nutrition and culture of entomophagous insects.}, journal = {Annual review of entomology}, volume = {44}, number = {}, pages = {561-592}, doi = {10.1146/annurev.ento.44.1.561}, pmid = {15012382}, issn = {0066-4170}, abstract = {This article reviews the current state of knowledge concerning the nutrition of entomophagous insects and other arthropods. Early nutritional investigations focused principally on the basic dietary and nutritional requirements for beneficial insects. Based on these findings, the first attempts were made to develop mass culture methods and to formulate artificial diets that would allow rearing of parasitoids and predators in the absence of host or prey, as well as the latter's food sources. Although limited success was achieved, these studies established the nutritional foundation for later advances. Recently, attention has focused on the interaction between nutrition, physiology, behavior, and ecology of the different life stages of entomophagous species within a unified concept of nutritional ecology. This approach has resulted in more comprehensive understanding of nutrition, which in turn has facilitated the continuous artificial culture of several parasites and predators. Additional studies have confirmed the importance of supplemental feeding of the adult stages of beneficial insects for maximizing reproduction and longevity. Applications of nutritional ecology to biological control are discussed.}, } @article {pmid14993321, year = {2004}, author = {Zervakis, GI and Moncalvo, JM and Vilgalys, R}, title = {Molecular phylogeny, biogeography and speciation of the mushroom species Pleurotus cystidiosus and allied taxa.}, journal = {Microbiology (Reading, England)}, volume = {150}, number = {Pt 3}, pages = {715-726}, doi = {10.1099/mic.0.26673-0}, pmid = {14993321}, issn = {1350-0872}, mesh = {Base Sequence ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/genetics ; Genetic Variation ; Molecular Sequence Data ; Phylogeny ; Pleurotus/*classification/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Members of the mushroom genus Pleurotus form a heterogeneous group of edible species of high commercial importance. Subgenus Coremiopleurotus includes taxa that produce synnematoid fructifications (anamorphic state). Several species, subspecies and varieties have been described in Coremiopleurotus: These taxa are discriminated by minute morphological differences and correspond to Pleurotus cystidiosus sensu lato. A worldwide geographical sampling of Coremiopleurotus taxa and nucleotide sequence data from the internal transcribed spacer of the nuclear rRNA genes (ITS) were used to produce a molecular phylogeny for the group. Also conducted were new interfertility studies, and a summary of the mating data currently available in the literature is provided. Both ITS phylogeny and mating data supported the distinction between Pleurotus australis (a species apparently endemic to New Zealand and Australia) and P. cystidiosus sensu lato. Within P. cystidiosus sensu lato, ITS phylogeny showed a deep split between Old and New World isolates and clearly distinguished four distinct clades that strongly corresponded to the geographical origin of the strains. In the Old World, one clade is composed of isolates from Europe and Africa, and one clade is composed of isolates from Asia (including collections from Hawaii). In the New World, one clade is restricted to isolates from Mexico, and one clade includes all the authors' North America isolates, one collection from Japan and one collection from South Africa. Mating data revealed a high level of interfertility among strains of P. cystidiosus sensu lato, except that isolates from Mexico were nearly fully intersterile with the other collections. Nucleotide sequence divergence in the ITS1-5.8S rDNA-ITS2 regions among intercompatible P. cystidiosus collections was very high (0-6.9 %) in comparison to that reported in other biological species of basidiomycetes (0-3 %), indicating significant genetic divergence between geographically isolated populations of the P. cystidiosus group. The phylogenetic species concept, as well as molecular, mating and geographical evidence, was used to recognize five species in the subgenus Coremiopleurotus: P. australis (in New Zealand and Australia), Pleurotus abalonus (in Asia and Hawaii), Pleurotus fuscosquamulosus (in Africa and Europe), Pleurotus smithii (in Mexico) and Pleurotus cystidiosus sensu stricto (in North America). However, geographical boundaries between these species are not strict, as rare events of long distance dispersal have occurred.}, } @article {pmid21148857, year = {2004}, author = {Lu, B and Druzhinina, IS and Fallah, P and Chaverri, P and Gradinger, C and Kubicek, CP and Samuels, GJ}, title = {Hypocrea/Trichoderma species with pachybasium-like conidiophores: teleomorphs for T. minutisporum and T. polysporum and their newly discovered relatives.}, journal = {Mycologia}, volume = {96}, number = {2}, pages = {310-342}, pmid = {21148857}, issn = {0027-5514}, abstract = {We describe or redescribe species of Hypocrea/Trichoderma (Ascomycetes, Hypocreales) having hyaline ascospores and pachybasium-like conidiophores. Teleomorphs are reported for Trichoderma minutisporum (Hypocrea minutispora sp. nov.) and T. polysporum (H. pachybasioides). Hypocrea pilulifera/T. piluliferum is redescribed. Trichoderma croceum is synonymized with T. polysporum. The new species H. parapilulifera, H. stellata and H. lacuwombatensis are described. All of these species fall within the morphological concept of Trichoderma sect. Pachybasium and within the phylogenetic group pachybasium B5 of Kullnig-Gradinger et al (2002). Parsimony analysis of nucleotide sequences from three unlinked loci-ITS1 and 2, endochitinase (ech42) and translation elongation factor 1-alpha (tef1)-detects two distinct phylogenetic lineages within the group pachybasium B5. One comprises H. pachybasioides/T. polysporum, H. pilulifera/T. piluliferum, H. parapilulifera and H. stellata; this group, the "polysporum" lineage, is characterized by having conidia that are white in mass and is the only lineage within Hypocrea characterized by such conidia. The second group includes the green conidial T. minutisporum and H. lacuwombatensis. The partition homogeneity test reveals significant recombination within the "polysporum" lineage but not within the "minutisporum" lineage.}, } @article {pmid21148856, year = {2004}, author = {Kropp, BR and Matheny, PB}, title = {Basidiospore homoplasy and variation in the Inocybe chelanensis group in North America.}, journal = {Mycologia}, volume = {96}, number = {2}, pages = {295-309}, pmid = {21148856}, issn = {0027-5514}, abstract = {We present a morphological and phylogenetic study of Inocybe chelanensis and other North American species of Inocybe that have unusually elongated nodulose spores. Taxonomy and illustrations of these species are provided, along with a key to these and similar species found in Europe and North America. The species concept of I. chelanensis is broadened to include the range of variation occurring for the species in North America. Despite similar basidiospore morphologies, I. chelanensis and I. candidipes are not closely related. Inocybe chelanensis is related more closely to I. stellatospora and I. candidipes is related to I. glabrodisca based on RPB1 and nLSU-rDNA nucleotide sequences. Distal enlongation of Inocybe basidiospores was achieved independently in at least two separate lineages of Inocybe. Inocybe candidipes and I. sierraensis are described as new.}, } @article {pmid14988931, year = {2004}, author = {Reydon, TA}, title = {Why does the species problem still persist?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {26}, number = {3}, pages = {300-305}, doi = {10.1002/bies.10406}, pmid = {14988931}, issn = {0265-9247}, mesh = {Animals ; *Biological Evolution ; Humans ; Models, Theoretical ; *Phylogeny ; }, abstract = {Despite many years of discussion, the species problem has still not been adequately resolved. Why is this the case? Here I discuss two recent suggested answers to this question that place the blame on the species problem's empirical aspects or on its philosophical aspects. In contrast, I argue that neither of these two faces of the species problem constitute the principal cause of the species problem's persistence. Rather, they are merely symptoms of the real cause: the species problem has not yet gone away because of a failure to recognize that not one but a number of distinct concepts are at the heart of the problem. To illustrate this point, a recently proposed solution to the problem is examined: the suggestion to understand the concept of species as a family resemblance concept.}, } @article {pmid14965906, year = {2004}, author = {Ricklefs, RE and Fallon, SM and Bermingham, E}, title = {Evolutionary relationships, cospeciation, and host switching in avian malaria parasites.}, journal = {Systematic biology}, volume = {53}, number = {1}, pages = {111-119}, doi = {10.1080/10635150490264987}, pmid = {14965906}, issn = {1063-5157}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Birds/*genetics/*parasitology ; Cytochromes b/genetics ; Haemosporida/*genetics ; Host-Parasite Interactions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {We used phylogenetic analyses of cytochrome b sequences of malaria parasites and their avian hosts to assess the coevolutionary relationships between host and parasite lineages. Many lineages of avian malaria parasites have broad host distributions, which tend to obscure cospeciation events. The hosts of a single parasite or of closely related parasites were nonetheless most frequently recovered from members of the same host taxonomic family, more so than expected by chance. However, global assessments of the relationship between parasite and host phylogenetic trees, using Component and ParaFit, failed to detect significant cospeciation. The event-based approach employed by TreeFitter revealed significant cospeciation and duplication with certain cost assignments for these events, but host switching was consistently more prominent in matching the parasite tree to the host tree. The absence of a global cospeciation signal despite conservative host distribution most likely reflects relatively frequent acquisition of new hosts by individual parasite lineages. Understanding these processes will require a more refined species concept for malaria parasites and more extensive sampling of parasite distributions across hosts. If parasites can disperse between allopatric host populations through alternative hosts, cospeciation may not have a strong influence on the architecture of host-parasite relationships. Rather, parasite speciation may happen more often in conjunction with the acquisition of new hosts followed by divergent selection between host lineages in sympatry. Detailed studies of the phylogeographic distributions of hosts and parasites are needed to characterize these events.}, } @article {pmid14726456, year = {2004}, author = {Xiao, L and Fayer, R and Ryan, U and Upton, SJ}, title = {Cryptosporidium taxonomy: recent advances and implications for public health.}, journal = {Clinical microbiology reviews}, volume = {17}, number = {1}, pages = {72-97}, pmid = {14726456}, issn = {0893-8512}, mesh = {Animals ; Biological Evolution ; Cryptosporidium/*classification/genetics/isolation & purification ; *Genes, Protozoan ; Host-Parasite Interactions ; Humans ; Public Health/standards/trends ; Terminology as Topic ; }, abstract = {There has been an explosion of descriptions of new species of Cryptosporidium during the last two decades. This has been accompanied by confusion regarding the criteria for species designation, largely because of the lack of distinct morphologic differences and strict host specificity among Cryptosporidium spp. A review of the biologic species concept, the International Code of Zoological Nomenclature (ICZN), and current practices for Cryptosporidium species designation calls for the establishment of guidelines for naming Cryptosporidium species. All reports of new Cryptosporidium species should include at least four basic components: oocyst morphology, natural host specificity, genetic characterizations, and compliance with the ICZN. Altogether, 13 Cryptosporidium spp. are currently recognized: C. muris, C. andersoni, C. parvum, C. hominis, C. wrairi, C. felis, and C. cannis in mammals; C. baïleyi, C. meleagridis, and C. galli in birds; C. serpentis and C. saurophilum in reptiles; and C. molnari in fish. With the establishment of a framework for naming Cryptosporidium species and the availability of new taxonomic tools, there should be less confusion associated with the taxonomy of the genus Cryptosporidium. The clarification of Cryptosporidium taxonomy is also useful for understanding the biology of Cryptosporidium spp., assessing the public health significance of Cryptosporidium spp. in animals and the environment, characterizing transmission dynamics, and tracking infection and contamination sources.}, } @article {pmid21148834, year = {2004}, author = {Peever, TL and Su, G and Carpenter-Boggs, L and Timmer, LW}, title = {Molecular systematics of citrus-associated Alternaria species.}, journal = {Mycologia}, volume = {96}, number = {1}, pages = {119-134}, pmid = {21148834}, issn = {0027-5514}, abstract = {The causal agents of Alternaria brown spot of tangerines and tangerine hybrids, Alternaria leaf spot of rough lemon and Alternaria black rot of citrus historically have been referred to as Alternaria citri or A. alternata. Ten species of Alternaria recently were described among a set of isolates from leaf lesions on rough lemon (Citrus jambhiri) and tangelo (C. paradisi × C. reticulata), and none of these isolates was considered representative of A. alternata or A. citri. To test the hypothesis that these newly described morphological species are congruent with phylogenetic species, selected Alternaria brown spot and leaf spot isolates, citrus black rot isolates (post-harvest pathogens), isolates associated with healthy citrus tissue and reference species of Alternaria from noncitrus hosts were scored for sequence variation at five genomic regions and used to estimate phylogenies. These data included 432 bp from the 5' end of the mitochondrial ribosomal large subunit (mtLSU), 365 bp from the 5' end of the beta-tubulin gene, 464 bp of an endopolygalacturonase gene (endoPG) and 559 and 571 bp, respectively, of two anonymous genomic regions (OPA1-3 and OPA2-1). The mtLSU and beta-tubulin phylogenies clearly differentiated A. limicola, a large-spored species causing leaf spot of Mexican lime, from the small-spored isolates associated with citrus but were insufficiently variable to resolve evolutionary relationships among the small-spored isolates from citrus and other hosts. Sequence analysis of translation elongation factor alpha, calmodulin, actin, chitin synthase and 1, 3, 8-trihydroxynaphthalene reductase genes similarly failed to uncover significant variation among the small-spored isolates. Phylogenies estimated independently from endoPG, OPA1-3 and OPA2-1 data were congruent, and analysis of the combined data from these regions revealed nine clades, eight of which contained small-spored, citrus-associated isolates. Lineages inferred from analysis of the combined dataset were in general agreement with described morphospecies, however, three clades contained more than one morphological species and one morphospecies (A. citrimacularis) was polyphyletic. Citrus black rot isolates also were found to be members of more than a single lineage. The number of morphospecies associated with citrus exceeded that which could be supported under a phylogenetic species concept, and isolates in only five of nine phylogenetic lineages consistently were correlated with a specific host, disease or ecological niche on citrus. We advocate collapsing all small-spored, citrus-associated isolates of Alternaria into a single phylogenetic species, A. alternata.}, } @article {pmid14651462, year = {2004}, author = {Gould, F and Schliekelman, P}, title = {Population genetics of autocidal control and strain replacement.}, journal = {Annual review of entomology}, volume = {49}, number = {}, pages = {193-217}, doi = {10.1146/annurev.ento.49.061802.123344}, pmid = {14651462}, issn = {0066-4170}, mesh = {Animals ; *Animals, Genetically Modified ; Female ; *Genes, Insect ; Genetic Engineering ; Genetics, Population ; Infertility, Male/genetics ; Insecta/genetics/*physiology ; Male ; Mutagenesis, Insertional ; Pest Control, Biological/*methods ; Transgenes ; Translocation, Genetic ; }, abstract = {The concept that an insect species' genome could be altered in a manner that would result in the control of that species (i.e., autocidal control) or in the replacement of a pestiferous strain of the species with a more benign genotype was first proposed in the mid-twentieth century. A major research effort in population genetics and ecology followed and led to the development of a set of classical genetic control approaches that included use of sterile males, conditional lethal genes, translocations, compound chromosomes, and microbe-mediated infertility. Although there have been a number of major successes in application of classical genetic control, research in this area has declined in the past 20 years for technical and societal reasons. Recent advances in molecular biology and transgenesis research have renewed interest in genetically based control methods because these advances may remove some major technical problems that have constrained effective genetic manipulation of pest species. Population genetic analyses suggest that transgenic manipulations may enable development of strains that would be 10 to over 100 times more efficient than strains developed by classical methods. Some of the proposed molecular approaches to genetic control involve modifications of classical approaches such as conditional lethality, whereas others are novel. Experience from the classical era of genetic control research indicates that the population structure and population dynamics of the target population will determine which, if any, genetic control approaches would be appropriate for addressing a specific problem. As such, there continues to be a need for ongoing communication between scientists who are developing strains and those who study the native pest populations.}, } @article {pmid14640415, year = {2003}, author = {Wertz, JE and Goldstone, C and Gordon, DM and Riley, MA}, title = {A molecular phylogeny of enteric bacteria and implications for a bacterial species concept.}, journal = {Journal of evolutionary biology}, volume = {16}, number = {6}, pages = {1236-1248}, doi = {10.1046/j.1420-9101.2003.00612.x}, pmid = {14640415}, issn = {1010-061X}, support = {GM58433/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Bacterial ; Enterobacteriaceae/*genetics ; *Evolution, Molecular ; Genotype ; *Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {A molecular phylogeny for seven taxa of enteric bacteria (Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, and Serratia plymuthica) was made from multiple isolates per taxa taken from a collection of environmental enteric bacteria. Sequences from five housekeeping genes (gapA, groEL, gyrA, ompA, and pgi) and the 16S rRNA gene were used to infer individual gene trees and were concatenated to infer a composite molecular phylogeny for the species. The isolates from each taxa formed tight species clusters in the individual gene trees, suggesting the existence of 'genotypic' clusters that correspond to traditional species designations. These sequence data and the resulting gene trees and consensus tree provide the first data set with which to assess the utility of the recently proposed core genome hypothesis (CGH). The CGH provides a genetically based approach to applying the biological species concept to bacteria.}, } @article {pmid14635856, year = {2003}, author = {Lee, MS}, title = {Species concepts and species reality: salvaging a Linnaean rank.}, journal = {Journal of evolutionary biology}, volume = {16}, number = {2}, pages = {179-188}, doi = {10.1046/j.1420-9101.2003.00520.x}, pmid = {14635856}, issn = {1010-061X}, mesh = {*Classification ; *Phylogeny ; Reproduction/*genetics ; Species Specificity ; }, abstract = {The validity of the species category (rank) as a distinct level of biological organization has been questioned. Phenetic, cohesion and monophyletic species concepts do not delimit species-level taxa that are qualitatively distinct from lower or higher taxa: all organisms throughout the tree of life exhibit varying degrees of similarity, cohesion, and monophyly. In contrast, interbreeding concepts delimit species-level taxa characterized by a phenomenon (regular gene flow) not found in higher taxa, making the species category a distinct level of biological organization. Only interbreeding concepts delimit species-level taxa that are all comparable according to a biologically meaningful criterion and qualitatively distinct from entities assigned to other taxonomic categories. Consistent application of interbreeding concepts can result in counterintuitive taxonomies--e.g. many wide polytypic species in plants and narrow cryptic species in animals. However, far from being problematic, such differences are biologically illuminating--reflecting differing barriers to gene flow in different clades. Empirical problems with interbreeding concepts exist, but many of these also apply to other species concepts, whereas others are not as severe as some have argued. A monistic view of species using interbreeding concepts will encounter strong historical inertia, but can save the species category from redundancy with other categories, and thus justify continued recognition of the species category.}, } @article {pmid14613500, year = {2003}, author = {Gibson, W}, title = {Species concepts for trypanosomes: from morphological to molecular definitions?.}, journal = {Kinetoplastid biology and disease}, volume = {2}, number = {1}, pages = {10}, pmid = {14613500}, issn = {1475-9292}, abstract = {The way species and subspecies names are applied in African trypanosomes of subgenera Trypanozoon and Nannomonas is reviewed in the light of data from molecular taxonomy. In subgenus Trypanozoon the taxonomic importance of pathogenicity, host range and distribution appear to have been inflated relative to actual levels of genetic divergence. The opposite is true for subgenus Nannomonas, where current taxonomic usage badly underrepresents genetic diversity. Data from molecular characterisation studies are revealing a growing number of genotypes, which may represent distinct taxa. Unfortunately few of these genotypes are yet supported by sufficient biological data to be recognized taxonomically. But we may be missing fundamental epidemiological information, because of our inability to distinguish these trypanosomes in host blood morphologically or in tsetse by their developmental cycle. Molecular taxonomy has led the way in identifying these new genotypes and now offers the key to elucidating the biology of these organisms.}, } @article {pmid14613497, year = {2003}, author = {Momen, H}, title = {Concepts of species in trypanosomatids.}, journal = {Kinetoplastid biology and disease}, volume = {2}, number = {1}, pages = {13}, pmid = {14613497}, issn = {1475-9292}, abstract = {This paper is a commentary on "Species concepts for trypanosomes: from morphological to molecular definitions?" by Wendy Gibson published in this journal 1. Taxonomy has been traditionally based on expert opinion which is influenced among other factors by the philosophical and educational background of the expert concerned. This has resulted in widely different criteria for species among the trypanosomatids when compared to the actual genetic diversity involved. Gibson's paper presents an example of this within the trypanosome sub-genera. Although attempts have been made to put taxonomy on a more objective basis expert opinion still appears to dominate in the actual classifications in use.}, } @article {pmid14595903, year = {2003}, author = {Cardinali, G}, title = {Measure of species variability for a microbial taxonomy based on the relative resemblance.}, journal = {Rivista di biologia}, volume = {96}, number = {2}, pages = {271-291}, pmid = {14595903}, issn = {0035-6050}, mesh = {Animals ; Bacteria/*classification ; Confidence Intervals ; Species Specificity ; }, abstract = {The concept of species currently in use in microbial taxonomy is based on sex because derives from that developed in zoology and botany. The absence of sex as the only system to reproduce does not allow to use the hybridization as the test to assess the conspecificity of microbial strains, forcing microbial taxonomists to use relative resemblance among strains as the only tool to define microbial species and to classify new microorganisms. Relative resemblance can be intuitively defined as the situation in which two strains of the same species must be more similar than each of them with a strain of any other species. Unfortunately, there are several algorithms to define the similarity between two strains, but none can be used to estimate the average distance between several members of the same species. This paper describes the problems inherent with the definition of species without hybridization tests and proposes two algorithms for a standard estimation of the overall variability of a species with the data obtained from a sample of strains. These measures will allow the non-subjective determination of the overall similarity among members of the same species using results from both phenotypic and molecular analyses. Both algorithms are based on a bootsrapping procedure implemented by RHO and SMA, two software applications freely available from the internet. These applications allow an easy evaluation of parameters such as the overall variability and levels of confidence associated with the sample of strains and the panel of characters under study.}, } @article {pmid14571066, year = {2003}, author = {Arrese, JE and Piérard, GE}, title = {Treatment failures and relapses in onychomycosis: a stubborn clinical problem.}, journal = {Dermatology (Basel, Switzerland)}, volume = {207}, number = {3}, pages = {255-260}, doi = {10.1159/000073086}, pmid = {14571066}, issn = {1018-8665}, mesh = {Administration, Oral ; Administration, Topical ; Antifungal Agents/*administration & dosage ; Biopsy, Needle ; Controlled Clinical Trials as Topic ; Female ; Foot Dermatoses ; Hand Dermatoses ; Humans ; Immunohistochemistry ; Male ; Onychomycosis/diagnosis/*drug therapy/*pathology ; Prognosis ; Recurrence ; Risk Assessment ; Severity of Illness Index ; Treatment Failure ; }, abstract = {The therapeutic outcome of onychomycoses is uncertain. Comparative short-term efficacy studies on antifungals abound and report contradictory findings. Few unbiased follow-up studies have scrutinized the long-term outcome. Basically, none of the current antifungals can guarantee cure in all instances. In addition, relapses are not rare. The causes of therapeutic failure in onychomycoses are multiple. The most important are the lack of diagnostic accuracy, inadequate antifungal choice or delivery modality, and presence of dormant conidia, sequestrated mycelium pockets or resistant fungal species. The concept of fungicidal drug derived from selected in vitro studies appears irrelevant in clinical practice.}, } @article {pmid14532858, year = {2003}, author = {Aikawa, K and Leggett, R and Levin, RM}, title = {Effect of age on hydrogen peroxide mediated contraction damage in the male rat bladder.}, journal = {The Journal of urology}, volume = {170}, number = {5}, pages = {2082-2085}, doi = {10.1097/01.ju.0000081461.73156.48}, pmid = {14532858}, issn = {0022-5347}, mesh = {Age Factors ; Animals ; Carbachol/pharmacology ; Cellular Senescence/*drug effects/physiology ; Culture Techniques ; Dose-Response Relationship, Drug ; Electric Stimulation ; Hydrogen Peroxide/*toxicity ; Isometric Contraction/*drug effects/physiology ; Male ; Malondialdehyde/metabolism ; Muscle, Smooth/*drug effects/physiopathology ; Potassium Chloride/pharmacology ; Rats ; Rats, Sprague-Dawley ; Reactive Oxygen Species/*toxicity ; Urinary Bladder/*drug effects/physiopathology ; Urinary Bladder Neck Obstruction/physiopathology ; }, abstract = {PURPOSE: Recent studies introduced the concept that reactive oxygen species (ROS) may be a major factor in the progressive deterioration of bladder function induced by benign prostatic hyperplasia in men and following partial outlet obstruction in animals. We determined whether bladder contraction sensitivity to ROS changes with aging. Using H2O2 to simulate ROS damage we compared the sensitivity of the contractile responses of bladder smooth muscle isolated from young and elderly rats to H2O2.

MATERIALS AND METHODS: Male 3-month-old (young) and 12-month-old (elderly) Sprague-Dawley rats were used for this study with 24 per group. Each rat was anesthetized and the bladder was excised. Two longitudinal strips were cut from the bladder body. Each strip was placed in individual 15 ml baths containing oxygenated Tyrode's solution at 37C. Each strip was stimulated at 32 Hz for 20 seconds with pulses 1 millisecond in duration at 80 V. After electrical field stimulation (EFS) the response to 20 microM carbachol and 120 mM KCl was determined. The bath solution was then exchanged for H2O2 solutions of 6 different concentrations including 0%, 0.0625%, 0.125%, 0.25%, 0.5% and 1.0%. After 1 hour of exposure to H2O2 the tissues were washed free of H2O2, and the response to EFS, carbachol and KCl were measured again. At the end of the experiment the strips were weighed and frozen at -70C for malondialdehyde analysis.

RESULTS: The magnitude of the contractile responses of the young and elderly rats to all forms of stimulation were equal. Hydrogen peroxide caused a dose dependent decrease in the contractile responses of bladder strips to all forms of stimulation. Contractile responses to carbachol and KCl were more sensitive to H2O2 than to EFS. Contractile responses of bladder strips isolated from elderly rats were significantly more sensitive to H2O2 damage than strips isolated from young rats. Malondialdehyde generation of bladder strips isolated from elderly rats was significantly greater than those from young rats.

CONCLUSIONS: It is suggested that aging increases the sensitivity of detrusor contraction to oxidative damage.}, } @article {pmid14529174, year = {2003}, author = {Rosselló-Mora, R}, title = {Opinion: the species problem, can we achieve a universal concept?.}, journal = {Systematic and applied microbiology}, volume = {26}, number = {3}, pages = {323-326}, doi = {10.1078/072320203322497347}, pmid = {14529174}, issn = {0723-2020}, mesh = {Bacteria/*classification/genetics ; Biodiversity ; Classification/*methods ; DNA, Ribosomal ; Genotype ; Phenotype ; Phylogeny ; Sequence Homology ; Terminology as Topic ; }, abstract = {One of the so called 'species problems' is that no universal concept exists. There is a tendency among microbiologists to criticize the hitherto devised concept. It is considered by some researchers as being too conservative and not suitable to be compared with those for eukaryotes. However, such problem is not only restricted to prokaryotes, but among other taxonomies comparisons seem to be impossible. As it is argued, the underlying cause to this problem is the reductionistic and monistic use of taxonomy. Analyzing the more than 22 devised concepts it seems possible to achieve a universal species concept. However, this might not be pragmatic. For the time being, a pluralistic sense of the species concept might be accepted, and one will have to recognize that any comparison among different taxonomies will be difficult.}, } @article {pmid14520888, year = {2003}, author = {Khalturin, MD and Litvinchuk, SN and Borkin, LIa and Rozanov, IuM and Mil'to, KD}, title = {[Genetic variation in two forms of the common spadefoot toad Pelobates fuscus (Pelobatidae, Anura, Amphibia) distinguished by genome size].}, journal = {Tsitologiia}, volume = {45}, number = {3}, pages = {308-323}, pmid = {14520888}, issn = {0041-3771}, mesh = {Animals ; Anura/*genetics ; Azerbaijan ; Electrophoresis, Polyacrylamide Gel ; Enzymes/*genetics ; *Genetic Variation ; *Genome ; Heterozygote ; Latvia ; Liver/enzymology ; Muscles/enzymology ; Russia ; Species Specificity ; Ukraine ; }, abstract = {Genetic differences (presumed 23 loci) between two cryptic forms of Pelobates fuscus, differing in genome size, were examined by means of polyacrylamide-gel electrophoresis. This method allowed to discriminate between these forms. Average genetic distance (DN) between both the forms was equal to 0.311, ranging from 0.055 to 0.563. As a rule, differences within these groups were smaller (0.021-0.388). The data show obvious genetic differentiation between these two cryptic forms of P. fuscus. Differences between these forms and P. syriacus were significantly higher (in average 0.943). Genetic distances in relation to speciation and species concepts are discussed.}, } @article {pmid14519574, year = {2003}, author = {de Meeûs, T and Durand, P and Renaud, F}, title = {Species concepts: what for?.}, journal = {Trends in parasitology}, volume = {19}, number = {10}, pages = {425-427}, doi = {10.1016/s1471-4922(03)00195-8}, pmid = {14519574}, issn = {1471-4922}, mesh = {Animals ; *Biodiversity ; Biological Evolution ; Classification ; Ecosystem ; Parasites/*classification ; Species Specificity ; }, } @article {pmid12965008, year = {2003}, author = {Kvist, L and Martens, J and Higuchi, H and Nazarenko, AA and Valchuk, OP and Orell, M}, title = {Evolution and genetic structure of the great tit (Parus major) complex.}, journal = {Proceedings. Biological sciences}, volume = {270}, number = {1523}, pages = {1447-1454}, pmid = {12965008}, issn = {0962-8452}, mesh = {Animals ; Asia ; Cluster Analysis ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Europe ; *Evolution, Molecular ; Geography ; Hybridization, Genetic ; Locus Control Region/genetics ; *Phylogeny ; Songbirds/*genetics ; }, abstract = {The great tit complex is divided into four groups, each containing several subspecies. Even though the groups are known to differ markedly on morphological, vocal and behavioural characters, some hybridization occurs in the regions where they meet. The great tit has often been referred to as an example of a ring species, although this has later been questioned. Here, we have studied the genetic structure and phylogenetic relationships of the subspecies groups to clarify the evolutionary history of the complex using control region sequences of the mitochondrial DNA. The subspecies groups were found to be monophyletic and clearly distinct in mitochondrial haplotypes, and therefore must have had long-independent evolutionary histories. This conflicts with the ring species assignment and supports the formation of secondary contact zones of previously temporarily isolated groups. According to the phylogenetic species concept, all the subspecies groups could be considered as separate species, but if the definition of the biological species concept is followed, none of the subspecies groups is a true species because hybridization still occurs.}, } @article {pmid12963468, year = {2003}, author = {Wiese, H}, title = {Iconic and non-iconic stages in number development: the role of language.}, journal = {Trends in cognitive sciences}, volume = {7}, number = {9}, pages = {385-390}, doi = {10.1016/s1364-6613(03)00192-x}, pmid = {12963468}, issn = {1879-307X}, abstract = {Is language the key to number? This article argues that the human language faculty provides the cognitive equipment that enables humans to develop a systematic number concept. Importantly, the number concept is based on non-iconic representations that involve relations between relations: relations between numbers are linked with relations between objects. In contrast to this, language-independent numerosity concepts provide only iconic representations. The pattern of forming relations between relations lies at the heart of our language faculty, suggesting that it is language that enables humans to make the step from these iconic representations, which we share with other species, to a generalized concept of number.}, } @article {pmid12957516, year = {2003}, author = {McCoy, KD}, title = {Sympatric speciation in parasites--what is sympatry?.}, journal = {Trends in parasitology}, volume = {19}, number = {9}, pages = {400-404}, pmid = {12957516}, issn = {1471-4922}, mesh = {Animals ; Biological Evolution ; Host-Parasite Interactions ; Models, Biological ; Parasites/classification/*genetics/physiology ; Species Specificity ; }, abstract = {Parasites account for a large part of known species diversity and are considered to have a high potential for sympatric speciation. However, the frequency of sympatric divergence in these organisms will depend on the definition of sympatry that one uses. Like many of our current species concepts, the typical definition of sympatry is not widely applicable to parasites. Revisiting the historically defined conditions for sympatric speciation and considering the situations in which we might regard parasites as being sympatric leads us to question the classic prediction that parasites have a greater tendency to speciate in sympatry than do free-living organisms.}, } @article {pmid12952629, year = {2003}, author = {Rohlfs, M and Hoffmeister, TS}, title = {An evolutionary explanation of the aggregation model of species coexistence.}, journal = {Proceedings. Biological sciences}, volume = {270 Suppl 1}, number = {Suppl 1}, pages = {S33-5}, pmid = {12952629}, issn = {0962-8452}, mesh = {Animals ; *Biological Evolution ; Drosophila/classification/*physiology ; Ecosystem ; Female ; *Models, Biological ; Oviposition/physiology ; Population Density ; Species Specificity ; }, abstract = {In ecology, the 'aggregation model of coexistence' provides a powerful concept to explain the unexpectedly high species richness of insects on ephemeral resources like dung pats, fruits, etc. It suggests that females aggregate their eggs across resource patches, which leads to an increased intraspecific competition within occupied patches and a relatively large number of patches that remain unoccupied. This provides competitor-free patches for heterospecifics, facilitating species coexistence. At first glance, deliberately causing competition among the females' own offspring and leaving resources to heterospecific competitors seems altruistic and incompatible with individual fitness maximization, raising the question of how natural selection operates in favour of egg aggregation on ephemeral resource patches. Allee effects that lead to fitness maxima at intermediate egg densities have been suggested, but not yet detected. Using drosophilid flies on decaying fruits as a study system, we demonstrate a hump-shaped relationship between egg density and individual survival probability, with maximum survivorship at intermediate densities. This pattern clearly selects for egg aggregation and resolves the possible conflict between the ecological concept of species coexistence on ephemeral resources and evolutionary theory.}, } @article {pmid12951793, year = {2003}, author = {Peintner, U and Ladurner, H and Simonini, G}, title = {Xerocomus cisalpinus sp. nov., and the delimitation of species in the X. chrysenteron complex based on morphology and rDNA-LSU sequences.}, journal = {Mycological research}, volume = {107}, number = {Pt 6}, pages = {659-679}, doi = {10.1017/s0953756203007901}, pmid = {12951793}, issn = {0953-7562}, mesh = {Basidiomycota/*classification/genetics/*ultrastructure ; DNA, Fungal/analysis ; DNA, Ribosomal/*analysis ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; *Mycological Typing Techniques ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Trees/microbiology ; }, abstract = {Species delimitation is still controversial in the Xerocomus chrysenteron complex. We have therefore established comprehensible and reliable species concepts based on statistical evaluation of morphological and ecological characters. We examined many collections from different geographical regions and different developmental stages within collections. Quantitative micromorphological characters (basidiospores, pileipellis end cells) were measured in statistically relevant numbers. The same material was used to generate 24 rDNA-LSU sequences,and the results of phylogenetic analyses clearly confirmed our species concepts: spore size and ornamentation, length of the pileipellis end cells and 'pruinatus-hyphae' are most valuable characters for the delimitation of species in this complex. Molecular data demonstrated that the X. chrysenteron complex is a monophyletic group. All the examined species (X. chrysenteron, X. cisalpinus, X. pruinatus, X. ripariellus, X. dryophilus, X. fennicus, X. porosporus, and X. rubellus) represent independent lineages. The faintly striate spores, a key character characterising species of section Striatulispori, probably evolved independently. In addition, the 'pruinatus-hyphae' have multiple origins, and truncate spore apices are derived at least twice. Xerocomus cisalpinus sp. nov. is characterised by striate spores, the presence of 'pruinatus-hyphae' and a pileipellis strongly reminiscent of X. chrysenteron. For reasons of discussion, microscopical data are presented on Boletellus episcopalis for the first time. Xerocomus fennicus (Boletellus) comb, nov. is proposed. We provide descriptions to all included taxa. Our results once more demonstrate that reliably identified and characterised voucher collections are the basic requirement for meaningful phylogenetic studies.}, } @article {pmid12909693, year = {2003}, author = {Kültz, D}, title = {Evolution of the cellular stress proteome: from monophyletic origin to ubiquitous function.}, journal = {The Journal of experimental biology}, volume = {206}, number = {Pt 18}, pages = {3119-3124}, doi = {10.1242/jeb.00549}, pmid = {12909693}, issn = {0022-0949}, support = {DK59470/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Cell Physiological Phenomena ; Conserved Sequence ; DNA Damage/*physiology ; *Evolution, Molecular ; Heat-Shock Proteins/*physiology ; Homeostasis ; Phylogeny ; *Proteome ; Stress, Physiological/*physiopathology ; }, abstract = {Cells respond to acute environmental change by activating a stress response that is widely studied. However, knowledge of this stress response is fragmentary, and a unifying concept explaining its universality for many different species and types of stress is lacking. The need for a holistic view emphasizing the key aspects of the stress response is addressed by the following hypothesis. The cellular stress response is a reaction to any form of macromolecular damage that exceeds a set threshold, independent of the underlying cause. It is aimed at temporarily increasing tolerance limits towards macromolecular damage by utilizing a phylogenetically conserved set of genes and pathways that mediate global macromolecular stabilization and repair to promote cellular and organismal integrity under suboptimal conditions. This mechanism affords time for a separate set of stressor-specific adaptations, designed to re-establish cellular homeostasis, to take action. Supporting evidence, emerging conclusions, and ways to test this hypothesis are presented.}, } @article {pmid12815215, year = {2003}, author = {Zietara, MS and Lumme, J}, title = {The crossroads of molecular, typological and biological species concepts: two new species of Gyrodactylus Nordmann, 1832 (Monogenea: Gyrodactylidae).}, journal = {Systematic parasitology}, volume = {55}, number = {1}, pages = {39-52}, pmid = {12815215}, issn = {0165-5752}, mesh = {Animals ; Base Sequence ; Cestoda/anatomy & histology/*classification/genetics ; DNA, Helminth/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Genetic Variation ; Microscopy, Phase-Contrast ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Alignment ; Smegmamorpha/parasitology ; }, abstract = {Nucleotide sequences of nuclear ribosomal DNA internal transcribed spacers (ITS) were used to confirm morphological identification of Gyrodactylus species in Fennoscandia. Three pairs of morphologically similar or cryptic species are compared in this study. G. branchicus Malmberg, 1964 and G. rarus Wegener, 1910, hosted by the sticklebacks Gasterosteus aculeatus L. and Pungitius pungitius (L.), respectively, displayed a genetic divergence of 0.9-1.3% along 774 nucleotides of ITS (Jukes & Cantor distance). G. branchicus isolates from the Baltic, White Sea and Scottish North Sea were invariable, but a Belgian North Sea population with a 0.4% divergence in ITS sequence has been collected. The species status of G. branchicus and G. rarus is supported by host-specificity in sympatric habitats and consistent morphological difference in the marginal hook sickles. Among Gyrodactylus on burbot Lota lota (L.) specimens were collected with their 792 bp long ITS sequences differing by 8.5%. This has led to the splitting of G. lotae Gusev, 1953 into two species, G. lotae and G. alexgusevi n. sp. The species are morphologically separable, and a similar range of variation was found in both the anchors and the marginal hooks in other collections and in the original description. Among G. macronychus-like parasites of minnow Phoxinus phoxinus (L.), divergent ITS sequences indicate two cryptic species. By comparison with the type-specimens, one was identified as G. macronychus Malmberg, 1957; the other is here designated as G. jussii n. sp., differing by 21.8% in 950-973 bp long ITS. The consequences of these findings for the species concept and species identification of Gyrodactylus are discussed.}, } @article {pmid12766949, year = {2003}, author = {Pigliucci, M}, title = {Species as family resemblance concepts: the (dis-)solution of the species problem?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {25}, number = {6}, pages = {596-602}, doi = {10.1002/bies.10284}, pmid = {12766949}, issn = {0265-9247}, mesh = {*Biological Evolution ; Models, Biological ; Models, Genetic ; Models, Theoretical ; Species Specificity ; }, abstract = {The so-called "species problem" has plagued evolutionary biology since before Darwin's publication of the aptly titled Origin of Species. Many biologists think the problem is just a matter of semantics; others complain that it will not be solved until we have more empirical data. Yet, we don't seem to be able to escape discussing it and teaching seminars about it. In this paper, I briefly examine the main themes of the biological and philosophical literatures on the species problem, focusing on identifying common threads as well as relevant differences. I then argue two fundamental points. First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require-but cannot be settled by-empirical evidence. Second, the (dis-)solution lies in explicitly adopting Wittgenstein's idea of "family resemblance" or cluster concepts, and to consider species as an example of such concepts. This solution has several attractive features, including bringing together apparently diverging themes of discussion among biologists and philosophers. The current proposal is conceptually independent (though not incompatible) with the pluralist approach to the species problem advocated by Mishler, Donoghue, Kitcher and Dupré, which implies that distinct aspects of the species question need to be emphasized depending on the goals of the researcher. From the biological literature, the concept of species that most closely matches the philosophical discussion presented here is Templeton's cohesion idea.}, } @article {pmid12761808, year = {2003}, author = {Baroli, B and Shastri, VP and Langer, R}, title = {A method to protect sensitive molecules from a light-induced polymerizing environment.}, journal = {Journal of pharmaceutical sciences}, volume = {92}, number = {6}, pages = {1186-1195}, doi = {10.1002/jps.10378}, pmid = {12761808}, issn = {0022-3549}, support = {DE13023/DE/NIDCR NIH HHS/United States ; }, mesh = {Acrylates/*chemistry ; Chemistry, Pharmaceutical ; Enzyme Stability ; Horseradish Peroxidase/chemistry/*radiation effects ; *Light ; Methacrylates ; Molecular Weight ; Polyethylene Glycols/*chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/*methods ; Technology, Pharmaceutical ; Time Factors ; alpha-Glucosidases/chemistry/*radiation effects ; }, abstract = {Systems that can be polymerized in situ upon exposure to light radiation may have significant applications in tissue engineering and drug delivery. However, the light-induced polymerization step, which is the requisite for this technology, could be potentially deleterious to sensitive bioactive agents (e.g., enzymes, cytokines, matrix metalloproteinases) being entrapped. In this study, a method to protect sensitive molecules from a light-induced polymerizing environment is proposed. This method is based on the idea that nonaccessible substances cannot interact with the polymerizing species. To examine this concept, two model enzymes-namely, horseradish peroxidase and alpha-glucosidase-were protected by gelatin-based wet granulation and incorporated within a cured polyethylene glycol dimethacrylate, a photocurable monomer, under different conditions. Unprotected enzymes were used as controls. Enzymes were then allowed to diffuse out of the polymerized matrices. The activity and total enzyme recovered from these matrices by passive diffusion were compared to ascertain the extent of activity retention. Matrix assisted laser desorption ionization mass spectrometry combined with time of flight mass spectrometry (MALDI-TOF) was used to determine changes in enzyme molecular weight. During the first 24 h of diffusion from the polymerized matrices, unprotected enzymes consistently showed a loss of activity ranging from 10-66%, depending on the matrix composition and enzyme properties. In contrast, protected enzymes retained over 94% of their activity irrespective of the experimental setting. The loss of activity appears to be a direct consequence of the polymerizing environment.}, } @article {pmid12748049, year = {2003}, author = {Spírek, M and Yang, J and Groth, C and Petersen, RF and Langkjaer, RB and Naumova, ES and Sulo, P and Naumov, GI and Piskur, J}, title = {High-rate evolution of Saccharomyces sensu lato chromosomes.}, journal = {FEMS yeast research}, volume = {3}, number = {4}, pages = {363-373}, doi = {10.1016/S1567-1356(02)00204-0}, pmid = {12748049}, issn = {1567-1356}, mesh = {Base Sequence ; Chromosomes, Fungal/*genetics ; DNA, Fungal/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; Evolution, Molecular ; Genetic Variation/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/chemistry/genetics ; Saccharomyces/*genetics ; Sequence Alignment ; }, abstract = {Forty isolates belonging to the Saccharomyces sensu lato complex were analyzed for one nuclear and two mitochondrial sequences, and for their karyotypes. These data are useful for description and definition of yeast species based on the phylogenetic species concept. The deduced phylogenetic relationships among isolates based on the nuclear and mitochondrial sequences were usually similar, suggesting that horizontal transfer/introgression has not been frequent. The highest degree of polymorphism was observed at the chromosome level. Even isolates which had identical nuclear and mitochondrial sequences often exhibited variation in the number and size of their chromosomes. Apparently, yeast chromosomes have been frequently reshaped and therefore also the position of genes has been dynamic during the evolutionary history of yeasts.}, } @article {pmid12727458, year = {2003}, author = {Cressman, R and Garay, J}, title = {Evolutionary stability in Lotka-Volterra systems.}, journal = {Journal of theoretical biology}, volume = {222}, number = {2}, pages = {233-245}, doi = {10.1016/s0022-5193(03)00032-8}, pmid = {12727458}, issn = {0022-5193}, mesh = {Animals ; *Biological Evolution ; *Ecosystem ; Game Theory ; *Models, Genetic ; Phenotype ; Population Dynamics ; Systems Theory ; }, abstract = {The Lotka-Volterra model of population ecology, which assumes all individuals in each species behave identically, is combined with the behavioral evolution model of evolutionary game theory. In the resultant monomorphic situation, conditions for the stability of the resident Lotka-Volterra system, when perturbed by a mutant phenotype in each species, are analysed. We develop an evolutionary ecology stability concept, called a monomorphic evolutionarily stable ecological equilibrium, which contains as a special case the original definition by Maynard Smith of an evolutionarily stable strategy for a single species. Heuristically, the concept asserts that the resident ecological system must be stable as well as the phenotypic evolution on the "stationary density surface". The conditions are also shown to be central to analyse stability issues in the polymorphic model that allows arbitrarily many phenotypes in each species, especially when the number of species is small. The mathematical techniques are from the theory of dynamical systems, including linearization, centre manifolds and Molchanov's Theorem.}, } @article {pmid21156637, year = {2003}, author = {Kretzer, AM and Luoma, DL and Molina, R and Spatafora, JW}, title = {Taxonomy of the Rhizopogon vinicolor species complex based on analysis of ITS sequences and microsatellite loci.}, journal = {Mycologia}, volume = {95}, number = {3}, pages = {480-487}, pmid = {21156637}, issn = {0027-5514}, abstract = {We are re-addressing species concepts in the Rhizopogon vinicolor species complex (Boletales, Basidiomycota) using sequence data from the internal-transcribed spacer (ITS) region of the nuclear ribosomal repeat, as well as genotypic data from five microsatellite loci. The R. vinicolor species complex by our definition includes, but is not limited to, collections referred to as R. vinicolor Smith, R. diabolicus Smith, R. ochraceisporus Smith, R. parvulus Smith or R. vesiculosus Smith. Holo- and/or paratype material for the named species is included. Analyses of both ITS sequences and microsatellite loci separate collections of the R. vinicolor species complex into two distinct clades or clusters, suggestive of two biological species that subsequently are referred to as R. vinicolor sensu Kretzer et al and R. vesiculosus sensu Kretzer et al. Choice of the latter names, as well as morphological characters, are discussed.}, } @article {pmid12702321, year = {2002}, author = {Gadanho, M and Sampaio, JP}, title = {Polyphasic taxonomy of the basidiomycetous yeast genus Rhodotorula: Rh. glutinis sensu stricto and Rh. dairenensis comb. nov.}, journal = {FEMS yeast research}, volume = {2}, number = {1}, pages = {47-58}, doi = {10.1111/j.1567-1364.2002.tb00068.x}, pmid = {12702321}, issn = {1567-1356}, mesh = {Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/*analysis/genetics ; Rhodotorula/*classification/genetics ; Sequence Analysis, DNA ; Spores, Fungal/growth & development ; }, abstract = {The phenotypic and genetic heterogeneity of the basidiomycetous yeast species Rhodotorula glutinis was investigated in a group of 109 isolates. A polyphasic taxonomic approach was followed which included PCR fingerprinting, determination of sexual compatibility, 26S and ITS rDNA sequence analysis, DNA-DNA reassociation experiments and reassessment of micromorphological and physiological attributes. The relationships with species of the teleomorphic genus Rhodosporidium were studied and isolates previously identified as Rh. glutinis were found to belong to Rhodosporidium babjevae, Rhodosporidium diobovatum and Rhodosporidium sphaerocarpum. Other isolates included in the study were found to belong to Rh. glutinis var. dairenensis, which is elevated to the species level, or to undescribed species. The concept of Rh. glutinis sensu stricto is proposed due to the close phenetic and phylogenetic proximity detected for Rh. glutinis, Rhodotorula graminis and R. babjevae.}, } @article {pmid12660443, year = {2003}, author = {Rehkämper, G and Kart, E and Frahm, HD and Werner, CW}, title = {Discontinuous variability of brain composition among domestic chicken breeds.}, journal = {Brain, behavior and evolution}, volume = {61}, number = {2}, pages = {59-69}, doi = {10.1159/000069352}, pmid = {12660443}, issn = {0006-8977}, mesh = {Animals ; *Biological Evolution ; Biometry ; Body Weight/genetics ; Brain/*anatomy & histology ; Chickens/*anatomy & histology/genetics ; Female ; Genetic Variation/genetics ; Male ; Organ Size/genetics ; Pedigree ; Species Specificity ; }, abstract = {In 80 domestic chickens from 8 breeds, the volumes of 12 brain parts were identified as dimensions in a cluster analysis. Based on Euclidean metrics and the Ward algorithm at least 2 groups were found that are congruent with the breeds 'White Crested Polish chicken' and 'Breda', although the breed identity was not a variable used in the cluster analysis. Domestication is interpreted as evolution which includes the possibility of speciation. It is hypothesized that White Crested Polish chickens and Bredas are becoming new species in terms of a biospecies concept.}, } @article {pmid12651455, year = {2000}, author = {Bartelink, HH}, title = {Effects of stand composition and thinning in mixed-species forests: a modeling approach applied to Douglas-fir and beech.}, journal = {Tree physiology}, volume = {20}, number = {5_6}, pages = {399-406}, doi = {10.1093/treephys/20.5-6.399}, pmid = {12651455}, issn = {1758-4469}, abstract = {Models estimating growth and yield of forest stands provide important tools for forest management. Pure stands have been modeled extensively and successfully for decades; however, relatively few models for mixed-species stands have been developed. A spatially explicit, mechanistic model (COMMIX) is presented that simulates growth of mixed-species forest stands, and takes account of the effects of management on stand dynamics. Previously, it was shown that COMMIX satisfactorily reproduced the development of monospecific stands. In the present study, the model was used to simulate growth and yield in mixed stands differing in the proportions of species present. The concept of a "replacement series" was used to compare productivities of the mixed stands. The model was also used to analyze effects of thinning regimes and stand composition on productivity. Model simulations indicate that productivity of a mixed stand will generally be intermediate between the productivities of monospecific stands of the contributing species. However, stand composition, and especially thinning regime, will strongly affect stand productivity. The simulations are discussed with reference to the effects of resource partitioning, canopy stratification, complementarity, spatial pattern, crown dynamics, and phenology on the growth and yield of mixed stands. The study highlights the value of using mechanistic approaches to predict mixed stand development in relation to management regime.}, } @article {pmid19265985, year = {2003}, author = {Eyualem, A and Blaxter, M}, title = {Comparison of biological, molecular, and morphological methods of species identification in a set of cultured panagrolaimus isolates.}, journal = {Journal of nematology}, volume = {35}, number = {1}, pages = {119-128}, pmid = {19265985}, issn = {0022-300X}, abstract = {We have developed a molecular barcode system that uses the small subunit ribosomal RNA (SSU) sequence to define molecular operational taxonomic units (MOTU) of soil nematodes. Here we attempt to differentiate five cultured isolates of a taxonomically difficult genus, Panagrolaimus, using morphological, molecular, and biological (breeding) criteria. The results indicated that the five culture populations belonged to two reproductively isolated species. The available morphological criteria, including scanning electron microscopy (SEM), were insufficient to differentiate among them, and all five could be classified as one morphospecies. Within-culture variation of the morphometrical data did not discern between the two biological species. Sequence data clearly separated the populations into two groups that supported the breeding results. Given this study represented only five populations of one genus, we suggest a congruence of MOTU analysis with the biological species concept. This multifaceted approach is promising for future identification of nematodes as it is simple, comparable, and transferable.}, } @article {pmid12573062, year = {2002}, author = {Smith, PF and Kornfield, I}, title = {Phylogeography of Lake Malawi cichlids of the genus Pseudotropheus: significance of allopatric colour variation.}, journal = {Proceedings. Biological sciences}, volume = {269}, number = {1509}, pages = {2495-2502}, pmid = {12573062}, issn = {0962-8452}, mesh = {Alleles ; Animals ; Cichlids/*classification/genetics/*physiology ; Color ; Evolution, Molecular ; *Fresh Water ; *Genetic Variation ; Genetics, Population ; Malawi ; Male ; Microsatellite Repeats/*genetics ; Phenotype ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {One of the most compelling features of the cichlid fishes of the African Great Lakes is the seemingly endless diversity of male coloration. Colour diversification has been implicated as an important factor driving cichlid speciation. Colour has also been central to cichlid taxonomy and, thus, to our concept of species diversity. We undertook a phylogeographical examination of several allopatric populations of the Lake Malawi cichlid Pseudotropheus zebra in order to reconstruct the evolutionary history of the populations, which exhibit one of two dorsal fin colours. We present evidence that populations with red dorsal fins (RT) are not monophyletic. The RT population defining the northern limit of the distribution has evidently originated independently of the southern RT populations, which share a common ancestry. This evidence of species-level colour convergence is an important discovery in our understanding of cichlid evolution. It implies that divergence in coloration may accompany speciation, and that allopatric populations with similar coloration cannot be assumed to be conspecific. In addition to this finding, we have observed evidence for introgression, contributing to current evidence that this phenomenon may be extremely widespread. Thus, in species-level phylogenetic reconstructions, including our own, consideration must be given to the potential effects of introgression.}, } @article {pmid12555775, year = {2002}, author = {Ortíz-Barrientos, D and Reiland, J and Hey, J and Noor, MA}, title = {Recombination and the divergence of hybridizing species.}, journal = {Genetica}, volume = {116}, number = {2-3}, pages = {167-178}, pmid = {12555775}, issn = {0016-6707}, support = {58060//PHS HHS/United States ; }, mesh = {*Biological Evolution ; Epistasis, Genetic ; Genetic Linkage ; *Hybridization, Genetic ; Phylogeny ; *Recombination, Genetic ; }, abstract = {The interplay between hybridization and recombination can have a dramatic effect on the likelihood of speciation or persistence of incompletely isolated species. Many models have suggested recombination can oppose speciation, and several recent empirical investigations suggest that reductions in recombination between various components of reproductive isolation and/or adaptation can allow species to persist in the presence of gene flow. In this article, we discuss these ideas in relation to speciation models, phylogenetic analyses, and species concepts. In particular, we revisit genetic architectures and population mechanisms that create genetic correlations and facilitate divergence in the face of gene flow. Linkage among genes contributing to adaptation or reproductive isolation due to chromosomal rearrangements as well as pleiotropy or proximity of loci can greatly increase the odds of species divergence or persistence. Finally, we recommend recombination to be a focus of inquiry when studying the origins of biological diversity.}, } @article {pmid12548332, year = {2003}, author = {Ambrose, L}, title = {Three acoustic forms of Allen's galagos (primates; Galagonidae) in the Central African region.}, journal = {Primates; journal of primatology}, volume = {44}, number = {1}, pages = {25-39}, doi = {10.1007/s10329-002-0004-x}, pmid = {12548332}, issn = {0032-8332}, mesh = {Africa, Central ; Animals ; Environment ; Galago/*classification/*physiology ; Geography ; Social Behavior ; Species Specificity ; *Vocalization, Animal ; }, abstract = {This study identifies populations currently classified as Allen's galago (Galago alleni) at ten locations in Gabon, Cameroon and Bioko Island. Morphological diversity was evident both within and between populations. Attention to the loud calls revealed three distinct vocal profiles which are consistent within biogeographical regions. This work is based on the Recognition Concept of Species which refers to a Specific Mate Recognition System. Galagos rely less on visual signals than diurnal primates and recognise each other principally by means of auditory and olfactory signals. Galagos possess repertoires of loud calls relating to contact and alarm which are thought to be species-specific. Other studies of nocturnal prosimians (galagos, tarsiers) have demonstrated that the unique loud call repertoires are reliable indicators of species boundaries; whereas characters such as body size and pelage coloration are highly variable, even within populations. The vocal data in this study provide evidence of at least three acoustic forms of galago within the Allen's group which are predicted to represent three distinct species: the Allen's form on Bioko Island and south-west Cameroon, the Gabon form in southern Cameroon and northern Gabon and the Makandé form in Gabon south of the Ogooué river. Some populations may be vulnerable to extinction due to limited distributions and habitat destruction.}, } @article {pmid12539825, year = {2002}, author = {Folgarait, PJ and Bruzzone, OA and Patrock, RJ and Gilbert, LE}, title = {Developmental rates and host specificity for Pseudacteon parasitoids (Diptera: Phoridae) of fire ants (Hymenoptera: Formicidae) in Argentina.}, journal = {Journal of economic entomology}, volume = {95}, number = {6}, pages = {1151-1158}, doi = {10.1603/0022-0493-95.6.1151}, pmid = {12539825}, issn = {0022-0493}, mesh = {Animals ; Ants/*parasitology ; Argentina ; Diptera/*growth & development ; *Pest Control, Biological ; Species Specificity ; }, abstract = {This study extends our comparative knowledge of Pseudacteon interactions with Solenopsis fire ant workers. Reported in this work are development times for seven Argentinean parasitoid species reared on two hosts, Solenopsis richteri Forel and Solenopsis invicta Buren, under laboratory temperature regimes comparable with those of the climatic zones occupied by these host species. Developmental times spanned 31-66 d across phorid species, and in general did not differ between genders or host species, but were longer at lower temperatures. The size distribution of flies reared was bimodal, with a group of large (Pseudacteon borgmeieri, Pseudacteon nocens, Pseudacteon obtusus and Pseudacteon tricuspis) and small (Pseudacteon cultellatus, Pseudacteon curvatus, and Pseudacteon nudicornis) species. P. borgmeieri was exceptional with respect to length of developmental time. Also reported are results of initial oviposition and developmental studies of some of these phorid species on other Argentinean Solenopsis ant species; P. curvatus was the only species able to complete its development on nonhost fire ants. These results support the concept of incorporating several complementary species of Pseudacteon in the biological control of pest fire ants.}, } @article {pmid12533720, year = {2003}, author = {Zhou, X and Xie, Y and Tao, X and Zhang, Z and Li, Z and Fauquet, CM}, title = {Characterization of DNAbeta associated with begomoviruses in China and evidence for co-evolution with their cognate viral DNA-A.}, journal = {The Journal of general virology}, volume = {84}, number = {Pt 1}, pages = {237-247}, doi = {10.1099/vir.0.18608-0}, pmid = {12533720}, issn = {0022-1317}, mesh = {Base Sequence ; China ; DNA, Viral/analysis/*genetics ; Evolution, Molecular ; Geminiviridae/classification/*genetics/*pathogenicity ; Lycopersicon esculentum/virology ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/virology ; *Recombination, Genetic ; Sequence Analysis, DNA ; Tobacco/virology ; }, abstract = {Eighteen samples of begomoviruses isolated from tobacco, tomato and weed species in Yunnan, China were found to be associated with DNAbeta molecules, for which the complete nucleotide sequences were found to contain 1333-1355 nt. The 18 DNAbeta molecules identified consist of three main types, each associated with a different begomovirus species: 72-99 % nucleotide identity was found within one type, but only 39-57 % identity was found between types. All the DNAbeta molecules reported here and elsewhere contain a 115 nt conserved region that has 93-100 % identity with a consensus sequence, and have a common ORF encoding 118 amino acids on the complementary strand (designated C1). Co-agroinoculation of the DNA-A component of Tomato yellow leaf curl China virus tobacco isolate Y10, with its associated DNAbeta (Y10beta), shows this DNAbeta to be involved in symptom induction in tobacco and tomato. The in-frame ATG mutation of C1 of Y10beta caused much milder symptoms as compared with wild Y10beta, indicating a functional role for this ORF. Pairwise nucleotide sequence identity comparisons of DNAbeta molecules and their cognate viral DNA-A molecules indicate that DNAbeta molecules have co-evolved with their cognate helper viruses. Recombination between DNAbeta molecules is documented and a DNAbeta species concept is proposed and discussed.}, } @article {pmid12519911, year = {2003}, author = {Germond, JE and Lapierre, L and Delley, M and Mollet, B and Felis, GE and Dellaglio, F}, title = {Evolution of the bacterial species Lactobacillus delbrueckii: a partial genomic study with reflections on prokaryotic species concept.}, journal = {Molecular biology and evolution}, volume = {20}, number = {1}, pages = {93-104}, doi = {10.1093/molbev/msg012}, pmid = {12519911}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; *Biological Evolution ; Galactose/metabolism ; *Genome, Bacterial ; Lactobacillus/classification/*genetics/physiology ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Sequence Analysis, DNA ; }, abstract = {The species Lactobacillus delbrueckii consists at present of three subspecies, delbrueckii, lactis and bulgaricus, showing a high level of DNA-DNA hybridization similarity but presenting markedly different traits related to distinct ecological adaptation. The internal genetic heterogeneity of the bacterial species L. delbrueckii was analyzed. Phenotypic and several genetic traits were investigated for 61 strains belonging to this species. These included 16S rDNA sequence mutations, expression of beta-galactosidase and of the cell wall-anchored protease, the characterization of the lactose operon locus and of the sequence of lacR gene, galactose metabolism, and the distribution of insertion sequences. The high genetic heterogeneity of taxa was confirmed by every trait investigated: the lac operon was completely deleted in the subsp. delbrueckii, different mutation events in the repressor gene of the operon led to a constitutive expression of lacZ in the subsp. bulgaricus. Structural differences in the same genetic locus were probably due to the presence of different IS elements in the flanking regions. The different expression of the cell wall-anchored protease, constitutive in the subsp. bulgaricus, inducible in the subsp. lactis, and absent in the subsp. delbrueckii was also a consequence of mutations at the gene level. The galT gene for galactose metabolism was found only in the subsp. lactis, while no specific amplification product was detected in the other two subspecies. All these data, together with the absence of a specific IS element, ISL6, from the major number of strains belonging to the subsp. bulgaricus, confirmed a deep internal heterogeneity among the three subspecies. Moreover, this evidence and the directional mutations found in the 16S rDNA sequences suggested that, of the three subspecies, L. delbrueckii subsp. lactis is the taxon closer to the ancestor. Limitations of the current prokaryotic species definition were also discussed, based on presented evidences. Our results indicate the need for an accurate investigation of internal heterogeneity of bacterial species. This study has consequences on the prokaryotic species concept, since genomic flexibility of prokaryotes collides with a stable classification, necessary from a scientific and applied point of view.}, } @article {pmid21156589, year = {2003}, author = {Challen, MP and Kerrigan, RW and Callac, P}, title = {A phylogenetic reconstruction and emendation of Agaricus section Duploannulatae.}, journal = {Mycologia}, volume = {95}, number = {1}, pages = {61-73}, doi = {10.1080/15572536.2004.11833132}, pmid = {21156589}, issn = {0027-5514}, abstract = {Agaricus section Duploannulatae comprises the group of species allied with A. bisporus and A. bitorquis. Disagreement exists in the literature regarding the composition of this group. We used DNA sequence data from the ITS segments of the nuclear ribosomal DNA region, in a sample of European and North American isolates, to identify characters shared by this group, to further delimit species-level taxa within the section, and to develop a phylogenetic hypothesis. Shared polymorphisms that suggest a natural limit for section Duploannulatae were found. ITS1 data were assessed using parsimony, distance and maximum likelihood methods of phylogeny. The section Duploannulatae comprised six robust clades. Five clades corresponded to well characterized species from the temperate Northern Hemisphere (A. bisporus, A. subfloccosus, A. bitorquis, A. vaporarius, A. cupressicola). The sixth clade encompassed an A. devoniensis complex. Species concepts, nomenclature, and relationships are discussed and compared with prior reports.}, } @article {pmid12501391, year = {1999}, author = {Tamura, M and Hamamoto, M and Canete-Gibas, CF and Sugiyama, J and Nakase, T}, title = {Genetic relatedness among species in Aspergillus section Clavati as measured by electrophoretic comparison of enzymes, DNA base composition, and DNA-DNA hybridization.}, journal = {The Journal of general and applied microbiology}, volume = {45}, number = {2}, pages = {77-83}, doi = {10.2323/jgam.45.77}, pmid = {12501391}, issn = {1349-8037}, abstract = {Aspergillus subgenus Clavati has four recognized species: A. clavatus (the type species), A. clavatonanicus, A. giganteus, and A. longivesica. These species are strictly anamorphic (mitotic) and defined by the morphological species concept. However, their genealogical relationships remain uncertain. In this study, we examined the genetic relatedness among the four species in this section, using electrophoretic comparison of enzymes, DNA base composition, and DNA-DNA hybridization. In a dendrogram based on the calculated similarity values of four enzymes, 10 strains in section Clavati, 3 strains in the xerophilic species, a strain in section Ornati, and a strain in section Cremei were separated into nine major clusters at a 60% similarity level. A. longivesica JCM 10186(T) had Q-10 in our analysis, but Kuraishi et al. (1990) reported A. longivesica JCM 1720(T) had Q-9 (49%) and Q-10 (46%). The G+C contents of the four species of section Clavati ranged from 48 to 50 mol%. The degree of the intraspecific reassociation among the DNAs from the strains of these species ranged from 77 to 99%, whereas the degrees of interspecific relative binding among strains of the four species ranged from 30 to 59%. Our data from enzyme patterns and DNA relatedness support the validity of the three species in section Clavati, except for A. longivesica.}, } @article {pmid12425634, year = {2002}, author = {Kuznetsov, AE and Zhai, HJ and Wang, LS and Boldyrev, AI}, title = {Peculiar antiaromatic inorganic molecules of tetrapnictogen in Na+Pn4- (Pn = P, As, Sb) and important consequences for hydrocarbons.}, journal = {Inorganic chemistry}, volume = {41}, number = {23}, pages = {6062-6070}, doi = {10.1021/ic020426+}, pmid = {12425634}, issn = {0020-1669}, abstract = {Although aromaticity has been observed in inorganic and all-metal species, the concept of antiaromaticity has not been extended beyond organic molecules. Here, we present theoretical and experimental evidence that the 6 -electron tetrapnictogen dianions in Na+Pn42- (Pn = P, As, Sb) undergo a transition from being aromatic to antiaromatic upon electron detachment, yielding the first inorganic antiaromatic Na+Pn4- molecules. Two types of antiaromatic structures were characterized, the conventional rectangular species and a new peculiar quasiplanar rhombus species. Aromaticity and antiaromaticity in the tetrapnictogen molecules were derived from molecular orbital analyses and verified by experimental photodetachment spectra of Na+Pn42-. On the basis of our findings for the tetrapnictogen clusters, we predicted computationally that the organic C4H4- anion also possesses two antiaromatic structures: rectangular and rhombus. Moreover, only the rhombus antiaromatic minimum was found for the radical NC3H4, thus extending the peculiar rhombus antiaromatic structure first uncovered in inorganic clusters into organic chemistry.}, } @article {pmid12414145, year = {2002}, author = {Moreno, E and Cloeckaert, A and Moriyón, I}, title = {Brucella evolution and taxonomy.}, journal = {Veterinary microbiology}, volume = {90}, number = {1-4}, pages = {209-227}, doi = {10.1016/s0378-1135(02)00210-9}, pmid = {12414145}, issn = {0378-1135}, mesh = {*Biological Evolution ; Brucella/*classification/*genetics ; Brucella melitensis/classification/genetics ; Classification ; DNA, Bacterial/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {The genus Brucella contains alpha-Proteobacteria adapted to intracellular life within cells of a variety of mammals. Controversy has arisen concerning Brucella internal taxonomy, and it has been proposed that the DNA-DNA hybridization-based genomospecies concept be applied to the genus. According to this view, only one species, Brucella melitensis, should be recognized, and the classical species should be considered as biovars (B. melitensis biovar melitensis; B. melitensis biovar abortus; etc.). However, a critical reappraisal of the species concept, a review of the population structure of bacteria and the analysis of Brucella genetic diversity by methods other than DNA-DNA hybridization show that there are no scientific grounds to apply the genomospecies concept to this genus. On the other hand, an enlarged biological species concept allows the definition of Brucella species that are consistent with molecular analyses and support the taxonomical standing of most classical species. Both the host range as a long-recognized biological criterion and the presence of species-specific markers in outer membrane protein genes and in other genes show that B. melitensis, B. abortus, B. ovis, B. canis and B. neotomae are not mere pathovars (or nomenspecies) but biologically meaningful species. The status of B. suis is, however, less clear. These approaches should be useful to define species for the marine mammal Brucella isolates, as illustrated by the grouping of the isolates from pinnipeds or from cetaceans by omp2 gene analysis. It is shown that a correct Brucella species definition is important to understand the evolution of the genus.}, } @article {pmid21156574, year = {2002}, author = {Steenkamp, ET and Wingfield, BD and Desjardins, AE and Marasas, WF and Wingfield, MJ}, title = {Cryptic speciation in Fusarium subglutinans.}, journal = {Mycologia}, volume = {94}, number = {6}, pages = {1032-1043}, pmid = {21156574}, issn = {0027-5514}, abstract = {Fusarium isolates that form part of the Gibberella fujikuroi species complex have been classified using either a morphological, biological, or phylogenetic species concept. Problems with the taxonomy of Fusarium species in this complex are mostly experienced when the morphological and biological species concepts are applied. The most consistent identifications are obtained with the phylogenetic species concept. Results from recent studies have presented an example of discordance between the biological and phylogenetic species concepts, where a group of F. subglutinans sensu stricto isolates, i.e., isolates belonging to mating population E of the G. fujikuroi complex, could be sub-divided into more than one phylogenetic lineage. The aim of this study was to determine whether this sub-division represented species divergence or intraspecific diversity in F. subglutinans. For this purpose, we included 29 F. subglutinans isolates belonging to the E-mating population that were collected from either maize or teosinte, from a wide geographic range. DNA sequence data for six nuclear regions in each of these isolates were obtained and used in phylogenetic concordance analyses. These analyses revealed the presence of two major groups representing cryptic species in F. subglutinans. These cryptic species were further sub-divided into a number of smaller groups that appear to be reproductively isolated in nature. This suggests not only that the existing F. subglutinans populations are in the process of divergence, but also that each of the resulting lineages are undergoing separation into distinct taxa. These divergences did not appear to be linked to geographic origin, host, or phenotypic characters such as morphology.}, } @article {pmid21156569, year = {2002}, author = {Adams, GC and Surve-Iyer, RS and Iezzoni, AF}, title = {Ribosomal DNA sequence divergence and group I introns within the Leucostoma species L. cinctum, L. persoonii, and L. parapersoonii sp. nov., ascomycetes that cause Cytospora canker of fruit trees.}, journal = {Mycologia}, volume = {94}, number = {6}, pages = {947-967}, pmid = {21156569}, issn = {0027-5514}, abstract = {Leucostoma species that are the causal agents of Cytospora canker of stone and pome fruit trees were studied in detail. DNA sequence of the internal transcribed spacer regions and the 5.8S of the nuclear ribosomal DNA operon (ITS rDNA) supplied sufficient characters to assess the phylogenetic relationships among species of Leucostoma, Valsa, Valsella, and related anamorphs in Cytospora. Parsimony analysis of the aligned sequence divided Cytospora isolates from fruit trees into clades that generally agreed with the morphological species concepts, and with some of the phenetic groupings (PG 1-6) identified previously by isozyme analysis and cultural characteristics. Phylogenetic analysis inferred that isolates of L. persoonii formed two well-resolved clades distinct from isolates of L. cinctum. Phylogenetic analysis of the ITS rDNA, isozyme analysis, and cultural characteristics supported the inference that L. persoonii groups PG 2 and PG 3 were populations of a new species apparently more genetically different from L. persoonii PG 1 than from isolates representative of L. massariana, L. niveum, L. translucens, and Valsella melastoma. The new species, L. parapersoonii, was described. A diverse collection of isolates of L. cinctum, L. persoonii, and L. parapersoonii were examined for genetic variation using restriction fragment length polymorphism (RFLP) analysis of the ITS rDNA and the five prime end of the large subunit of the rDNA (LSU rDNA). HinfI and HpaII endonucleases were each useful in dividing the Leucostoma isolates into RFLP profiles corresponding to the isozyme phenetic groups, PG 1-6. RFLP analysis was more effective than isozyme analysis in uncovering variation among isolates of L. persoonii PG 1, but less effective within L. cinctum populations. Isolates representative of seven of the L. persoonii formae speciales proposed by G. Défago in 1935 were found to be genetically diverse isolates of PG 1. Two large insertions, 415 and 309 nucleotides long, in the small subunit (SSU) of the nuclear rDNA of L. cinctum were identified as Group 1 introns; intron 1 at position 943 and intron 2 at position 1199. The two introns were found to be consistently present in isolates of L. cinctum PG 4 and PG 5 and absent from L. cinctum PG 6 isolates, despite the similarity of the ITS sequence and teleomorph morphology. Intron 1 was of subgroup 1C1 whereas intron 2 was of an unknown subgroup. RFLP patterns and presence/absence of introns were useful characters for expediting the identification of cultures of Leucostoma isolated from stone and pome fruit cankers. RFLP patterns from 13 endonucleases provided an effective method for selecting an array of diverse PG 1 isolates useful in screening plant germplasm for disease-resistance.}, } @article {pmid12402523, year = {2001}, author = {Morgan-Ryan, UM and Monis, P and Possenti, A and Crisanti, A and Spano, F}, title = {Cloning and phylogenetic analysis of the ribosomal internal transcribed spacer-1 (ITS1) of Cryptosporidium wrairi and its relationship to C. parvum genotypes.}, journal = {Parassitologia}, volume = {43}, number = {4}, pages = {159-163}, pmid = {12402523}, issn = {0048-2951}, mesh = {Animals ; Base Sequence ; Cattle ; Cloning, Molecular ; Cryptosporidiosis/parasitology/veterinary ; Cryptosporidium/classification/*genetics ; Cryptosporidium parvum/genetics ; DNA, Protozoan/*genetics ; DNA, Ribosomal Spacer/*genetics ; Disease Outbreaks ; Genotype ; Guinea Pigs ; Humans ; Likelihood Functions ; Mice ; Molecular Sequence Data ; Phylogeny ; Rodent Diseases/parasitology ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; Transcription, Genetic ; }, abstract = {We have cloned and sequenced the ribosomal internal transcribed spacer-1 (ITS1) of Cryptosporidium wrairi. Phylogenetic analysis of this region provided further support to the validity of C. wrairi as a distinct species and also to the concept that many of the genotypes recently identified within C. parvum are in fact separate species. Analysis placed the "cattle" and "mouse" genotypes of C. parvum as each other's closest relatives and C. wrairi as a sister group to these two genotypes, followed by the "human" genotype.}, } @article {pmid12383748, year = {2002}, author = {Soto-Adames, FN}, title = {Molecular phylogeny of the Puerto Rican Lepidocyrtus and Pseudosinella (Hexapoda: Collembola), a validation of Yoshii's "color pattern species".}, journal = {Molecular phylogenetics and evolution}, volume = {25}, number = {1}, pages = {27-42}, doi = {10.1016/s1055-7903(02)00250-6}, pmid = {12383748}, issn = {1055-7903}, mesh = {Animals ; Codon/genetics ; DNA/chemistry/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Geography ; Haplotypes ; Insecta/anatomy & histology/classification/*genetics ; Molecular Sequence Data ; *Phylogeny ; Puerto Rico ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {Color pattern was one of the most important characters used to diagnose species in the genus Lepidocyrtus until the introduction of chaetotaxy to Collembola taxonomy. Chaetotaxy confirmed most species diagnoses based only on color patterns, but a number of populations with distinct pigmentation patterns have been found to be identical in all other morphological characters. The absence of individuals showing intermediate color patterns prompted Yoshii to suggest that, despite chaetotaxic identity, populations with distinct color forms represent valid species (implying reproductive isolation and therefore biological species) in what he designated as "color pattern species." In Puerto Rico Lepidocyrtus biphasis, L. dispar, and L. caprilesi show a remarkable variation in pigmentation and as a group include 11 different color forms. Here I present a phylogenetic analysis of the cytochrome oxidase I gene (COI) in 17 species of Lepidocyrtus and Pseudosinella, including 11 species and 10 color forms of Puerto Rican Lepidocyrtus, to test Yoshii's color pattern species concept. The analysis shows large genetic distances between species defined based on morphology alone (morphospecies) and between most color variants within morphospecies. The most often used calibration for the COI molecular clock (2.3% sequence divergence per million years) suggests that morphospecies diverged between 20 and 25 million years before present while color forms within morphospecies diverged between 8 and 19 million years ago. This indicates that changes in climate and sea levels during the Pleistocene were irrelevant to the speciation process in the Puerto Rican Lepidocyrtus. Examination of the genetic variation, phylogenetic relationships, and collection data in light of the biological and phylogenetic species concepts supports the hypothesis that most populations of morphospecies differing only in color pattern are distinct species, thus validating Yoshii's color pattern species concept. As a result it is suggested that morphological characters traditionally used in species diagnoses are very conservative indicators of genetic divergence, that the diversity of springtails has been greatly underestimated, and that studies concerned with identifying factors promoting speciation in Collembola could be misled if they do not include analysis of mitochondrial markers.}, } @article {pmid12377592, year = {2002}, author = {Paul, R}, title = {Species concepts versus species criteria.}, journal = {Trends in parasitology}, volume = {18}, number = {10}, pages = {439-40; author reply 440}, doi = {10.1016/s1471-4922(02)02319-x}, pmid = {12377592}, issn = {1471-4922}, mesh = {Animals ; Biological Evolution ; *Classification ; Parasites/classification ; *Phylogeny ; }, } @article {pmid12353748, year = {2002}, author = {Hudson, RR and Coyne, JA}, title = {Mathematical consequences of the genealogical species concept.}, journal = {Evolution; international journal of organic evolution}, volume = {56}, number = {8}, pages = {1557-1565}, doi = {10.1111/j.0014-3820.2002.tb01467.x}, pmid = {12353748}, issn = {0014-3820}, support = {GM58260/GM/NIGMS NIH HHS/United States ; HG02107/HG/NHGRI NIH HHS/United States ; }, mesh = {Alleles ; Biological Evolution ; *Genetics, Population ; Mathematics ; *Models, Biological ; *Phylogeny ; Species Specificity ; }, abstract = {A genealogical species is defined as a basal group of organisms whose members are all more closely related to each other than they are to any organisms outside the group ("exclusivity"), and which contains no exclusive group within it. In practice, a pair of species is so defined when phylogenies of alleles from a sample of loci shows them to be reciprocally monophyletic at all or some specified fraction of the loci. We investigate the length of time it takes to attain this status when an ancestral population divides into two descendant populations of equal size with no gene exchange, and when genetic drift and mutation are the only evolutionary forces operating. The number of loci used has a substantial effect on the probability of observing reciprocal monophyly at different times after population separation, with very long times needed to observe complete reciprocal monophyly for a large number of loci. In contrast, the number of alleles sampled per locus has a relatively small effect on the probability of reciprocal monophyly. Because a single mitochondrial or chloroplast locus becomes reciprocally monophyletic much faster than does a single nuclear locus, it is not advisable to use mitochondrial and chloroplast DNA to recognize genealogical species for long periods after population divergence. Using a weaker criterion of assigning genealogical species status when more than 50% of sampled nuclear loci show reciprocal monophyly, genealogical species status depends much less on the number of sampled loci, and is attained at roughly 4-7 N generations after populations are isolated, where N is the historically effective population size of each descendant. If genealogical species status is defined as more than 95% of sampled nuclear loci showing reciprocal monophyly, this status is attained after roughly 9-12 N generations.}, } @article {pmid12349851, year = {2002}, author = {Silva, MB and Barbosa, HS and Jurberg, J and Galvão, C and Carcavallo, RU}, title = {Comparative ultrastructural analysis of the antennae of Triatoma guazu and Triatoma jurbergi (Hemiptera: Reduviidae) during the nymphal stage development.}, journal = {Journal of medical entomology}, volume = {39}, number = {5}, pages = {705-715}, doi = {10.1603/0022-2585-39.5.705}, pmid = {12349851}, issn = {0022-2585}, mesh = {Animals ; Nymph/ultrastructure ; Triatoma/*ultrastructure ; }, abstract = {The specific concept of two triatominae species of epidemiological importance in the Mato Grosso Region (Brasil), Triatoma guazu Lent & Wygodzinsky, 1979 and Triatoma jurbergi Carcavallo, Galvão & Lent, 1998, the antenniferous tubercle and the four antennal segments of nymphs from the first to fifth instar were morphologically compared by scanning electron microscopy. The main differences observed were that the antenniferous tubercle in T. guazu did not present a smaller tubercle in the base of the larger tubercle. The first antennal segment in the fifth instar had sensilla distributed with an alternating array and the trichobothria in the first instar had half of its length reaching the third antennal segment. However, in T. jurbergi the antenniferous tubercle had two smaller tubercles in the base of the two larger tubercles. The first antennal segment in the fifth instar presents sensilla distributed in pairs, and the trichobothria in the first instar has only a small portion of the structure reaching the third antennal segment. These structures differentiated the nymphs of T. guazu and T. jurbergi.}, } @article {pmid12227994, year = {2002}, author = {Li, JP and Balazs, ME and Parks, GT and Clarkson, PJ}, title = {A species conserving genetic algorithm for multimodal function optimization.}, journal = {Evolutionary computation}, volume = {10}, number = {3}, pages = {207-234}, doi = {10.1162/106365602760234081}, pmid = {12227994}, issn = {1063-6560}, mesh = {*Algorithms ; Genetics, Population ; *Models, Genetic ; Population Density ; }, abstract = {This paper introduces a new technique called species conservation for evolving parallel subpopulations. The technique is based on the concept of dividing the population into several species according to their similarity. Each of these species is built around a dominating individual called the species seed. Species seeds found in the current generation are saved (conserved) by moving them into the next generation. Our technique has proved to be very effective in finding multiple solutions of multimodal optimization problems. We demonstrate this by applying it to a set of test problems, including some problems known to be deceptive to genetic algorithms.}, } @article {pmid12175808, year = {2002}, author = {Wolf, YI and Rogozin, IB and Grishin, NV and Koonin, EV}, title = {Genome trees and the tree of life.}, journal = {Trends in genetics : TIG}, volume = {18}, number = {9}, pages = {472-479}, doi = {10.1016/s0168-9525(02)02744-0}, pmid = {12175808}, issn = {0168-9525}, mesh = {Animals ; Computational Biology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation/genetics ; *Genome ; Humans ; Models, Genetic ; Phylogeny ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Genome comparisons indicate that horizontal gene transfer and differential gene loss are major evolutionary phenomena that, at least in prokaryotes, involve a large fraction, if not the majority, of genes. The extent of these events casts doubt on the feasibility of constructing a 'Tree of Life', because the trees for different genes often tell different stories. However, alternative approaches to tree construction that attempt to determine tree topology on the basis of comparisons of complete gene sets seem to reveal a phylogenetic signal that supports the three-domain evolutionary scenario and suggests the possibility of delineation of previously undetected major clades of prokaryotes. If the validity of these whole-genome approaches to tree building is confirmed by analyses of numerous new genomes, which are currently being sequenced at an increasing rate, it would seem that the concept of a universal 'species' tree is still appropriate. However, this tree should be reinterpreted as a prevailing trend in the evolution of genome-scale gene sets rather than as a complete picture of evolution.}, } @article {pmid12169615, year = {2002}, author = {Lawrence, JG and Hatfull, GF and Hendrix, RW}, title = {Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches.}, journal = {Journal of bacteriology}, volume = {184}, number = {17}, pages = {4891-4905}, pmid = {12169615}, issn = {0021-9193}, support = {R01 GM051975/GM/NIGMS NIH HHS/United States ; GM 47795/GM/NIGMS NIH HHS/United States ; R01 AI028927/AI/NIAID NIH HHS/United States ; GM 51975/GM/NIGMS NIH HHS/United States ; AI 28927/AI/NIAID NIH HHS/United States ; R01 GM047795/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteriophages/*classification/genetics ; Biological Evolution ; Gene Transfer, Horizontal ; Mosaicism ; Recombination, Genetic ; }, abstract = {The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.}, } @article {pmid12144664, year = {2002}, author = {Wilke, T and Pfenninger, M}, title = {Separating historic events from recurrent processes in cryptic species: phylogeography of mud snails (Hydrobia spp.).}, journal = {Molecular ecology}, volume = {11}, number = {8}, pages = {1439-1451}, doi = {10.1046/j.1365-294x.2002.01541.x}, pmid = {12144664}, issn = {0962-1083}, mesh = {Animals ; Biological Evolution ; Data Interpretation, Statistical ; Ecosystem ; Environment ; *Genetic Variation ; Likelihood Functions ; Molecular Sequence Data ; Phylogeny ; Snails/classification/*genetics ; }, abstract = {The present study combines methods that were designed to infer intraspecific relationships (e.g. nested-clade analysis (NCA), mismatch distributions and maximum likelihood gene flow analysis) to analyse historic events and recurrent processes in the cryptic mud snail species Hydrobia acuta and H. glyca. Specifically, we test the proposed allopatry of cryptic species and whether the peculiar range-subdivision of the putative subspecies H. a. acuta and H. a. neglecta is a result of long-distance dispersal or continuous range expansion. The NCA indicates a past fragmentation of the two H. acuta subspecies as well as past fragmentations within H. glyca. Gene-flow analyses show extensive gene flow in an E-W direction (towards the Atlantic) in the Mediterranean H. a. acuta, generally low gene flow in a W-E direction in the Atlantic H. a. neglecta and complex gene-flow pattern in a N-S but also in a S-N direction (against the Gulf Stream) in H. glyca. Based on these data and supportive ecological and oceanographical data, we hypothesize that the separation of the two H. acuta subspecies was not caused by long-distance dispersal but by a range shift and/or range expansion of the closely related competitor H. glyca as a result of an interglacial warming with a subsequent range shift in H. acuta. Moreover, our data do not show evidence for a long-term, stable sympatry of Hydrobia species, supporting the concept of allopatric relationships within cryptic radiations. NCA and gene-flow analyses indicate that the only sympatric population found in our study is the result of a recent dispersal event from the nearby Mediterranean. It is assumed that allopatric relationships in ephemeral Hydrobia populations constitute an evolutionary advantage relative to competition, recruitment and re-establishment of habitats. Mechanisms that could be of relevance for maintaining allopatry are discussed.}, } @article {pmid12144656, year = {2002}, author = {Márquez, LM and Van Oppen, MJ and Willis, BL and Reyes, A and Miller, DJ}, title = {The highly cross-fertile coral species, Acropora hyacinthus and Acropora cytherea, constitute statistically distinguishable lineages.}, journal = {Molecular ecology}, volume = {11}, number = {8}, pages = {1339-1349}, doi = {10.1046/j.1365-294x.2002.01526.x}, pmid = {12144656}, issn = {0962-1083}, mesh = {Animals ; Anthozoa/classification/*genetics/physiology ; DNA/analysis/genetics ; DNA, Mitochondrial/analysis ; *Genetic Variation ; Haplotypes ; Introns/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {A major challenge for understanding the evolutionary genetics of mass-spawning corals is to explain the maintenance of discrete morphospecies in view of high rates of interspecific fertilization in vitro and nonmonophyletic patterns in molecular phylogenies. In this study, we focused on Acropora cytherea and A. hyacinthus, which have one of the highest potentials for interspecific fertilization. Using sequences of a nuclear intron, we performed phylogenetic and nested clade analyses (NCA). Both species were polyphyletic in molecular phylogenies, but the NCA indicated that they constitute statistically distinguishable lineages. Phylogenetic analysis using an intergenic region of the mitochondrial DNA (mtDNA), was inconclusive because of low levels of variability in this marker. The position of these two species differed between the nuclear DNA (nDNA) and mtDNA phylogenies and was also at odds with a cladistic analysis based on morphology. We conclude that despite the potential for high levels of hybridization and introgression, A. cytherea and A. hyacinthus constitute statistically distinguishable lineages and their taxonomic status is consistent with the cohesion species concept.}, } @article {pmid12142474, year = {2002}, author = {Cohan, FM}, title = {What are bacterial species?.}, journal = {Annual review of microbiology}, volume = {56}, number = {}, pages = {457-487}, doi = {10.1146/annurev.micro.56.012302.160634}, pmid = {12142474}, issn = {0066-4227}, mesh = {Bacteria/*classification/*genetics ; Cluster Analysis ; Genetic Variation ; Multigene Family ; Phenotype ; Phylogeny ; Sequence Analysis/trends ; Species Specificity ; }, abstract = {Bacterial systematics has not yet reached a consensus for defining the fundamental unit of biological diversity, the species. The past half-century of bacterial systematics has been characterized by improvements in methods for demarcating species as phenotypic and genetic clusters, but species demarcation has not been guided by a theory-based concept of species. Eukaryote systematists have developed a universal concept of species: A species is a group of organisms whose divergence is capped by a force of cohesion; divergence between different species is irreversible; and different species are ecologically distinct. In the case of bacteria, these universal properties are held not by the named species of systematics but by ecotypes. These are populations of organisms occupying the same ecological niche, whose divergence is purged recurrently by natural selection. These ecotypes can be discovered by several universal sequence-based approaches. These molecular methods suggest that a typical named species contains many ecotypes, each with the universal attributes of species. A named bacterial species is thus more like a genus than a species.}, } @article {pmid12109272, year = {2002}, author = {Veracini, C and Galleni, L and Forti, M}, title = {The concept of species and the foundations of biology, a case study: the Callithrix jacchus group (Primates-Platyrrhini).}, journal = {Rivista di biologia}, volume = {95}, number = {1}, pages = {75-100}, pmid = {12109272}, issn = {0035-6050}, mesh = {Animals ; Biology ; Callithrix/*classification/genetics ; *Models, Theoretical ; }, abstract = {The axiomatic theory presented in Galleni and Forti [1999], being part of the foundational programme of Ennio De Giorgi, is based on the fundamental notions of quality, relation, operation and collection, and provides a very general axiomatization of the biological notions of living object, generation, species and speciation. Within this theoretical framework we consider here a difficult case of classification of species: the Callithrix jacchus group of the New World monkeys. Although the morphological analysis strongly suggests the individuation of six different species, nevertheless several experiments of crossing give evidence to fertility of hybrids. Since both the morphological and the hybridological criteria have shown to be of enormous importance in actual classification of species, this apparent contradiction seems very disappointing. Our axiomatization of speciation processes as operations acting in special time intervals permits to avoid the contradiction by allowing for individuals which, during such special periods, may belong to more than one species. Therefore we assume that one or more speciation processes are developing, starting from a unique protospecies and differentiating in six new ones. In order to obtain more evidence of these processes, new observations and suitable experiments are needed.}, } @article {pmid21156539, year = {2002}, author = {Câmara, MP and O'Neill, NR and van Berkum, P}, title = {Phylogeny of Stemphylium spp. based on ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences.}, journal = {Mycologia}, volume = {94}, number = {4}, pages = {660-672}, doi = {10.1080/15572536.2003.11833194}, pmid = {21156539}, issn = {0027-5514}, abstract = {The phylogenetic relationships among 44 isolates representing 16 species of Stemphylium were inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase (gpd) sequence data. The results generally agree with morphological species concepts. There was strong support for monophyly of the genus Stemphylium. Analysis of the gpd fragment in particular was useful for establishing well-supported relationships among the species and isolates of Stemphylium. Species of Stemphylium that appear to have lost the ability to produce a sexual state are scattered among the species with the ability to reproduce sexually (Pleospora spp.). Species that are pathogenic to alfalfa are resolved into two groups. Stemphylium botryosum and two isolates with morphological characters similar to S. globuliferum had identical sequences at both loci. These two loci in S. vesicarium, S. alfalfae and S. herbarum are nearly identical but differ from S. botryosum. The separation of S. vesicarium, S. herbarum and S. alfalfae into separate species by morphometric evidence was not supported by the molecular data. Morphological and developmental characters such as size and shape of conidia, conidiophores, and ascospores, and size and time of maturation of pseudothecia are useful for diagnosing species. However, other morphological characters such as septum development and small variations in conidial wall ornamentation are not as useful.}, } @article {pmid21156534, year = {2002}, author = {Grubisha, LC and Trappe, JM and Molina, R and Spatafora, JW}, title = {Biology of the ectomycorrhizal genus Rhizopogon. VI. Re-examination of infrageneric relationships inferred from phylogenetic analyses of ITS sequences.}, journal = {Mycologia}, volume = {94}, number = {4}, pages = {607-619}, doi = {10.1080/15572536.2003.11833189}, pmid = {21156534}, issn = {0027-5514}, abstract = {Rhizopogon (Basidiomycota, Boletales) is a genus of hypogeous fungi that form ectomycorrhizal associations mostly with members of the Pinaceae. This genus comprises an estimated 100(+) species, with the greatest diversity found in coniferous forests of the Pacific northwestern United States. Maximum parsimony analyses of 54 nuclear ribosomal DNA internal transcribed spacer (ITS) sequences including 27 Rhizopogon and 10 Suillus species were conducted to test sectional relationships in Rhizopogon and examine phylogenetic relationships with the closely related epigeous genus, Suillus. Sequences from 10 Rhizopogon type collections were included in these analyses. Rhizopogon and Suillus were both monophyletic. Rhizopogon section Rhizopogon is not monophyletic and comprised two clades, one of which consisted of two well supported lineages characterized by several long insertions. Rhizopogon sections Amylopogon and Villosuli formed well supported groups, but certain species concepts within these sections were unresolved. Four species from section Fulviglebae formed a strongly supported clade within section Villosuli. Subgeneric taxonomic revisions are presented.}, } @article {pmid12067592, year = {2002}, author = {Roy, AK and Oh, T and Rivera, O and Mubiru, J and Song, CS and Chatterjee, B}, title = {Impacts of transcriptional regulation on aging and senescence.}, journal = {Ageing research reviews}, volume = {1}, number = {3}, pages = {367-380}, doi = {10.1016/s1568-1637(02)00006-5}, pmid = {12067592}, issn = {1568-1637}, support = {R01DK-14744/DK/NIDDK NIH HHS/United States ; R37AG-10486/AG/NIA NIH HHS/United States ; T32AG-00165/AG/NIA NIH HHS/United States ; }, mesh = {Aging/genetics/*physiology ; Animals ; Cellular Senescence/*physiology ; Gene Expression Regulation/physiology ; Humans ; Transcription Factors/genetics/*physiology ; Transcription, Genetic/*physiology ; }, abstract = {The genetic makeup of the organism appears to dictate the species-specific rate of aging and the maximum life-span potential. The genotype is converted to phenotype through transcriptional and translational regulation. A group of gene regulatory proteins (transcription factors) play critical roles in controlling the rates of transcription of specific genes by directly interacting with regulatory sequences at gene promoters. Here, we review the basic mechanism of transcriptional control and the role of a number of transcription factors whose level and/or activity alter with age. Among these age-dependent transcription factors, many are involved in the regulation of stress and inflammatory responses and are subjected to functional alterations by reactive oxygen species (ROSs). A progressive rise of oxidative stress, impaired ability to cope with stressful stimuli and prolongation of the inflammatory response are some of the hallmarks of the senescent phenotype. Results published to date are supportive of the concept that a species-specific program of the temporal regulation of genes with additional modulation by a number of epigenetic factors, mediates the age-dependent deterioration of physiological functions and development of the senescent phenotype.}, } @article {pmid12058383, year = {2002}, author = {Cazzaniga, NJ}, title = {Old species and new concepts in the taxonomy of Pomacea (Gastropoda: Ampullariidae).}, journal = {Biocell : official journal of the Sociedades Latinoamericanas de Microscopia Electronica ... et. al}, volume = {26}, number = {1}, pages = {71-81}, pmid = {12058383}, issn = {0327-9545}, mesh = {Animals ; Snails/anatomy & histology/*classification ; Species Specificity ; Terminology as Topic ; }, abstract = {The taxonomic history of the South American genus Pomacea Perry, 1810, and some shifts of systematic concepts during recent decades are briefly reviewed. Too many pre-evolutionist, shell-defined species created a gibberish, the only acceptable solution of which being perhaps a conventional, somewhat authoritarian decision based on expertise. The addition of other sources of morphological, biochemical, ecological or genetic information should not solve the problem if it is not accompanied by a sound reappraisal of the species concepts. Since the assumptions of each concept differ, any correspondence between them is irrelevant, and may drive to incompatible results. The shell variability of Pomacea canaliculata was acknowledged for most authors throughout more than a century. A recent insight into its life-history traits demonstrated they are as variable as the morphology. These findings stress the need of determining the ecological identity of any pest apple-snail population at a local scale, because its invading ability may be not exactly correlated to its taxonomical identity. Probably, all the canaliculata-like apple snails constitute a single, very variable "species" in most senses, even though different subsets may be recognized under other incommensurable concepts.}, } @article {pmid12055858, year = {2002}, author = {Bañuls, AL and Hide, M and Tibayrenc, M}, title = {Evolutionary genetics and molecular diagnosis of Leishmania species.}, journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene}, volume = {96 Suppl 1}, number = {}, pages = {S9-13}, doi = {10.1016/s0035-9203(02)90045-3}, pmid = {12055858}, issn = {0035-9203}, mesh = {Animals ; *Biological Evolution ; Genetic Variation ; Leishmania/classification/*genetics ; Leishmaniasis/*diagnosis/parasitology ; Species Specificity ; }, abstract = {An extensive study has been performed on various natural populations of Leishmania from the 'Old' and 'New Worlds' using multilocus enzyme electrophoresis and random amplification of polymorphic deoxyribonucleic acid. The data are interpreted in evolutionary genetic terms in order to give a firm basis to studies dealing with the relevant medical properties of pathogens. We confirm that Leishmania undergoes clonal evolution with occasional phenomena of hybridization. This suggests that the microorganism genotypes are stable in space and time and consequently have epidemiological and medical relevance. It is crucial to have a clear definition of the taxa to be identified. In the case of Leishmania, there is at present no firm consensus on the species concept. We propose that any new species of Leishmania should correspond to a 'discrete typing unit' that exhibits specific medical and/or epidemiological characters. Based on this approach, the species status of L. peruviana can be supported. On the contrary, L. panamensis cannot be clearly distinguished from L. guyanensis. Our studies on the genetic diversity of Leishmania show that a given stock is not representative of the genus, the subgenera, or any species. We suggest that the genetic polymorphism of Leishmania has a strong impact on the parasite's biomedical properties.}, } @article {pmid12054245, year = {2002}, author = {Lanoot, B and Vancanneyt, M and Cleenwerck, I and Wang, L and Li, W and Liu, Z and Swings, J}, title = {The search for synonyms among streptomycetes by using SDS-PAGE of whole-cell proteins. Emendation of the species Streptomyces aurantiacus, Streptomyces cacaoi subsp. cacaoi, Streptomyces caeruleus and Streptomyces violaceus.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 3}, pages = {823-829}, doi = {10.1099/00207713-52-3-823}, pmid = {12054245}, issn = {1466-5026}, mesh = {Bacterial Proteins/*analysis ; Bacterial Typing Techniques ; Electrophoresis, Polyacrylamide Gel ; Nucleic Acid Hybridization ; Phenotype ; Species Specificity ; Streptomyces/*chemistry/*classification/genetics ; }, abstract = {A collection of 93 Streptomyces reference strains were investigated using SDS-PAGE of whole-cell proteins. Computer-assisted numerical analysis revealed 24 clusters encompassing strains with very similar protein profiles. Five of them grouped several type strains with visually identical patterns. DNA-DNA hybridizations revealed homology values higher than 70% among these type strains. According to the current species concept, it is proposed that Streptomyces albosporeus subsp. albosporeus LMG 19403T is considered as a subjective synonym of Streptomyces aurantiacus LMG 19358T, that Streptomyces aminophilus LMG 19319T is considered as a subjective synonym of Streptomyces cacaoi subsp. cacaoi LMG 19320T, that Streptomyces niveus LMG 19395T and Streptomyces spheroides LMG 19392T are considered as subjective synonyms of Streptomyces caeruleus LMG 19399T, and that Streptomyces violatus LMG 19397T is considered as a subjective synonym of Streptomyces violaceus LMG 19360T.}, } @article {pmid12054028, year = {2002}, author = {Santín-Durán, M and de la Fuente, C and Alunda, JM and Rosenthal, BM and Hoberg, EP}, title = {Identical ITS-1 and ITS-2 sequences suggest Spiculopteragia asymmetrica and Spiculopteragia quadrispiculata (Nematoda: Trichostrongylidae) constitute morphologically distinct variants of a single species.}, journal = {The Journal of parasitology}, volume = {88}, number = {2}, pages = {417-418}, doi = {10.1645/0022-3395(2002)088[0417:IIAISS]2.0.CO;2}, pmid = {12054028}, issn = {0022-3395}, mesh = {Animals ; Base Sequence ; DNA, Helminth/chemistry/*genetics ; DNA, Ribosomal Spacer/chemistry/*genetics ; Deer/*parasitology ; Male ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; Species Specificity ; Trichostrongyloidea/chemistry/classification/*genetics ; }, abstract = {Sequences of ITS-1 and ITS-2 rDNA for adult males of Spiculopteragia asymmetrica and Spiculopteragia quadrispiculata in red deer (Cervus elaphus) were determined. They were found to be identical, suggesting that S. asymmetrica and S. quadrispiculata represent a single species and do not refute the concept of dimorphic species in the Spiculopteragia.}, } @article {pmid12033429, year = {2002}, author = {Giles, GI and Jacob, C}, title = {Reactive sulfur species: an emerging concept in oxidative stress.}, journal = {Biological chemistry}, volume = {383}, number = {3-4}, pages = {375-388}, doi = {10.1515/BC.2002.042}, pmid = {12033429}, issn = {1431-6730}, mesh = {Animals ; Nitrogen ; Oxidants/*metabolism ; Oxidative Stress/*physiology ; Sulfides/*metabolism ; Sulfur/*metabolism ; }, abstract = {The ingredients of oxidative stress include a variety of reactive species such as reactive oxygen and reactive nitrogen species (ROS, RNS). While sulfur is usually considered as part of cellular antioxidant systems there is mounting evidence that reactive sulfur species (RSS) with stressor properties similar to the ones found in ROS are formed under conditions of oxidative stress. Thiols as well as disulfides are easily oxidised to sulfur species with sulfur in higher oxidation states. Such agents include thiyl radicals, disulfides, sulfenic acids and disulfide-S-oxides. They rapidly oxidise and subsequently inhibit thiol-proteins and enzymes and can be considered as a separate class of oxidative stressors providing new antioxidant drug targets.}, } @article {pmid11989683, year = {2002}, author = {Ballard, JW and Chernoff, B and James, AC}, title = {Divergence of mitochondrial dna is not corroborated by nuclear dna, morphology, or behavior in Drosophila simulans.}, journal = {Evolution; international journal of organic evolution}, volume = {56}, number = {3}, pages = {527-545}, doi = {10.1111/j.0014-3820.2002.tb01364.x}, pmid = {11989683}, issn = {0014-3820}, mesh = {Animals ; Base Sequence ; Behavior, Animal/*physiology ; Cell Nucleus/*genetics ; DNA/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Drosophila/classification/*genetics/physiology ; *Evolution, Molecular ; Female ; Genetic Variation ; Geography ; *Phylogeny ; Reproduction/physiology ; Wolbachia/classification/genetics/physiology ; X Chromosome ; }, abstract = {We ask whether the observed mitochondrial DNA (mtDNA) population subdivision of Drosophila simulans is indicative of organismal structure or of specific processes acting on the mitochondrial genome. Factors either intrinsic or extrinsic to the host genome may influence the evolutionary dynamics of mtDNA. Potential intrinsic factors include adaptation of the mitochondrial genome and of nucleomitochondrial gene complexes specific to the local environment. An extrinsic force that has been shown to influence mtDNA evolution in invertebrates is the bacterial endosymbiont Wolbachia. Evidence presented in this study suggests that mtDNA is not a good indicator of organismal subdivision in D. simulans. Furthermore, there is no evidence to suggest that Wolbachia causes any reduction in nuclear gene flow in this species. The observed differentiation in mtDNA is not corroborated by data from NADH: ubiquinone reductase 75kD subunit precursor or the Alcohol dehydrogenase-related loci, from the shape or size of the male genital arch, or from assortative premating behavior. We discuss these results in relation to a mitochondrial genetic species concept and the potential for Wolbachia-induced incompatibility to be a mechanism of speciation in insects. We conclude with an iterated appeal to include phylogenetic and statistical tests of neutrality as a supplement to phylogenetic and population genetic analyses when using mtDNA as an evolutionary marker.}, } @article {pmid11934048, year = {2002}, author = {ter, SP and Ueckert, JE}, title = {Debating the biological reality of modelling preservation.}, journal = {International journal of food microbiology}, volume = {73}, number = {2-3}, pages = {409-414}, doi = {10.1016/s0168-1605(01)00665-1}, pmid = {11934048}, issn = {0168-1605}, mesh = {Bacteria/*growth & development ; Flow Cytometry ; Food Microbiology ; Food Preservation/*methods/standards ; Models, Biological ; Models, Theoretical ; Risk Assessment ; }, abstract = {Predictive food microbiology is a rapidly developing science and has made great advances. The aim is to debate a number of issues in modelling preservation: (1) inoculum and prehistory effects on lag times and process susceptibility; (2) mechanistic vs. empirical modelling; and (3) concluding remarks (the Species concept, methodology and biovariability). Increasing the awareness in these issues may bridge the gap between the complex reality in food microbial physiology and the application potential of predictive models. The challenge of bringing integrated preservation or risk analysis further and developing ways to truly model and link biological susceptibility distributions from raw ingredients via process survival to outgrowth probabilities in the final product remains.}, } @article {pmid11924504, year = {2002}, author = {Brower, AV}, title = {Cladistics, populations and species in geographical space: the case of Heliconius butterflies.}, journal = {EXS}, volume = {}, number = {92}, pages = {5-15}, doi = {10.1007/978-3-0348-8114-2_1}, pmid = {11924504}, issn = {1023-294X}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Butterflies/*classification/genetics ; Cluster Analysis ; DNA, Mitochondrial/genetics ; Geography ; Molecular Sequence Data ; }, abstract = {The paradox of the species in evolutionary thought has promoted much debate and numerous incompatible definitions and concepts. This chapter argues that although the phylogenetic species concept (the author's version of it, at least) is no more accurate a description of "speciesness" than any other species concept (indeed, the notion of accuracy is irrelevant, as will be seen), it links species definition to species diagnosis via explicit criteria, which renders phylogenetic species more amenable to empirical testing than species defined by other concepts. The practical implications of cladistic species concepts for determining the boundaries between geographically differentiated sister taxa are explored using the example of Heliconius, based on my work and the recent studies of Mallet and others. The problem of circumscription is also addressed, with particular reference to the concepts of subspecies and geographical races.}, } @article {pmid11924493, year = {2002}, author = {Goldstein, PZ and Brower, AV}, title = {Molecular systematics and the origin of species: new syntheses or methodological introgressions?.}, journal = {EXS}, volume = {}, number = {92}, pages = {147-161}, doi = {10.1007/978-3-0348-8114-2_11}, pmid = {11924493}, issn = {1023-294X}, mesh = {Animals ; *Phylogeny ; Species Specificity ; }, abstract = {The advent of molecular phylogenetics stimulated the need to reprise for many discussions surrounding species concepts. The interpretation of cladograms as accurate representations of phylogeny, when the characters upon which they are based exhibit a reticulate pattern, is inconsistent with the epistemological axiom of hierarchy we assign to the cladistic method (Brower, 2000c). Discrepancies in the interpretation of cladograms would appear to account for differences in the kinds of questions to which they are applied. The philosophical and empirical issues surrounding this subject are examined in this chapter.}, } @article {pmid11922967, year = {2002}, author = {Striedter, GF}, title = {Brain homology and function: an uneasy alliance.}, journal = {Brain research bulletin}, volume = {57}, number = {3-4}, pages = {239-242}, doi = {10.1016/s0361-9230(01)00692-x}, pmid = {11922967}, issn = {0361-9230}, mesh = {Animals ; *Biological Evolution ; Birds/physiology ; Brain/*physiology ; Hippocampus/physiology ; Humans ; Mammals/physiology ; Models, Neurological ; Phylogeny ; }, abstract = {Current efforts to homologize brain regions across species are often motivated by the expectation that "functional homology" can be deduced from structural homology. Research guided by this "extrapolationist" assumption has been quite successful in molecular biology and, to a lesser extent, in comparative neurobiology. For example, several studies have shown that the hippocampal formation performs similar behavioral functions in birds and mammals, despite significant differences in both anatomy and physiology. However, the extrapolationist assumption can also impede progress because it disregards the possibility that brain regions may change their function during the course of evolution. For example, data gathered at the end of the 19th century on the behavioral effects of large telencephalic lesions were quite confusing until Ferrier recognized that the lesion effects simply differ between species. This realization gave rise to the concept of "functional encephalization," according to which behavioral functions generally shift from "lower" to "higher" brain regions as one ascends the so-called phylogenetic scale. This idea is now discredited, but there is still no adequate theory to explain the species differences in lesion effects. The present paper outlines how one might begin to construct a theory of evolutionary changes in brain function.}, } @article {pmid11912222, year = {2002}, author = {Gastal, F and Lemaire, G}, title = {N uptake and distribution in crops: an agronomical and ecophysiological perspective.}, journal = {Journal of experimental botany}, volume = {53}, number = {370}, pages = {789-799}, doi = {10.1093/jexbot/53.370.789}, pmid = {11912222}, issn = {0022-0957}, mesh = {Agriculture ; Biomass ; Carbon/metabolism ; Crops, Agricultural/drug effects/*physiology ; *Ecology ; Light ; Nitrogen/*metabolism/pharmacology ; Photosynthesis/drug effects/*physiology ; Plant Leaves/drug effects/physiology ; Plant Roots/drug effects/physiology ; Plant Stems/drug effects/physiology ; Plants/classification ; Soil/analysis ; Time Factors ; }, abstract = {The rate of N uptake of crops is highly variable during crop development and between years and sites. However, under ample soil N availability, crop N accumulation is highly related to crop growth rate and to biomass accumulation. Critical N concentration has been defined as the minimum N concentration which allows maximum growth rate. Critical N concentration declines during crop growth. The relationship between critical N concentration and biomass accumulation over the growth period of a crop is broadly similar within major C(3) and C(4) cultivated species. Therefore, the critical N concentration concept is widely used in agronomy as the basis of the diagnosis of crop N status, and allows discrimination between situations of sub-optimal and supra-optimal N supply. The relationship between N and biomass accumulation in crops, relies on the interregulation of multiple crop physiological processes. Among these processes, N uptake, crop C assimilation and thus growth rate, and C and N allocation between organs and between plants, play a particular role. Under sub-optimal N supply, N uptake of the crop depends on soil mineral N availability and distribution, and on root distribution. Under ample N supply, N uptake largely depends on growth rate via internal plant regulation. Carbon assimilation of the crop is related to crop N through the distribution of N between mature leaves with consequences for leaf and canopy photosynthesis. However, although less commonly emphasized, carbon assimilation of the crop also depends on crop N through leaf area development. Therefore, crop growth rate fundamentally relies on the balance of N allocation between growing and mature leaves. Nitrogen uptake and distribution also depends on C allocation between organs and N composition of these organs. Within shoots, allocation of C to stems generally increases in relation to C allocation to the leaves over the crop growth period. Allocation of C and N between shoots and roots also changes to a large extent in relation to soil N and/or crop N. These alterations in C and N allocation between plant organs have implications, together with soil availability and carbon assimilation, on N uptake and distribution in crops. Therefore, N uptake and distribution in plants and crops involves many aspects of growth and development. Regulation of nitrogen assimilation needs to be considered in the context of these interregulatory processes.}, } @article {pmid11903888, year = {2001}, author = {Fraser, DJ and Bernatchez, L}, title = {Adaptive evolutionary conservation: towards a unified concept for defining conservation units.}, journal = {Molecular ecology}, volume = {10}, number = {12}, pages = {2741-2752}, pmid = {11903888}, issn = {0962-1083}, mesh = {Animals ; *Biological Evolution ; Conservation of Natural Resources/*methods ; Ecology ; Fishes/genetics ; Genetic Variation ; Moths/genetics ; Phylogeny ; }, abstract = {Recent years have seen a debate over various methods that could objectively prioritize conservation value below the species level. Most prominent among these has been the evolutionarily significant unit (ESU). We reviewed ESU concepts with the aim of proposing a more unified concept that would reconcile opposing views. Like species concepts, conflicting ESU concepts are all essentially aiming to define the same thing: segments of species whose divergence can be measured or evaluated by putting differential emphasis on the role of evolutionary forces at varied temporal scales. Thus, differences between ESU concepts lie more in the criteria used to define the ESUs themselves rather than in their fundamental essence. We provide a context-based framework for delineating ESUs which circumvents much of this situation. Rather than embroil in a befuddled debate over an optimal criterion, the key to a solution is accepting that differing criteria will work more dynamically than others and can be used alone or in combination depending on the situation. These assertions constitute the impetus behind adaptive evolutionary conservation.}, } @article {pmid11884161, year = {2002}, author = {Porter, BA and Cavender, TM and Fuerst, PA}, title = {Molecular phylogeny of the snubnose darters, subgenus Ulocentra (genus Etheostoma, family Percidae).}, journal = {Molecular phylogenetics and evolution}, volume = {22}, number = {3}, pages = {364-374}, doi = {10.1006/mpev.2001.1069}, pmid = {11884161}, issn = {1055-7903}, mesh = {Animals ; DNA, Mitochondrial/chemistry/*genetics ; Haplotypes ; Molecular Sequence Data ; Perches/classification/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer, Phe/genetics ; Sequence Analysis, DNA ; }, abstract = {Snubnose darters comprise one of the largest subgenera of the percid genus Etheostoma. Many species are described based on differences in male breeding coloration. Few morphological synapomorphies have been proposed for the subgenus and their relatives, making it difficult to delineate monophyletic clades. The phylogenetic relationships of the 20 snubnose darter species of the subgenus Ulocentra and 11 members of its proposed sister subgenus Etheostoma were investigated with partial mitochondrial DNA sequences including 1033 bp encompassing the entire mitochondrial control region, the tRNA-Phe gene, and part of the 12S rRNA gene. Two hypotheses on the relationship and monophyly of the two subgenera were evaluated. Both maximum-parsimony and neighbor-joining analyses supported monophyly of the subgenus Ulocentra and resolved some species-level relationships. The banded darter, E. zonale, and its sister taxon, E. lynceum, were not closely related to the snubnose darters and appear to be diverged from the other members of the subgenus Etheostoma, fitting their former distinction as the recognized subgenus Nanostoma. The sister group to Ulocentra appears to be a restricted species assemblage within the subgenus Etheostoma containing E. blennioides, E. rupestre, E. blennius, and the E. thalassinum species group. The placement of the harlequin darter, E. histrio, is problematic, and it may represent a basal member of Ulocentra or of the restricted subgenus Etheostoma. Despite recent estimates of divergence times between nominal Ulocentra taxa, each species exhibits its own unique set of mtDNA haplotypes, providing no direct evidence for current genetic exchange between species. The nominal taxa of snubnose darters thus appear to be evolving independently from each other and therefore constitute valid species under the Phylogenetic Species Concept.}, } @article {pmid11878886, year = {2001}, author = {El-Attar, L and Dhaliwal, W and Howard, CR and Bridger, JC}, title = {Rotavirus cross-species pathogenicity: molecular characterization of a bovine rotavirus pathogenic for pigs.}, journal = {Virology}, volume = {291}, number = {1}, pages = {172-182}, doi = {10.1006/viro.2001.1222}, pmid = {11878886}, issn = {0042-6822}, mesh = {Amino Acid Sequence ; Animals ; *Antigens, Viral ; Base Sequence ; Capsid/genetics ; *Capsid Proteins ; Cattle ; DNA, Viral ; Diarrhea/epidemiology/*veterinary/virology ; Disease Outbreaks/*veterinary ; Genome, Viral ; Glycoproteins/genetics ; Molecular Sequence Data ; Rotavirus/classification/*genetics/pathogenicity ; Rotavirus Infections/epidemiology/*veterinary/virology ; Sequence Homology, Amino Acid ; Swine ; Toxins, Biological ; United Kingdom/epidemiology ; Viral Nonstructural Proteins/genetics ; }, abstract = {Rotaviruses which cause disease in heterologous animal species have been reported but the molecular basis of cross-species infectivity and disease is not established. We report the molecular characterization of a cloned rotavirus, PP-1, which was originally obtained from cattle and which had been biologically characterized in vivo in two target animal species, gnotobiotic pigs and calves. In pigs, PP-1 caused severe clinical disease but in experimental calves it replicated subclinically. PP-1 was characterized as a G3 reassortant with a porcine VP4 and NSP4 but a bovine NSP1. The PP-1 VP4 had 96 to 97% deduced amino acid identity to P[7] porcine rotaviruses and P[7] specificity was confirmed with VP4-specific monoclonal antibodies. Sequence analysis of the PP-1 NSP1 showed 94 to 99.6% deduced amino acid identity to bovine rotaviruses but the NSP4 protein had 94 to 98% identity to the NSP4 genotype B porcine rotaviruses. G-typing PCR initially classified PP-1 as a G10 rotavirus but sequence analysis revealed 92 to 96% identity of the PP-1 VP7 with porcine, simian, and human G3 rotaviruses. These results, combined with the in vivo properties of PP-1 in the two target species, supported the concept that species-specific VP4 and NSP4, but not NSP1, are required to induce rotavirus disease, at least in calves and pigs. The results illustrate experimentally that rotaviruses circulating in one animal species can pose a risk to another by the emergence of a pathogenic reassortant rotavirus under appropriate conditions.}, } @article {pmid11844580, year = {2002}, author = {Tavares, MC and Tomaz, C}, title = {Working memory in capuchin monkeys (Cebus apella).}, journal = {Behavioural brain research}, volume = {131}, number = {1-2}, pages = {131-137}, doi = {10.1016/s0166-4328(01)00368-0}, pmid = {11844580}, issn = {0166-4328}, mesh = {Animals ; Cebus ; Conditioning, Operant/physiology ; Female ; Male ; Memory, Short-Term/*physiology ; Psychomotor Performance/physiology ; }, abstract = {It has been suggested that delayed (non-) matching to sample (DNMTS/DMTS) tasks using trial-unique stimuli and short, as well as longer delay intervals, can provide important insights into animal cognition. Therefore, this research examined the capability of the New World capuchin monkey (Cebus apella) in perform trial-unique DMTS and DNMTS tasks across delay intervals ranging between 8 s and 10 min. Subjects were tested using a version of the Wisconsin General Test Apparatus mounted in front of the animal's home cage. They were first trained on a basic DMTS/DNMTS task with an 8 s interval until they reached a learning criterion of nine correct responses in ten consecutive trials. All subjects reached the learning criterion in both DMTS/DNMTS tasks, and the number of trials to criterion did not differ between tasks. After reaching the criterion, subject's memory performance was successively assessed at delay intervals of 15 s, 60 s, 120 s and 10 min. For both DMTS/DNMTS tasks, the mean percentage of correct responses across delays was above chance and, interestingly, performance did not significantly decrease as function of delay increments. Comparisons based on each group's scores, averaged across the four delays, showed no difference between DMTS and DNMTS memory performance. These results indicate that capuchin monkeys are able to learn DMTS/DNMTS tasks in which they are required to respond to new pairs of stimuli on every trial. This demonstrates the capability of 'concept' learning in this species. Moreover, above chance performance on the memory tests indicates a working memory ability similar to that reported for the genus Macaca. Taken together, these data indicates that capuchin monkeys can be a valuable alternative model for investigations of the neuropsychological basis of memory.}, } @article {pmid11795597, year = {2001}, author = {Pani, G and Bedogni, B and Colavitti, R and Anzevino, R and Borrello, S and Galeotti, T}, title = {Cell compartmentalization in redox signaling.}, journal = {IUBMB life}, volume = {52}, number = {1-2}, pages = {7-16}, doi = {10.1080/15216540252774702}, pmid = {11795597}, issn = {1521-6543}, mesh = {Animals ; Apoptosis ; *Cell Compartmentation ; Cell Respiration ; Cellular Senescence ; Humans ; Mitochondria/metabolism ; NADPH Oxidases/metabolism ; *Oxidation-Reduction ; Oxidative Stress ; *Signal Transduction ; Superoxides/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; ras Proteins/metabolism ; }, abstract = {From a growing body of evidence on the role of Reactive Oxygen Species as intracellular signaling molecules, the concept starts to emerge that cell responses to redox changes are function of the intracellular site where oxidants are produced and/or meet their molecular targets. In particular, a major distinction between oxidative events in the cytosolic versus the mitochondrial compartment appears to exist in terms of physiological stimuli, signaling mechanisms and functional consequences. Experimental data supporting this view are reviewed here, and the potential implications of this new perspective in redox signaling are discussed.}, } @article {pmid11786995, year = {2001}, author = {Jolly, CJ}, title = {A proper study for mankind: Analogies from the Papionin monkeys and their implications for human evolution.}, journal = {American journal of physical anthropology}, volume = {Suppl 33}, number = {}, pages = {177-204}, doi = {10.1002/ajpa.10021}, pmid = {11786995}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical/trends ; *Biological Evolution ; Ecology ; Genetic Variation ; Hominidae/*physiology ; Humans ; Models, Theoretical ; Papio/*physiology ; Phylogeny ; Physiology, Comparative ; }, abstract = {This paper's theme is that analogies drawn from the cercopithecine tribe Papionini, especially the African subtribe Papionina (baboons, mangabeys, and mandrills), can be a valuable source of insights about the evolution of the human tribe, Hominini, to complement homologies found in extant humans and/or African apes. Analogies, involving a "likeness of relations" of the form "A is to B, as X is to Y," can be usefully derived from nonhomologous (homoplastic) resemblances in morphology, behavior, ecology, or population structure. Pragmatically, the papionins are a fruitful source of analogies for hominins because they are phylogenetically close enough to share many basic attributes by homology, yet far enough that homoplastic modifications of these features are easily recognized as such. In "The Seedeaters," an analogy between Theropithecus among baboons and Australopithecus africanus among hominines was the source of a widely discussed (and often misrepresented) diet-based scenario of hominin origins that explained previously unassociated hominin apomorphies, interpreted basal hominins as nonhuman rather than prehuman primates, and accommodated a basal hominin adaptive radiation of at least two lines. Current usage recognizes an even more extensive evolutionary radiation among the basal hominins, originating no earlier than about 7 ma, with multiple lineages documented or inferred by 2.5 ma. Although multilineage clades (especially the Paranthropus clade) within this complex are widely recognized, and emerge from sophisticated, parsimony-based analyses, it is suspected that in many cases, developmental or functional homoplasies are overwhelming the phylogenetic signal in the data. The papionin analogy (specifically the splitting of the traditional, morphology-based genera Cercocebus and Papio mandated by molecular evidence) illustrates the power of these factors to produce erroneous cladograms. Moreover, the rapid deployment of basal hominins across varied African habitats was an ideal scenario for producing morphologically undetectable homoplasy. There seems to be no foolproof way to distinguish, a priori, homologous from homoplastic resemblances in morphology, but one pragmatic strategy is to severely censor the datset, retaining only resemblances or differences (often apparently trivial ones) that cannot be reasonably explained on the basis of functional resemblance or difference, respectively. This strategy may eliminate most morpological data, and leave many fossil taxa incertae sedis, but this is preferable to unwarranted phylogenetic confidence. Another source of phylogenetic uncertainty is the possibility of gene-flow by occasional hybridization between hominins belonging to ecologically and adaptively distinct species or even genera. Although the evidence is unsatisfactorily sparse, it suggests that among catarrhines generally, regardless of major chromosomal rearrangements, intersterility is roughly proportional to time since cladogenetic separation. On a papionin analogy, especially the crossability of Papio hamadryas with Macaca mulatta and Theropithecus gelada, crossing between extant hominine genera is unlikely to produce viable and fertile offspring, but any hominine species whose ancestries diverged less than 4 ma previously may well have been able to produce hybrid offspring that could, by backcrossing, introduce alien genes with the potential of spreading if advantageous. Selection against maladaptive traits would maintain adaptive complexes against occasional genetic infiltration, and the latter does not justify reducing the hybridizing forms to a conspecific or congeneric rank. Whether reticulation could explain apparent parallels in hominin dentition and brain size is uncertain, pending genetic investigation of these apparently complex traits. Widespread papionin taxa (such as Papio baboons and species-groups of the genus Macaca), like many such organisms, are distributed as a "patchwork" of nonoverlapping but often parapatric forms (allotaxa). Morphologically diagnosable, yet not reproductively isolated, most allotaxa would be designated species by the phylogenetic species concept, but subspecies by the biological species concept, and use of the term "allotaxa" avoids this inconsistency. A line of contact between allotaxa typically coincides with an ecotone, with neighboring allotaxa occupying similar econiches in slightly different habitats, and often exhibiting subtle, adaptive, morphological differences as well as their defining differences of pelage. "Hybrid zones," with a wide variety of internal genetic structures and dynamics, typically separate parapatric allotaxa. Current models attribute the formation and maintenance of allotaxa to rapid pulses of population expansion and contraction to and from refugia, driven by late Neogene climatic fluctuations. An overall similarity in depth of genetic diversity suggests that papionin taxa such as Papio baboons, rather than extant humans, may present the better analogy for human population structure of the "prereplacement" era. Neandertals and Afro-Arabian "premodern" populations may have been analogous to extant baboon (and macaque) allotaxa: "phylogenetic" species, but "biological" subspecies. "Replacement," in Europe, probably involved a rapidly sweeping hybrid zone, driven by differential population pressure from the "modern" side. Since the genetic outcome of hybridization at allotaxon boundaries is so variable, the problem of whether any Neandertal genes survived the sweep, and subsequent genetic upheavals, is a purely empirical one; if any genes passed "upstream" across the moving zone, they are likely to be those conferring local adaptive advantage, and markers linked to these. In general, extant papionin analogies suggest that the dynamics and interrelationships among hominin populations now known only from fossils are likely to have been more complex than we are likely to be able to discern from the evidence available, and also more complex than can be easily expressed in conventional taxonomic terminology.}, } @article {pmid11774887, year = {2001}, author = {McOuat, G}, title = {From cutting nature and its joints to measuring it: new kinds and new kinds of people in biology.}, journal = {Studies in history and philosophy of science}, volume = {32}, number = {4}, pages = {613-643}, doi = {10.1016/s0039-3681(01)00027-9}, pmid = {11774887}, issn = {0039-3681}, mesh = {Biology/*history ; *Historiography ; History, 19th Century ; History, 20th Century ; Natural History/*history ; Research Design/*trends ; }, abstract = {In the received version of the development of science, natural kinds are established in the preliminary stages (natural history) and made more precise by measurement (exact science). By examining the move from nineteenth- to twentieth-century biology, this paper unpacks the notion of species as 'natural kinds' and grounds for discourse, questioning received notions about both kinds and species. Life sciences in the nineteenth century established several 'monster-barring' techniques to block disputes about the precise definition of species. Counterintuitively, precision and definition brought dispute and disrupted exchange. Thus, any attempt to add precision was doomed to failure. By intervening and measuring, the new experimental biology dislocated the established links between natural kinds and kinds of people and institutions. New kinds were built in new places. They were made to measure from the very start. This paper ends by claiming that there was no long-standing 'species problem' in the history of biology. That problem is a later construction of the 'modern synthesis', well after the disruption of 'kinds' and kinds of people. Only then would definitions and precision matter. A new, non-linguistic, take on the incommensurability thesis is hinted at.}, } @article {pmid11773531, year = {2001}, author = {Mori, IC and Pinontoan, R and Kawano, T and Muto, S}, title = {Involvement of superoxide generation in salicylic acid-induced stomatal closure in Vicia faba.}, journal = {Plant & cell physiology}, volume = {42}, number = {12}, pages = {1383-1388}, doi = {10.1093/pcp/pce176}, pmid = {11773531}, issn = {0032-0781}, mesh = {1,2-Dihydroxybenzene-3,5-Disulfonic Acid Disodium Salt/pharmacology ; Fabaceae/*physiology ; Oxygen/metabolism ; Peroxidases/metabolism ; Plant Epidermis/drug effects/physiology ; Reactive Oxygen Species/metabolism ; Salicylamides/pharmacology ; Salicylic Acid/*pharmacology ; Signal Transduction ; Superoxide Dismutase/pharmacology ; Superoxides/*metabolism ; }, abstract = {Salicylic acid (SA), the known mediator of systemic acquired resistance, induced stomatal closure of Vicia faba L. Application of SA to the epidermal peels evoked an elevation of chemiluminescence of Cripridina lucigenin-derived chemiluminescent reagent (CLA) which is sensitive to superoxide anion (O(2)(.-)). The SA-induced generation of chemiluminescence was suppressed by O(2)(.-)-specific scavengers superoxide dismutase (SOD) and 4,5-dihydroxy-1,3-benzenedisulfonic acid (Tiron). These results suggest that O(2)(.-) was generated in epidermal peels by SA-treatment. A peroxidase inhibitor salicylhydroxamic acid (SHAM) inhibited guaiacol peroxidase activity and suppressed the SA-induced CLA chemiluminescence in the epidermal peels, suggesting that O(2)(.-) generation occurred by the peroxidase-catalyzed reaction as proposed for SA-treated tobacco cell suspension culture [Kawano et al. (1998) Plant Cell Physiol. 39: 721]. SOD, Tiron or SHAM suppressed the SA-induced stomatal closure. Moreover, application of superoxide-generating system also induced stomatal closure. These results support the concept of involvement of reactive oxygen species in signal transduction in SA-induced stomatal closure.}, } @article {pmid11748652, year = {2002}, author = {Devereux, HL and Burke, A and Lee, CA and Johnson, MA}, title = {In vivo HIV-1 compartmentalisation: drug resistance-associated mutation distribution.}, journal = {Journal of medical virology}, volume = {66}, number = {1}, pages = {8-12}, doi = {10.1002/jmv.2104}, pmid = {11748652}, issn = {0146-6615}, mesh = {Adult ; *Antiretroviral Therapy, Highly Active ; Autopsy ; Drug Resistance, Viral/*genetics ; Genotype ; HIV Infections/drug therapy/virology ; HIV Protease/genetics ; HIV Reverse Transcriptase/genetics ; HIV-1/classification/*drug effects/genetics/isolation & purification ; Humans ; Middle Aged ; Molecular Sequence Data ; *Mutation ; *Organ Specificity ; Sequence Analysis, DNA ; Viral Load ; }, abstract = {Four patients who had received highly active antiretroviral therapy (HAART), and had postmortem samples stored, were tested for genotypic resistance using consensus sequencing. One patient was further investigated using single-copy sequencing. Patients 1, 3, and 4 showed a relatively uniform distribution of resistance-associated mutations, with only a small number (one to three) of protease mutations detectable. Patient 2 had a number of detectable mutations (four to eight, depending on the tissue) with similar distributions between the tissues. The exception was viruses detected in the esophagus, which were more diverse. Plasma was a moderately representative tissue of the viruses circulating in these individuals. However, some mutations detectable in some tissues were not seen in plasma (e.g., M46I and D30N in the protease). Single-copy sequencing revealed a wide distribution of quasi-species and a number of defective viruses in the proviral DNA and RNA. This study supports the concept that a wide variety of quasi-species circulate in each individual and that there may be viruses evolving independently in different body compartments.}, } @article {pmid19265874, year = {2001}, author = {Adams, BJ}, title = {The species delimitation uncertainty principle.}, journal = {Journal of nematology}, volume = {33}, number = {4}, pages = {153-160}, pmid = {19265874}, issn = {0022-300X}, abstract = {If, as Einstein said, "it is the theory which decides what we can observe," then "the species problem" could be solved by simply improving our theoretical definition of what a species is. However, because delimiting species entails predicting the historical fate of evolutionary lineages, species appear to behave according to the Heisenberg Uncertainty Principle, which states that the most philosophically satisfying definitions of species are the least operational, and as species concepts are modified to become more operational they tend to lose their philosophical integrity. Can species be delimited operationally without losing their philosophical rigor? To mitigate the contingent properties of species that tend to make them difficult for us to delimit, I advocate a set of operations that takes into account the prospective nature of delimiting species. Given the fundamental role of species in studies of evolution and biodiversity, I also suggest that species delimitation proceed within the context of explicit hypothesis testing, like other scientific endeavors. The real challenge is not so much the inherent fallibility of predicting the future but rather adequately sampling and interpreting the evidence available to us in the present.}, } @article {pmid11701822, year = {1999}, author = {Taylor, J and Jacobson, D and Fisher, M}, title = {THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification.}, journal = {Annual review of phytopathology}, volume = {37}, number = {}, pages = {197-246}, doi = {10.1146/annurev.phyto.37.1.197}, pmid = {11701822}, issn = {1545-2107}, abstract = {Phylogenetic and population genetic methods that compare nucleic acid variation are being used to identify species and populations of pathogenic fungi and determine how they reproduce in nature. These studies show that asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior, and that fungi with all types of reproductive morphologies and behaviors can be accommodated by a phylogenetic species concept. Although approximately one fifth of described fungi have been thought to be asexual and clonal, recent studies have shown that they are also recombining. Whether a particular pathogen reproduces clonally or by recombination depends on factors relating to its biology and its distribution in space and time. Knowing the identity of species and populations and their reproductive modes, while taking a broad view of pathogen behavior in space and time, should enhance the ability of pathologists to control pathogens and even predict their behavior.}, } @article {pmid11668452, year = {2001}, author = {Browning, ST and Shuler, ML}, title = {Towards the development of a minimal cell model by generalization of a model of Escherichia coli: use of dimensionless rate parameters.}, journal = {Biotechnology and bioengineering}, volume = {76}, number = {3}, pages = {187-192}, doi = {10.1002/bit.10007}, pmid = {11668452}, issn = {0006-3592}, mesh = {Computer Simulation ; Escherichia coli/growth & development/*physiology ; Glucose/metabolism ; Kinetics ; *Models, Biological ; }, abstract = {A model of a minimal cell would be a valuable tool in identifying the organizing principles that relate the static sequence information of the genome to the dynamic functioning of the living cell. Our approach for developing a minimal cell model is to first generalize an existing model of Escherichia coli by expressing reaction rates as ratios to a set of reference parameters. This generalized model is a prototype minimal cell model that will be developed by adding detail to explicitly include each chemical species. We tested the concept of a generalized model by testing the effect of scaling all enzyme-catalyzed reactions in the E. coli model. The scaling has little effect on cellular function for a wide range of kinetic ratios, where the kinetic ratio is defined as the rate of all enzyme-catalyzed reactions in a given model relative to those in the E. coli model.}, } @article {pmid11594617, year = {2001}, author = {Wright, D and Prickett, T and Helm, RF and Potts, M}, title = {Form species Nostoc commune (Cyanobacteria).}, journal = {International journal of systematic and evolutionary microbiology}, volume = {51}, number = {Pt 5}, pages = {1839-1852}, doi = {10.1099/00207713-51-5-1839}, pmid = {11594617}, issn = {1466-5026}, mesh = {Base Sequence ; Cyanobacteria/*classification/*genetics ; Evolution, Molecular ; Introns/*genetics ; Leucine ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Transfer, Amino Acid-Specific/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The form species concept for the Cyanobacteria was evaluated using a comprehensive set of Nostoc samples that were collected during the past two centuries, from all continents, including regions from the Tropics to the Poles. Phylogenies were constructed based upon the conserved regions of tRNALeu (UAA) group I intron DNA sequences. Thirty-four forms contained a tRNALeu (UAA) intron of 284 nt. These 284-nt introns contained 200 nt of conserved sequence that, in most cases, shared 100% sequence identity, they had three variable regions (I, II and III) amounting to 84 nt, contained no hypervariable region and formed a discrete cluster in phylogenetic analysis. These forms represented 31 independent populations in both hemispheres and constitute examples of form species Nostoc commune. Multiple introns were obtained from several of the populations. Ten populations contained introns of 287-340 nt with a hypervariable region, 8 to 59 nt in length, located between variable regions I and II. Alignments identified 15 examples where 5'-AAAAUCC-3' occurred at the hypervariable region-variable region II boundary; this sequence is identical to the conserved sequence at the 3' intron-exon boundary (splice site) within the tRNALeu (UAA) gene. The possibility that hypervariable regions were removed from the primary intron through secondary splicing was tested in vitro but proved to be negative under the experimental conditions used. Shared morphologies of genetically different strains, dissimilar morphologies in strains that share identical genetic markers, incorrect naming of culture collection strains and genetic drift in cultured strains emphasize that the successful delineation of cyanobacterial species requires the application of multiple taxonomic criteria.}, } @article {pmid11572457, year = {2001}, author = {Voigt, K and Jedryczka, M and Wöstemeyer, J}, title = {Strain typing of polish Leptosphaeria maculans isolates supports at the genomic level the multi-species concept of aggressive and non-aggressive strains.}, journal = {Microbiological research}, volume = {156}, number = {2}, pages = {169-177}, doi = {10.1078/0944-5013-00099}, pmid = {11572457}, issn = {0944-5013}, mesh = {Ascomycota/*classification/enzymology/genetics/*pathogenicity ; Brassica napus/microbiology ; Cellulase/metabolism ; DNA, Fungal/analysis ; Electrophoresis, Gel, Pulsed-Field ; Mycological Typing Techniques ; Piperazines/metabolism ; Plant Diseases/microbiology ; Polymerase Chain Reaction ; Random Amplified Polymorphic DNA Technique ; Virulence/genetics ; }, abstract = {47 Polish isolates of the blackleg fungus Leptosphaeria maculans (Phoma lingam) were compared with eight well-defined reference strains from Germany, France, Denmark, Australia and one Polish isolate of Phoma nigrificans. The isolates were tested (i) for growth characteristics, (ii) for their ability to form sirodesmins, (iii) for cellulolytic enzymes, and (iv) for pathotype-differentiating molecular markers generated by RAPD-PCR, PCR analysis with pathotype-specific primer pairs and PFGE. With two exceptions all Polish isolates do not form sirodesmins. grow rapidly without penetrating into the substrate and form in most cases yellow or brown pigments in Czapek-Dox liquid cultures. With respect to cellulase secretion and molecular fingerprinting Polish A strains (aggressive) fit into the general picture of the aggressive pathotype group, whereas the NA isolates (non-aggressive) display a higher degree of heterogeneity. This matches with inoculation tests on rape seedlings, which revealed a considerable number of isolates ranging in aggressivity between the conventional A and NA pathotype group. Molecular fingerprinting techniques unequivocally sorted intermediately aggressive isolates into the NA pathotype group. Isolate Ph Bial, which produces sirodesmin but groups within NA isolates according to molecular and physiological markers, may represent a novel third group besides A and NA strains with intermediate aggressivity (IA). We hybridized Southern blots of electrophoretically separated chromosomes with radioactively labelled PCR fragments used for differentiation between A and NA isolates. The specificity of diagnostic PCR amplicons is reflected at the genomic level. The A probe reveals a single hybridizing chromosome exclusively in A strains. The NA probe reveals several chromosomes and is specific for the NA pathotype group. Chromosomes from intermediately aggressive strains are equally well recognized by the NA probe as are Polish isolates with low aggressivity and give no signal with the A probe. Both diagnostic DNA sequences are highly specific for the pathotype group they were derived from. The lack of correspondence of both genetic elements between A and NA strains strongly supports the idea of ascribing the pathotype groups to different species. Whereas the A pathotype group is genetically homogeneous and congruent with the species Leptosphaeria maculans, the NA group needs to be revised taxonomically. NA isolates will presumably have to be split into several independent species.}, } @article {pmid11569147, year = {2001}, author = {Pavlinov, IIa}, title = {[Concepts of taxonomy and concepts of biodiversity: the problem of interaction].}, journal = {Zhurnal obshchei biologii}, volume = {62}, number = {4}, pages = {362-366}, pmid = {11569147}, issn = {0044-4596}, mesh = {*Classification ; *Ecosystem ; Phylogeny ; }, abstract = {There is, or there should be, an interaction between concepts of taxonomy and biodiversity. On the one hand, taxonomy develops some general and particular classificatory paradigms, which own diversity is to be taken into account to understand the nature of variety of natural kinds. On the other hand, analysis of the properties of biodiversity may put forward nontrivial problems for taxonomy that cannot be deduced directly from its own statements. From the point view of taxonomy, it is argued that the current concept of biodiversity based entirely on the species concept is deeply rooted in reductionistic view of nature. It is outdated epistemologically and should be replaced by the modern taxonomic concept of the hierarchical phylogenetic pattern. Operationally, the latter presumes a possibility for each species to be assigned a certain "phylogenetic weight", according to its phylogenetic uniqueness. From the point view of biodiversity, it is argued that the global biodiversity is a three component entity, as it includes, in addition to phylogenetic and ecological hierarchies, a biomorphic hierarchy, as well. This calls for taxonomy to elaborate the general principles of classification of biomorphs.}, } @article {pmid11567550, year = {2001}, author = {Carter, DA and Taylor, JW and Dechairo, B and Burt, A and Koenig, GL and White, TJ}, title = {Amplified single-nucleotide polymorphisms and a (GA)(n) microsatellite marker reveal genetic differentiation between populations of Histoplasma capsulatum from the Americas.}, journal = {Fungal genetics and biology : FG & B}, volume = {34}, number = {1}, pages = {37-48}, doi = {10.1006/fgbi.2001.1283}, pmid = {11567550}, issn = {1087-1845}, mesh = {Genetic Markers ; Genotype ; Histoplasma/*classification/genetics ; Histoplasmosis/microbiology ; Humans ; Microsatellite Repeats ; North America ; *Polymorphism, Single Nucleotide ; South America ; Species Specificity ; }, abstract = {Histoplasma capsulatum has a worldwide distribution but is particularly concentrated in the midwestern United States and throughout Central and South America. Genetic differences between isolates resident in separate parts of the world have been reported, but the relationship between the isolates and the level of migration between different endemic foci has not been clear. In this study we used multilocus genotypes based on amplified polymorphic loci and one microsatellite to quantify the level of genetic differentiation occurring between North and South American populations of H. capsulatum. Significant genetic differentiation occurred between isolates obtained from Indiana and Alabama, and a marked division was seen between the Indiana population and the Class 1 isolates from St. Louis. Strong genetic differentiation occurred between the two North American populations and the Colombian population. This study supports the separation of North and South American H. capsulatum into different species, which has been proposed under the phylogenetic species concept.}, } @article {pmid11553454, year = {2001}, author = {Reid, G and Howard, J and Gan, BS}, title = {Can bacterial interference prevent infection?.}, journal = {Trends in microbiology}, volume = {9}, number = {9}, pages = {424-428}, doi = {10.1016/s0966-842x(01)02132-1}, pmid = {11553454}, issn = {0966-842X}, mesh = {Antibiosis/*physiology ; Bacterial Adhesion ; Bacterial Infections/complications/*microbiology/*prevention & control/therapy ; Bacterial Vaccines/immunology/therapeutic use ; Biofilms/growth & development ; Digestive System/microbiology ; Humans ; Lactobacillus/physiology ; Probiotics/therapeutic use ; Urogenital System/microbiology ; }, abstract = {The concept that one bacterial species can interfere with the ability of another to colonize and infect the host has at its foundation the prerequisite that bacteria must attach to biological surfaces to cause infection. Although this is an over-simplification of pathogenesis, it has led to studies aimed at creating vaccines that block adhesion events. Arguably, the use of commensal bacteria (also referred to as "normal flora", "indigenous" or "autochthonous" microorganisms) to inhibit pathogens has even greater potential than vaccine use, because these bacteria are natural competitors of pathogens and their action does not require host immune stimulation. Exogenous application of commensal organisms (probiotics) has been shown to reduce the risk of infections in the gut, urogenital tract and wound sites. To manipulate and optimize these effects, further studies are required to understand cell signaling amongst commensals and pathogens within biofilms adherent to host tissues. The potential for new therapeutic regimens using probiotics is significant and worthy of further study.}, } @article {pmid11553453, year = {2001}, author = {Lan, R and Reeves, PR}, title = {When does a clone deserve a name? A perspective on bacterial species based on population genetics.}, journal = {Trends in microbiology}, volume = {9}, number = {9}, pages = {419-424}, doi = {10.1016/s0966-842x(01)02133-3}, pmid = {11553453}, issn = {0966-842X}, mesh = {Bacteria/*classification/*genetics/pathogenicity ; Clone Cells/classification/metabolism ; Gene Transfer, Horizontal ; Genetic Variation/genetics ; *Genetics, Population ; Humans ; Mycobacterium/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Terminology as Topic ; Yersinia/genetics ; }, abstract = {Molecular population-genetic analysis has revealed that for several human diseases, including tuberculosis, plague and shigellosis, the generally accepted taxonomic status of the organisms involved does not fit the usually accepted genus or species criteria. This raises the question of what species concept to apply to bacteria. We suggest that the species definition in bacteria should be based on analysis of sequence variation in housekeeping genes, and also that the "clone" be given official status in bacterial nomenclature. This will allow demotion of the species or genus status of several traditionally recognized human pathogens, but retention of current names of anomalous species and genera as clone names.}, } @article {pmid11544775, year = {2001}, author = {Nazarenko, AA}, title = {[Is a unified concept of species in ornithology possible? (An opinion of a practicing taxonomist)].}, journal = {Zhurnal obshchei biologii}, volume = {62}, number = {2}, pages = {180-186}, pmid = {11544775}, issn = {0044-4596}, mesh = {Animals ; Birds/*classification ; Classification/methods ; }, abstract = {An analysis of current publications on species problem reveals the radical discrepancy between the statements of species reality in nature and different number of these "realities" in light of different species concepts. It has been shown, that the only realities are populations, and "species" is only logical construct--the notion. A concept of species is a system of interconnected notions, where the main element--ontology of species has been always given a priori to the real biodiversity. For that reason every concept of species creates its own "virtual reality". Various concepts of species are not mutually comparable, and can not be criticized from each other's views and from position of "reality". Biological and Phylogenetic Species Concepts competing in ornithology exclude each other completely, and the unified concept of species is principally impossible. But as generally accepted species "standard" is needed, the unified convention of species must take the place of the various concepts of species.}, } @article {pmid11527463, year = {2001}, author = {Richard, M and Thorpe, RS}, title = {Can microsatellites be used to infer phylogenies? Evidence from population affinities of the Western Canary Island lizard (Gallotia galloti).}, journal = {Molecular phylogenetics and evolution}, volume = {20}, number = {3}, pages = {351-360}, doi = {10.1006/mpev.2001.0981}, pmid = {11527463}, issn = {1055-7903}, mesh = {Alleles ; Animals ; DNA/genetics ; DNA, Mitochondrial/genetics ; Gene Frequency ; Genetics, Population ; Lizards/*genetics ; Microsatellite Repeats/*genetics ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; Random Amplified Polymorphic DNA Technique ; }, abstract = {Population phylogeographic studies are generally based solely on mtDNA without corroboration, from an independent segregating unit (i.e., nuclear genes), that the mtDNA gene tree represents the organismal phylogeny. This paper attempts to evaluate the utility of microsatellites for this process by use of the Western Canary Island lacertid (Gallotia galloti) as a model. The geological times of island eruptions are known, and well-supported mtDNA phylogenies exist (corroborated as the organismal phylogeny rather than just a gene tree by nuclear random amplified polymorphic DNAs (RAPDs)). The allelic variation in 12 populations from four islands (representing five haplotype lineages) was investigated in five unlinked microsatellite loci. Analysis of molecular variance showed this data to be highly structured. A series of genetic distances among populations was computed based on both the variance in allele frequency (i.e., F(st) related) and the variance in repeat numbers (i.e., R(st) related). The genetic distances based on the former were more highly correlated with the mtDNA genetic distances than those based on the latter. All trees based on both models supported the primary division shown by mtDNA and RAPDs, which is dated at ca. 2.8 to 5.6 mybp (depending on calibration of the mtDNA clock) and which could, under the evolutionary species concept, be regarded separate species. This was achieved despite theoretical problems posed by the use of few loci, suspected bottlenecks, and large population sizes. The finer details were less consistently represented. Nevertheless, this study demonstrates that even a small number of microsatellites can be useful in corroborating the deeper divisions of a population phylogeny.}, } @article {pmid11526093, year = {2001}, author = {Shiratori, I and Matsumoto, M and Tsuji, S and Nomura, M and Toyoshima, K and Seya, T}, title = {Molecular cloning and functional characterization of guinea pig IL-12.}, journal = {International immunology}, volume = {13}, number = {9}, pages = {1129-1139}, doi = {10.1093/intimm/13.9.1129}, pmid = {11526093}, issn = {0953-8178}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Guinea Pigs ; Hematopoietic Stem Cells/immunology ; Humans ; Interferon-gamma ; Interleukin-12/*genetics/*immunology ; Lymphocytes/immunology ; Macrophages, Peritoneal/immunology ; Male ; Molecular Sequence Data ; Recombinant Proteins ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; Spleen/cytology/immunology ; Testis/immunology ; Tissue Distribution ; }, abstract = {IL-12 is a heterodimeric cytokine that plays a central role in cell-mediated immunity. We cloned complete cDNAs of guinea pig homologues of IL-12 p35 and p40 subunits, and compared their functional properties with human IL-12. Both p35 and p40 mRNA were constitutively expressed in the testis and peritoneal macrophages. On immunoblotting, anti-guinea pig p40 antibody detected the constitutive expression of p40 protein in the testis, while in macrophages it was induced in response to lipopolysaccharide. An unidentified 200-kDa macromolecule was also expressed in the testis. All recombinant hybrid heterodimer p70 (guinea pig p70, human p70 and two interspecies heterodimers) exerted proliferative activity toward concanavalin A-primed guinea pig and human lymphoblasts in a dose-dependent manner. A similar tendency was observed in IFN-gamma production in IL-2-treated human lymphocytes. All hybrid heterodimers also induced IFN-gamma mRNA from IL-2-treated guinea pig splenocytes. Thus, unlike the current concept that the p35 subunit determines the species incompatibility of IL-12 in humans and mice, p35 has marginal ability to define its species-specific functional expression between humans and guinea pigs. In addition, constitutive expression of IL-12 or related molecules in the testis indicated a potential role of this molecule in regulation of physiological or pathophysiological conditions in the reproductive system.}, } @article {pmid11518323, year = {2001}, author = {Kang, JC and Crous, PW and Schoch, CL}, title = {Species concepts in the Cylindrocladium floridanum and Cy. spathiphylli complexes (Hypocreaceae) based on multi-allelic sequence data, sexual compatibility and morphology.}, journal = {Systematic and applied microbiology}, volume = {24}, number = {2}, pages = {206-217}, doi = {10.1078/0723-2020-00026}, pmid = {11518323}, issn = {0723-2020}, mesh = {Alleles ; DNA, Ribosomal Spacer/*genetics ; Genes, Fungal ; Genes, rRNA ; Histones/*genetics ; Hypocreales/*classification/genetics/physiology/ultrastructure ; Molecular Sequence Data ; Phylogeny ; *Sequence Analysis, DNA ; Species Specificity ; Tubulin/*genetics ; }, abstract = {Much attention has recently been devoted to the delimitation of species units in Cylindrocladium (Cy.). In this regard the present study focuses on the taxa within the unresolved Cy. floridanum and Cy. spathiphylli species complexes. Maximum parsimony analyses of DNA sequences of ITS, beta-tubulin and histone regions of rRNA genes, and mating experiments revealed a geographically isolated species of Cylindrocladium in the Cy. spathiphylli (teleomorph: Calonectria spathiphylli) species complex. Cy. pseudospathiphylli sp. nov. (teleomorph: Ca. pseudospathiphylli sp. nov.) is described as a new phylogenetic, biological and morphological species. It is distinguished from Cy. spathiphylli by being homothallic, having smaller macroconidia, and distinct DNA sequences of beta-tubulin and histone genes. Similarly, parsimony analysis of a combined data set also indicated several phylogenetic species to exist within Cy. floridanum (teleomorph: Ca. kyotensis). Based on differences in vesicle morphology and conidium dimensions, the Canadian population of Cy. floridanum, formerly known as Cy. floridanum Group 2, is described as Cy. canadense sp. nov., while a further collection from Hawaii is described as Cy. pacificum sp. nov.}, } @article {pmid11475051, year = {2001}, author = {Perry, WL and Feder, JL and Dwyer, G and Lodge, DM}, title = {Hybrid zone dynamics and species replacement between Orconectes crayfishes in a northern Wisconsin lake.}, journal = {Evolution; international journal of organic evolution}, volume = {55}, number = {6}, pages = {1153-1166}, doi = {10.1111/j.0014-3820.2001.tb00635.x}, pmid = {11475051}, issn = {0014-3820}, mesh = {Animals ; Astacoidea/*genetics ; Conservation of Natural Resources ; Crosses, Genetic ; DNA Primers ; Female ; Fertility/genetics ; Fresh Water ; Kinetics ; Linkage Disequilibrium ; Male ; Michigan ; Polymerase Chain Reaction/methods ; Sex Ratio ; Species Specificity ; Wisconsin ; }, abstract = {Hybrid zones that result in the genetic assimilation (replacement) of one species by another are underrepresented in the animal literature, most likely due to their transient nature. One such zone involves the rusty crayfish, Orconectes rusticus, and its congener O. propinquus. Orconectes rusticus was recently introduced into northern Wisconsin and Michigan lakes and streams, where it is hybridizing with and displacing resident O. propinquus. Here we report on a study investigating the dynamics of a hybrid zone between the two crayfish in Trout Lake, Wisconsin, where both the time (circa 1979) and location of the initial introduction are known. Our prediction was that hybridization should hasten the demise of O. propinquus because we expected that male O. rusticus (which are larger than congeners) would outcompete male O. propinquus for mates of both species. If hybrid progeny are unfit, then the result would be decreased reproductive output of O. propinquus females. However, we found a pattern of cytonuclear disequilibrium between allozymes and mtDNA suggesting that a majority (94.5%) of F1 hybrids resulted from matings between O. rusticus females and O. propinquus males. Also contrary to expectations, fecundity (O. rusticus and O. propinquus) and early hybrid survivorship did not differ significantly from nonhybrids. Moreover, adults of mixed ancestry were superior to both O. rusticus and O. propinquus in competition for a limiting food resource. Using a single-locus model, we estimated that hybridization increases the advance of O. rusticus genes in Trout Lake between 4.8% and 36.3% above that due to the previously documented ecological interactions. Consequently, whereas hybridization may be hastening the elimination of genetically pure O. propinquus, introgression is nevertheless slowing the loss of O. propinquus nuclear genes. Although our results suggest that O. rusticus and O. propinquus may not be true species under the biological concept, their ecological differences are of great conservation importance.}, } @article {pmid11468795, year = {2001}, author = {Müller-Wille, S}, title = {Gardens of paradise.}, journal = {Endeavour}, volume = {25}, number = {2}, pages = {49-54}, doi = {10.1016/s0160-9327(00)01358-2}, pmid = {11468795}, issn = {0160-9327}, mesh = {Botany/*history ; History, 18th Century ; Sweden ; }, abstract = {Two hundred and fifty years ago, the Swedish naturalist Carolus Linnaeus (1707-1778) published his Philosophia botanica. This textbook in botanical science was widely read well into the 19th century. Today it is remembered mainly for two things: the introduction of binomial nomenclature and the formulation of a fixist and creationist species concept. While the former achievement is seen as a practical tool, still applicable for purposes of identification and information retrieval, the latter is usually deemed to have been one of the main obstacles to scientific progress in biology. That both achievements were not independent of each other, but interlocked theoretically and grounded in a specific scientific practice still thriving today--the collection of plant specimens in botanical gardens--is usually overlooked. The following article tries to uncover these connections and to demonstrate the significance that Linnaeus' achievements had for modern biology.}, } @article {pmid11413654, year = {2000}, author = {Perkins, SL}, title = {Species concepts and malaria parasites: detecting a cryptic species of Plasmodium.}, journal = {Proceedings. Biological sciences}, volume = {267}, number = {1459}, pages = {2345-2350}, pmid = {11413654}, issn = {0962-8452}, mesh = {Animals ; Base Sequence ; Caribbean Region ; Cytochrome b Group/genetics ; DNA Primers/genetics ; DNA, Protozoan/genetics ; Lizards/parasitology ; Phylogeny ; Plasmodium/*classification/*genetics/isolation & purification ; Species Specificity ; }, abstract = {Species of malaria parasite (phylum Apicomplexa: genus Plasmodium) have traditionally been described using the similarity species concept (based primarily on differences in morphological or life-history characteristics). The biological species concept (reproductive isolation) and phylogenetic species concept (based on monophyly) have not been used before in defining species of Plasmodium. Plasmodium azurophilum, described from Anolis lizards in the eastern Caribbean, is actually a two-species cryptic complex. The parasites were studied from eight islands, from Puerto Rico in the north to Grenada in the south. Morphology of the two species is very similar (differences are indistinguishable to the eye), but one infects only erythrocytes and the other only white blood cells. Molecular data for the cytochrome b gene reveal that the two forms are reproductively isolated; distinct haplotypes are present on each island and are never shared between the erythrocyte-infecting and leucocyte-infecting species. Each forms a monophyletic lineage indicating that they diverged before becoming established in the anoles of the eastern Caribbean. This comparison of the similarity, biological and phylogenetic species concepts for malaria parasites reveals the limited value of using only similarity measures in defining protozoan species.}, } @article {pmid11403874, year = {2001}, author = {Benton, MJ and Pearson, PN}, title = {Speciation in the fossil record.}, journal = {Trends in ecology & evolution}, volume = {16}, number = {7}, pages = {405-411}, doi = {10.1016/s0169-5347(01)02149-8}, pmid = {11403874}, issn = {1872-8383}, abstract = {It is easy to claim that the fossil record says nothing about speciation because the biological species concept (which relies on interbreeding) cannot be applied to it and genetic studies cannot be carried out on it. However, fossilized organisms are often preserved in sufficient abundance for populations of intergrading morphs to be recognized, which, by analogy with modern populations, are probably biological species. Moreover, the fossil record is our only reliable documentation of the sequence of past events over long time intervals: the processes of speciation are generally too slow to be observed directly, and permanent reproductive isolation can only be verified with hindsight. Recent work has shown that some parts of the fossil record are astonishingly complete and well documented, and patterns of lineage splitting can be examined in detail. Marine plankton appear to show gradual speciation, with subsequent morphological differentiation of lineages taking up to 500000 years to occur. Marine invertebrates and vertebrates more commonly show punctuated patterns, with periods of rapid speciation followed by long-term stasis of species lineages.}, } @article {pmid11403864, year = {2001}, author = {Hey, J}, title = {The mind of the species problem.}, journal = {Trends in ecology & evolution}, volume = {16}, number = {7}, pages = {326-329}, doi = {10.1016/s0169-5347(01)02145-0}, pmid = {11403864}, issn = {1872-8383}, abstract = {The species problem is the long-standing failure of biologists to agree on how we should identify species and how we should define the word 'species'. The innumerable attacks on the problem have turned the often-repeated question 'what are species?' into a philosophical conundrum. Today, the preferred form of attack is the well-crafted argument, and debaters seem to have stopped inquiring about what new information is needed to solve the problem. However, our knowledge is not complete and we have overlooked something. The species problem can be overcome if we understand our own role, as conflicted investigators, in causing the problem.}, } @article {pmid11403386, year = {2001}, author = {Kunz, W}, title = {Taking more care in using different species concepts--an opinion.}, journal = {Parasitology research}, volume = {87}, number = {5}, pages = {413-416}, doi = {10.1007/s004360000372}, pmid = {11403386}, issn = {0932-0113}, mesh = {Animals ; *Classification ; DNA, Ribosomal/analysis ; Parasitology/*methods ; Phylogeny ; Schistosoma/*classification/cytology/genetics ; Species Specificity ; }, } @article {pmid11353392, year = {2001}, author = {Rieder, S and Taourit, S and Mariat, D and Langlois, B and Guérin, G}, title = {Mutations in the agouti (ASIP), the extension (MC1R), and the brown (TYRP1) loci and their association to coat color phenotypes in horses (Equus caballus).}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {12}, number = {6}, pages = {450-455}, doi = {10.1007/s003350020017}, pmid = {11353392}, issn = {0938-8990}, mesh = {3' Untranslated Regions ; 5' Untranslated Regions ; Adaptor Proteins, Signal Transducing ; Alleles ; Animals ; Base Sequence ; *Carrier Proteins ; *Cell Adhesion Molecules ; Cell Cycle Proteins ; Cloning, Molecular ; Color ; DNA Mutational Analysis ; Exons ; Frameshift Mutation ; Genotype ; Helminth Proteins/chemistry/*genetics ; Horses ; Introns ; Membrane Glycoproteins/chemistry/*genetics ; Methionine/chemistry ; Models, Genetic ; Molecular Sequence Data ; *Mutation ; Phenotype ; Polymerase Chain Reaction ; Receptors, Pituitary Hormone/chemistry/*genetics ; Sequence Analysis, DNA ; Threonine/chemistry ; }, abstract = {Coat color genetics, when successfully adapted and applied to different mammalian species, provides a good demonstration of the powerful concept of comparative genetics. Using cross-species techniques, we have cloned, sequenced, and characterized equine melanocortin-1-receptor (MC1R) and agouti-signaling-protein (ASIP), and completed a partial sequence of tyrosinase-related protein 1 (TYRP1). The coding sequences and parts of the flanking regions of those genes were systematically analyzed in 40 horses and mutations typed in a total of 120 horses. Our panel represented 22 different horse breeds, including 11 different coat colors of Equus caballus. The comparison of a 1721-bp genomic fragment of MC1R among the 11 coat color phenotypes revealed no sequence difference apart from the known chestnut allele (C901T). In particular, no dominant black (ED) mutation was found. In a 4994-bp genomic fragment covering the three putative exons, two introns and parts of the 5'- and 3'-UTRs of ASIP, two intronic base substitutions (SNP-A845G and C2374A), a point mutation in the 3'-UTRs (A4734G), and an 11-bp deletion in exon 2 (ADEx2) were detected. The deletion was found to be homozygous and completely associated with horse recessive black coat color (Aa/Aa) in 24 black horses out of 9 different breeds from our panel. The frameshift initiated by ADEx2 is believed to alter the regular coding sequence, acting as a loss-of-function ASIP mutation. In TYRP1 a base substitution was detected in exon 2 (C189T), causing a threonine to methionine change of yet unknown function, and an SNP (A1188G) was found in intron 2.}, } @article {pmid11348499, year = {2001}, author = {Bond, JE and Hedin, MC and Ramirez, MG and Opell, BD}, title = {Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus.}, journal = {Molecular ecology}, volume = {10}, number = {4}, pages = {899-910}, doi = {10.1046/j.1365-294x.2001.01233.x}, pmid = {11348499}, issn = {0962-1083}, mesh = {Animals ; Biological Evolution ; California ; DNA, Mitochondrial/genetics ; Ecosystem ; Female ; *Genetics, Population ; Geography ; Haplotypes/*genetics ; Likelihood Functions ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spiders/anatomy & histology/classification/*genetics/physiology ; }, abstract = {Aptostichus simus is a trapdoor spider endemic to the coastal dunes of central and southern California and, on morphological grounds, is recognized as a single species. Mitochondrial DNA 16S rRNA sequences demonstrate that most populations are fixed for the same haplotype and that the population haplotypes from San Diego County, Los Angeles County, Santa Rosa Island, and Monterey County are extremely divergent (6-12%), with estimated separation times ranging from 2 to 6 million years. A statistical cluster analysis of morphological features demonstrates that this genetic divergence is not reflected in anatomical features that might signify ecological differentiation among these lineages. The species status of these divergent populations of A. simus depends upon the species concept utilized. If a time-limited genealogical perspective is employed, A. simus would be separated at the base into two genetically distinct species. This study suggests that species concepts based on morphological distinctiveness, in spider groups with limited dispersal capabilities, probably underestimate true evolutionary diversity.}, } @article {pmid11331468, year = {2001}, author = {Mochizuki, T and Sugita, Y and Makimura, K and Kim, JA and Kano, R and Takahashi, I and Okeke, CN and Kawasaki, M}, title = {[Advances in molecular biology of dermatophytes].}, journal = {Nihon Ishinkin Gakkai zasshi = Japanese journal of medical mycology}, volume = {42}, number = {2}, pages = {81-86}, doi = {10.3314/jjmm.42.81}, pmid = {11331468}, issn = {0916-4804}, mesh = {Actins/genetics ; Animals ; Arthrodermataceae/classification/genetics/*isolation & purification ; Cell Survival ; DNA, Ribosomal Spacer/genetics ; Humans ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single-Stranded Conformational ; RNA, Messenger/analysis ; Random Amplified Polymorphic DNA Technique ; }, abstract = {During the 44th meeting of The Japanese Society for Medical Mycology in Nagasaki, 2000, a forum was held entitled Advances in Molecular Biology of Dermatophytes. Based on the subject, target molecules and kind of approach, we selected seven presentations from over 100 of the poster abstracts. Six of them concerned identification and one concerned viability. Summaries of the 7 presentations are given in this article. Of presentations on the identification methods, 5 demonstrated their usefulness: 1) A sequence analysis of ITS 1 region in ribosomal DNA of several Microsporum species showed ITS 1 genospecies Arthroderma otae to be composed of A. otae, M. canis, M. equinum and M. audouinii. 2) RAPD may be useful for identifying isolates which are not clearly identifiable by conventional biological techniques. 3) Sequence analysis of CHS 1 was shown to be a rapid tool for species level identification of M. gypseum. 4) PCR-SSCP analysis was also useful for discrimination of dermatophytes with high reproducibility and sensitivity. 5) Strain identification of A. benhamiae isolates may be possible using RFLP analysis of NTS regions in ribosomal DNA. The other presentation concerning identification pointed out some important problems: RFLP of mitochondrial DNA and ITS sequencing of A. benhamiae showed that the results are sometimes in conflict with those obtained from biological techniques, or in some cases, between other molecular techniques. This implies that our concept of fungal species needs to be re-examined and perhaps amended. The presentation on viability introduced quantitative analysis of mRNA of ACT gene, a new application of a molecular technique. Since the mRNA expresses only in living cells, the method is highly useful as an indicator of fungal viability.}, } @article {pmid11331465, year = {2001}, author = {Makimura, K}, title = {Species identification system for dermatophytes based on the DNA sequences of nuclear ribosomal internal transcribed spacer 1.}, journal = {Nihon Ishinkin Gakkai zasshi = Japanese journal of medical mycology}, volume = {42}, number = {2}, pages = {61-67}, doi = {10.3314/jjmm.42.61}, pmid = {11331465}, issn = {0916-4804}, mesh = {Arthrodermataceae/*classification/genetics/isolation & purification ; Cluster Analysis ; DNA, Ribosomal Spacer/*genetics ; Humans ; *Sequence Analysis, DNA ; }, abstract = {This describes a new and reliable species identification and classification system for dermatophytes based on the cluster analysis of nuclear ribosomal internal transcribed spacer 1 (ITS1) DNA sequences. In this system, some phenotypically similar species construct a compact monophyleic cluster which seems to be a species. This ITS1 sequence based species is called an ITS1-genospecies. The classification of genospecies is a practical concept for DNA sequence based species identification. It is possible to perform species identification and/or strain typing of 25 major dermatophytes (anamorphic genera Trichophyton, Microsporum, Epidermophyton, and the teleomorphic genus Arthroderma), some of which are hard to identify from their morphological features, by demonstrating their dendrogram using this system.}, } @article {pmid11304947, year = {2001}, author = {Leng, YJ and Zhang, LM}, title = {Chinese phlebotomine sandflies of subgenus Adlerius nitzulescu, 1931 (Diptera: Psychodidae) and the identity of Phlebotomus sichuanensis Leng & Yin, 1983. Part I--Taxonomical study and geographical distribution.}, journal = {Parasite (Paris, France)}, volume = {8}, number = {1}, pages = {3-9}, doi = {10.1051/parasite/2001081003}, pmid = {11304947}, issn = {1252-607X}, mesh = {Animals ; China ; Female ; Male ; Phlebotomus/anatomy & histology/*classification ; Species Specificity ; }, abstract = {Four species of Adlerius phlebotomine sandflies have been recorded in China, namely: P. chinensis Newstead, 1916 (Pc), P. fengi Leng & Zhang, 1994; P. longiductus Parrot, 1928 and P. sichuanensis Leng & Yin, 1983 (Ps). Adlerius phlebotomies are the main vectors of visceral leishmaniasis (VL) in China; three of them are acknowledged as VL vectors and P. fengi is considered a potential VL vector for southwestern mountainous region. Different opinion has been raised to the validity of identity of Ps by some investigators from Shanghai and Shanxi who consider Ps to be a large type of Pc instead of an isolate species. The center of controversy is whether Ps is an isolate taxon or a large type of Pc. The present authors have carried out a series of comparative studies for these two flies on: 1 quantitative and qualitative morphological characters of four Chinese Adlerius phlebotomies; and 2. differences in geographical distribution. All specimens of Pc and Ps used in the present study are collected where their holotypes-paratypes were produced--West Mountain, West Suburb, Beijing and Lixian County, Sichuan Province. The results have forcefully proved that Ps is an isolate species instead of a so-called large type Pc according to the concept of species. The clarification of their taxonomical identities is meaningful because both of them are VL vectors in different epidemic areas in China; especially Ps is an important VL vector in high mountainous regions of southwestern China and some extend to the Loess Plateau of northwestern China, where VL still exists and it is also the first Phlebotomine sandfly discovered in Tibet, the locality being near Assam in India (Leng et al. 1990).}, } @article {pmid11298987, year = {2001}, author = {Templeton, AR}, title = {Using phylogeographic analyses of gene trees to test species status and processes.}, journal = {Molecular ecology}, volume = {10}, number = {3}, pages = {779-791}, doi = {10.1046/j.1365-294x.2001.01199.x}, pmid = {11298987}, issn = {0962-1083}, mesh = {Animals ; DNA/genetics ; *Evolution, Molecular ; *Genetic Variation ; Geography ; Humans ; *Phylogeny ; Species Specificity ; }, abstract = {A gene tree is an evolutionary reconstruction of the genealogical history of the genetic variation found in a sample of homologous genes or DNA regions that have experienced little or no recombination. Gene trees have the potential of straddling the interface between intra- and interspecific evolution. It is precisely at this interface that the process of speciation occurs, and gene trees can therefore be used as a powerful tool to probe this interface. One application is to infer species status. The cohesion species is defined as an evolutionary lineage or set of lineages with genetic exchangeability and/or ecological interchangeability. This species concept can be phrased in terms of null hypotheses that can be tested rigorously and objectively by using gene trees. First, an overlay of geography upon the gene tree is used to test the null hypothesis that the sample is from a single evolutionary lineage. This phase of testing can indicate that the sampled organisms are indeed from a single lineage and therefore a single cohesion species. In other cases, this null hypothesis is not rejected due to a lack of power or inadequate sampling. Alternatively, this null hypothesis can be rejected because two or more lineages are in the sample. The test can identify lineages even when hybridization and lineage sorting occur. Only when this null hypothesis is rejected is there the potential for more than one cohesion species. Although all cohesion species are evolutionary lineages, not all evolutionary lineages are cohesion species. Therefore, if the first null hypothesis is rejected, a second null hypothesis is tested that all lineages are genetically exchangeable and/or ecologically interchangeable. This second test is accomplished by direct contrasts of previously identified lineages or by overlaying reproductive and/or ecological data upon the gene tree and testing for significant transitions that are concordant with the previously identified lineages. Only when this second null hypothesis is rejected is a lineage elevated to the status of cohesion species. By using gene trees in this manner, species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation. When one or more of the null hypotheses cannot be rejected, this procedure also provides specific guidance for future work that will be needed to judge species status.}, } @article {pmid11258098, year = {2000}, author = {Silverstein, AM}, title = {Pasteur, Pastorians, and the dawn of immunology: the importance of specificity.}, journal = {History and philosophy of the life sciences}, volume = {22}, number = {1}, pages = {29-41}, pmid = {11258098}, issn = {0391-9714}, mesh = {Allergy and Immunology/*history ; Animals ; Bacteriology/*history ; France ; History, 19th Century ; Humans ; Species Specificity ; }, abstract = {Throughout his career, the problems that attracted Louis Pasteur almost invariably involved considerations of specificity of structure and/or of action. Thus, his work on asymmetric crystals showed that chemical form not only specifies crystalline structure, but affects the affinity of ferments as well. In his studies of diseases of silkworms, of beer, and of wine, he could unerringly distinguish with the microscope the specific agents of disease. From this emerged his concept of the specificity of species and against the nonspecificity of spontaneous generation, whence the germ theory of disease. It was in the new field of immunology, however, where the manifestations of an exquisite specificity were most clearly seen. Here, Pasteur's vaccines worked because he chose the specific pathogen in order to induce a specific immunity, and he succeeded each time. But the two most prominent Pastorian successors in immunology, Elie Metchnikoff and Jules Bordet, were not equally successful. Although each contributed significantly to the birth of immunology, each advanced a theory that neglected the principle of specificity and paid a price in consequence. Metchnikoff's phagocytic theory of immunity could not survive the demonstrable specificity of humoral antibodies, while Bordet's physical adsorptive concept of the antibody-cell interaction quickly fell to Paul Ehrlich's demonstration of the stereochemical determination of immunological specificity.}, } @article {pmid11199480, year = {2000}, author = {Schweiger, M and Erhard, MH and Amselgruber, WM}, title = {Cell-specific localization of the cholecystokininA receptor in the porcine pancreas.}, journal = {Anatomia, histologia, embryologia}, volume = {29}, number = {6}, pages = {357-361}, doi = {10.1046/j.1439-0264.2000.00286.x}, pmid = {11199480}, issn = {0340-2096}, mesh = {Animals ; Immunohistochemistry ; Intestinal Mucosa/metabolism ; Islets of Langerhans/*anatomy & histology/physiology ; Pancreas/*anatomy & histology/metabolism ; Receptor, Cholecystokinin A ; Receptors, Cholecystokinin/*isolation & purification/physiology ; Staining and Labeling ; Swine ; }, abstract = {Cholecystokinin (CCK) produced in the mucosa of the upper small intestine exerts several biological functions. Its secretion in physiological amounts is modulated by the interaction of extracellular regulators and by binding to intracellular receptors of the target cells. The relative affinity of CCK to its receptor has been characterized in various biological and pharmacological studies and it is now well established that CCK has a higher affinity to the CCKA than to the CCKB receptor. Furthermore CCK influences the secretion of pancreatic enzymes in several species but very little is known about the relationship between CCK and the islet hormone-producing cells in the pig pancreas. The localization of this receptor at the cellular level showed conflicting results in animal studies and has not been described in pigs. The aim of the present study was to characterize the precise cellular location of the CCKA receptor in the porcine pancreas. Polyclonal antiserum was raised against the N-terminal epitope of the CCKA receptor molecule and used for localization studies. Using immunohistochemistry on methanol/acetic acid-fixed, paraffin-embedded pancreas, the CCKA receptor could successfully be localized in islet cells. Parallel staining of serial sections with antibodies directed against insulin and glucagon revealed colocalization with glucagon in alpha cells. No immunoreaction was found in the exocrine pancreas. Our results support the concept that in the porcine species the stimulation of the exocrine pancreas is mediated by the CCKB rather than the CCKA receptor, as it is known for the rat species.}, } @article {pmid11159132, year = {2000}, author = {Spooner, DM and Van Den Berg, RG and Miller, JT}, title = {Species and series boundaries of Solanum series Longipedicellata (Solanaceae) and phenetically similar species in ser. Demissa and ser. Tuberosa: implications for a practical taxonomy of Section Petota.}, journal = {American journal of botany}, volume = {88}, number = {1}, pages = {113-130}, pmid = {11159132}, issn = {1537-2197}, abstract = {Species boundaries were assessed by phenetic analyses of morphological data for all species of wild potatoes (SOLANUM: section PETOTA:) assigned to ser. LONGIPEDICELLATA: S. fendleri, S. hjertingii, S. matehualae, S. papita, S. polytrichon, and S. stoloniferum. These six tetraploid species grow in the southeastern United States (S. fendleri) and Mexico (all six species). We also analyzed morphologically similar species in ser. DEMISSA: (S. demissum) and ser. TUBEROSA: (S. avilesii, S. gourlayi, S. verrucosum). We chose S. verrucosum and S. demissum as Mexican representatives, and S. avilesii and S. gourlayi as South American representatives of other series that are difficult to distinguish from ser. LONGIPEDICELLATA: We also analyzed morphologically more dissimilar species in ser. TUBEROSA: (S. berthaultii) and ser. YUNGASENSIA: (S. chacoense). The results support only three species in ser. LONGIPEDICELLATA: (1) S. polytrichon, (2) S. hjertingii + S. matehualae, (3) S. fendleri + S. papita + S. stoloniferum. Solanum avilesii, S. gourlayi, and to a lesser extent S. demissum and S. verrucosum are very similar to members of ser. LONGIPEDICELLATA: and are difficult to distinguish practically from them, despite differences in chromosome numbers and crossability relationships. These data help document and explain the extensive taxonomic difficulty in sect. Petota, highlight conflicts between biological and morphological species concepts, and add to a growing body of evidence that too many wild potato species are recognized.}, } @article {pmid11157162, year = {2001}, author = {Li, XL and Kuznetsov, AE and Zhang, HF and Boldyrev, AI and Wang, LS}, title = {Observation of all-metal aromatic molecules.}, journal = {Science (New York, N.Y.)}, volume = {291}, number = {5505}, pages = {859-861}, doi = {10.1126/science.291.5505.859}, pmid = {11157162}, issn = {0036-8075}, abstract = {Aromaticity is a concept invented to account for the unusual stability of an important class of organic molecules: the aromatic compounds. Here we report experimental and theoretical evidence of aromaticity in all-metal systems. A series of bimetallic clusters with chemical composition MAl4- (M = Li, Na, or Cu), was created and studied with photoelectron spectroscopy and ab initio calculations. All the MAl4- species possess a pyramidal structure containing an M+ cation interacting with a square Al4(2-) unit. Ab initio studies indicate that Al4(2-) exhibits characteristics of aromaticity with two delocalized pi electrons (thus following the 4n + 2 electron counting rule) and a square planar structure and maintains its structural and electronic features in all the MAl4- complexes. These findings expand the aromaticity concept into the arena of all-metal species.}, } @article {pmid11152940, year = {2001}, author = {Rosselló-Mora, R and Amann, R}, title = {The species concept for prokaryotes.}, journal = {FEMS microbiology reviews}, volume = {25}, number = {1}, pages = {39-67}, doi = {10.1111/j.1574-6976.2001.tb00571.x}, pmid = {11152940}, issn = {0168-6445}, mesh = {Bacteria/*classification/genetics ; Nucleic Acid Hybridization ; Phenotype ; *Phylogeny ; Prokaryotic Cells/*classification ; Species Specificity ; }, abstract = {The species concept is a recurrent controversial issue that preoccupies philosophers as well as biologists of all disciplines. Prokaryotic species concept has its own history and results from a series of empirical improvements parallel to the development of the techniques of analysis. Among the microbial taxonomists, there is general agreement that the species concept currently in use is useful, pragmatic and universally applicable within the prokaryotic world. However, this empirically designed concept is not encompassed by any of the, at least, 22 concepts described for eukaryotes. The species could be described as 'a monophyletic and genomically coherent cluster of individual organisms that show a high degree of overall similarity in many independent characteristics, and is diagnosable by a discriminative phenotypic property'. We suggest to refer it as a phylo-phenetic species concept. Here, we discuss the validity of the concept in use which we believe is more pragmatic in comparison with those concepts described for eukaryotes.}, } @article {pmid11118132, year = {2000}, author = {Taylor, JW and Jacobson, DJ and Kroken, S and Kasuga, T and Geiser, DM and Hibbett, DS and Fisher, MC}, title = {Phylogenetic species recognition and species concepts in fungi.}, journal = {Fungal genetics and biology : FG & B}, volume = {31}, number = {1}, pages = {21-32}, doi = {10.1006/fgbi.2000.1228}, pmid = {11118132}, issn = {1087-1845}, mesh = {Evolution, Molecular ; Fungi/*classification/genetics/physiology ; *Phylogeny ; Species Specificity ; }, abstract = {The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.}, } @article {pmid11091315, year = {2000}, author = {Rosenbaum, HC and Brownell, RL and Brown, MW and Schaeff, C and Portway, V and White, BN and Malik, S and Pastene, LA and Patenaude, NJ and Baker, CS and Goto, M and Best, PB and Clapham, PJ and Hamilton, P and Moore, M and Payne, R and Rowntree, V and Tynan, CT and Bannister, JL and DeSalle, R}, title = {World-wide genetic differentiation of Eubalaena: questioning the number of right whale species.}, journal = {Molecular ecology}, volume = {9}, number = {11}, pages = {1793-1802}, doi = {10.1046/j.1365-294x.2000.01066.x}, pmid = {11091315}, issn = {0962-1083}, mesh = {Animals ; Atlantic Ocean ; Base Sequence ; DNA, Mitochondrial/genetics ; Databases, Factual ; Genetic Variation ; Genetics, Population ; Pacific Ocean ; Phylogeny ; Species Specificity ; Whales/*genetics ; }, abstract = {Few studies have examined systematic relationships of right whales (Eubalaena spp.) since the original species descriptions, even though they are one of the most endangered large whales. Little morphological evidence exists to support the current species designations for Eubalaena glacialis in the northern hemisphere and E. australis in the southern hemisphere. Differences in migratory behaviour or antitropical distribution between right whales in each hemisphere are considered a barrier to gene flow and maintain the current species distinctions and geographical populations. However, these distinctions between populations have remained controversial and no study has included an analysis of all right whales from the three major ocean basins. To address issues of genetic differentiation and relationships among right whales, we have compiled a database of mitochondrial DNA control region sequences from right whales representing populations in all three ocean basins that consist of: western North Atlantic E. glacialis, multiple geographically distributed populations of E. australis and the first molecular analysis of historical and recent samples of E. glacialis from the western and eastern North Pacific Ocean. Diagnostic characters, as well as phylogenetic and phylogeographic analyses, support the possibility that three distinct maternal lineages exist in right whales, with North Pacific E. glacialis being more closely related to E. australis than to North Atlantic E. glacialis. Our genetic results provide unequivocal character support for the two usually recognized species and a third distinct genetic lineage in the North Pacific under the Phylogenetic Species Concept, as well as levels of genetic diversity among right whales world-wide.}, } @article {pmid11023890, year = {2000}, author = {Zhu, C and Williams, TE}, title = {Modeling concurrent binding of multiple molecular species in cell adhesion.}, journal = {Biophysical journal}, volume = {79}, number = {4}, pages = {1850-1857}, pmid = {11023890}, issn = {0006-3495}, support = {AI38282/AI/NIAID NIH HHS/United States ; GM08433/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Binding, Competitive ; Biophysical Phenomena ; Biophysics ; Cell Adhesion/*physiology ; Kinetics ; Ligands ; *Models, Biological ; Receptors, Cell Surface/physiology ; }, abstract = {Cell adhesion provides not only physical linkage but also communication between the cell and its environment. As such, it is important to many cellular functions. Recently, the probability distribution of forming a low number of specific adhesive bonds in a short-duration contact has been described (Chesla et al., Biophys. J. , 1998, 75:1553-1572). This model assumes that binding occurs between a single receptor species and a single ligand species. However, cell adhesion molecules rarely work alone in physiological settings. To account for these in vivo situations, we extended the previous model to include concurrent interactions of multiple receptor-ligand species, introducing the concept of independent binding. Closed-form solutions have been obtained for cases where competition is absent or can be neglected. In two companion papers (Williams et al., Biophys. J., 2000, 79:1858-1866; 2000, 79:1867-1875), the model developed herein has been applied to analyze two sets of experiments designed such that the validity of the theory was also tested.}, } @article {pmid11016897, year = {2000}, author = {Zawalich, WS and Bonnet-Eymard, M and Zawalich, KC}, title = {Insulin secretion, inositol phosphate levels, and phospholipase C isozymes in rodent pancreatic islets.}, journal = {Metabolism: clinical and experimental}, volume = {49}, number = {9}, pages = {1156-1163}, doi = {10.1053/meta.2000.8613}, pmid = {11016897}, issn = {0026-0495}, support = {NIDDK 41230/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Blotting, Western ; Carbachol/pharmacology ; Enzyme Activation/drug effects ; Glucose/metabolism/pharmacology ; Inositol Phosphates/*metabolism ; Insulin/*metabolism ; Insulin Secretion ; Islets of Langerhans/chemistry/drug effects/*physiology ; Isoenzymes/*metabolism ; Keto Acids/pharmacology ; Kinetics ; Male ; Mice ; Proteins/analysis ; Rats ; Rats, Sprague-Dawley ; Type C Phospholipases/*metabolism ; }, abstract = {During a dynamic perifusion, 20 mmol/L glucose, 20 mmol/L alpha-ketoisocaproate (KIC) or 20 mmol/L methyl pyruvate (MP) stimulate biphasic insulin secretory responses from collagenase-isolated rat islets. Peak first-phase insulin responses were comparable for all 3 nutrient agonists. The largest second-phase insulin secretory response was evoked by 20 mmol/L glucose (30-fold above basal release rates), and this response was more sustained than that observed with either 20 mmol/L KIC or 20 mmol/L MP. When mouse islets were perifused under similar conditions, KIC stimulated the largest first-phase insulin response, while comparable acute insulin secretion rates were obtained with glucose- or MP-stimulated islets. In contrast to rat islets, the sustained second phase of insulin secretion from mouse islets was minimal regardless of the nutrient secretagogue used. This anomalous response of mouse islets as compared with rat islets could not be ascribed to any obvious difference in the glucose usage rate or insulin content between these 2 species. Glucose, KIC, or MP stimulated significant increases in 3H-inositol phosphates in rat islets. Significantly smaller increases were measured in mouse islets. Comparative Western blot analyses showed pronounced species differences in the expression of phospholipase Cbeta1 (PLCbeta1), PLCbeta2, PLCbeta3, and PLCdelta1 but not PLCgamma1 or protein kinase Calpha (PKCalpha) between rat and mouse islets. PLCbeta4 or PLCdelta2 could not be identified in either species. These findings are consistent with the concept that the underexpression of the nutrient-activated PLC isozyme may account for the minimal inositol phosphate (IP) and second-phase insulin secretory response from mouse islets.}, } @article {pmid11004945, year = {1999}, author = {Stamos, DN}, title = {Darwin's species category realism.}, journal = {History and philosophy of the life sciences}, volume = {21}, number = {2}, pages = {137-186}, pmid = {11004945}, issn = {0391-9714}, mesh = {*Biological Evolution ; Breeding ; *Classification ; Fertility ; History, 19th Century ; Selection, Genetic ; *Species Specificity ; }, abstract = {Ever since Charles Darwin's On the Origin of Species was published, the received view has been that Darwin literally thought of species as not extra-mentally real. In 1969 Michael Ghiselin upset the received view by interpreting Darwin to mean that species taxa are indeed real but not the species category. In 1985 John Beatty took Ghiselin's thesis a step further by providing a strategy theory to explain why Darwin would say one thing (his repeated nominalistic definition of species) and do another (hold that species taxa are real). In the present paper I attempt to take this line of interpretation to a new level. Guided by the principle of charity, I provide and analyze a considerable amount of evidence from Darwin's mature writings (both private and published) to show that (contra Ghiselin and Beatty) Darwin did not simply accept the species delimitations of his fellow naturalists but actually employed, repeatedly and consistently, a species concept in a thoroughly modern sense, albeit with an implicit definition, a concept uniquely his own and fully in accord with his theory of evolution by natural selection. This implicit concept and definition is carefully reconstructed in the present paper. A new strategy theory is then provided to account for why Darwin would define species (both taxa and category) nominalistically on the one hand but delimit species realistically on the other.}, } @article {pmid10989306, year = {2000}, author = {Lan, R and Reeves, PR}, title = {Intraspecies variation in bacterial genomes: the need for a species genome concept.}, journal = {Trends in microbiology}, volume = {8}, number = {9}, pages = {396-401}, doi = {10.1016/s0966-842x(00)01791-1}, pmid = {10989306}, issn = {0966-842X}, mesh = {Bacteria/*classification/genetics ; Biological Evolution ; Enterobacteriaceae/genetics ; *Genetic Variation ; *Genome, Bacterial ; Helicobacter pylori/genetics ; Neisseria meningitidis/genetics ; *Species Specificity ; }, abstract = {Bacterial populations are clonal. Their evolution involves not only divergence between orthologous genes but also gain of genes from other clones or species, which has only recently been widely appreciated through macrorestriction mapping, genomic subtraction and complete genome sequencing. Genes can also be lost in response to selection or by random mutation after becoming redundant. The bacterial genome is a dynamic structure and intraspecies variation needs to be included in genome analysis if we are to gain insight into the full species genome.}, } @article {pmid10984836, year = {2000}, author = {Singh, RS and Kulathinal, RJ}, title = {Sex gene pool evolution and speciation: a new paradigm.}, journal = {Genes & genetic systems}, volume = {75}, number = {3}, pages = {119-130}, doi = {10.1266/ggs.75.119}, pmid = {10984836}, issn = {1341-7568}, mesh = {Animals ; *Evolution, Molecular ; *Gene Pool ; Humans ; Reproduction/genetics/physiology ; Sex Characteristics ; *Sex Determination Processes ; Species Specificity ; }, abstract = {In this paper, we review the literature on the growing body of data demonstrating the rapid evolution of sex and reproduction related (SRR) genes and show how a paradigm shift to the study of SRR genes can provide new approaches to solving some of the old problems in evolutionary biology. The argument is based on (1) the growing scope and importance of sexual selection in evolution, (2) the growing number of case studies showing rapid evolution of sexual traits in a wide variety of taxa, (3) the faster rate of DNA sequence divergence in genes affecting sexual function and fertility, (4) the evidence for the involvement of novel traits/genes in sexual functions, and (5) a proposed sex/non-sex dichotomy of the gene pool affecting viability versus fertility. It is argued that the adoption of the sex/non-sex dichotomy of genes/traits can provide new perspectives on such problems as species concepts, modes (allopatric/sympatric) of speciation, Haldane's rule, reinforcement, and the founder effect. It is proposed that the evolutionary study of genes affecting viability versus fertility is the key to understanding the genetic basis of speciation.}, } @article {pmid10971688, year = {2000}, author = {Koh, HS and Lee, WJ and Kocher, TD}, title = {The genetic relationships of two subspecies of striped field mice, Apodemus agrarius coreae and Apodemus agrarius chejuensis.}, journal = {Heredity}, volume = {85 (Pt 1)}, number = {}, pages = {30-36}, doi = {10.1046/j.1365-2540.2000.00723.x}, pmid = {10971688}, issn = {0018-067X}, mesh = {Animals ; Body Constitution ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Variation ; Genotype ; Haplotypes ; Mice/*genetics ; Models, Genetic ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {We obtained 282 base pairs of sequence for the mitochondrial control region of 70 individuals of Korean striped field mice Apodemus agrarius coreae and Apodemus agrarius chejuensis to determine the levels of genetic divergence between these morphologically distinct taxa. The DNA sequences showed more genetic diversity (pi) in A. agrarius coreae (2.98%) than in A. agrarius chejuensis (1.86%). Our data do not support the current concept that the two morphotypes are different species, but phylogenetic analysis indicates that animals of A. agrarius coreae with large body size from Wan Island cluster with the large-bodied A. agrarius chejuensis, and should be included in that taxon. As currently accepted A. agrarius coreae is not strictly monophyletic, because the large-bodied samples cluster within the range of mitochondrial variation of A. agrarius chejuensis. The fact that the two morphotypes do not share mitochondrial haplotypes (chi2=66, P < 0.001) suggests that there is little gene flow between them. A molecular clock estimate suggests that the two subspecies might have been isolated at the time of separation of the islands from the mainland.}, } @article {pmid10955909, year = {2000}, author = {Varga, J and Tóth, B and Rigó, K and Téren, J and Hoekstra, RF and Kozakiewicz, Z}, title = {Phylogenetic analysis of Aspergillus section Circumdati based on sequences of the internal transcribed spacer regions and the 5.8 S rRNA gene.}, journal = {Fungal genetics and biology : FG & B}, volume = {30}, number = {1}, pages = {71-80}, doi = {10.1006/fgbi.2000.1204}, pmid = {10955909}, issn = {1087-1845}, mesh = {Aspergillus/classification/*genetics/physiology ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/*genetics ; Evolution, Molecular ; Genes, rRNA/genetics ; Phenotype ; *Phylogeny ; RNA, Ribosomal, 5.8S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Phenotypic features and sequences of the internal transcribed spacer (ITS) regions and the 5.8 S rRNA gene of type or neotype strains and other isolates of the 17 species currently assigned to Aspergillus section Circumdati and some potentially related species were analyzed. Parsimony analysis of sequence data indicated that Aspergillus section Circumdati is paraphyletic. Aspergillus campestris, A. lanosus, and A. dimorphicus with A. sepultus were found to be more closely related to Aspergillus sections Candidi, Flavi, and Cremei, respectively. These results were also supported by phenotypic data. A. robustus and A. ochraceoroseus were found not to be related to any of the species examined. Species of the proposed revised Aspergillus section Circumdati formed two main clades, which could also be distinguished based on phenotypic methods. Phylogenetic analysis of sequence data of other isolates assigned to species of the revised section indicates that either some of these isolates were misidentified or species concepts of A. ochraceus, A. melleus, and A. petrakii should be reconsidered.}, } @article {pmid10912248, year = {2000}, author = {van den Berg, M and Peterson, RE and Schrenk, D}, title = {Human risk assessment and TEFs.}, journal = {Food additives and contaminants}, volume = {17}, number = {4}, pages = {347-358}, doi = {10.1080/026520300283414}, pmid = {10912248}, issn = {0265-203X}, mesh = {Animals ; Benzofurans/adverse effects ; Dibenzofurans, Polychlorinated ; Dioxins/*adverse effects ; Environmental Pollutants/*adverse effects ; Humans ; Polychlorinated Biphenyls/adverse effects ; Polychlorinated Dibenzodioxins/adverse effects/analogs & derivatives ; Risk Assessment/methods/standards ; Species Specificity ; }, abstract = {The concept of toxic equivalency factors (TEFs) has been developed to facilitate risk assessment and regulatory control of exposure to complex PCDD, PCDF and PCB mixtures. Recently the European Centre for Environment and Health of the World Health Organization (WHO-ECEH) and the International Programme on Chemical Safety (IPCS) jointly re-evaluated the TEFs of PCDDs, PCDFs and dioxin-like PCBs for mammals and derived consensus TEFs for birds and fish (Stockholm, 1997). From a mechanistic point of view it can be concluded that, although the quantitative response will vary depending on the congener involved, the occurrence of a common mechanism (binding to the Ah receptor) legitimates the use of the TEF concept across species. But there also is criticism regarding the TEF concept. Pharmacokinetic differences between species can significantly influence the TEF value, and uncertainties due to additive or non-additive interactions, to differences in species responsiveness and to differences in the shape of the dose-response curve might hamper the derivation of consensus TEF values. In this context it should be noted, however, that using TCDD alone, as the only measure of exposure to dioxin-like PCDDs, PCDFs and PCBs, would severely underestimate the risk from exposure to these compounds. Therefore, it can be concluded that, for pragmatic reasons, the TEF concept remains the most feasible approach for risk assessment purposes, in spite of the uncertainties associated with its use.}, } @article {pmid10906700, year = {2000}, author = {Vanderhorst, VG and Terasawa, E and Ralston, HJ and Holstege, G}, title = {Monosynaptic projections from the nucleus retroambiguus to motoneurons supplying the abdominal wall, axial, hindlimb, and pelvic floor muscles in the female rhesus monkey.}, journal = {The Journal of comparative neurology}, volume = {424}, number = {2}, pages = {233-250}, doi = {10.1002/1096-9861(20000821)424:2<233::aid-cne4>3.0.co;2-c}, pmid = {10906700}, issn = {0021-9967}, support = {NS 23347/NS/NINDS NIH HHS/United States ; RR00167/RR/NCRR NIH HHS/United States ; }, mesh = {Abdominal Muscles/*innervation/physiology ; Animals ; Back/*innervation/physiology ; Female ; Hindlimb/*innervation/physiology ; Lumbar Vertebrae ; Macaca mulatta/*anatomy & histology/physiology ; Medulla Oblongata/*cytology/physiology ; Motor Neurons/physiology/*ultrastructure ; Neural Pathways/physiology/*ultrastructure ; Pelvic Floor/*innervation/physiology ; Presynaptic Terminals/physiology/ultrastructure ; Respiratory Center/*cytology/physiology ; Sexual Behavior, Animal/physiology ; Spinal Cord/physiology/*ultrastructure ; }, abstract = {The nucleus retroambiguus (NRA) consists of premotor neurons in the caudal medulla. It is involved in expiration, vomiting, vocalization, and probably reproductive behavior by means of projections to distinct motoneuronal cell groups. Because no information is available about the NRA and its efferent pathways in primates, the present study examines NRA projections to the lumbosacral spinal cord in female rhesus monkeys. To identify the NRA, wheat germ agglutinin-horseradish peroxidase (WGA-HRP) was injected into the lumbosacral cord in three monkeys. To study the distribution of NRA axons in the lumbosacral cord, WGA-HRP injections were made into the NRA in seven monkeys. To identify motoneuronal cell groups receiving input from the NRA, the same seven monkeys also received cholera toxin subunit b (CTb) injections into different hindlimb, axial, and pelvic floor muscles. The results show that NRA neurons projecting to the lumbosacral cord are mainly located between 1 to 4 mm caudal to the obex. They send numerous axons to external oblique and pelvic floor motoneurons, whereas projections to iliopsoas and axial motoneurons are less numerous. The projections are bilateral, but show a clear contralateral predominance in the iliopsoas, axial, and pelvic floor motoneuronal cell groups. At the ultrastructural level, NRA-terminal profiles make asymmetrical contacts with labeled and unlabeled dendrites in these motoneuronal cell groups and contain large amounts of spherical and a few dense core vesicles. It is concluded that the NRA is well developed in the monkey and that there exists a direct pathway from the NRA to lumbosacral motoneurons in this species. The finding that the NRA projects to a somewhat different set of motoneuronal cell groups compared with other species fits the concept that it is not only involved in expiration-related activities but also in species specific receptive and submissive behavior.}, } @article {pmid10904411, year = {2000}, author = {Dujardin, JC and Henriksson, J and Victoir, K and Brisse, S and Gamboa, D and Arevalo, J and Le Ray, D}, title = {Genomic rearrangements in trypanosomatids: an alternative to the "one gene" evolutionary hypotheses?.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {95}, number = {4}, pages = {527-534}, doi = {10.1590/s0074-02762000000400015}, pmid = {10904411}, issn = {0074-0276}, mesh = {Animals ; *Evolution, Molecular ; *Gene Rearrangement ; *Genome, Protozoan ; Karyotyping ; Leishmania braziliensis/cytology/genetics ; Polymorphism, Genetic ; Trypanosoma cruzi/cytology/genetics ; Trypanosomatina/*genetics ; }, abstract = {Most molecular trees of trypanosomatids are based on point mutations within DNA sequences. In contrast, there are very few evolutionary studies considering DNA (re) arrangement as genetic characters. Waiting for the completion of the various parasite genome projects, first information may already be obtained from chromosome size-polymorphism, using the appropriate algorithms for data processing. Three illustrative models are presented here. First, the case of Leishmania (Viannia) braziliensis/L. (V.) peruviana is described. Thanks to a fast evolution rate (due essentially to amplification/deletion of tandemly repeated genes), molecular karyotyping seems particularly appropriate for studying recent evolutionary divergence, including eco-geographical diversification. Secondly, karyotype evolution is considered at the level of whole genus Leishmania. Despite the fast chromosome evolution rate, there is qualitative congruence with MLEE- and RAPD-based evolutionary hypotheses. Significant differences may be observed between major lineages, likely corresponding to major and less frequent rearrangements (fusion/fission, translocation). Thirdly, comparison is made with Trypanosoma cruzi. Again congruence is observed with other hypotheses and major lineages are delineated by significant chromosome rearrangements. The level of karyotype polymorphism within that "species" is similar to the one observed in "genus" Leishmania. The relativity of the species concept among these two groups of parasites is discussed.}, } @article {pmid10901844, year = {1999}, author = {Eloit, M}, title = {[Anthropozoonozes: the species barrier].}, journal = {Medecine tropicale : revue du Corps de sante colonial}, volume = {59}, number = {4 Pt 2}, pages = {435-441}, pmid = {10901844}, issn = {0025-682X}, mesh = {Animals ; Ecosystem ; Environmental Exposure ; Humans ; Mutation/genetics ; RNA Viruses/genetics/physiology ; Risk Factors ; Species Specificity ; Virus Diseases/immunology/*transmission ; Virus Replication/physiology ; Zoonoses/transmission/*virology ; }, abstract = {Various animal virus can infect humans with a wide range of clinical manifestations from subclinical to fatal. In theory transmission is also possible in a number of poorly defined situations. Several examples of interspecific contamination in animals and the emergence of new viral infections in animals have documented the ability of some viruses to cross the species barrier. The barrier concept is based on epidemiological factors lowering the probability of exposition to risk and molecular factors limiting or preventing viral replication in alien hosts. Although these mechanisms are generally effective, they can fail under circumstances. This is notably the case when changes in the ecosystem lead to the development of variants able to replicate in different hosts including man. An analysis of several mechanisms underlying the species barrier is also presented. Some viruses are prevented from entering the organism by the absence of suitable receptors, but development is possible if entrance is forced. Other viruses can enter but the organism but are unable to complete their developmental cycle. Study has shown that these inhibitory mechanisms correspond to interactions involving a small number of amino acids. Such a blockage could be leaky, especially for RNA viruses with a high mutation rate.}, } @article {pmid10901843, year = {1999}, author = {Baranowski, E and Ruiz-Jarabo, CM and Escarmis, C and Domingo, E}, title = {[Variability and development of viral populations: assessment and implications].}, journal = {Medecine tropicale : revue du Corps de sante colonial}, volume = {59}, number = {4 Pt 2}, pages = {430-434}, pmid = {10901843}, issn = {0025-682X}, mesh = {Antibiosis ; Antiviral Agents/therapeutic use ; Epitopes/immunology ; Genetic Variation ; Genome, Viral ; Humans ; Molecular Biology ; Mutation/genetics ; RNA Virus Infections/prevention & control ; RNA Viruses/genetics/immunology/*physiology ; Selection, Genetic ; Viral Load ; Viral Vaccines/immunology ; Virus Replication/genetics ; }, abstract = {RNA virus populations consist of complex distributions of closely related but not identical genomes known as viral quasi-species. The quasi-species concept describes the dynamics of these genomes subjected to a continuous process of variation, competition, and selection. Quasi-species dynamics has broad implications not only in the understanding of the molecular mechanisms underlying adaptation of RNA viruses but also in the design of strategies for control and prevention of viral disease. Viral load and genetic heterogeneity have a determinant influence on the adaptation of RNA virus to their environment. Vaccines designed to control diseases caused by highly variable viruses must contain several B and T epitopes to provide an ample and diversified immune response. Similarly, antiviral drugs should be used in combination therapy to minimize selection of resistant viruses. The theoretical model of quasi-species has opened the way for new antiviral therapies based on augmentation of the mutation rate during replication of viral RNA. Finally the quasi-species concept provides the basis for defining the selective factors that could influence the evolution of RNA virus and promote the emergence or reemergence of viral diseases.}, } @article {pmid10880860, year = {2000}, author = {Garay, J and Varga, Z}, title = {Strict ESS for n-species systems.}, journal = {Bio Systems}, volume = {56}, number = {2-3}, pages = {131-137}, doi = {10.1016/s0303-2647(00)00080-0}, pmid = {10880860}, issn = {0303-2647}, mesh = {Animals ; *Biological Evolution ; Humans ; *Models, Theoretical ; }, abstract = {A system of n asexual populations is considered where both intra- and interspecific frequency-dependent game conflicts with lack of information take place. The concept of a strict n-species ESS is introduced which implies local asymptotic stability of the replicator dynamics of pure phenotypes. The dynamical concept of strict stability is also introduced which turns out to be equivalent to the strict n-species ESS concept. The above notions are also related to similar concepts considered in the literature for the same biological situation.}, } @article {pmid10836510, year = {2000}, author = {Zander, CD and Reimer, LW and Barz, K and Dietel, G and Strohbach, U}, title = {Parasite communities of the Salzhaff (Northwest Mecklenburg, Baltic Sea) II. Guild communities, with special regard to snails, benthic crustaceans, and small-sized fish.}, journal = {Parasitology research}, volume = {86}, number = {5}, pages = {359-372}, doi = {10.1007/s004360050681}, pmid = {10836510}, issn = {0932-0113}, mesh = {Animals ; Baltic States ; Crustacea/*parasitology ; Ecosystem ; Fish Diseases/parasitology ; Fishes/*parasitology ; Host-Parasite Interactions ; Parasites/classification/*physiology ; Parasitic Diseases, Animal/epidemiology/*parasitology ; Prevalence ; *Seawater ; Snails/*parasitology ; }, abstract = {Metazoan parasites of guilds of benthic snails and crustaceans and of four fish families--Gobiidae, Gasterosteidae, Syngnathidae, and Zoarcidae--were investigated off the brackish Salzhaff area (Southwest Baltic) in the semienclosed Salzhaff and the near Rerik Riff in the free Baltic. Comparisons revealed greater similarities in parasite populations and communities within the fish guilds than between them. According to an evaluation of the core-/satellite-species concept using abundance values, the most important parasites of fish were some generalists, such as Cryptocotyle spp., Podocotyle atomon, and Diplostomum spathaceum, as well as some specialists, such as Acanthostomum balthicum, Thersitina gasterostei, and Aphalloides timmi. These specialists revealed high degrees of prevalence in their main hosts and lower degrees in one or two by-hosts. Additional importance is assigned to parasites that cause harm to their hosts due to their large size, e.g., Schistocephalus spp., or via massive infestation, e.g., several digenean metacercariae. Because specialists were more prominent in snails and fish from the Rerik Riff, the correlation of host numbers with prevalence resulted in only a slight increase instead of a more rapid rise in regression among crustaceans and fish from the entire Salzhaff, where the generalists were more prevalent. The selected host guilds demonstrated the entire life cycles of three digeneans (P. atomon, A. balthicum, A. timmi), one acanthocephalan (Echinorhynchus gadi), and one nematode (Hysterothylacium sp.). The prevalence increased in these cycles from host level to host level and attained relatively high values in all guilds. The parasite fauna of the Salzhaff area is influenced by eutrophication stress, which leads to a high level of productivity and, consequently, to great densities in primary consumers such as snails and crustaceans. These are attractive for several secondary consumers such as fish and birds, which is the reason for the existence of at least 24 autogenic and 20 allogenic parasite species at this locality. The slight surplus of the first category indicates a yet-balanced environment in the investigation area.}, } @article {pmid19270959, year = {2000}, author = {Kaplan, DT and Thomas, WK and Frisse, LM and Sarah, JL and Stanton, JM and Speijer, PR and Marin, DH and Opperman, CH}, title = {Phylogenetic Analysis of Geographically Diverse Radopholus similis via rDNA Sequence Reveals a Monomorphic Motif.}, journal = {Journal of nematology}, volume = {32}, number = {2}, pages = {134-142}, pmid = {19270959}, issn = {0022-300X}, abstract = {The nucleic acid sequences of rDNA ITS1 and the rDNA D2/D3 expansion segment were compared for 57 burrowing nematode isolates collected from Australia, Cameroon, Central America, Cuba, Dominican Republic, Florida, Guadeloupe, Hawaii, Nigeria, Honduras, Indonesia, Ivory Coast, Puerto Rico, South Africa, and Uganda. Of the 57 isolates, 55 were morphologically similar to Radopholus similis and seven were citrus-parasitic. The nucleic acid sequences for PCR-amplified ITS1 and for the D2/D3 expansion segment of the 28S rDNA gene were each identical for all putative R. similis. Sequence divergence for both the ITS1 and the D2/D3 was concordant with morphological differences that distinguish R. similis from other burrowing nematode species. This result substantiates previous observations that the R. similis genome is highly conserved across geographic regions. Autapomorphies that would delimit phylogenetic lineages of non-citrus-parasitic R. similis from those that parasitize citrus were not observed. The data presented herein support the concept that R. similis is comprised of two pathotypes-one that parasitizes citrus and one that does not.}, } @article {pmid10817815, year = {2000}, author = {Amanullah, A and Jüsten, P and Davies, A and Paul, GC and Nienow, AW and Thomas, CR}, title = {Agitation induced mycelial fragmentation of Aspergillus oryzae and Penicillium chrysogenum.}, journal = {Biochemical engineering journal}, volume = {5}, number = {2}, pages = {109-114}, doi = {10.1016/s1369-703x(99)00059-5}, pmid = {10817815}, issn = {1369-703X}, abstract = {Given the impact of mycelial morphology on fermentation performance, it is important to understand the factors that influence it, including agitation-induced fragmentation. The successful application of the energy dissipation/circulation function (EDC) to correlate fragmentation of Penicillium chrysogenum with agitation intensity and with different impeller types [5] has already been demonstrated. The EDC function takes into account the specific energy dissipation rate in the impeller swept volume and the frequency of mycelial circulation through that volume. In order to explore whether the EDC function can be used more generally to correlate fragmentation of different filamentous species, the present study extended the concept to agitation-induced, off-line fragmentation of Aspergillus oryzae grown in chemostat culture. The work shows that at EDC values off-line greater than that in the chemostat, fragmentation with different impellers can be correlated with the EDC. For EDC values less than those used in the chemostat, fragmentation did not occur. The earlier results of Jüsten et al. [5] with Penicillium chrysogenum are also reconsidered and found to behave similarly.}, } @article {pmid10811211, year = {2000}, author = {Darling, KF and Wade, CM and Stewart, IA and Kroon, D and Dingle, R and Brown, AJ}, title = {Molecular evidence for genetic mixing of Arctic and Antarctic subpolar populations of planktonic foraminifers.}, journal = {Nature}, volume = {405}, number = {6782}, pages = {43-47}, doi = {10.1038/35011002}, pmid = {10811211}, issn = {0028-0836}, mesh = {Animals ; Antarctic Regions ; Arctic Regions ; Base Sequence ; Cold Climate ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; Genetics, Population ; Genotype ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Plankton/classification/*genetics ; RNA, Ribosomal/genetics ; }, abstract = {Bipolarity, the presence of a species in the high latitudes separated by a gap in distribution across the tropics, is a well-known pattern of global species distribution. But the question of whether bipolar species have evolved independently at the poles since the establishment of the cold-water provinces 16-8 million years ago, or if genes have been transferred across the tropics since that time, has not been addressed. Here we examine genetic variation in the small subunit ribosomal RNA gene of three bipolar planktonic foraminiferal morphospecies. We identify at least one identical genotype in all three morphospecies in both the Arctic and Antarctic subpolar provinces, indicating that trans-tropical gene flow must have occurred. Our genetic analysis also reveals that foraminiferal morphospecies can consist of a complex of genetic types. Such occurrences of genetically distinct populations within one morphospecies may affect the use of planktonic foraminifers as a palaeoceanographic proxy for climate change and necessitate a reassessment of the species concept for the group.}, } @article {pmid10799776, year = {2000}, author = {Brown, IH}, title = {The epidemiology and evolution of influenza viruses in pigs.}, journal = {Veterinary microbiology}, volume = {74}, number = {1-2}, pages = {29-46}, doi = {10.1016/s0378-1135(00)00164-4}, pmid = {10799776}, issn = {0378-1135}, mesh = {Animals ; *Evolution, Molecular ; Genetic Variation ; Humans ; Orthomyxoviridae/*genetics/pathogenicity ; Orthomyxoviridae Infections/epidemiology/*veterinary ; Swine ; Swine Diseases/*virology ; Turkeys ; Zoonoses/*transmission/virology ; }, abstract = {Pigs serve as major reservoirs of H1N1 and H3N2 influenza viruses which are endemic in pig populations world-wide and are responsible for one of the most prevalent respiratory diseases in pigs. The maintenance of these viruses in pigs and the frequent exchange of viruses between pigs and other species is facilitated directly by swine husbandry practices, which provide for a continual supply of susceptible pigs and regular contact with other species, particularly humans. The pig has been a contender for the role of intermediate host for reassortment of influenza A viruses of avian and human origin since it is the only domesticated mammalian species which is reared in abundance and is susceptible to, and allows productive replication, of avian and human influenza viruses. This can lead to the generation of new strains of influenza, some of which may be transmitted to other species including humans. This concept is supported by the detection of human-avian reassortant viruses in European pigs with some evidence for subsequent transmission to the human population. Following interspecies transmission to pigs, some influenza viruses may be extremely unstable genetically, giving rise to variants which could be conducive to the species barrier being breached a second time. Eventually, a stable lineage derived from the dominant variant may become established in pigs. Genetic drift occurs particularly in the genes encoding the external glycoproteins, but does not usually result in the same antigenic variability that occurs in the prevailing strains in the human population. Adaptation of a 'newly' transmitted influenza virus to pigs can take many years. Both human H3N2 and avian H1N1 were detected in pigs many years before they acquired the ability to spread rapidly and become associated with disease epidemics in pigs.}, } @article {pmid10792699, year = {2000}, author = {Gómez-Zurita, J and Petitpierre, E and Juan, C}, title = {Nested cladistic analysis, phylogeography and speciation in the Timarcha goettingensis complex (Coleoptera, chrysomelidae).}, journal = {Molecular ecology}, volume = {9}, number = {5}, pages = {557-570}, doi = {10.1046/j.1365-294x.2000.00900.x}, pmid = {10792699}, issn = {0962-1083}, mesh = {Animals ; Base Sequence ; Coleoptera/classification/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Europe ; Genetics, Population ; Geography ; *Haplotypes ; Molecular Sequence Data ; Population Dynamics ; }, abstract = {The Timarcha goettingensis complex is a monophyletic assemblage of closely related leaf beetles (Chrysomelidae), distributed from the north half of the Iberian Peninsula to Central Europe. Oligophagy, mountainous habitat and apterism are factors which are assumed to promote speciation in these beetles. We have used cytochrome oxidase subunit II mitochondrial DNA genealogies obtained from 31 sampling localities and a nested geographical distance analysis to assess the population structure and demographic factors explaining the geographical distributions of the mtDNA haplotypes in the T. goettingensis complex. The results show that there is a significant association between genetic structuring and geography. Inferences about the historical population processes in the species complex are discussed, being in general in accordance with contiguous range expansions and past fragmentations. The use of the cohesion species concept approach suggests the existence of several systematic ranks among the different T. goettingensis populations, which is in part supported by ecological traits such as trophic selection and altitudinal distribution.}, } @article {pmid10703554, year = {1999}, author = {Wyner, YM and Amato, G and Desalle, R}, title = {Captive breeding, reintroduction, and the conservation genetics of black and white ruffed lemurs, Varecia variegata variegata.}, journal = {Molecular ecology}, volume = {8}, number = {12 Suppl 1}, pages = {S107-15}, doi = {10.1046/j.1365-294x.1999.00815.x}, pmid = {10703554}, issn = {0962-1083}, mesh = {Animal Husbandry ; Animals ; Animals, Zoo/genetics ; Base Sequence ; Conservation of Natural Resources ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; Lemur/*genetics ; Madagascar ; Male ; Pregnancy ; }, abstract = {A character-based phylogenetic species concept approach was used to examine conservation unit status for three wild populations of black and white ruffed lemurs, Varecia vareigata variegata, from Betampona (N = 3), Manombo (N = 6), and Ranomafana (N = 14), Madagascar. Population aggregation analysis was performed on 548 bp from the control region (D-loop) of the mitochondrial DNA (mtDNA). Twenty-one diagnostic sites were found to differentiate the Betampona (northern) population from the Manombo/Ranomafana (southern) populations. Additionally, individuals from the North American captive population (N = 11) and from Parc Ivoloina, Madagascar (N = 6) were examined for the same mtDNA fragment. The captive animals more closely resembled the southern populations and the Parc Ivoloina animals were more similar to the northern population. However, the inclusion of these ex situ animals reduced the number of diagnostic sites differentiating the northern and southern populations. Our genetic data were used to assess the ongoing management strategy for reintroducing individuals into the Betampona population and for introducing new founders into the ex situ population. This study demonstrates the utility of combining genetic information with a consideration of conservation priorities in evaluating the implementation of management strategies.}, } @article {pmid10697840, year = {1999}, author = {Besansky, NJ}, title = {Complexities in the analysis of cryptic taxa within the genus Anopheles.}, journal = {Parassitologia}, volume = {41}, number = {1-3}, pages = {97-100}, pmid = {10697840}, issn = {0048-2951}, mesh = {Animals ; Anopheles/*classification/genetics ; Genetic Variation ; Humans ; Phylogeny ; }, abstract = {Grassi's discovery one hundred years ago brought to light the puzzle of anophelism without malaria in Europe. With the discovery of the European Anopheles maculipennis complex the puzzle was solved but the 'species problem' has not gone away. Meaningful epidemiologic studies and effective vector control programs depend upon efficient methods for discriminating among the major vectors, lesser vectors and non-vectors of ubiquitous anopheline sibling species complexes. We now have a variety of techniques for identifying cryptic species, ranging from crossing studies through morphological, cytogenetic, allozyme and repetitive DNA-based strategies. However, cytogenetic and molecular data can also be used to infer evolutionary relationships among cryptic taxa. This approach has been crucial to understanding the biology of the vector, and may illuminate the speciation process and the human impact upon this process. Nevertheless, the analysis of cryptic taxa has proven unexpectedly complex. Studies of An. funestus and An. gambiae reveal conflicts among classes of markers and between different genomic locations. The data are consistent with a model of speciation in which gene flow may still occur in parts of the genome, and they suggest that caution should be exercised in the interpretation of results from small numbers of loci, only one type of marker, and markers located in specific genomic regions such as chromosomal inversions.}, } @article {pmid10651909, year = {1999}, author = {Berlocher, SH}, title = {Host race or species? Allozyme characterization of the 'flowering dogwood fly', a member of the Rhagoletis pomonella complex.}, journal = {Heredity}, volume = {83 (Pt 6)}, number = {}, pages = {652-662}, doi = {10.1046/j.1365-2540.1999.00591.x}, pmid = {10651909}, issn = {0018-067X}, mesh = {Animals ; Data Interpretation, Statistical ; Enzymes/*genetics ; Fruit ; *Genetic Variation ; Genetics, Population ; Insecta/*genetics ; Trees ; }, abstract = {The term 'flowering dogwood fly' has been used in the literature for a poorly understood member of the Rhagoletis pomonella sibling species complex infesting the fruits of flowering dogwood (Cornus florida). Electrophoretic analysis of 17 allozyme loci in 21 populations reveals significant frequency differences between the flowering dogwood fly and its closest relative the apple maggot fly, R. pomonella, and between it and the somewhat more distant 'sparkleberry fly'. Frequency differences between the flowering dogwood fly and R. pomonella are as great as 0.817 in the north, but are less in the south, with a maximum difference at one site of only 0.328. No fixed allozyme differences distinguish the flowering dogwood fly anywhere; its only consistent, unique feature is the highest frequency of Aat-259 in the pomonella species group. Population structure of the flowering dogwood fly is moderate with FST=0.084 and fewer latitudinal clines than R. pomonella. The conclusion from the allozyme and life history data is that the flowering dogwood fly is a species, although some interspecific gene flow may be occurring. Additional issues discussed include how to estimate interspecific gene flow when genetic markers are under divergent selection, the appropriate species concept when there is gene flow, and the future of the flowering dogwood fly in the face of the dogwood anthracnose epidemic. The possible utility of a new species concept for phytophagous insects, using as a criterion the capacity of a host race to regenerate the ancestral population, is also discussed.}, } @article {pmid10576566, year = {1999}, author = {Banũls, AL and Hide, M and Tibayrenc, M}, title = {Molecular epidemiology and evolutionary genetics of Leischmania parasites.}, journal = {International journal for parasitology}, volume = {29}, number = {8}, pages = {1137-1147}, doi = {10.1016/s0020-7519(99)00083-1}, pmid = {10576566}, issn = {0020-7519}, mesh = {Animals ; Biological Evolution ; Genes, Protozoan ; Humans ; Leishmania/*classification/*genetics/pathogenicity ; Leishmaniasis/*epidemiology/*parasitology ; Molecular Epidemiology ; Phylogeny ; }, abstract = {In order to illustrate the relevance of the concepts and methods of evolutionary genetics in the understanding of the epidemiology of pathogenic agents, we develop in this paper the case of the Leishmania, a genus of parasitic protozoa. An extensive study of various natural populations of Leishmania in different countries (Old and New World) was carried out by using Multilocus Enzyme Electrophoresis (MLEE) and Random Amplified Polymorphic DNA fingerprinting (RAPD) as genetic markers. The data have been interpreted in evolutionary genetic terms. The main benefit of this approach has been to better define the concept of species in the genus Leishmnania, on rigorous phylogenetic bases. As a matter of fact, a sound taxonomical background is a prerequisite for any epidemiological approach. Since the biological concept of species is difficult or impossible to apply for most pathogenic microorganisms, we recommend relying on criteria of both phylogenetic discreteness and of epidemiological/medical relevance to describe new species of Leishmania. Through this approach, for example, we have shown that the species status of L. (V.) perzzl.ianza can be supported. On the contrary, we have been unable to clearly distinguish L. (V.) panamensis from L. (V.) guyanensis with genetic tools. Additionally, we have shown that the epidemiological inferences based on a limited set of genetic markers can be misleading. As a matter of fact, we have demonstrated that a collection of L. (L.) infantum stocks identified as zymodeme 'MON 1' by other authors present additional genetic heterogeneity and do not correspond to a distinct 'Discrete Typing Unit' DTU, and are actually polyphyletic. Lastly, in the samples that were conveniently designed, we have confirmed that Leishmania parasites have a basically clonal population structure. As the clonal model specifies it, occasional bouts of genetic exchange remain nevertheless possible. Telling comparisons are drawn with the evolutionary genetics of other pathogens Trypanosoma cruzi and Trypanosoma congolense.}, } @article {pmid10565922, year = {1999}, author = {Summerbell, RC and Haugland, RA and Li, A and Gupta, AK}, title = {rRNA gene internal transcribed spacer 1 and 2 sequences of asexual, anthropophilic dermatophytes related to Trichophyton rubrum.}, journal = {Journal of clinical microbiology}, volume = {37}, number = {12}, pages = {4005-4011}, pmid = {10565922}, issn = {0095-1137}, mesh = {Arthrodermataceae/*genetics ; Base Sequence ; DNA, Fungal/genetics ; DNA, Ribosomal/*genetics ; Genes, rRNA/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 5.8S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Trichophyton/*genetics ; }, abstract = {The ribosomal region spanning the two internal transcribed spacer (ITS) regions and the 5.8S ribosomal DNA region was sequenced for asexual, anthropophilic dermatophyte species with morphological similarity to Trichophyton rubrum, as well as for members of the three previously delineated, related major clades in the T. mentagrophytes complex. Representative isolates of T. raubitschekii, T. fischeri, and T. kanei were found to have ITS sequences identical to that of T. rubrum. The ITS sequences of T. soudanense and T. megninii differed from that of T. rubrum by only a small number of base pairs. Their continued status as species, however, appears to meet criteria outlined in the population genetics-based cohesion species concept of A. R. Templeton. The ITS sequence of T. tonsurans differed from that of the biologically distinct T. equinum by only 1 bp, while the ITS sequence of the recently described species T. krajdenii had a sequence identical to that of T. mentagrophytes isolates related to the teleomorph Arthroderma vanbreuseghemii.}, } @article {pmid10565281, year = {1999}, author = {Ni, J and Lipert, RJ and Dawson, GB and Porter, MD}, title = {Immunoassay readout method using extrinsic Raman labels adsorbed on immunogold colloids.}, journal = {Analytical chemistry}, volume = {71}, number = {21}, pages = {4903-4908}, doi = {10.1021/ac990616a}, pmid = {10565281}, issn = {0003-2700}, mesh = {Adsorption ; Animals ; Antibodies/chemistry ; Antigens/analysis ; Benzoates/chemistry ; Fluorescence ; Gold Colloid/chemistry ; Immunoassay/instrumentation/*methods ; Immunoglobulin G/chemistry/immunology ; Naphthalenes/chemistry ; Phenols/chemistry ; Rabbits ; Rats ; Sensitivity and Specificity ; Spectrum Analysis, Raman/instrumentation/*methods ; Sulfhydryl Compounds/chemistry ; }, abstract = {An immunoassay readout method based on surface-enhanced Raman scattering (SERS) is described. The method exploits the SERS-derived signal from reporter molecules that are coimmobilized with biospecific species on gold colloids. This concept is demonstrated in a dualanalyte sandwich assay, in which two different antibodies covalently bound to a solid substrate specifically capture two different antigens from an aqueous sample. The captured antigens in turn bind selectively to their corresponding detection antibodies. The detection antibodies are conjugated with gold colloids that are labeled with different Raman reporter molecules, which serve as extrinsic labels for each type of antibody. The presence of a specific antigen is established by the characteristic SERS spectrum of the reporter molecule. A near-infrared diode laser was used to excite efficiently the SERS signal while minimizing fluorescence interference. We show that, by using different labels with little spectral overlap, two different antigenic species can be detected simultaneously. The potential of this concept to function as a readout strategy for multiple analytes is briefly discussed.}, } @article {pmid10564451, year = {1999}, author = {Oyler-McCance, SJ and Kahn, NW and Burnham, KP and Braun, CE and Quinn, TW}, title = {A population genetic comparison of large- and small-bodied sage grouse in colorado using microsatellite and mitochondrial DNA markers.}, journal = {Molecular ecology}, volume = {8}, number = {9}, pages = {1457-1465}, doi = {10.1046/j.1365-294x.1999.00716.x}, pmid = {10564451}, issn = {1365-294X}, abstract = {Sage grouse (Centrocercus urophasianus) from southwestern Colorado and southeastern Utah (United States) are 33% smaller than all other sage grouse and have obvious plumage and behavioural differences. Because of these differences, they have been tentatively recog-nized as a separate 'small-bodied' species. We collected genetic evidence to further test this proposal, using mitochondrial sequence data and microsatellite markers to determine whether there was gene flow between the two proposed species. Significant differences in the distribution of alleles between the large- and small-bodied birds were found in both data sets. Analysis of molecular variance (AMOVA) revealed that 65% of the variation in mitochondrial DNA (mtDNA) haplotypes could be explained by the large- vs. small-bodied distinction. Genetic distances and neighbour-joining trees based on allelic frequency data showed a distinct separation between the proposed species, although cladistic analysis of the phylogenetic history of the mitochondrial sequence haplotypes has shown a lack of reciprocal monophyly. These results further support the recognition of the small-bodied sage grouse as a distinct species based on the biological species concept, providing additional genetic evidence to augment the morphological and behavioural data. Furthermore, small-bodied sage grouse had much less genetic variation than large-bodied sage grouse, which may have implications for conservation issues.}, } @article {pmid10479119, year = {1999}, author = {Fulhorst, CF and Ksiazek, TG and Peters, CJ and Tesh, RB}, title = {Experimental infection of the cane mouse Zygodontomys brevicauda (family Muridae) with guanarito virus (Arenaviridae), the etiologic agent of Venezuelan hemorrhagic fever.}, journal = {The Journal of infectious diseases}, volume = {180}, number = {4}, pages = {966-969}, doi = {10.1086/315029}, pmid = {10479119}, issn = {0022-1899}, support = {AI-33983/AI/NIAID NIH HHS/United States ; AI-41435/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antibodies, Viral/blood ; Arenaviridae/isolation & purification/*pathogenicity ; Arenaviruses, New World/isolation & purification/*pathogenicity ; Hemorrhagic Fever, American/pathology/*physiopathology/urine ; Muridae ; Oropharynx/virology ; Spleen/virology ; Venezuela ; }, abstract = {Chronic infections in specific rodents appear to be crucial to the long-term persistence of arenaviruses in nature. The cane mouse, Zygodontomys brevicauda, is a natural host of Guanarito virus (family Arenaviridae), the etiologic agent of Venezuelan hemorrhagic fever. The purpose of this study was to elucidate the natural history of Guanarito virus infection in Z. brevicauda. Thirty-nine laboratory-reared cane mice each were inoculated subcutaneously with 3.0 log10 plaque-forming units of the Guanarito virus prototype strain INH-95551. No lethality was associated with infection in any animal, regardless of age at inoculation. The 13 newborn, 14 weanling, and 8 of the 12 adult animals developed chronic viremic infections characterized by persistent shedding of infectious virus in oropharyngeal secretions and urine. These findings indicate that Guanarito virus infection in Z. brevicauda can be chronic and thus support the concept that this rodent species is the natural reservoir of Guanarito virus.}, } @article {pmid21662900, year = {1999}, author = {Hasegawa, T}, title = {Detection of minute chemical species by principal-component analysis.}, journal = {Analytical chemistry}, volume = {71}, number = {15}, pages = {3085-3091}, doi = {10.1021/ac981430z}, pmid = {21662900}, issn = {0003-2700}, abstract = {A novel analytical technique based on the detection of minute bands in a mixture spectrum with the use of principal-component analysis (PCA) is presented. This new aspect of PCA indicates that overlapped spectra of some components can be separated with no a priori knowledge of the components when the absorbances of the components vary greatly. This technique can be used for the detection of minute chemical species. The concept was confirmed by computer simulations. In the simulations, abstract spectra (loading vectors) were successfully obtained, and the changes of the component absorbances were also successfully followed semiquantitatively by calculating their scores. The method developed with PCA was applied to the analysis of infrared reflection-absorption (RA) spectra to study molecular interaction mechanism between alkyl-deuterated dipalmitoylphosphatidylcholine (DPPC-d(62)) monolayer and sucrose. The samples were Langmuir-Blodgett (LB) films of the DPPC-d(62) monolayer that was prepared on a sucrose solution. The LB films consisted of the following phases: air/DPPC-d(62) + sucrose/sucrose/substrate (gold). The abstract spectra corresponding to "DPPC-d(62) + sucrose" and "sucrose" phases were successfully separated by PCA, and the absorbance change of sucrose in each phase was semiquantitatively calculated from the score. The absorbance change was experimentally confirmed with quartz-crystal microbalance (QCM) experiments. In addition, minute water molecules that remained in the LB films after drying were readily detected from an abstract spectrum, and their binding site was found to be the phospholipid moiety in the head group of DPPC-d(62).}, } @article {pmid10417214, year = {1999}, author = {Wood, BD and Whitaker, S}, title = {Cellular growth in biofilms.}, journal = {Biotechnology and bioengineering}, volume = {64}, number = {6}, pages = {656-670}, doi = {10.1002/(sici)1097-0290(19990920)64:6<656::aid-bit4>3.0.co;2-n}, pmid = {10417214}, issn = {0006-3592}, mesh = {Biofilms/*growth & development ; Biological Transport ; Cell Division/physiology ; Mechanics ; *Models, Biological ; }, abstract = {In this paper we develop a macroscopic evolutionary equation for the growth of the cellular phase starting from a microscopic description of mass transport and a simple structured model for product formation. The methods of continuum mechanics and volume averaging are used to develop the macroscopic representation by carefully considering the fluxes of chemical species that pertain to cell growth. The concept of structured models is extended to include the transport of reacting chemical species at the microscopic scale. The resulting macroscopic growth model is similar in form to previously published models for the transport of a single substrate and electron donor and for the production of cellular mass and exopolymer. The method of volume averaging indicates under what conditions the developed growth model is valid and provides an explicit connection between the relevant microscopic model parameters and their corresponding macroscopic counterparts.}, } @article {pmid10373615, year = {1999}, author = {Medina, M and Weil, E and Szmant, AM}, title = {Examination of the Montastraea annularis Species Complex (Cnidaria: Scleractinia) Using ITS and COI Sequences.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {1}, number = {1}, pages = {89-97}, doi = {10.1007/pl00011756}, pmid = {10373615}, issn = {1436-2236}, abstract = {: The Caribbean coral Montastraea annularis has recently been proposed to be a complex of at least three sibling species. To test the validity of this proposal, we sequenced the ITS region of the nuclear ribosomal RNA gene family (ITS-1, 5.8S, and ITS-2), and a portion of the mitochondrial DNA gene cytochrome c oxidase subunit I (COI) from the three proposed species (M. annularis, M. faveolata, and M. franksi) from Florida reefs. The ITS fragment was 665 nucleotides long and had 19 variable sites, of which 6 were parsimony-informative sites. None of these sites was fixed within the proposed species. The COI fragment was 658 nucleotides long with only two sites variable in one individual. Thus, under both the biological species concept and the phylogenetic species concept, the molecular evidence gathered in this study indicates the Montastraea annularis species complex to be a single evolutionary entity as opposed to three distinct species. The three proposed Montastraea species can interbreed, ruling out prezygotic barriers to gene flow (biological species concept), and the criterion of monophyly is not satisfied if hybridization is occurring among taxa (phylogenetic species concept).}, } @article {pmid19270883, year = {1999}, author = {Wheeler, QD}, title = {Why the phylogenetic species concept?-Elementary.}, journal = {Journal of nematology}, volume = {31}, number = {2}, pages = {134-141}, pmid = {19270883}, issn = {0022-300X}, abstract = {Although species play a number of unique and necessary roles in biology, none are more important than as the elements of phylogeny, nomenclature, and biodiversity study. Species are not divisible into any smaller units among which shared derived characters can be recognized with fidelity. Biodiversity inventory, assessment, and conservation are dependent upon a uniformly applicable species concept. Species are the fundamental units in formal Linnaean classification and zoological nomenclature. The Biological Species Concept, long given nominal support by most zoologists, forced an essentialy taxonomic problem (what are species?) into a population genetics framework (why are there species?). Early efforts at a phylogenetic species concept focused on correcting problems in the Biological Species Concept associated with ancestral populations, then applying phylogenetic logic to species themselves. Subsequently, Eldredge and Cracraft, and Nelson and Platnick, each proposed essentially identical and truly phylogenetic species concepts that permitted the rigorous recognition of species prior to and for the purposes of phylogenetic analysis, yet maintained the integrity of the Phylogenetic Species Concept outside of cladistic analysis. Such phylogenetic elements have many benefits, including giving to biology a unit species concept applicable across all kinds of living things including sexual and asexual forms. This is possible because the Phylogenetic Species Concept is based on patterns of character distributions and is therefore consistent with the full range of possible evolutionary processes that contribute to species formation, including both biotic and abiotic (even random) factors.}, } @article {pmid19270882, year = {1999}, author = {Brooks, DR and McLennan, DA}, title = {Species: turning a conundrum into a research program.}, journal = {Journal of nematology}, volume = {31}, number = {2}, pages = {117-133}, pmid = {19270882}, issn = {0022-300X}, abstract = {The most appropriate ontological basis for understanding the role of species in evolutionary biology is the Evolutionary Species Concept. The ESC is not an operational concept, but one version of the Phylogenetic Species Concept is. Linking the ontology of species with the epistemological basis of actual biological studies requires that we specify both a discovery mode for identifying collections of organisms that we believe are evolutionary species, and a series of evaluation criteria for assessing those entities we have discovered. Simply naming a collection of specimens, no matter how strong one's evolutionary beliefs, is not sufficient for declaring that evolutionary species have been discovered. All operational historical species concepts represent discovery modes with minimal evaluation criteria; all operational non-dimensional species concepts represent evaluation criteria that do not specify discovery modes. Thus, both categories of knowledge are necessary and neither is sufficient for assigning species status. This leads naturally to a hierarchical research program in historical ecology, beginning with phylogenetic analysis of a group of entities postulated to be evolutionary species, which provides a productive arena for our arguments about species concepts.}, } @article {pmid19270881, year = {1999}, author = {Mayden, RL}, title = {Consilience and a hierarchy of species concepts: advances toward closure on the species puzzle.}, journal = {Journal of nematology}, volume = {31}, number = {2}, pages = {95-116}, pmid = {19270881}, issn = {0022-300X}, abstract = {Numerous concepts exist for biological species. This diversity of ideas derives from a number of sources ranging from investigative study of particular taxa and character sets to philosophical aptitude and world view to operationalism and nomenclatorial rules. While usually viewed as counterproductive, in reality these varied concepts can greatly enhance our efforts to discover and understand biological diversity. Moreover, this continued "turf war" and dilemma over species can be resolved if the various concepts are viewed in a hierarchical system and each evaluated for its inherent level of consilience. Under this paradigm a theoretically appropriate, highly consilient concept of species capable of colligating the abundant types of species diversity offers the best guidance for developing and employing secondary operational concepts for identifying diversity. Of all the concepts currently recognized, only the non-operational Evolutionary Species Concept corresponds to the requisite parameters and, therefore, should serve as the theoretical concept appropriate for the category Species. As operational concepts, the remaining ideas have been incompatible with one another in their ability to encompass species diversity because each has restrictive criteria as to what qualifies as a species. However, the operational concepts can complement one another and do serve a vital role under the Evolutionary Species Concept as fundamental tools necessary for discovering diversity compatible with the primary theoretical concept. Thus, the proposed hierarchical system of primary and secondary concepts promises both the most productive framework for mutual respect for varied concepts and the most efficient and effective means for revealing species diversity.}, } @article {pmid19270880, year = {1999}, author = {Ferris, VR}, title = {Species concepts do matter in nematology.}, journal = {Journal of nematology}, volume = {31}, number = {2}, pages = {93-94}, pmid = {19270880}, issn = {0022-300X}, abstract = {Nematology is a taxon-based science, and a correct understanding of species and their relationships is basic to all nematological research. Modern methods of systematic analysis have reshaped issues concerning species recognition.}, } @article {pmid10333320, year = {1999}, author = {Monis, PT}, title = {The importance of systematics in parasitological research.}, journal = {International journal for parasitology}, volume = {29}, number = {3}, pages = {381-388}, doi = {10.1016/s0020-7519(98)00216-1}, pmid = {10333320}, issn = {0020-7519}, mesh = {Animals ; Genetic Techniques ; Giardia/classification/genetics ; Parasites/*classification/*genetics ; Phylogeny ; Research ; }, abstract = {The discipline of systematics plays a central role in all branches of biology. In today's technology-orientated research world, it is important to realise the continuing value of systematics, the basic tenet of which is to combine diverse types of data to produce classifications that reflect the natural history of living organisms. Accurate classification systems are crucial in the field of parasitology, not only because they provide the means to identify species and strains of parasites, but also because they provide a framework around which a parasite's biology can be studied. The construction of such a classification system is often hampered by the parasite's biology, which may preclude the application of traditional techniques or concepts (such as morphological differentiation or the biological species concept) to delineate species. It is often the case that these difficulties can be overcome by the use of molecular systematic techniques. In this paper, it is proposed that a detailed understanding of the phylogeny of a group of organisms can be used as a basis to examine other aspects of their systematics. This is illustrated using the protozoan parasite Giardia intestinalis. Data gathered using the complementary techniques of allozyme electrophoresis and nucleotide sequencing have been used to infer the phylogenetic relationships of G. intestinalis isolated from various host species. The results, supported by biological data, suggest that G. intestinalis is a species-complex. As we move towards the year 2000, molecular systematics will play an increasingly important role in elucidating host-parasite relationships. However, its use as a taxonomic tool will require a general acceptance by parasitologists and the adoption of formal procedures to allow the description of new species by these methods. The aim of this approach is not to dismiss traditional methods, but to use them in combination with contemporary methods in the true spirit of the discipline of systematics.}, } @article {pmid10090711, year = {1999}, author = {van der Schalie, WH and Gardner, HS and Bantle, JA and De Rosa, CT and Finch, RA and Reif, JS and Reuter, RH and Backer, LC and Burger, J and Folmar, LC and Stokes, WS}, title = {Animals as sentinels of human health hazards of environmental chemicals.}, journal = {Environmental health perspectives}, volume = {107}, number = {4}, pages = {309-315}, pmid = {10090711}, issn = {0091-6765}, mesh = {Animals ; Biological Assay ; Environmental Exposure/*adverse effects ; *Environmental Health ; Environmental Monitoring/*methods ; Environmental Pollutants/*adverse effects ; Humans ; Risk Assessment ; *Sentinel Surveillance/veterinary ; Species Specificity ; United States ; }, abstract = {A workshop titled "Using Sentinel Species Data to Address the Potential Human Health Effects of Chemicals in the Environment," sponsored by the U.S. Army Center for Environmental Health Research, the National Center for Environmental Assessment of the EPA, and the Agency for Toxic Substances and Disease Registry, was held to consider the use of sentinel and surrogate animal species data for evaluating the potential human health effects of chemicals in the environment. The workshop took a broad view of the sentinel species concept, and included mammalian and nonmammalian species, companion animals, food animals, fish, amphibians, and other wildlife. Sentinel species data included observations of wild animals in field situations as well as experimental animal data. Workshop participants identified potential applications for sentinel species data derived from monitoring programs or serendipitous observations and explored the potential use of such information in human health hazard and risk assessments and for evaluating causes or mechanisms of effect. Although it is unlikely that sentinel species data will be used as the sole determinative factor in evaluating human health concerns, such data can be useful as for additional weight of evidence in a risk assessment, for providing early warning of situations requiring further study, or for monitoring the course of remedial activities. Attention was given to the factors impeding the application of sentinel species approaches and their acceptance in the scientific and regulatory communities. Workshop participants identified a number of critical research needs and opportunities for interagency collaboration that could help advance the use of sentinel species approaches.}, } @article {pmid10075268, year = {1999}, author = {Sarmini, K and Kenndler, E}, title = {Ionization constants of weak acids and bases in organic solvents.}, journal = {Journal of biochemical and biophysical methods}, volume = {38}, number = {2}, pages = {123-137}, doi = {10.1016/s0165-022x(98)00033-5}, pmid = {10075268}, issn = {0165-022X}, mesh = {Acids/*analysis ; Cations, Monovalent/analysis ; Dose-Response Relationship, Drug ; Electrophoresis, Capillary/methods ; Ethanol/pharmacology ; Hydrogen-Ion Concentration ; *Ions ; Models, Statistical ; Solvents/*analysis/classification ; Thermodynamics ; }, abstract = {A discussion of the influence of organic solvents on pKa values is presented. Enthalpy and entropy of ionization in organic solvents are compared with aqueous systems. The impact of the solvent on the ionization constants is interpreted based on the free energy of transfer applied to all particles involved in the ionization reaction of acids and bases, and the concept of the 'medium effect' on these species. The limitation of Born's approach (which takes into account only electrostatic effects on the ionization equilibrium) is demonstrated and the importance of solute-solvent interactions on the change of the pKa values emphasized.}, } @article {pmid10066488, year = {1998}, author = {Ward, DM}, title = {A natural species concept for prokaryotes.}, journal = {Current opinion in microbiology}, volume = {1}, number = {3}, pages = {271-277}, doi = {10.1016/s1369-5274(98)80029-5}, pmid = {10066488}, issn = {1369-5274}, mesh = {Bacteria/*classification/genetics ; *DNA, Ribosomal ; *Ecology ; *Evolution, Molecular ; }, abstract = {Direct molecular analyses of natural microbial populations reveal patterns that should compel microbiologists to adopt a more natural species concept that has been known to biologists for decades. The species debate can be exploited to address a larger issue - microbiologists need, in general, to take a more natural view of the organisms they study.}, } @article {pmid10030448, year = {1998}, author = {Josephy, PD and Coomber, BL}, title = {The 1996 Veylien Henderson Award of the Society of Toxicology of Canada. Current concepts: neutrophils and the activation of carcinogens in the breast and other organs.}, journal = {Canadian journal of physiology and pharmacology}, volume = {76}, number = {7-8}, pages = {693-700}, doi = {10.1139/cjpp-76-7-8-693}, pmid = {10030448}, issn = {0008-4212}, mesh = {Animals ; Biotransformation ; Breast Neoplasms/*etiology/genetics ; Carcinogens/*metabolism/toxicity ; Environmental Pollutants/*metabolism/toxicity ; Epithelium/drug effects/pathology ; Female ; Humans ; Mammary Neoplasms, Experimental/etiology/genetics ; Mutagenicity Tests ; Mutation ; Neutrophils/*metabolism ; Peroxidases/genetics ; }, abstract = {Many chemical carcinogens target epithelial tissues, but the biological and biochemical bases of carcinogen specificity remain largely unknown. Focusing on the mammary gland, we discuss the concept that neutrophils metabolize carcinogens to reactive species that damage adjacent epithelial cells. This mechanism may help to explain why epithelial cells are sensitive targets for chemical carcinogenesis, despite their limited bioactivation capacity.}, } @article {pmid9987897, year = {1999}, author = {Lyons, LA and Kehler, JS and O'Brien, SJ}, title = {Development of comparative anchor tagged sequences (CATS) for canine genome mapping.}, journal = {The Journal of heredity}, volume = {90}, number = {1}, pages = {15-26}, doi = {10.1093/jhered/90.1.15}, pmid = {9987897}, issn = {0022-1503}, mesh = {Animals ; Chromosome Banding/veterinary ; Chromosome Mapping/methods/*veterinary ; Dogs/*genetics ; Genetic Markers ; Polymerase Chain Reaction/veterinary ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single-Stranded Conformational ; *Sequence Tagged Sites ; }, abstract = {The development of a useful genetic map of the domestic dog would benefit by the inclusion of type I markers; coding genes that can connect the canine map to the homologous gene maps of other mammalian species. A group of 280 comparative anchor tagged sequences (CATS), and universal mammalian sequence tagged sites (UM-STS), were optimized for canine assessment. One hundred and five were screened for genetic polymorphism among nine canine breeds and three wild species of Canis in an attempt to promote gene mapping of comparative type I markers. Three categories of variation--size, restriction fragment length polymorphism (RFLP), and single-strand conformation polymorphism (SSCP)--were assessed. The data showed that 50% of the type I markers discriminate between species and 40% showed genetic variation among dog breeds. Although polymorphism incidence between nominated breeds for gene mapping is more limited than found for established reference pedigrees in other species, the concept and application of these CATS and UM-STS markers is useful in capturing the comparative information required for the full application and efficacy of the dog gene map.}, } @article {pmid9986828, year = {1999}, author = {Kasuga, T and Taylor, JW and White, TJ}, title = {Phylogenetic relationships of varieties and geographical groups of the human pathogenic fungus Histoplasma capsulatum Darling.}, journal = {Journal of clinical microbiology}, volume = {37}, number = {3}, pages = {653-663}, pmid = {9986828}, issn = {0095-1137}, support = {HL55953/HL/NHLBI NIH HHS/United States ; }, mesh = {AIDS-Related Opportunistic Infections/microbiology ; Animals ; Base Sequence ; DNA, Fungal/genetics/isolation & purification ; Fungal Proteins/genetics ; *Genes, Fungal ; Genotype ; Geography ; Histoplasma/*classification/*genetics/isolation & purification ; Histoplasmosis/etiology/*microbiology ; Humans ; Molecular Sequence Data ; North America ; Panama ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Soil Microbiology ; South America ; }, abstract = {The phylogeny of 46 geographically diverse Histoplasma capsulatum isolates representing the three varieties capsulatum, duboisii, and farciminosum was evaluated using partial DNA sequences of four protein coding genes. Parsimony and distance analysis of the separate genes were generally congruent and analysis of the combined data identified six clades: (i) class 1 North American H. capsulatum var. capsulatum, (ii) class 2 North American H. capsulatum var. capsulatum, (iii) Central American H. capsulatum var. capsulatum, (iv) South American H. capsulatum var. capsulatum group A, (v) South American H. capsulatum var. capsulatum group B, and (vi) H. capsulatum var. duboisii. Although the clades were generally well supported, the relationships among them were not resolved and the nearest outgroups (Blastomyces and Paracoccidioides) were too distant to unequivocally root the H. capsulatum tree. H. capsulatum var. farciminosum was found within the South American H. capsulatum var. capsulatum group A clade. With the exception of the South American H. capsulatum var. capsulatum group A clade, genetic distances within clades were an order of magnitude lower than those between clades, and each clade was supported by a number of shared derived nucleotide substitutions, leading to the conclusion that each clade was genetically isolated from the others. Under a phylogenetic species concept based on possession of multiple shared derived characters, as well as concordance of four gene genealogies, H. capsulatum could be considered to harbor six species instead of three varieties.}, } @article {pmid9927681, year = {1999}, author = {Avise, JC and Walker, D}, title = {Species realities and numbers in sexual vertebrates: perspectives from an asexually transmitted genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {3}, pages = {992-995}, pmid = {9927681}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Female ; *Genome ; Male ; Phylogeny ; Reproduction/*genetics ; Vertebrates/classification/*genetics/physiology ; }, abstract = {A literature review is conducted on the phylogenetic discontinuities in mtDNA sequences of 252 taxonomic species of vertebrates. About 140 of these species (56%) were subdivided clearly into two or more highly distinctive matrilineal phylogroups, the vast majority of which were localized geographically. However, only a small number (two to six) of salient phylogeographic subdivisions (those that stand out against mean within-group divergences) characterized individual species. A previous literature summary showed that vertebrate sister species and other congeners also usually have pronounced phylogenetic distinctions in mtDNA sequence. These observations, taken together, suggest that current taxonomic species often agree reasonably well in number (certainly within an order-of-magnitude) and composition with biotic entities registered in mtDNA genealogies alone. In other words, mtDNA data and traditional taxonomic assignments tend to converge on what therefore may be "real" biotic units in nature. All branches in mtDNA phylogenies are nonanastomose, connected strictly via historical genealogy. Thus, patterns of historical phylogenetic connection may be at least as important as contemporary reproductive relationships per se in accounting for microevolutionary unities and discontinuities in sexually reproducing vertebrates. Findings are discussed in the context of the biological and phylogenetic species concepts.}, } @article {pmid9916005, year = {1999}, author = {Bodensteiner, KJ and Clay, CM and Moeller, CL and Sawyer, HR}, title = {Molecular cloning of the ovine Growth/Differentiation factor-9 gene and expression of growth/differentiation factor-9 in ovine and bovine ovaries.}, journal = {Biology of reproduction}, volume = {60}, number = {2}, pages = {381-386}, doi = {10.1095/biolreprod60.2.381}, pmid = {9916005}, issn = {0006-3363}, mesh = {Amino Acid Sequence ; Animals ; Bone Morphogenetic Protein 15 ; *Cattle ; *Cloning, Molecular ; DNA/analysis/chemistry ; Female ; *Gene Expression ; Growth Differentiation Factor 9 ; Growth Substances/chemistry/*genetics ; Humans ; In Situ Hybridization ; *Intercellular Signaling Peptides and Proteins ; Mice ; Molecular Sequence Data ; Ovary/*metabolism ; RNA, Messenger/analysis ; Restriction Mapping ; Sequence Homology ; *Sheep ; Transforming Growth Factor beta/genetics ; }, abstract = {Recently a novel member of the transforming growth factor beta (TGFbeta) superfamily termed growth/differentiation factor-9 (GDF-9) was shown to be expressed in ovaries of mice and humans, and to be essential for normal follicular development beyond the primary (type 2) follicle stage in mice. In the present study, the gene for ovine GDF-9 was isolated and characterized, and expression of GDF-9 mRNA in ovaries of domestic ruminants was examined. The predicted amino acid sequence of ovine GDF-9 is 77% and 66% homologous to human and mouse GDF-9, respectively. Specific hybridization using homologous 35S-antisense probes was restricted to oocytes. In contrast to similar studies in mice in which GDF-9 was first detected beginning at the primary (type 2) follicle stage, in ovine and bovine ovaries GDF-9 mRNA was expressed beginning at the primordial (type 1) follicle stage. The observed timing and pattern of GDF-9 expression in oocytes of domestic ruminants is consistent with a role for GDF-9 in the initiation and maintenance of folliculogenesis in these species, and supports the general concept that early stages of follicular growth and development are regulated by intraovarian factors.}, } @article {pmid9879007, year = {1998}, author = {Mitrofanov, VG and Sidorova, NV and Grigor'eva, GA and Falileeva, LI}, title = {[Genetic control of isolating mechanisms in the genus Drosophila].}, journal = {Genetika}, volume = {34}, number = {9}, pages = {1189-1199}, pmid = {9879007}, issn = {0016-6758}, mesh = {Animals ; Behavior, Animal/*physiology ; Drosophila/*genetics ; *Ecosystem ; Genotype ; *Hybridization, Genetic ; Infertility/*physiopathology ; }, abstract = {Published data on the genetic control of isolating mechanisms in the genus Drosophila are discussed. The main isolation types of genetic mechanisms (ecological isolation, behavioral isolation, hybrid sterility, and the inviability or impaired development of interspecific hybrids) are considered. It is shown that each of the isolation barriers between different species is controlled by a small number of genes. However, as each pair of sibling species is usually separated by several barriers, the total number of isolation genes is about 20 to 30. The probable sequence of events in the appearance of isolation barriers during the divergence of novel species is discussed. A concept of the consolidation of a new species is proposed. This concept is based on the assumption of the genetic determination of behavior that promotes crossing between individuals of the new genotype and constrains their crosses with individuals of the ancestral genotype.}, } @article {pmid9873135, year = {1998}, author = {Podesser, BK and Neumann, F and Neumann, M and Schreiner, W and Wollenek, G and Mallinger, R}, title = {Outer radius-wall thickness ratio, a postmortem quantitative histology in human coronary arteries.}, journal = {Acta anatomica}, volume = {163}, number = {2}, pages = {63-68}, doi = {10.1159/000046485}, pmid = {9873135}, issn = {0001-5180}, mesh = {Adult ; Coronary Vessels/*anatomy & histology ; Humans ; Image Processing, Computer-Assisted ; Male ; }, abstract = {Although the anatomy, histology and pathology of human coronary arteries have been studied extensively, little is known about the functional relationship between vessel radius and wall thickness. It is the purpose of this study to present detailed measurements and to describe this relationship covering the range from the feeding coronary artery to the arterioles. Human hearts of 10 adults less than 36 +/- 3 years old were investigated immediately postmortem. Ten cubic tissue blocks, measuring about 10 mm in length on each side, were dissected from the left ventricular wall. After fixation by immersion, 15-microm sections were prepared and outer and inner perimeters of 52 arterial segments were digitalized. Vessel radius and wall thickness were calculated and plotted to show their relationship over the whole range of vessel calibers. Outer vessel radii ranged from 100 to 3,000 microm and wall thickness from 80 to 800 microm. Plotting the outer vessel radius against the wall thickness, the data points were found to cluster around a straight line. A significant correlation between the two parameters was found (R2 = 0.79). This mathematical correlation and the good agreement of the presented results with data from other species indicate a common physiologic concept.}, } @article {pmid9865591, year = {1998}, author = {Canbolat, O and Fandrey, J and Jelkmann, W}, title = {Effects of modulators of the production and degradation of hydrogen peroxide on erythropoietin synthesis.}, journal = {Respiration physiology}, volume = {114}, number = {2}, pages = {175-183}, doi = {10.1016/s0034-5687(98)00080-2}, pmid = {9865591}, issn = {0034-5687}, mesh = {Carcinoma, Hepatocellular/metabolism ; Catalase/antagonists & inhibitors/metabolism/pharmacology ; Erythropoietin/antagonists & inhibitors/*biosynthesis ; Free Radical Scavengers/pharmacology ; Glutathione Peroxidase/metabolism ; Humans ; Hydrogen Peroxide/*metabolism/pharmacology ; Hypoxia/metabolism ; Reactive Oxygen Species/metabolism ; Superoxide Dismutase/metabolism ; Tumor Cells, Cultured ; }, abstract = {Erythropoietin (Epo) synthesis is suppressed in normoxia and stimulated in hypoxia. To test the hypothesis that the cellular H2O2 level is important in the control of Epo synthesis, we have studied effects of modulators of H2O2 generation and degradation on Epo production in human hepatic cell cultures (hepatoma lines HepG2 and Hep3B). In addition, we measured the activities of antioxidant enzymes (catalase, superoxide dismutase, glutathione peroxidase) in cultures following hypoxia exposure or H2O2 treatment. The results show that the formation of immunoreactive Epo was stimulated in normoxic cultures by treatment with exogenous catalase thus mimicking the effect of hypoxia (24 h incubation periods). Epo production was also stimulated when scavengers of reactive O2 species (tetramethylthiourea, dihydrorhodamine) were added to the cells. On the other hand, stimulators of H2O2 generation (xanthine oxidase, glucose oxidase, NADH, NADPH) lowered Epo production in hypoxic cultures. Hypoxia exposure decreased superoxide dismutase activity and H2O2 treatment reduced catalase activity thus influencing the endogenous antioxidant defense system. These findings support the concept that reactive O2 species, primarily H2O2, act as messengers in the O2-dependent control of the hepatic production of Epo. Changes in the cellular activities of antioxidant enzymes appear to play only a minor role in this process.}, } @article {pmid9862257, year = {1998}, author = {Hansen, PJ}, title = {Regulation of uterine immune function by progesterone--lessons from the sheep.}, journal = {Journal of reproductive immunology}, volume = {40}, number = {1}, pages = {63-79}, doi = {10.1016/s0165-0378(98)00035-7}, pmid = {9862257}, issn = {0165-0378}, support = {HD 20671/HD/NICHD NIH HHS/United States ; HD 26421/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Female ; Glycoproteins/immunology ; Humans ; Lymphocytes/immunology ; Models, Biological ; Pregnancy ; Progesterone/*immunology ; *Serpins ; Sheep ; Uterus/cytology/*immunology ; }, abstract = {Survival of the fetal allograft results from orchestrated adjustments in activity of maternal lymphoid cells as well as in trophoblast gene expression. One molecule that regulates uterine immune responsiveness is progesterone. In fact, uterine skin graft survival and susceptibility to bacterial infections are increased by progesterone. This review focuses on the role of progesterone in regulation of uterine immune function in the sheep. While the importance of progesterone as a regulator of immune function likely varies between species, concepts derived from the sheep model may prove pertinent to other species also. The actions of progesterone on uterine immune function in the ewe change during pregnancy. Before day 50 of gestation, i.e. when the uterus is still dependent upon the corpus luteum as a source of progesterone, concentrations of progesterone are probably not high enough at the maternal fetal interface to inhibit lymphocyte activation. During this early period of pregnancy, progesterone inhibits uterine immune function by inducing endometrial secretion of a protein called uterine milk protein (UTMP) that itself is inhibitory to lymphocyte function. After day 50 of pregnancy, it is likely that the placenta produces sufficient amounts of progesterone to directly inhibit lymphocyte proliferation. Additional inhibition is achieved because of sustained synthesis of UTMP. Accordingly, progesterone acts to regulate uterine immune function in ways that allows for inhibition of immune responses at the utero-placental interface without systemic immunosuppression.}, } @article {pmid9787782, year = {1998}, author = {Jones, JH}, title = {Optimization of the mammalian respiratory system: symmorphosis versus single species adaptation.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology}, volume = {120}, number = {1}, pages = {125-138}, doi = {10.1016/s0305-0491(98)00027-3}, pmid = {9787782}, issn = {1096-4959}, mesh = {Adaptation, Biological/*physiology ; Animals ; Horses/*physiology ; Models, Biological ; Oxygen/pharmacokinetics ; Oxygen Consumption/physiology ; Respiratory System/*metabolism ; }, abstract = {Taylor and Weibel's principle of symmorphosis hypothesized optimal design of the mammalian respiratory system, with no excess structure relative to its maximal O2 flux, VO2max. Although they found symmorphosis not to be a general principle of design, it might apply to a highly adapted aerobic athlete, e.g. the Thoroughbred racehorse. Using a mathematical model based on empirical data of the equine O2 transport system at normoxic VO2max, the fraction of the total limitation to O2 flux contributed by each of the respiratory transport steps is calculated as either the fractional change (F) in VO2max for a 1% change in each component, or as the fraction of total O2 pressure drop (R(int)) across each component at VO2max. When calculated as F, alveolar ventilation (VA) and pulmonary diffusing capacity (DLO2) are major limiting factors, circulatory convection (Q) is nearly as limiting, and peripheral tissue diffusing capacity (DTO2) is only one-third as important. When calculated as R(int), DLO2 is the major factor, VA and DTO2 contribute significantly, and Q is smallest. These patterns contrast with analogous studies in humans, in which Q is the single major limiting factor. The results suggest that strong selection for aerobic power in horses has maximized the malleable components of their respiratory systems until the least malleable structure, the lungs, has become a major limitation to O2 flux. Symmorphosis cannot determine if such a design is or is not optimized, as every system falls on a continuous distribution of relative optimization among species. However, the concept of symmorphosis is useful for establishing a framework within which a single species can be compared with a quantitatively defined hypothesis of optimal animal design, and compared with other species according to those criteria.}, } @article {pmid9787780, year = {1998}, author = {Brooks, GA}, title = {Mammalian fuel utilization during sustained exercise.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology}, volume = {120}, number = {1}, pages = {89-107}, doi = {10.1016/s0305-0491(98)00025-x}, pmid = {9787780}, issn = {1096-4959}, support = {AR 42906/AR/NIAMS NIH HHS/United States ; DK 19577/DK/NIDDK NIH HHS/United States ; }, mesh = {Blood Glucose/metabolism ; Energy Metabolism/*physiology ; Fatty Acids/metabolism ; Glycolysis/physiology ; Humans ; Lactic Acid/metabolism ; Oxygen Consumption/physiology ; Physical Exertion/*physiology ; }, abstract = {The 'crossover' and 'lactate shuttle' concepts of substrate utilization in humans during exercise are extended to describe metabolic responses on other mammalian species. The 'crossover concept' is that lipid plays a predominant role in sustaining efforts requiring half or less aerobic capacity (VO2max); however, greater relative efforts depend increasingly on blood glucose and muscle glycogen as substrates. Thus, as exercise intensity increases from mild to moderate and hard, fuel selection switches (crosses over) from lipid to carbohydrate dependence. Glycogen and glucose catabolic rates are best described as exponential functions of exercise intensity, but with a greater gain in slope of the glycogen than glucose response. In contrast, plasma free fatty acid flux is described as an inverted hyperbola with vertex at approximately 50% VO2max. Both endocrine and intra-cellular factors play critical roles in determining substrate balance during sustained exercise. Moreover, genotypic adaptation for aerobic capacity as well as phenotypic adaptations to short- and long-term chronic activity affect the balance of substrate utilization during exercise. The concept of a 'lactate shuttle' is that during hard exercise, as well as other conditions of accelerated glycolysis, glycolytic flux in muscle involves lactate formation regardless of the state of oxygenation. Further, according to the lactate shuttle concept, lactate represents a major means of distributing carbohydrate potential energy for oxidation and gluconeogenesis. In humans and other mammals, the formation, distribution and disposal of lactate (not pyruvate) represent key steps in the regulation of intermediary metabolism during sustained exercise.}, } @article {pmid9785350, year = {1998}, author = {Gereben, B and Leuhuber, K and Rausch, WD and Gálfi, P and Jancsik, V and Rudas, P}, title = {Inverse hierarchy of vimentin epitope expression in primary cultures of chicken and rat astrocytes: a double-immunofluorescence study.}, journal = {Neurobiology (Budapest, Hungary)}, volume = {6}, number = {2}, pages = {141-150}, pmid = {9785350}, issn = {1216-8068}, mesh = {Animals ; Astrocytes/*immunology ; Blotting, Western ; Cells, Cultured ; Chick Embryo ; Epitopes/*analysis ; Fluorescent Antibody Technique ; Rats ; Rats, Sprague-Dawley ; Species Specificity ; Vimentin/*immunology ; }, abstract = {Vimentin contributes to the cytoskeleton of different cell-types, among them glial cells. We report here that different forms of this protein, distinguishable by the monoclonal antibodies Vim3B4 and V9, are species-specifically expressed in cultures of glial fibrillary acidic protein (GFAP) positive, primary astrocytes of the chicken and rat. Most cells in the cultures co-expressed GFAP and one of the two vimentin epitopes. The Vim3B4 positive epitope was present in chicken astrocytes, while the V9 positive was not. Inverse situation was found in the astrocytes of rat. In vitro age of the cells did not influence the hierarchy of vimentin epitope expression with respect to species-specificity. Our result shows that the different vimentin expression program of cultured astrocytes of the chicken and rat is preserved under in vitro conditions. The presented data support the concept of the species-specific regulation of vimentin forms in glial cells of the central nervous system.}, } @article {pmid9785043, year = {1998}, author = {Abraham, EJ and Morris-Hardeman, JN and Swenson, LM and Knoppel, EL and Ramanathan, B and Wright, KJ and Grieger, DM and Minton, JE}, title = {Pituitary function in the acute phase response in domestic farm animals: cytokines, prostaglandins, and secretion of ACTH.}, journal = {Domestic animal endocrinology}, volume = {15}, number = {5}, pages = {389-396}, doi = {10.1016/s0739-7240(98)00020-4}, pmid = {9785043}, issn = {0739-7240}, mesh = {Acute-Phase Reaction/immunology/physiopathology/*veterinary ; Adrenocorticotropic Hormone/*metabolism ; Amino Acid Sequence ; Animals ; *Animals, Domestic ; Cattle ; Cytokines/*immunology/physiology ; Dinoprostone/*immunology/physiology ; Humans ; Immunity, Innate/physiology ; Indomethacin/pharmacology ; Interleukin-6/immunology/physiology ; Lipopolysaccharides/pharmacology ; Macrophage Migration-Inhibitory Factors/immunology/physiology ; Mice ; Molecular Sequence Data ; Pituitary Gland, Anterior/*immunology/metabolism/physiology ; Pituitary-Adrenal System/immunology/metabolism/physiology ; Rats ; Sequence Homology, Amino Acid ; Swine ; }, abstract = {Contained in this report is a review of available data on pituitary cytokines in domestic species of agricultural importance. The concept is advanced that the pituitary gland is essential to appropriate generation of host defense mechanisms and thus should be considered among other tissues contributing to innate immunity. The functions of these intrapituitary cytokines, principally IL-6, are discussed in the context of potential regulation of the pituitary-adrenal axis (ACTH secretion) via intrapituitary PGE2 generation during the acute-phase response to infectious/inflammatory stimuli. Data from other species are cited as appropriate for comparative purposes and elaboration of proposed mechanisms. However, the scope of the review is not intended to comprehensively cover the vast literature on proinflammatory cytokines and prostaglandins generated peripherally and centrally during host responses to inflammatory stimuli.}, } @article {pmid9762560, year = {1998}, author = {Southgate, VR and Jourdane, J and Tchuenté, LA}, title = {Recent studies on the reproductive biology of the schistosomes and their relevance to speciation in the Digenea.}, journal = {International journal for parasitology}, volume = {28}, number = {8}, pages = {1159-1172}, doi = {10.1016/s0020-7519(98)00021-6}, pmid = {9762560}, issn = {0020-7519}, mesh = {Animals ; Disorders of Sex Development ; Host-Parasite Interactions ; Humans ; Hybridization, Genetic/physiology ; Parthenogenesis ; Reproduction/physiology ; Schistosoma/*physiology ; Sexual Behavior, Animal ; Species Specificity ; }, abstract = {The members of the family Schistosomatidae, dioecious Digenea, are discussed with regard to their distribution, intermediate and definitive host-parasite relationships. The biological species concept is considered together with the difficulties of its application to Schistosoma spp. and the Digenea. The correlation between pairing of adult schistosomes, physical and sexual development and the maintenance of reproductive potential is emphasised. Development of the female reproductive system does not depend upon species-specific pairing. In some combinations, e.g., Schistosoma haematobium/Schistosoma intercalatum and Schistosoma bovis/Schistosoma curassoni, a specific mate choice system apparently does not exist, whereas it does in other combinations, e.g., Schistosoma mansoni/Schistosoma intercalatum. In mixed infections change of mate may occur and when the opportunity arises heterospecific pairs of worms will change partners to conspecific pairs. Interspecific pairing in adult schistosomes will lead to either hybridisation or parthenogenesis. Yet the majority of schistosomes that inhabit the same definitive host maintain their genetic identity: specific mate recognition, site selection within the host and heterologous immunity have been suggested as isolating mechanisms. Experimental intraspecific crosses have enabled evaluation of the degree to which some populations separated and became reproductively isolated through pre-mating isolating mechanisms, indicative of incipient speciation, e.g., the Lower Guinea and Zaire strains of S. intercalatum. The occurrence and significance of parthenogenesis in schistosomes and other species of Digenea are discussed. The consequences of interspecific mating interactions in schistosomes with regard to parasite epidemiology, interspecific competition and genetic heterogeneity are debated. Geographical isolation and host specificity represent important pre-zygotic isolating mechanisms. It is suggested that site selection within the host and heterologous immunity may both reduce interspecific genetic interchange when digenean parasites utilise the same definitive host.}, } @article {pmid9714215, year = {1998}, author = {Zarlenga, DS and Hoberg, EP and Stringfellow, F and Lichtenfels, JR}, title = {Comparisons of two polymorphic species of Ostertagia and phylogenetic relationships within the Ostertagiinae (Nematoda: Trichostrongyloidea) inferred from ribosomal DNA repeat and mitochondrial DNA sequences.}, journal = {The Journal of parasitology}, volume = {84}, number = {4}, pages = {806-812}, pmid = {9714215}, issn = {0022-3395}, mesh = {Animals ; Base Sequence ; Cattle ; Cloning, Molecular ; Consensus Sequence ; DNA, Helminth/*chemistry ; DNA, Mitochondrial/*chemistry ; DNA, Ribosomal/*chemistry ; Deer ; Electron Transport Complex IV/genetics ; Female ; Male ; Molecular Sequence Data ; Ostertagia/*classification/enzymology/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; *Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; }, abstract = {The first internal transcribed spacer DNA (ITS-1) (rDNA) and the mitochondrial (mt) DNA-derived cytochrome oxidase I gene (COX-1) were enzymatically amplified, cloned and sequenced from 6 nominal species of Ostertagiinae as well as Haemonchus contortus and Haemonchus placei. The portion of the COX-1 gene analyzed was 393 base pairs (bp) in length and contained 33 within species polymorphic base changes at 28 synonymous sites. The ITS-1 rDNA consensus sequences ranged from 392 bp (Ostertagia ostertagi/Ostertagia lyrata, Teladorsagia circumcincta) to 404 bp (H. contortus, H. placei). These data were used both in a distance analysis to assess the concept of polymorphic species within the genus Ostertagia and in parsimony analysis to assess phylogenetic relationships within a limited group of Ostertagiinae. Pairwise similarity scores of both ITS-1 and COX-1 data showed the highest number of conserved sites between the proposed dimorphic species of Ostertagia. The level of similarity was lower in the COX-1 data due to the high number of synonymous base changes. Analysis by maximum parsimony of the same data did not refute O. ostertagi/O. lyrata and Ostertagia mossil/Ostertagia dikmansi as dimorphic species and supported monophyly of these ostertagiines relative to representatives of the haemonchine outgroup. In the single most parsimonious tree from ITS-1 rDNA data, a subclade of Ostertagia spp. included forms possessing parallel synlophes and long esophageal valves that typically occur in cervid hosts.}, } @article {pmid9673868, year = {1998}, author = {Adlard, RD and O'Donoghue, PJ}, title = {Perspectives on the biodiversity of parasitic protozoa in Australia.}, journal = {International journal for parasitology}, volume = {28}, number = {6}, pages = {887-897}, doi = {10.1016/s0020-7519(98)00043-5}, pmid = {9673868}, issn = {0020-7519}, mesh = {Amphibians/parasitology ; Animals ; Australia ; Birds/parasitology ; *Ecosystem ; Eukaryota/*classification ; Fishes/parasitology ; Host-Parasite Interactions ; Mammals/parasitology ; Protozoan Infections, Animal/*parasitology ; Reptiles/parasitology ; }, abstract = {Biodiversity is a term applied to described the number, variety and variability of organisms. Its colloquial application is usually as a measure of species diversity of species richness. Thus, the concepts of "species" and "species boundaries" are integral to any discussion on biodiversity, and with them, the basal question of what constitutes meaningful variation. Protozoan taxonomy is an evolving mix of morphological and molecular characters, and is based largely on decisions made intuitively and arbitrarily using multiple characters. Where to draw species boundaries has become more difficult in the face of a bewildering level of variation uncovered in recent years, due largely to an increase in the resolution of our taxonomic techniques (e.g., ultrastructural and genetic studies). A major challenge for contemporary protozoan taxonomists is to update the existing systematic framework to incorporate our current level of knowledge and to decide on the relative importance of parasite morphology, genetics and biology to the concept of the protozoan "species". This task is compounded by the relative paucity of information on our endemic protozoan parasites. In Australia, even in vertebrate hosts, little is known of the biodiversity of parasitic protozoa. Not surprisingly, what knowledge we do have is linked to clinical disease, e.g., detailed knowledge of some species of coccidia and of some enteric ciliates, flagellates and amoebae of mammals. We have some knowledge of a few species of haemosporidia of reptiles and birds but, even here, molecular studies and experimental work are required to identify species boundaries. In view of these limitations, the best estimate of the biodiversity of Australia's parasitic protozoa in at least the vertebrate fauna of Australia, is that less than one third of the total species have been discovered to date.}, } @article {pmid9653737, year = {1998}, author = {Tchesnova, L}, title = {Socio-economic and scientific premises for forming the strategies against malaria in Russia under Soviet power.}, journal = {Parassitologia}, volume = {40}, number = {1-2}, pages = {103-108}, pmid = {9653737}, issn = {0048-2951}, mesh = {Animals ; Anopheles ; History, 20th Century ; Humans ; Malaria/*history/prevention & control ; Mosquito Control/history ; Russia ; USSR ; }, abstract = {The rapid spread of malaria in the 1920s-early '30s in the USSR was a result of Stalin's social and demographic policy. The Soviet government needed to elaborate the special complex of organisational and applied scientific measures concerning the eradication of malaria. The Central Malaria Commission and a network of antimalaria stations were created. In the 1930s and '40s malaria studies were institutionalised. A system of Medical Research Institutes was set up in the Soviet Union. Antimalaria congresses and periodical special issues helped coordinate their activities. Russian parasitologists worked out new approaches and methods of the comprehensive control of malaria foci. During World War II (1941-1945), the epidemiological situation was aggravated and antimalaria measures reduced. In the years 1945-1960 Beklemishev with his scientific school worked out the concept of landscape malariology and of "vital scheme of the species". This concept formed the basis for realising the malaria eradication strategy. In 1961 the WHO Malaria Eradication Department ascertained the liquidation of all types of malaria in Russia as epidemics.}, } @article {pmid9608515, year = {1997}, author = {Borrego, JJ and Figueras, MJ}, title = {Microbiological quality of natural waters.}, journal = {Microbiologia (Madrid, Spain)}, volume = {13}, number = {4}, pages = {413-426}, pmid = {9608515}, issn = {0213-4101}, mesh = {Animals ; Bacteria/classification/isolation & purification ; Bacteriophages/isolation & purification ; Communicable Diseases/microbiology/parasitology/transmission ; Eukaryota/classification/isolation & purification ; Feces/microbiology/parasitology ; Fresh Water ; Humans ; Sewage ; Viruses/classification/isolation & purification ; Water/parasitology ; *Water Microbiology ; Water Pollution/analysis ; }, abstract = {Several aspects of the microbiological quality of natural waters, especially recreational waters, have been reviewed. The importance of the water as a vehicle and/or a reservoir of human pathogenic microorganisms is also discussed. In addition, the concepts, types and techniques of microbial indicator and index microorganisms are established. The most important differences between faecal streptococci and enterococci have been discussed, defining the concept and species included. In addition, we have revised the main alternative indicators used to measure the water quality.}, } @article {pmid9595694, year = {1998}, author = {Masters, JC}, title = {Speciation in the lesser galagos.}, journal = {Folia primatologica; international journal of primatology}, volume = {69 Suppl 1}, number = {}, pages = {357-370}, doi = {10.1159/000052724}, pmid = {9595694}, issn = {0015-5713}, mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; Ecology ; *Galago ; Models, Biological ; Sexual Behavior, Animal ; Species Specificity ; Vocalization, Animal ; }, abstract = {Species and their origins remain one of the outstanding enigmas of evolutionary biology. Many different views of the problem exist, but few have concrete predictions that open the problem to investigation. This study formalises predictions arising from the Recognition Concept of species (RC) and the Organization Theory of Speciation (OTS), and applies them to the pattern demonstrated by the lesser galago radiation. The RC and OTS are in agreement that one of the primary adaptive responses during animal speciation events involves the system of sexual recognition and reproduction, and indeed the lesser galago taxa show significant divergences in their communication systems relating to specific-mate recognition. On the other hand, only the RC predicts a concomitant adaptive response to the ecological conditions prevailing during speciation, and there are strong indications of shifts in habitat preference among these taxa. The predictions of the RC are supported above those of the OTS.}, } @article {pmid9584889, year = {1998}, author = {Ahern, JC}, title = {Underestimating intraspecific variation: the problem with excluding Sts 19 from Australopithecus africanus.}, journal = {American journal of physical anthropology}, volume = {105}, number = {4}, pages = {461-480}, doi = {10.1002/(SICI)1096-8644(199804)105:4<461::AID-AJPA5>3.0.CO;2-R}, pmid = {9584889}, issn = {0002-9483}, mesh = {Animals ; Anthropology, Physical ; Anthropometry ; *Fossils ; Hominidae/*classification ; Humans ; Phylogeny ; Skull/anatomy & histology ; }, abstract = {Two analyses conclude that Sts 19 cannot be accommodated within the Australopithecus africanus hypodigm (Kimbel and Rak [1993] In Kimbel and Martin [eds.]: Species, Species Concepts, and Primate Evolution. New York: Plenum, pp. 461-484; Sarmiento [1993] Am. J. Phys. Anthropol. [Suppl.] 16:173). Both studies exclude Sts 19 because it possesses synapomorphies with Homo. Furthermore, according to Kimbel and Rak (1993), including Sts 19 in A. africanus results in an unacceptably high degree of polymorphism. This study aims to refute the null hypothesis that Sts 19 belongs to A. africanus. Twelve basicranial characters, as defined and implemented in Kimbel and Rak's study, were scored for casts of seven A. africanus and seven Homo habilis basicranial specimens. These characters were also examined on specimens from a large (N = 87) sample of African pongids. Contrary to Kimbel and Rak's (1993) findings, the null hypothesis is not refuted. The degree of polymorphism among A. africanus with Sts 19 included is less than that seen in Pan troglodytes. In addition, Sts 19 shares only one apomorphy with Homo. However, when treated metrically, Sts 19's morphology for this character is not significantly divergent from other A. africanus specimens.}, } @article {pmid9520404, year = {1998}, author = {Vaz, AD and McGinnity, DF and Coon, MJ}, title = {Epoxidation of olefins by cytochrome P450: evidence from site-specific mutagenesis for hydroperoxo-iron as an electrophilic oxidant.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {7}, pages = {3555-3560}, pmid = {9520404}, issn = {0027-8424}, support = {AA-06221/AA/NIAAA NIH HHS/United States ; DK-10339/DK/NIDDK NIH HHS/United States ; }, mesh = {Alkenes/*metabolism ; Animals ; Binding Sites/genetics ; Cytochrome P-450 Enzyme System/genetics/*metabolism ; Escherichia coli ; Mutagenesis, Site-Directed ; Oxidants/metabolism ; Oxidation-Reduction ; Rats ; Substrate Specificity/genetics ; }, abstract = {P450 cytochromes (P450) catalyze many types of oxidative reactions, including the conversion of olefinic substrates to epoxides by oxygen insertion. In some instances epoxidation leads to the formation of products of physiological importance from naturally occurring substrates, such as arachidonic acid, and to the toxicity, carcinogenicity, or teratogenicity of foreign compounds, including drugs. In the present mechanistic study, the rates of oxidation of model olefins were determined with N-terminal-truncated P450s 2B4 and 2E1 and their respective mutants in which the threonine believed to facilitate proton delivery to the active site was replaced by alanine. Styrene epoxidation, cyclohexene epoxidation and hydroxylation to give 1-cyclohexene-3-ol, and cis- or trans-butene epoxidation (without isomerization) and hydroxylation to give 2-butene-1-ol were all significantly decreased by the 2B4 T302A mutation. Reduced proton delivery in this mutant is believed to interfere with the activation of dioxygen to the oxenoid species, as shown earlier by decreased hydroxylation of several substrates and enhanced aldehyde deformylation via a presumed peroxo intermediate. Of particular interest, however, the T303A mutation of P450 2E1 resulted in enhanced epoxidation of all of the model olefins along with decreased allylic hydroxylation of cyclohexene and butene. These results and a comparison of the ratios of the rates of epoxidation and hydroxylation support the concept that two different species with electrophilic properties, hydroperoxo-iron (FeO2H)3+ and oxenoid-iron (FeO)3+, can effect olefin epoxidation. The ability of cytochrome P450 to use several different active oxidants generated from molecular oxygen may help account for the broad reaction specificity and variety of products formed by this versatile catalyst.}, } @article {pmid9565977, year = {1998}, author = {Sigmund, D}, title = {[Phenomenology of cycloid axis syndromes and their delineation from a schizophrenic core group].}, journal = {Der Nervenarzt}, volume = {69}, number = {3}, pages = {228-237}, doi = {10.1007/s001150050264}, pmid = {9565977}, issn = {0028-2804}, mesh = {Cyclothymic Disorder/classification/*diagnosis/psychology ; Delusions/classification/diagnosis/psychology ; Hallucinations/classification/diagnosis/psychology ; Humans ; Psychiatric Status Rating Scales/*statistics & numerical data ; Schizophrenia/classification/*diagnosis ; Schizophrenia, Paranoid/classification/diagnosis/psychology ; *Schizophrenic Psychology ; }, abstract = {The concept of cycloid psychoses means a certain species as part of the group of schizophrenias. From our clinical point of view, the subtypes of Leonard and their poles are axial syndromes. They can occur simultaneously or intermingle during one phase. In the present phenomenological study the inner connections of these axial syndromes are shown. Apart from these connections, cycloid psychoses can be differentiated from core schizophrenia by three conditions: (1) the lack of deformation of affect and affect expression; (2) the lack of deformaton of thought structure; and (3) the lack of certain movement deformations, e.g., parakinesis. Our concept of phenomenon is explained to criticize the current operational definitions of cycloid psychoses. A different approach is suggested.}, } @article {pmid9542098, year = {1998}, author = {de Barros Lopes, M and Soden, A and Martens, AL and Henschke, PA and Langridge, P}, title = {Differentiation and species identification of yeasts using PCR.}, journal = {International journal of systematic bacteriology}, volume = {48 Pt 1}, number = {}, pages = {279-286}, doi = {10.1099/00207713-48-1-279}, pmid = {9542098}, issn = {0020-7713}, mesh = {DNA Fingerprinting ; DNA Primers ; DNA, Fungal/*analysis ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Polymerase Chain Reaction/*methods ; Saccharomyces cerevisiae/*genetics/*isolation & purification ; Species Specificity ; Wine/*microbiology ; }, abstract = {A PCR-based method has been developed that permits both intraspecies differentiation and species identification of yeast isolates. Oligonucleotide primers that are complementary to intron splice sites were used to produce PCR fingerprints that display polymorphisms between different species of indigenous wine yeasts. Although polymorphisms existed between isolates of the same species, the banding patterns shared several amplification products that allowed species identification. Importantly, the method was able to distinguish between species of the closely related Saccharomyces sensu stricto yeasts. In two cases where isolates could not be positively identified there was discrepancy between the phenetic and phylogenetic species concept. The method has applications in yeast ecological studies, enabling the rapid grouping of isolates with related genomes and the investigation of population dynamics of strains of the same species.}, } @article {pmid9504344, year = {1998}, author = {Jackson, TF}, title = {Entamoeba histolytica and Entamoeba dispar are distinct species; clinical, epidemiological and serological evidence.}, journal = {International journal for parasitology}, volume = {28}, number = {1}, pages = {181-186}, doi = {10.1016/s0020-7519(97)00177-x}, pmid = {9504344}, issn = {0020-7519}, mesh = {Animals ; Dysentery, Amebic/*classification/*epidemiology ; Entamoeba/*classification ; Entamoeba histolytica/*classification ; Entamoebiasis/*classification/*epidemiology ; Humans ; Isoenzymes/analysis ; South Africa/epidemiology ; }, abstract = {The name of the causative organism of invasive amoebiasis, Entamoeba histolytica, was first introduced in 1903, even though this intestinal amoeba had been recognised since 1875. The marked disparity between the number of infected individuals and those with invasive amoebiasis resulted in a number of explanatory hypotheses being proposed. Although none of these were universally accepted, Brumpt's concept of two morphologically identical species gained increasing acceptance 50-60 years later when technology became available to investigate this anomaly. Sargeaunt spear-headed this drive by establishing the value of isoenzyme electrophoresis for studying the host-parasite relationship. From this foundation, incorporation of clinical, epidemiological and serological parameters to studies of the parasite resulted in the conclusion that a species complex comprising two morphologically identical amoebae was implicated with the disease. The two organisms have been named E. histolytica and Entamoeba dispar. The former is a pathogen and is responsible for invasive amoebiasis, while the latter is a gut commensal. Demonstration of the existence of this species complex has subsequently been confirmed by studies on the nucleic acids from several independent laboratories. The acceptance of E. histolytica and E. dispar as distinct species has had a major impact on our understanding of amoebiasis and its clinical management.}, } @article {pmid9504333, year = {1998}, author = {Finlay, BJ}, title = {The global diversity of protozoa and other small species.}, journal = {International journal for parasitology}, volume = {28}, number = {1}, pages = {29-48}, doi = {10.1016/s0020-7519(97)00167-7}, pmid = {9504333}, issn = {0020-7519}, mesh = {Animals ; Ciliophora/*classification ; Eukaryota/*classification ; Geography ; Water/parasitology ; }, abstract = {It is widely believed that the number of species of micro-organisms in the world is extremely large. Here, we offer the contrasting view--that the number may be quite modest. Most of the work reviewed refers to the ciliated protozoa. As with all microbial groups, we must define our concept of "species", and for ciliates, the "morphospecies" concept appears to be at least as robust as any other. Critical examination of published descriptions of ciliates provides a "best estimate" of 3744 for the global number of free-living morphospecies. Of these, 793 are associated with marine sediments, and 1370 with freshwater sediments. In an independent analysis based on extrapolation (assuming the ubiquity of species) from ecological datasets, we estimate the numbers of species in marine and freshwater sediments as 597 and 732, respectively (i.e. within a factor of two of the figures obtained from taxonomic analysis). This apparent convergence of independent estimates will strengthen if, as is likely, the number of nominal species is further reduced by taxonomic revision. These relatively low numbers of species are consistent with (a) the vast amount of published information indicating typically cosmopolitan distributions for ciliates and other microbes, and (b) recent experimental evidence that most free-living ciliates are rare or cryptic--seldom detectable, but present, and "waiting" for suitable conditions to arrive. In summary, most ciliates (and other micro-organisms) are probably ubiquitous, endemics are rare, global species richness is relatively low, and, at least in the case of the ciliates, most species have already been discovered.}, } @article {pmid9480733, year = {1998}, author = {Young, ND}, title = {Pacific Coast Iris species delimitation using three species definitions: biological, phylogenetic and genealogical.}, journal = {Biological journal of the Linnean Society. Linnean Society of London}, volume = {63}, number = {1}, pages = {99-120}, pmid = {9480733}, issn = {0024-4066}, abstract = {Morphological characters are used to discriminate the five Oregon species of the Pacific Coast irises (Iris series Californicae). In nearly every case, fixed differences were found between species, revealing that they are good phylogenetic species. However, when the biological species concept is applied, the whole series is found to be one biological species. Sequence data were generated from the chloroplast DNA region between the atpbeta and rbcL genes. For this 700 bp region, the maximum divergence observed in the series was one percent. These sequences, together with three restriction site characters, were used to produce a cladogram for multiple individuals of all species in the group. On the resulting consensus cladogram, the different individuals from each species do not cluster together. This could result from either introgressive hybridization or the retention of ancestral polymorphism. When the genealogical species concept is applied, only one species can be identified: the whole Series Californicae. There are therefore two natural levels at which taxa can be defined. It is recommended that the phylogenetic species be used as the taxonomic species in this group.Copyright 1998 The Linnean Society of London}, } @article {pmid19274196, year = {1998}, author = {Adams, BJ and Burnell, AM and Powers, TO}, title = {A phylogenetic analysis of heterorhabditis (nemata: rhabditidae) based on internal transcribed spacer 1 DNA sequence data.}, journal = {Journal of nematology}, volume = {30}, number = {1}, pages = {22-39}, pmid = {19274196}, issn = {0022-300X}, abstract = {Internal transcribed spacer 1 sequences were used to infer phylogenetic relationships among 8 of the 9 described species and one putative species of the entomopathogenic nematode genus Heterorhabditis. Sequences were aligned and optimized based on pairwise genetic distance and parsimony criteria and subjected to a variety of sequence alignment parameters. Phylogenetic trees were constructed with maximum parsimony, cladistic, distance, and maximum likelihood algorithms. Our results gave strong support for four pairs of sister species, while relationships between these pairs also were resolved but less well supported. The ITS1 region of the nuclear ribosomal repeat was a reliable source of homologous characters for resolving relationships between closely related taxa but provided more tenuous resolution among more divergent lineages. A high degree of sequence identity and lack of autapomorphic characters suggest that sister species pairs within three distinct lineages may be mutually conspecific. Application of these molecular data and current morphological knowledge to the delimitation of species is hindered by an incomplete understanding of their variability in natural populations.}, } @article {pmid19274195, year = {1998}, author = {Adams, BJ}, title = {Species concepts and the evolutionary paradigm in modem nematology.}, journal = {Journal of nematology}, volume = {30}, number = {1}, pages = {1-21}, pmid = {19274195}, issn = {0022-300X}, abstract = {Given the task of recovering and representing evolutionary history, nematode taxonomists can choose from among several species concepts. All species concepts have theoretical and (or) operational inconsistencies that can result in failure to accurately recover and represent species. This failure not only obfuscates nematode taxonomy but hinders other research programs in hematology that are dependent upon a phylogenetically correct taxonomy, such as biodiversity, biogeography, cospeciation, coevolution, and adaptation. Three types of systematic errors inherent in different species concepts and their potential effects on these research programs are presented. These errors include overestimating and underestimating the number of species (type I and II error, respectively) and misrepresenting their phylogenetic relationships (type III error). For research programs in hematology that utilize recovered evolutionary history, type II and III errors are the most serious. Linnean, biological, evolutionary, and phylogenefic species concepts are evaluated based on their sensitivity to systematic error. Linnean and biological species concepts are more prone to serious systematic error than evolutionary or phylogenetic concepts. As an alternative to the current paradigm, an amalgamation of evolutionary and phylogenetic species concepts is advocated, along with a set of discovery operations designed to minimize the risk of making systematic errors. Examples of these operations are applied to species and isolates of Heterorhabditis.}, } @article {pmid9367738, year = {1997}, author = {Marín, I}, title = {Sexual isolation in Drosophila. III. Estimating isolation using male-choice experiments.}, journal = {Journal of theoretical biology}, volume = {188}, number = {4}, pages = {515-524}, doi = {10.1006/jtbi.1997.0492}, pmid = {9367738}, issn = {0022-5193}, mesh = {Animals ; Drosophila/*physiology ; Female ; Male ; Models, Biological ; Phylogeny ; *Sexual Behavior, Animal ; Species Specificity ; }, abstract = {It has been generally assumed that "choice experiments" are useful to measure sexual isolation between Drosophila strains or species. Theoretical models have demonstrated however that the results obtained using one of these designs, namely multiple-choice experiments, are insufficient to determine the degree of isolation, even under very favorable assumptions. In this work, a simple behavioral model is developed to test whether male-choice experiments can be used to measure sexual isolation in Drosophila. This model shows that, although the outcome of male-choice experiments is affected by differences in female receptivities, a procedure to estimate the minimum degree of isolation using this experimental design can be established. The application of the methods derived from the theoretical model to previously reported experimental data demonstrates that a substantial degree of isolation frequently exists intraspecifically, while isolation is far from complete interspecifically. These results have important implications for discussions based on the comparative analysis of Drosophila behavior, both intra- and interspecifically. Most especially, they are in contradiction with the expectations of the Recognition concept of species.}, } @article {pmid9461398, year = {1997}, author = {Lönnig, WE and Saedler, H}, title = {Plant transposons: contributors to evolution?.}, journal = {Gene}, volume = {205}, number = {1-2}, pages = {245-253}, doi = {10.1016/s0378-1119(97)00397-1}, pmid = {9461398}, issn = {0378-1119}, mesh = {DNA ; *DNA Transposable Elements ; *Evolution, Molecular ; Plants/*genetics ; }, abstract = {A spectrum of different hypotheses has been presented by various authors, from plant transposable elements as major agents in evolution to the very opposite, transposons as mainly selfish DNA constituting a genetic burden for the organisms. The following review will focus on: (1) a short survey of the two main different assessments of transposable elements (TEs) concerning the origin of species (selfish vs useful DNA); (2) the significance of the hierarchy of gene functions and redundancies for TE activities (selfish in non-redundant parts of the genome, but as a source of variability in the rest); (3) the relevance of the results of TE research in Zea mays and Antirrhinum majus for species formation in the wild (contrast between artificial and natural selection); (4) three areas of research where a synthesis between the two different evaluations of TEs seems possible: regressive evolution, the origin of ecotypes and the origin of cultivated plants; and (5) some possible prospects regarding TE-induced species formation in the angiosperms in general, i.e., the basic difference between systematic and genetic species concepts and the conceivable origin of a large part of angiosperm morphospecies owing to loss of function and further mutations by TE activities.}, } @article {pmid9351269, year = {1997}, author = {Ito, Y and Hirano, T}, title = {The determination of the partial 18 S ribosomal DNA sequences of Cordyceps species.}, journal = {Letters in applied microbiology}, volume = {25}, number = {4}, pages = {239-242}, doi = {10.1046/j.1472-765x.1997.00203.x}, pmid = {9351269}, issn = {0266-8254}, mesh = {Animals ; Ascomycota/classification/genetics ; Base Sequence ; DNA Primers/genetics ; DNA, Fungal/*genetics ; DNA, Ribosomal/*genetics ; Hypocreales/classification/*genetics/pathogenicity ; Insecta/microbiology ; Medicine, Chinese Traditional ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Cordyceps species, which are used in Chinese traditional medicines, are fungal parasites of insects. In this study the partial nucleotide sequences of 18 S ribosomal DNA from four Cordyceps species were determined and compared with the sequences of published ascomycetes. The sequence data support the concept that Cordyceps species belong to the pyrenomycetes. Based on sequence data the phylogenetic tree was constructed using the neighbor-joining (NJ) method. Diversity in the phylogenetic tree was found for Cordyceps species. A new classification of Cordyceps species can be constructed based on the phylogenetic information obtained from such rDNA sequences.}, } @article {pmid9259512, year = {1997}, author = {Coombes, AG and Tasker, S and Lindblad, M and Holmgren, J and Hoste, K and Toncheva, V and Schacht, E and Davies, MC and Illum, L and Davis, SS}, title = {Biodegradable polymeric microparticles for drug delivery and vaccine formulation: the surface attachment of hydrophilic species using the concept of poly(ethylene glycol) anchoring segments.}, journal = {Biomaterials}, volume = {18}, number = {17}, pages = {1153-1161}, doi = {10.1016/s0142-9612(97)00051-3}, pmid = {9259512}, issn = {0142-9612}, mesh = {Biocompatible Materials/chemistry/*metabolism ; Dextrans/chemistry/*metabolism ; Drug Carriers ; *Drug Delivery Systems ; Drug Stability ; Emulsions ; Enzyme-Linked Immunosorbent Assay ; Lactic Acid/*metabolism ; Microscopy, Electron, Scanning ; Microspheres ; Particle Size ; Polyethylene Glycols/chemistry/*metabolism ; Polyglycolic Acid/*metabolism ; Polylactic Acid-Polyglycolic Acid Copolymer ; Polymers/*metabolism ; Solvents ; Spectrometry, X-Ray Emission ; Surface Properties ; Vaccines/*administration & dosage ; Volatilization ; }, abstract = {Poly(ethylene glycol)-dextran (PEG-DEX) conjugates have been used as a combined stabilizer and surface modifier to produce resorbable poly(DL-lactide-co-glycolide) (PLG) microparticles by an emulsification/solvent evaporation technique. The use of PEG or dextran polymers alone was incapable of producing microparticles. Particle size measurements revealed smaller mean particle sizes (480 nm) and improved polydispersity when using a 1.2% PEG substituted conjugate relative to a 9% substituted material (680 nm). PLG microparticles modified by post-adsorbed PEG-DEX conjugates flocculated in 0.01 M salt solutions, whereas PLG microparticles prepared using PEG-DEX as a surfactant were stable in at least 0.5 M NaCl solutions. Surface modification of PLG microparticles was confirmed by zeta potential measurements and surface analysis using X-ray photoelectron spectroscopy. The presence of surface exposed dextran was confirmed by an immunological detection method using a dextran-specific antiserum in an enzyme-linked immunosorbent assay. The findings support a model in which the PEG component of the PEG-DEX conjugate provides an anchor to the microparticle surface while the dextran component extends from the particle surface to contribute a steric stabilization function. This approach offers opportunities for attaching hydrophilic species such as targeting moieties to biodegradable microparticles to improve the interaction of drug carriers and vaccines with specific tissue sites.}, } @article {pmid9356324, year = {1997}, author = {Apaloo, J}, title = {Revisiting Strategic Models of Evolution: The Concept of Neighborhood Invader Strategies.}, journal = {Theoretical population biology}, volume = {77}, number = {1}, pages = {52-71}, doi = {10.1006/tpbi.1997.1318}, pmid = {9356324}, issn = {1096-0325}, abstract = {In game-theoretic or strategic models of species evolution, the phenotype of individual organisms in a population are regarded as alternate strategies for playing a competitive game. The evolutionary outcome is predicted to conform to the "solution" of that game. The most usual solution concept adopted for the evolutionary game is that of Maynard Smith, the so-called "evolutionary stable strategies" (ESS). In this paper we explore an alternative solution concept. We call it neighborhood invader strategy (NIS). A NIS is a phenotype which is capable of invading all established populations of its neighbors. This phenotype need not be, at the same time, an ESS; and the reverse is true as well. We shall analyze this concept for a single species whose evolutionary-possibility set is a one-dimensional continuum. Copyright 1997 Academic Press}, } @article {pmid9223259, year = {1997}, author = {Avise, JC and Wollenberg, K}, title = {Phylogenetics and the origin of species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, number = {15}, pages = {7748-7755}, pmid = {9223259}, issn = {0027-8424}, mesh = {Models, Genetic ; *Phylogeny ; Species Specificity ; }, abstract = {A recent criticism that the biological species concept (BSC) unduly neglects phylogeny is examined under a novel modification of coalescent theory that considers multiple, sex-defined genealogical pathways through sexual organismal pedigrees. A competing phylogenetic species concept (PSC) also is evaluated from this vantage. Two analytical approaches are employed to capture the composite phylogenetic information contained within the braided assemblages of hereditary pathways of a pedigree: (i) consensus phylogenetic trees across allelic transmission routes and (ii) composite phenograms from quantitative values of organismal coancestry. Outcomes from both approaches demonstrate that the supposed sharp distinction between biological and phylogenetic species concepts is illusory. Historical descent and reproductive ties are related aspects of phylogeny and jointly illuminate biotic discontinuity.}, } @article {pmid9296259, year = {1997}, author = {Palleroni, NJ}, title = {Prokaryotic diversity and the importance of culturing.}, journal = {Antonie van Leeuwenhoek}, volume = {72}, number = {1}, pages = {3-19}, doi = {10.1023/a:1000394109961}, pmid = {9296259}, issn = {0003-6072}, mesh = {*Bacteria/classification ; Bacteriological Techniques ; Biological Evolution ; *Ecosystem ; Prokaryotic Cells ; }, abstract = {Modern approaches based on the use of molecular techniques presumed to circumvent the need for culturing prokaryotes, fail to provide sufficient and reliable information for estimation of prokaryote diversity. Many properties that make these organisms important members of the living world are amenable to observation only through the study of living cultures. Since current culture techniques do not always satisfy the need of providing a balanced picture of the microflora composition, future developments in the study of bacterial diversity should include improvements in the culture methods to approach as closely as possible the conditions of natural habitats. Molecular methods of microflora analysis have an important role as guides for the isolation and characterization of new prokaryotic taxa. Although the species concept is central to biodiversity studies, it is extremely difficult to propose a definition applicable without constraints to all groups of living organisms. However, in prokaryote systematics much improvement has been achieved by comprehensive descriptions that include not only molecular data, but also the relevant aspects of the biology of the organisms under study (polyphasic approach).}, } @article {pmid9224882, year = {1997}, author = {Fussenegger, M and Rudel, T and Barten, R and Ryll, R and Meyer, TF}, title = {Transformation competence and type-4 pilus biogenesis in Neisseria gonorrhoeae--a review.}, journal = {Gene}, volume = {192}, number = {1}, pages = {125-134}, doi = {10.1016/s0378-1119(97)00038-3}, pmid = {9224882}, issn = {0378-1119}, mesh = {Antigenic Variation ; Bacterial Outer Membrane Proteins/metabolism ; Bacterial Proteins/*metabolism ; Biological Evolution ; DNA, Bacterial/metabolism ; Fimbriae Proteins ; Fimbriae, Bacterial/immunology/*metabolism ; Humans ; Membrane Glycoproteins/*metabolism ; Models, Genetic ; Neisseria gonorrhoeae/*genetics/immunology/*metabolism ; *Transformation, Bacterial ; }, abstract = {In Neisseria gonorrhoea (Ngo), the processes of type-4 pilus biogenesis and DNA transformation are functionally linked and play a pivotal role in the life style of this strictly human pathogen. The assembly of pili from its main subunit pilin (PilE) is a prerequisite for gonococcal infection since it allows the first contact to epithelial cells in conjunction with the pilus tip-associated PilC protein. While the components of the pilus and its assembly machinery are either directly or indirectly involved in the transport of DNA across the outer membrane, other factors unrelated to pilus biogenesis appear to facilitate further DNA transfer across the murein layer (ComL, Tpc) and the inner membrane (ComA) before the transforming DNA is rescued in the recipient bacterial chromosome in a RecA-dependent manner. Interestingly, PilE is essential for the first step of transformation, i.e., DNA uptake, and is itself also subject to transformation-mediated phase and antigenic variation. This short-term adaptive mechanism allows Ngo to cope with changing micro-environments in the host as well as to escape the immune response during the course of infection. Given the fact that Ngo has no ecological niche other than man, horizontal genetic exchange is essential for a successful co-evolution with the host. Horizontal exchange gives rise to heterogeneous populations harboring clones which better withstand selective forces within the host. Such extended horizontal exchange is reflected by a high genome plasticity, the existence of mosaic genes and a low linkage disequilibrium of genetic loci within the neisserial population. This led to the concept that rather than regarding individual Neisseria species as independent traits, they comprise a collective of species interconnected via horizontal exchange and relying on a common gene pool.}, } @article {pmid9458988, year = {1997}, author = {Moreno, E}, title = {In search of a bacterial species definition.}, journal = {Revista de biologia tropical}, volume = {45}, number = {2}, pages = {753-771}, pmid = {9458988}, issn = {0034-7744}, mesh = {Bartonella/*classification/genetics ; Brucella/*classification/genetics ; Rhizobium/*classification/genetics ; Rhodopseudomonas/*classification/genetics ; Species Specificity ; }, abstract = {The bacterial species concept was examined within the framework of plant and animal associated alpha-2 proteobacteria, taking into consideration the phylogenetic, taxonomic and biological approaches as well as the microbiologists' perception. The virtue of the phylogenetic approach is that it gives an evolutionary perspective of the bacterial lineage; however the methods used possess low resolution for defining species located at the terminal branches of the phylogenetic trees. The merit of the taxonomic approach is that species are defined on the basis of multiple characteristics allowing high resolution at the terminal branches of dendograms; its disadvantage is the inaccuracy in the earlier nodes. On an individual level, the qualitative biological characteristics used for the definition of species frequently reveal shortcomings because many of these properties are the result of coevolution, parallel evolution or the horizontal transfer of genes. Nevertheless, when considered together with the phylogenetic and taxonomic approaches, important uncertainties are discovered: these must be weighed if a practical definition of bacterial species is conceived. The microbiologists' perception is the criterion expressed by a group of sponsors who, based on scientific and practical grounds, propose a new bacterial species. The success of this new proposal is measured by its widespread acceptance and its permanence. A difficult problem concerned with defining bacterial species is how to distinguish if they are independent evolutionary units or if they are reticulate evolutionary units. In the first case the inherence is vertically transmitted as a result of binary fission and clonal expansion. This may be the case of some animal cell associated bacteria in which recombination appears to be precluded or exceptional. In the second case adaptive changes occurring within an individual can be horizontally transferred to many or all group members. This seems to be the condition of many intestinal and plant associated bacteria. Genetic drift and speciation in clonal bacteria will depend almost exclusively on mutation and internal genetic rearrangement processes, whereas speciation in reticulate bacteria will depend not only on these processes but in their genetic interactions with other bacterial strains. This uncertainty, which corresponds to the evolutionary process, is at the same time one of the key factors in defining a bacterial species.}, } @article {pmid9069002, year = {1997}, author = {Braun, J and Pein, M and Djonlagic, H and Dalhoff, K}, title = {Production of reactive oxygen species by central venous and arterial neutrophils in severe pneumonia and cardiac lung edema.}, journal = {Intensive care medicine}, volume = {23}, number = {2}, pages = {170-176}, doi = {10.1007/s001340050312}, pmid = {9069002}, issn = {0342-4642}, mesh = {Adult ; Aged ; Aged, 80 and over ; Female ; Humans ; Intensive Care Units ; Leukocyte Elastase/blood ; Luminescent Measurements ; Male ; Middle Aged ; Neutrophils/*metabolism/physiology ; Pneumonia/*blood/metabolism/mortality ; Pulmonary Edema/*blood/metabolism ; Reactive Oxygen Species/*metabolism ; Respiratory Distress Syndrome/blood/metabolism ; alpha 1-Antitrypsin/metabolism ; }, abstract = {OBJECTIVE: In pneumonia the influx of neutrophils to the lungs is thought to be of primary importance with regard to host defence and to complications like the adult respiratory distress syndrome. We wanted to evaluate the neutrophil function in patients in acute respiratory failure who required admission to the intensive care unit.

DESIGN: We determined the luminolenhanced chemiluminescence (CL) of neutrophils isolated both from central venous and arterial blood. In addition, the plasma-concentrations of alpha 1-proteinase inhibitor, (alpha 1PI), alpha 2-macroglobulin (alpha 2PI) and elastase-alpha 1PI-complex (elastase) were determined by chemiluminescence immunoassay, and the intracellular elastase content of blood neutrophils was determined using immuno activation assay.

PATIENTS: 28 Patients, 18 with acute pneumonia (group 1) and 10 with cardiac pulmonary edema (group 2).

MEASUREMENTS AND RESULTS: In group 1, luminol enhanced CL was significantly higher than in group 2 (mean 87.7 vs 30.4 x 10(6) counts per minute, p < 0.01). The production of reactive oxygen species was significantly higher in central venous than in arterial neutrophils in the patients with pneumonia (p < 0.03). In patients with pulmonary edema there was no such difference. The plasma concentration of elastase in group 1 was significantly higher than in group 2, that of alpha 2PI were significantly lower. The intracellular elastase content of neutrophils was lower in group 1 than in group 2. In group 1, there was a trend for a correlation between lower intracellular elastase content and a higher elastase plasma concentration. There were no central venous-arterial differences with regard to leukocyte count, cell differential or protein concentration in either group.

CONCLUSION: The central venous-arterial differences in neutrophil production of reactive oxygen species support the concept of compartmentalization of activated neutrophils from the systemic to the pulmonary compartment.}, } @article {pmid9060879, year = {1997}, author = {Brown, PD and Levett, PN}, title = {Differentiation of Leptospira species and serovars by PCR-restriction endonuclease analysis, arbitrarily primed PCR and low-stringency PCR.}, journal = {Journal of medical microbiology}, volume = {46}, number = {2}, pages = {173-181}, doi = {10.1099/00222615-46-2-173}, pmid = {9060879}, issn = {0022-2615}, mesh = {Animals ; DNA Fingerprinting ; DNA, Bacterial/*analysis/isolation & purification ; Dogs ; Humans ; Leptospira/*classification/genetics/isolation & purification ; *Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Prohibitins ; Rats ; Reproducibility of Results ; *Restriction Mapping ; Templates, Genetic ; }, abstract = {Reference strains from 30 serovars representing seven species of Leptospira and 48 recent isolates from human patients, dogs and rats, were characterised by polymerase chain reaction-restriction endonuclease analysis (PCR-REA), arbitrarily primed PCR (AP-PCR) and low stringency PCR (LS-PCR). PCR-REA analysis yielded seven groups among 29 serovars of pathogenic Leptospira; the non-pathogenic L. biflexa serovar patoc was not amplified with the primer pairs studied. AP-PCR and LS-PCR fingerprinting resulted in 25 and 21 distinct profiles, respectively, among the 30 reference strains. The results of the three PCR-based techniques were highly concordant and were in general agreement with those from previous DNA studies, confirming the high level of polymorphism among Leptospira species and serovars, and supported the concept of the serovar as the basic taxonomic unit of leptospiral classification. Results of the PCR-based typing methods for 11 randomised leptospiral strains, 36 clinical isolates from human patients and dogs and 12 survey isolates from trapped rats agreed with those from serological identification. With one exception, isolates of the same serovar gave identical profiles irrespective of the source. AP-PCR and LS-PCR are simple to perform and interpret, and appear to be useful for characterising isolates of Leptospira spp. for diagnostic and epidemiological purposes.}, } @article {pmid9039400, year = {1997}, author = {Gavrilets, S and Gravner, J}, title = {Percolation on the fitness hypercube and the evolution of reproductive isolation.}, journal = {Journal of theoretical biology}, volume = {184}, number = {1}, pages = {51-64}, doi = {10.1006/jtbi.1996.0242}, pmid = {9039400}, issn = {0022-5193}, support = {R01 GM 32130/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Genotype ; Models, Biological ; Phylogeny ; Reproduction/*genetics ; Species Specificity ; }, abstract = {We study the structure and properties of adaptive landscapes arising from the assumption that genotype fitness can only be 0 (inviable genotype) or 1 (viable genotype). An appropriate image of resulting ("holey") fitness landscapes is a (multidimensional) flat surface with many holes. We have demonstrated that in the genotype space there are clusters of viable genotypes whose members can evolve from any member by single substitutions and that there are "species" defined according to the biological species concept. Assuming that the number of genes, n, is very large while the proportion of viable genotypes among all possible genotypes, p, is very small, we have deduced many qualitative and quantitative properties of holey adaptive landscapes which may be related to the patterns of speciation. Relationship between p and n determines two qualitatively different regimes: subcritical and supercritical. The subcritical regime takes place if p is extremely small. In this case, the largest clusters of viable genotypes in the genotype space have size of order n and there are many of such size; typical members of a cluster are connected by a single ("evolutionary") path; the number of different (biological) species in the cluster has order n; the expected number of different species in the cluster within k viable substitutions from any its member is of order k. The supercritical regime takes place if p is small but not extremely small. In this case, there exists a cluster of viable genotypes (a "giant" component) that has size of order 2n/n; the giant component comes "near" every point of the genotype space; typical members of the giant component are connected by many evolutionary paths; the number of different (biological) species on the "giant" component has at least order n2; the expected number of different species on the "giant" component within k viable substitution from any its member is at least of order kn. At the boundary of two regimes all properties of adaptive landscapes undergo dramatic changes, a physical analogy of which is a phase transition. We have considered the most probable (within the present framework) scenario of biological evolution on holey landscapes assuming that it starts on a genotype from the largest connected component and proceeds along it by mutation and genetic drift. In this scenario, there is no need to cross any "adaptive valleys"; reproductive isolation between populations evolves as a side effect of accumulating different mutations. The rate of divergence is very fast: a few substitutions are sufficient to result in a new biological species. We argue that macroevolution and speciation on "rugged" fitness landscapes proceed according to the properties of the corresponding holey landscapes.}, } @article {pmid9342854, year = {1997}, author = {Parsons, PA}, title = {Stress-resistance genotypes, metabolic efficiency and interpreting evolutionary change.}, journal = {EXS}, volume = {83}, number = {}, pages = {291-305}, doi = {10.1007/978-3-0348-8882-0_16}, pmid = {9342854}, issn = {1023-294X}, mesh = {Animals ; *Biological Evolution ; Drosophila/genetics/physiology ; *Environment ; *Genotype ; *Models, Genetic ; Selection, Genetic ; *Stress, Physiological ; }, abstract = {Assuming stress levels to which free-living populations are normally exposed, an association between rapid development time, a long life, success in mating and size of sexual ornaments can be predicted. Fitness at one stage of the life cycle should therefore correlate with fitness at other stages under this environmental model. Assuming that stress targets energy carriers, high-energy efficiency underlain by stress-resistance genotypes that are likely to be heterozygous is the basis of this prediction. Stress-resistance genotypes therefore have a role in promoting the energy efficiency required for organisms to accommodate a stressed world. Selection for energy efficiency to utilize heterogenous resources implies that the process of speciation should normally occur rapidly and be rarely observed. It follows that the ecological species concept is primary to other species concepts. The intensity of selection for stress resistance goes from an extreme in the highly disturbed and stressful environments of living fossils to relatively stable abiotic habitats, where specialist diversifications and adaptive radiations are likely. Between these extremes, a punctuated pattern of evolutionary change may occur in perturbed environments during a transient phase of increased resources. In abiotically benign tropical habitats where energy constraints are low, specialization of resource utilization by learning appears possible.}, } @article {pmid9311567, year = {1997}, author = {Pisano, MR and Nicoli, J and Tolou, H}, title = {Homogeneity of yellow fever virus strains isolated during an epidemic and a post-epidemic period in West Africa.}, journal = {Virus genes}, volume = {14}, number = {3}, pages = {225-234}, pmid = {9311567}, issn = {0920-8569}, mesh = {Aedes/virology ; Animals ; Cote d'Ivoire/epidemiology ; *Disease Outbreaks ; Humans ; Mice ; Mutation ; Polymorphism, Genetic ; RNA, Viral/genetics ; Yellow Fever/epidemiology/*virology ; Yellow fever virus/*classification/genetics/isolation & purification ; }, abstract = {Three strains of yellow fever virus (YFV) were isolated in 1982 in The Ivory Coast, one from a human case and two from Aedes luteocephalus, during and subsequent to an epidemic. The complete genomic sequence of the human strain was determined and compared to that of the 1927 Asibi strain of YFV. The divergence observed was on average of 8.3%, ranging from 5.5 to 11.7% in the coding region. The transitions to transversions ratio was 5.9. Most mutations (84.3%) occurred on the third position of the codons, with synonymous mutations representing 92.5%. However, when partial sequences representing 60% of each genome were compared, homology between the three Ivory Coast strains was greater than 99%. These results demonstrate the homogeneity of the virus strains circulating in different hosts and vectors in a limited geographical region and validate the concept of topotype in viral quasi-species.}, } @article {pmid15275268, year = {1996}, author = {Lymbery, AJ and Thompson, RC}, title = {Species of Echinococcus: pattern and process.}, journal = {Parasitology today (Personal ed.)}, volume = {12}, number = {12}, pages = {486-491}, doi = {10.1016/s0169-4758(96)10071-5}, pmid = {15275268}, issn = {0169-4758}, abstract = {Although classification and nomenclature within the cestode genus Echinococcus has, historically, been controversial, the past 20-30 years have provided a period of relative stability. Recent calls for taxonomic revision in the genus have therefore created something of a stir. In this article, Alan Lymbery and Andrew Thompson describe the reasons for the new controversy, and suggest that the problem can only be resolved by agreement on an appropriate species concept and on operational procedures for implementing that concept.}, } @article {pmid8904889, year = {1996}, author = {Yang, M and Nazhat, NB and Jiang, X and Kelsey, SM and Blake, DR and Newland, AC and Morris, CJ}, title = {Adriamycin stimulates proliferation of human lymphoblastic leukaemic cells via a mechanism of hydrogen peroxide (H2O2) production.}, journal = {British journal of haematology}, volume = {95}, number = {2}, pages = {339-344}, doi = {10.1046/j.1365-2141.1996.d01-1901.x}, pmid = {8904889}, issn = {0007-1048}, mesh = {Cell Division/drug effects ; Dose-Response Relationship, Drug ; Doxorubicin/*pharmacology ; Electron Spin Resonance Spectroscopy ; Humans ; Hydrogen Peroxide/*metabolism ; Leukemia, Lymphoid/metabolism/*pathology ; Tumor Cells, Cultured ; }, abstract = {It is becoming clear that adriamycin cytotoxicity may be mediated by semiquinone-free radicals derived from the drug itself and reactive oxygen species (ROS). Recent evidence supports the concept that low concentrations of ROS are able to stimulate cell proliferation, and, based on the observation that subtoxic concentrations of adriamycin can also induce cell proliferation, we hypothesize that low concentrations of adriamycin stimulate cell proliferation by a ROS generation mechanism. We have employed spin-trapping and electron spin resonance (ESR) spectroscopy to investigate the nature of the adriamycin-generated ROS. The spin trap 3,5-dibromo-4-nitrosobenzenesulphonate (DBNBS), which is oxidized in the presence of H2O2 and peroxidase enzymes, was used to produce a characteristic three-line spectrum, and it was found that an identical spectrum was produced by human lymphoblastic leukaemic cells (CCRF-CEM cells) after exposure to adriamycin. We tested our hypothesis further by exposing CCRF-CEM cells to subtoxic concentrations of adriamycin (10(-8), 10(-9) and 10(-10) M) and low concentrations of H2O2 (10(-8), 10(-9) and 10(-10) M) and subsequently monitored cell proliferation. We found that low concentrations of both adriamycin and H2O2 significantly stimulate CCRF-CEM cell proliferation. We therefore conclude that subtoxic concentrations of adriamycin are likely to induce cell proliferation via an H2O2 mediated mechanism.}, } @article {pmid9246365, year = {1996}, author = {Silva-Benavides, AM}, title = {The use of water chemistry and benthic diatom communities for qualification of a polluted tropical river in Costa Rica.}, journal = {Revista de biologia tropical}, volume = {44}, number = {2A}, pages = {395-416}, pmid = {9246365}, issn = {0034-7744}, mesh = {Animals ; Costa Rica ; Diatoms/*classification/*isolation & purification ; Eutrophication ; Plankton/*isolation & purification ; *Tropical Climate ; Water Pollution/*analysis ; }, abstract = {The water quality of several sections of a tropical river subjected to severe pollution was studied through physico-chemical water analysis and benthic diatom assemblages. The methodology follows the concept of differential species groups and that of its modification for the groups of nutrient-differentiating species for rivers rich in both oxygen and inorganic nutrients. The trophic indication of the latter authors correspond clearly with the results of chemical observations made in this study. The most abundant species found in this river were Navicula goeppertiana, Gomphonema parvulum, Gomphonema sp. aff. pumilum, Nitzschia palea, Nitzschia amphibia, Nitzschia clausii Nitzschia inconspicua, Navicula seminulum, Navicula sp. aff. cryptocephala, Navicula schroeterii var. escambia, Cymbella sinuata and Surirella sp. aff. roba. These species are known to be tolerant to organic pollution and eutrophication. Therefore we may conclude that diatoms are useful for biological monitoring of disturbed tropical rivers.}, } @article {pmid8991530, year = {1996}, author = {Mirzoian, EN}, title = {[Ecology and genetics: at the sources of synthesis].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {4}, pages = {478-484}, pmid = {8991530}, issn = {1026-3470}, mesh = {Animals ; Biological Evolution ; *Ecology ; Genetics/*history ; History, 20th Century ; Humans ; }, abstract = {In the 1920s V. V. Stanchinskiĭ undertook an attempt at evolutionary synthesis on the basis of darwinism, new taxonomy, generalizations of population genetics of S. S. Chetverikov's school, the concept of Linnean species of N. I. Vavilov, ecological-genetic studies of the school of N. I. Vavilov, and data on biocenology. An original evolutionary-ecological concept was developed by V. V. Stanchinskiĭ on this basis.}, } @article {pmid8674535, year = {1996}, author = {Gaudu, P and Nivière, V and Pétillot, Y and Kauppi, B and Fontecave, M}, title = {The irreversible inactivation of ribonucleotide reductase from Escherichia coli by superoxide radicals.}, journal = {FEBS letters}, volume = {387}, number = {2-3}, pages = {137-140}, doi = {10.1016/0014-5793(96)00480-2}, pmid = {8674535}, issn = {0014-5793}, mesh = {Escherichia coli/*enzymology ; Free Radicals ; Oxidation-Reduction ; Ribonucleotide Reductases/*antagonists & inhibitors ; Superoxides/*pharmacology ; Tyrosine ; }, abstract = {The expression of superoxide dismutase in all aerobic living organisms supports the concept that superoxide radicals are toxic species. However, because of the limited chemical reactivity of superoxide, the mechanisms of this toxicity are still uncertain. Protein R2, the small component of ribonucleotide reductase, a key enzyme for DNA synthesis, is shown here to be irreversibly inactivated during incubation with an enzymatic generator of superoxide radicals, at neutral pH. During inactivation the essential tyrosyl radical of protein R2 is irreversibly destroyed. Full protection is afforded by superoxide dismutase. It is proposed that coupling between superoxide radicals and the radical protein R2 generates oxidized forms of tyrosine, tyrosine peroxide and 3,4-dihydroxyphenylalanine.}, } @article {pmid8674999, year = {1996}, author = {Sreenivasaprasad, S and Mills, PR and Meehan, BM and Brown, AE}, title = {Phylogeny and systematics of 18 Colletotrichum species based on ribosomal DNA spacer sequences.}, journal = {Genome}, volume = {39}, number = {3}, pages = {499-512}, doi = {10.1139/g96-064}, pmid = {8674999}, issn = {0831-2796}, mesh = {Base Sequence ; *DNA, Fungal ; *DNA, Ribosomal ; Genetic Variation ; Mitosporic Fungi/*classification/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {The potential use of the ribosomal DNA internal transcribed spacer (ITS) sequences in understanding the phylogeny and systematics of Colletotrichum species has been evaluated. Sequence data from a limited number of isolates revealed that in Colletotrichum species the ITS 1 region (50.3% variable sites) shows a greater degree of intra- and inter-specific divergence than ITS 2 (12.4% variable sites). Nucleotide sequences of the ITS 1 region from 93 isolates representing 18 Colletotrichum species were determined. Data for 71 of these isolates where molecular and morphological identities concurred were used for phylogenetic analysis. The size of the ITS 1 region varied from 159 to 185 base pairs. Maximum intraspecific divergence was recorded with C. acutatum (5.8%), and C. capsici showed the greatest level of interspecific divergence (8.9-23.3%). Parsimony and distance analyses gave similar tree topologies. The bootstrapped consensus parsimony tree divided the 18 Colletotrichum species into six phylogenetic groups, designated 1-6. These groups, however, are not congruent with species clusterings based on spore shape. For example, the straight cylindrical spored species were represented both in groups 1 and 6; group 6 also included the falcate fusiform spored species C. capsici. The molecular evidence suggests refinement of the species concepts of some of the taxa examined. In group 6, divergence between C. gloeosporioides and C. fuscum (0.6-3.0%) or C. kahawae (0.6-3.0%) or C. fragariae (0.6-4.2%) overlap the divergence (3.6%) within C. gloeosporioides. It is suggested that C. fuscum as well as C. kahawae and C. fragariae fall within the group species C. gloeosporioides. ITS 1 data enabled clear distinction (7.1%) of Colletotrichum isolates from maize and sorghum into C. graminicola and C. sublineolum, respectively (group 2). Species such as C. acutatum, C. coccodes, C. dematium, and C. trichellum can be clearly distinguished based on ITS 1 sequence divergence, but C. destructivum cannot be confidently separated (98% homology) from C. linicola. Colletotrichum dematium f. truncatum is distinct (12.9%) from C. dematium and should probably be called C. truncatum.}, } @article {pmid8610425, year = {1996}, author = {Diamond, LE and McCurry, KR and Martin, MJ and McClellan, SB and Oldham, ER and Platt, JL and Logan, JS}, title = {Characterization of transgenic pigs expressing functionally active human CD59 on cardiac endothelium.}, journal = {Transplantation}, volume = {61}, number = {8}, pages = {1241-1249}, doi = {10.1097/00007890-199604270-00021}, pmid = {8610425}, issn = {0041-1337}, support = {HL50985/HL/NHLBI NIH HHS/United States ; HL52297/HL/NHLBI NIH HHS/United States ; NRSA F32HL09046/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Animals, Genetically Modified ; CD59 Antigens/*biosynthesis/genetics ; Complement System Proteins/metabolism ; Endothelium/metabolism ; Gene Transfer Techniques ; Heart Transplantation ; Humans ; Myocardium/*metabolism ; Papio ; Swine ; }, abstract = {The critical shortage of human donor organs has generated interest in the potential for porcine to human xenotransplantation. The initial immunological barrier to xenotransplantation is hyperacute rejection, which is mediated by xenoreactive antibodies and complement, and results in rapid and irreversible tissue destruction. While endogenous complement regulatory proteins (CRPs) protect cells from injury caused by autologous complement, they are relatively species specific and most likely ineffectual in this setting. This has led to the hypothesis that expression of human CRPs in transgenic pigs may affect susceptibility to complement-mediated tissue injury in a porcine-to-human xenograft. Using specific lines of transgenic pigs that express low levels of human CD59, a CRP that acts at the terminal stage of the complement cascade, we present evidence that shows that the human CD59 protein inhibits membrane attack complex assembly and reduces tissue damage when the heart is transplanted to a baboon. Examination by immunohistochemistry of transgenic porcine hearts after transplantation revealed markedly reduced deposition of C5b and MAC, but a similar level of C3 deposition as compared with transplanted control hearts. This finding supports the concept that the species specific function of CRPs contributes to the humoral barrier to xenotransplantation and, given the low level of human CD59 protein expression in the porcine heart, argues that the human protein contributes a unique rather than an additive function in regulation of complement in a xenogeneic setting.}, } @article {pmid8861773, year = {1996}, author = {Manfredi Romanini, MG and Fraschini, A}, title = {Facts and paradoxes in current notions of nuclear organization and function.}, journal = {Histology and histopathology}, volume = {11}, number = {2}, pages = {513-519}, pmid = {8861773}, issn = {0213-3911}, mesh = {Animals ; Cell Compartmentation/*physiology ; Cell Nucleus/*physiology/ultrastructure ; Chromatin/*ultrastructure ; DNA/chemistry ; *DNA Replication ; Humans ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Invisible compartments, identified rather by their activities than by their morphology, seem to operate in the nucleus. These compartments interrelate somehow, including mediation by the nuclear matrix. As our knowledge about the nucleus increases, more paradoxes become evident. We here consider some of them: 1) the well-known C-paradox of Cavalier-Smith, concerning the disproportionate amount of nuclear DNA content in comparison with the amount of DNA potentially able to transcribe; 2) the DNA folding in the chromatin fibre and its superorganization within the nucleus, which seems to be in opposition with the transcribing and self-replicating activities; 3) the elusive role of the DNA sequences with different degrees of repetitivity; and 4) the compartmentalization in the nucleus and how it relates to transcription, processing and transport of transcripts, and to DNA reduplication. We conclude by introducing the concept of species specific, minimal, but essential genome components, i.e. the elusive few thousand DNA bases that, in our hypothesis, act as a functional bridge between the nuclear matrix and chromatin.}, } @article {pmid8846267, year = {1996}, author = {Wolin, MS}, title = {Reactive oxygen species and vascular signal transduction mechanisms.}, journal = {Microcirculation (New York, N.Y. : 1994)}, volume = {3}, number = {1}, pages = {1-17}, doi = {10.3109/10739689609146778}, pmid = {8846267}, issn = {1073-9688}, support = {HL31069/HL/NHLBI NIH HHS/United States ; HL43023/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Endothelium, Vascular/*metabolism ; Humans ; Muscle Tonus/physiology ; Reactive Oxygen Species/*metabolism ; Regional Blood Flow ; Signal Transduction/*physiology ; Vasomotor System/physiology ; }, abstract = {Sources of reactive O2 species in the vessel wall that potentially contribute to the control of vascular tone include NADPH oxidases, arachidonic acid metabolizing enzymes, xanthine oxidase, nitric oxide synthase and mitochondria. Specific physiological stimuli (such as changes in PO2) as well as pathophysiological stimuli control the production of reactive O2 species by many of these sources. Certain key reactive O2 species activate specific signalling mechanisms that control vascular tone, often through processes involving the metabolism of these species. The production of prostaglandins and cyclic GMP are some of the most sensitive systems regulated by hydrogen peroxide; whereas the conversion of nitric oxide (NO) to peroxynitrite (ONOO-) and inhibition of the stimulation of the cytosolic form of guanylate cyclase are processes that are very sensitive to superoxide anion (O2.-). High levels of NO production readily result in the formation of significant amounts of ONOO-, because NO competes with superoxide dismutase for the metabolism of cellular O2.- and thereby activates additional signalling mechanisms such as regulation through thiol nitrosation. As the levels of individual reactive O2 species increase, other signalling mechanisms likely to participate in vascular responses to oxidant injury seem to become activated. Thus, evidence is developing to support the concept that reactive O2 species are important contributors to the control of vascular tone.}, } @article {pmid8733475, year = {1996}, author = {Jongeling, TB}, title = {Self-organization and competition in evolution: a conceptual problem in the use of fitness landscapes.}, journal = {Journal of theoretical biology}, volume = {178}, number = {4}, pages = {369-373}, doi = {10.1006/jtbi.1996.0032}, pmid = {8733475}, issn = {0022-5193}, mesh = {Animals ; *Biological Evolution ; *Genetics, Population ; Models, Biological ; Paleontology ; Selection, Genetic ; }, abstract = {Recently it has been claimed that certain macroevolutionary patterns, such as the contrast between the Cambrian explosion and the Permian quiescence, can be explained as generic properties of selection processes, i.e. as features that are not caused by specific selection pressures, but that are to be expected in any selection process. The explanations are based on models of motions on randomly generated fitness landscapes, which are assumed to be representative of fitness landscapes in general. In this paper I show that such explanations of macroevolutionary patterns are conceptually flawed. If the concept of fitness used in the model is not the customary biological notion of fitness, there is no reason why organisms with higher fitness should displace organisms with lower fitness, and as a result the motion of a point representing a population is no longer determined by the shape of the fitness landscape. Nothing can be derived about the motions on the landscape, and the explanation collapses. If the model is based on the customary fitness concept, non-competing species have to be assigned the same fitnesses. As most species belonging to a radiation such as the Cambrian explosion are assumed to coexist, the majority of species will have the same fitness. A radiation of species can therefore not be modeled meaningfully on a fitness landscape.}, } @article {pmid11636468, year = {1996}, author = {Montiel, L}, title = {[The reasons for a fleeting resurrection: the natural historical method in the work of K. W. Stark (1787-1845) and F. Jahn (1804-1859)].}, journal = {Asclepio; archivo iberoamericano de historia de la medicina y antropologia medica}, volume = {48}, number = {2}, pages = {73-85}, doi = {10.3989/asclepio.1996.v48.i2.398}, pmid = {11636468}, issn = {0210-4466}, mesh = {Germany ; History, 19th Century ; Natural History/*history ; Pathology/*history ; Philosophy, Medical/*history ; *Terminology as Topic ; }, abstract = {This work analyses the methodological proposals of two German doctors in the first half of the XIX century, traditionally linked to the so-called "Naturalistic School". It aims especially to evaluate the importance given by each to the "Naturalistic method" applied to the classification of these diseases, taking into account the fact that both defended an ontologistic or "parasitic" conception of the same. This study illustrates how this undertaking responds to the challenge, expounded by the followers of Schelling's Naturphilosophie, of converting medicine into a natural science. Likewise, this undertaking was doomed to failure due to the existing contradiction between the utilization to the classificatory method, characteristic of eighteenth century Natural History, and the need for a physiological foundation of nosology, more in accordance with the nascent Biology, which will greatly reduce the epistemological soundness of the concept of morbid species. This very imbalance will be revealed, in the strictly medical aspect, in the doubts when giving epistemological priority to physiology or to the clinical observation.}, } @article {pmid8825233, year = {1996}, author = {Gadaleta, SJ and Paschalis, EP and Betts, F and Mendelsohn, R and Boskey, AL}, title = {Fourier transform infrared spectroscopy of the solution-mediated conversion of amorphous calcium phosphate to hydroxyapatite: new correlations between X-ray diffraction and infrared data.}, journal = {Calcified tissue international}, volume = {58}, number = {1}, pages = {9-16}, pmid = {8825233}, issn = {0171-967X}, support = {AR41325/AR/NIAMS NIH HHS/United States ; }, mesh = {Calcium Phosphates/*metabolism ; Durapatite/*metabolism ; Humans ; Solutions ; Spectroscopy, Fourier Transform Infrared/*methods ; Time Factors ; X-Ray Diffraction/*methods ; }, abstract = {Fourier Transform infrared spectroscopic analysis of maturing, poorly crystalline hydroxyapatite (HA) formed from the conversion of amorphous calcium phosphate (ACP) at constant pH or variable pH show only subtle changes in the v1, v3 phosphate absorption region (900 cm-1-1200 cm-1). This region is of interest because it can be detected by analysis of mineralized tissue sections using FT-IR microscopy. To evaluate the subtle spectral changes occurring during the maturation, second derivatives of the spectra were calculated. HA formed at constant pH showed little or no variation in the second derivative peak positions with bands occurring at 960 cm-1, 985 cm-1, 1030 cm-1, 1055 cm-1, 1075 cm-1, 1096 cm-1, 1116 cm-1, and 1145 cm-1. These bands can be assigned to molecular vibrations of the phosphate (PO4(3-)) moiety in an apatitic/stoichiometric environment of HA. In contrast, during the early stages of maturation of the HA formed at variable pH, second derivative peak positions occurring at 958 cm-1, 985 cm-1, 1020 cm-1, 1038 cm-1, 1112 cm-1, and 1127 cm-1 shifted in position with maturation, indicating that the environment of the phosphate species is changing as the crystals mature. Peaks at 1020 cm-1, 1038 cm-1, 1112 cm-1, and 1127 cm-1 were attributable to nonstoichiometry and/or the presence of acid phosphate-containing species. This concept was supported by the lower Ca:P molar ratios measured by chemical analysis of the synthetic material made at variable pH. Using the second derivative peak positions as initial input parameters, the v1, v3 phosphate region of the synthetic HAs prepared at constant pH were curve fit. X-ray diffraction patterns of these same materials were also curve fit to calculate the changes in crystallinty (size/perfection) in the c-axis 002 reflection as well as the 102, 210, 211, 112, 300, 202, and 301 planes. Linear regression analysis showed that the changes in the percent area of the underlying bands at 982 cm-1, 999 cm-1, 1030 cm-1, 1075 cm-1, 1096 cm-1, 1116 cm-1, and 1145 cm-1 were correlated with changes in crystallinity in one or more of the reflection planes. It is suggested that a combination of second-derivative and curve-fitting analysis of the v1, v3 phosphate contour allows the most reproducible evaluation of these spectra.}, } @article {pmid8754080, year = {1996}, author = {Gor'kov, VA}, title = {[The concepts and conceptual models of psychopharmacology].}, journal = {Vestnik Rossiiskoi akademii meditsinskikh nauk}, volume = {}, number = {4}, pages = {51-54}, pmid = {8754080}, issn = {0869-6047}, mesh = {Animals ; Clinical Trials as Topic ; Dose-Response Relationship, Drug ; Drug Evaluation, Preclinical ; Humans ; *Models, Biological ; *Psychopharmacology ; Psychotropic Drugs/pharmacology/therapeutic use ; }, abstract = {The present approaches to the testing and use of drugs, psychotropic ones in particular, are characterized by inadequate efficiency: the ratio of agents successfully undergone preclinical, clinical, and postclinical tests is 100:5:1 and in clinical psychopharmacotherapy, the proportion of drug-resistant patients and the incidence of side effects are rather high. The groundless supposition that interspecies- and intraspecies-specific sensitivity to drugs is equal may explain this notion, which contradicts the concept of the biochemical stability of species and to the principle of molecular economy in species-specific ratios. To enhance the efficiency of tests and pharmacotherapy, it is suggested that the existing conceptual model "concentration-effect" should be replaced by the extended one "sensitivity-concentration-effect" as it is more scientifically substantiated. Increases in the efficiency of psychopharmacotherapy may be, among other things, reached by individually predicting the most effective psychotropic agents with clinical, paraclinical, pharmacokinetic, and other predictors.}, } @article {pmid8684838, year = {1996}, author = {Thompson, RC and Lymbery, AJ}, title = {Genetic variability in parasites and host-parasite interactions.}, journal = {Parasitology}, volume = {112 Suppl}, number = {}, pages = {S7-22}, pmid = {8684838}, issn = {0031-1820}, mesh = {Animals ; Cryptosporidium/classification/*genetics/physiology ; Echinococcus/classification/*genetics/physiology ; Ecology ; Genetic Variation ; Giardia/classification/*genetics/physiology ; Host-Parasite Interactions ; Humans ; Parasitic Diseases/parasitology ; Virulence ; }, abstract = {We have examined genetic variability in parasites in the context of ecological interactions with the host. Recent research on Echinococcus, Giardia and Cryptosporidium has been used to illustrate: (i) the problems that parasite variability and species recognition pose for understanding the complex and often controversial relationship between parasite and host occurrence; (ii) the need for accurate parasite characterization and the application of appropriate molecular techniques to studies on parasite transmission if fundamental questions about zoonotic relationships and risk factors are to be answered; (iii) our lack of understanding about within-host interactions between genetically heterogeneous parasites at the inter- and intraspecific levels, and the significance of such interactions with respect to evolutionary considerations and the clinical outcome of parasite infections. If advances in molecular biology and mathematical ecology are to be realized, we need to give serious consideration to the development of appropriate species concepts and in vivo systems for testing the predictions and assumptions of theoretical models.}, } @article {pmid8640113, year = {1996}, author = {Stepanova, LV and Bodiak, ND and Surov, AV}, title = {[The morphofunctional characteristics of the harderian gland in some mammalian species].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {1}, pages = {56-62}, pmid = {8640113}, issn = {1026-3470}, mesh = {Animal Communication ; Animals ; Cricetinae ; Cricetulus ; Harderian Gland/metabolism/*ultrastructure ; Histocytochemistry ; Male ; Marmota ; Microscopy, Electron ; Phodopus ; Species Specificity ; }, abstract = {The structure of harderian glands was studied using electron microscopy and histochemistry in six rodent species, including three Phodopus species. Based on the concept of cell morphotype it was shown that the harderian glands of the studied mammalian species are lipid-secreting and have secretory cells of the species specific morphotypes. The secretory cells are distinguished by the ultrastructural features not only between different genera, but also between different species of the same genus. The data obtained allow species identification according to the ultrastructure of secretory cells. The role of harderian glands in chemical communication was shown for the golden hamster (Mesocricetus auratus). Their secretory substance contains information about the sexual and species identity of animals.}, } @article {pmid8541606, year = {1995}, author = {de Freitas Burity, CH and Mandarim-de-Lacerda, CA}, title = {The weight of the heart in Callithrix Erxleben, 1777.}, journal = {Bulletin de l'Association des anatomistes}, volume = {79}, number = {246}, pages = {21-24}, pmid = {8541606}, issn = {0376-6160}, mesh = {Animals ; Body Constitution/*physiology ; Callithrix/*anatomy & histology ; Female ; Linear Models ; Male ; Organ Size/physiology ; Statistics as Topic ; }, abstract = {The allometric relationship between the weight of the heart and the body measurements was analyzed in 31 primates of genus Callithrix (C. jacchus and C. penicillata). The data were analyzed after logarithmic transformation using the model: Ln Y = Ln a + (b) Ln X. We compared with the t-test the slopes of the males and females and the slopes of the C. Jacchus and C. penicillata. Positive allometry was found to the weight of the heart in relation to the body weight (except to females of C. penicillata = isometry) and to sitting height in females of C. jacchus and males of C. penicillata. The relationship of the weight of the heart with the sitting height was isometric in males of C. jacchus and negative in females of C. penicillata. We cannot reject the null hypothesis analyzing the differences between the slopes of males and females. Therefore, in these two species of Callithrix we accept the concept of monomorphism.}, } @article {pmid24234417, year = {1995}, author = {Aldrich, JR}, title = {Testing the "new associations" biological control concept with a tachinid parasitoid (Euclytia flava).}, journal = {Journal of chemical ecology}, volume = {21}, number = {7}, pages = {1031-1042}, doi = {10.1007/BF02033806}, pmid = {24234417}, issn = {0098-0331}, abstract = {Males of the spined soldier bug,Podisus maculiventris (Heteroptera: Pentatomidae), produce an attractant pheromone that is exploited as a host-finding kairomone by a complex of parasitic species. The capability to catch hundreds of a generalist tachinid fly parasitoid,Euclytia flava, alive in traps baited with the pheromone ofP. maculiventris provided an opportunity to test the premise of the "new associations" biological control concept. The hypothesis that host species newly associated with a parasitoid are maladapted relative to native-native associations was tested by givingE. flava females a choice between native and exotic stink bugs (Heteroptera: Pentatomidae). WildE. flava females preferred to oviposit on exotic pentatomid species rather than indigenous, known host species, both in field traps baited with the pheromone of a native host and in the laboratory. Data presented here demonstrate that an invader may be vulnerable to native parasitoids in one aspect of the parasitism process (acceptance), yet go unrecognized as a potential host.}, } @article {pmid21237047, year = {1995}, author = {Mallet, J}, title = {A species definition for the modern synthesis.}, journal = {Trends in ecology & evolution}, volume = {10}, number = {7}, pages = {294-299}, doi = {10.1016/0169-5347(95)90031-4}, pmid = {21237047}, issn = {0169-5347}, abstract = {One hundred and thirty-six years since On the Origin of Species 3., biologists might be expected to have an accepted theory of speciation. Instead, there is, if anything, more disagreement about speciation than ever before. Even more surprisingly, 60 years after the biological species concept, in which species were considered to be reproductive communities isolated from other such communities, we still do not all accept a common definition of what a species is. And yet, if speciation is to be any different from ordinary evolution, we must have a clear definition of species. The emerging solution to the species problem is an updated, genetic version of Darwin's own definition. This definition is useful and is already being used in taxonomy, in biodiversity studies and in evolution.}, } @article {pmid8526477, year = {1995}, author = {Haase, G and Sonntag, L and van de Peer, Y and Uijthof, JM and Podbielski, A and Melzer-Krick, B}, title = {Phylogenetic analysis of ten black yeast species using nuclear small subunit rRNA gene sequences.}, journal = {Antonie van Leeuwenhoek}, volume = {68}, number = {1}, pages = {19-33}, pmid = {8526477}, issn = {0003-6072}, mesh = {Ascomycota/genetics ; Base Sequence ; Exophiala/classification/genetics ; Fungi/*classification/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Fungal/chemistry/*genetics ; RNA, Ribosomal/chemistry/*genetics ; Sequence Analysis, DNA ; }, abstract = {The nuclear small subunit rRNA genes of authentic strains of the black yeasts Exophiala dermatitidis, Wangiella dermatitidis, Sarcinomyces phaemuriformis, Capronia mansonii, Nadsoniella nigra var. hesuelica, Phaeoannellomyces elegans, Phaeococcomyces exophialae, Exophiala jeanselmei var. jeanselmei and E. castellanii were amplified by PCR and directly sequenced. A putative secondary structure of the nuclear small subunit rRNA of Exophiala dermatitidis was predicted from the sequence data. Alignment with corresponding sequences from Neurospora crassa and Aureobasidium pullulans was performed and a phylogenetic tree was constructed using the neighbor-joining method. The obtained topology of the tree was confirmed by bootstrap analysis. Based upon this analysis all fungi studied formed a well-supported monophyletic group clustering as a sister group to one group of the Plectomycetes (Trichocomaceae and Onygenales). The analysis confirmed the close relationship postulated between Exophiala dermatitidis, Wangiella dermatitidis and Sarcinomyces phaeomuriformis. This monophyletic clade also contains the telemorph species Capronia mansonii thus confirming the concept of a teleomorph connection of the genus Exophiala to a member of the herpotrichiellaceae. However, Exophiala castellanii did not belong to this clade. Therefore, this species is not the anamorph of Capronia mansonii as it was postulated.}, } @article {pmid7582946, year = {1995}, author = {Atwell, GJ and Yaghi, BM and Turner, PR and Boyd, M and O'Connor, CJ and Ferguson, LR and Baguley, BC and Denny, WA}, title = {Synthesis, DNA interactions and biological activity of DNA minor groove targeted polybenzamide-linked nitrogen mustards.}, journal = {Bioorganic & medicinal chemistry}, volume = {3}, number = {6}, pages = {679-691}, doi = {10.1016/0968-0896(95)00049-m}, pmid = {7582946}, issn = {0968-0896}, mesh = {Alkylation ; Animals ; Antineoplastic Agents, Alkylating/chemistry/*pharmacology ; Base Sequence ; Benzamides/chemistry/*pharmacology ; DNA/chemistry/*drug effects ; Drug Screening Assays, Antitumor ; Hydrolysis ; Kinetics ; Leukemia P388/drug therapy ; Ligands ; Mechlorethamine/chemistry/*pharmacology ; Mice ; Molecular Sequence Data ; Structure-Activity Relationship ; }, abstract = {A series of polybenzamide DNA minor groove binding ligands bearing either one or two monofunctional mustards have been synthesised, and their cytotoxicities and interactions with DNA have been studied. Analogues with two alkylating functions (e.g. compounds 7 and 14) are the most cytotoxic, with 7 being 1000-fold more potent than the clinical mustard chlorambucil against P388 leukemia in culture, as well as being more potent in vivo. Monofunctional analogues were also significantly more cytotoxic than chlorambucil, despite bearing much less reactive mustard species. These results support the concept that targeting nitrogen mustard alkylating agents to DNA by attachment to DNA-affinic carriers can greatly enhance cytotoxicity due to alkylation, and that even for such DNA-targeted mustards, crosslinking is a more toxic event than monoalkylation. Close analogues of 7 differing only in their radius of curvature, appear to alkylate and crosslink DNA in similar fashion, yet have widely differing cytotoxicities. The most cytotoxic compound (7) possesses a geometry most complementary to that of duplex DNA, suggesting that the most toxic lesions are those which result in least DNA distortion, thus being less easily recognised by DNA repair systems.}, } @article {pmid7714195, year = {1995}, author = {Kapur, V and Sischo, WM and Greer, RS and Whittam, TS and Musser, JM}, title = {Molecular population genetic analysis of Staphylococcus aureus recovered from cows.}, journal = {Journal of clinical microbiology}, volume = {33}, number = {2}, pages = {376-380}, pmid = {7714195}, issn = {0095-1137}, mesh = {Alleles ; Animals ; Cattle/*microbiology ; Enzymes/genetics ; Female ; Genetic Variation ; Genetics, Population ; Genotype ; Humans ; Mastitis, Bovine/microbiology/prevention & control ; Molecular Biology ; Polymorphism, Genetic ; Species Specificity ; Staphylococcus aureus/enzymology/*genetics/*isolation & purification ; }, abstract = {Staphylococcus aureus is one of the most common causes of bovine mastitis. To estimate genetic relationships among S. aureus strains recovered from cows, 357 isolates from milk samples from worldwide localities were examined for electrophoretic variation at 13 metabolic-enzyme loci. Thirty-nine electrophoretic types which represented distinctive multilocus enzyme genotypes were identified, and nearly 90% of all isolates were assigned to one of eight clones. Genetic heterogeneity was found among organisms recovered from dairy herds from which multiple isolates were obtained, indicating that the S. aureus population in a single herd can be multiclonal. Although humans and cows shared 7 of the 39 S. aureus clones, each clone was predominantly associated with one of these host species. These results are consistent with the concept of host specialization among S. aureus clones and imply that successful transfer of bacteria between humans and cows is limited.}, } @article {pmid7857798, year = {1995}, author = {Varga, J and Vágvölgyi, C and Nagy, A and Pfeiffer, I and Ferenczy, L}, title = {Isoenzyme, restriction fragment length polymorphism, and random amplified polymorphic DNA characterization of Phaffia rhodozyma Miller et al.}, journal = {International journal of systematic bacteriology}, volume = {45}, number = {1}, pages = {173-177}, doi = {10.1099/00207713-45-1-173}, pmid = {7857798}, issn = {0020-7713}, mesh = {Base Sequence ; DNA, Fungal/*analysis ; *Gene Amplification ; Isoenzymes/*analysis ; Molecular Sequence Data ; *Polymorphism, Restriction Fragment Length ; Yeasts/*classification/enzymology/genetics ; }, abstract = {The validity of the species concept was examined with strains of Phaffia rhodozyma by comparing the isoenzyme profiles, ribosomal DNAs, and random amplified polymorphic DNA (RAPD) patterns of the strains. The isoenzyme profiles appeared to be more stable than the RAPD patterns or the electrophoretic karyotypes determined previously (A. Nagy, N. Garamszegi, C. Vágvölgyi, and L. Ferenczy, FEMS Microbiol. Lett., in press). The ribosomal DNA patterns revealed only a limited degree of variability, while RAPD analysis proved to be the most useful method for differentiating the strains studied. Strain CBS 5905T (T = type strain) produced characteristic RAPD patterns, which were different from those produced by the other strains. However, despite the high degree of variability observed, the isoenzyme data and the slightly variable ribosomal DNA hybridization profiles confirmed that the strains which we examined belong to one species.}, } @article {pmid7868154, year = {1994}, author = {Starzl, TE and Valdivia, LA and Murase, N and Demetris, AJ and Fontes, P and Rao, AS and Manez, R and Marino, IR and Todo, S and Thomson, AW}, title = {The biological basis of and strategies for clinical xenotransplantation.}, journal = {Immunological reviews}, volume = {141}, number = {}, pages = {213-244}, pmid = {7868154}, issn = {0105-2896}, support = {R01 DK029961-19/DK/NIDDK NIH HHS/United States ; DK 29961/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Graft Rejection/prevention & control ; Humans ; *Organ Transplantation ; Transplantation, Heterologous/*immunology ; }, abstract = {Recent discoveries have suggested that the exchange of multiple leukocyte lineages between grafts and host and subsequent long-term chimerism in both is the seminal mechanism of the acceptance of organs transplanted from the same (allografts) or different species (xenografts). This insight suggests new strategies which may allow xenotransplantation, the principal obstacle to which has been humoral rejection. We have defined humoral rejection as a family of complement activation syndromes afflicting allografts and xenografts in which there is a strong (but not invariable) association with performed antigraft antibodies, invariable evidence of complement activation, histopathologic stigmas of vascular endothelial damage, and a concomitant local or systemic coagulopathy. The generic descriptive term hyperacute rejection is a misnomer because a slow-motion version of the same "humoral" process can occur with some allografts and is the rule with the so-called concordant species xenotransplantations. The pathway of experience and discovery leading to this conclusion shows clearly that the distinction frequently made between allograft versus xenograft humoral rejection does not actually exist in principle, but only in details and intensity. Breaking down this barrier to xenotransplantation, whether or not it is associated with antibodies, is unrealistic. However, the possibility of avoiding the barrier has been exposed by showing that animal organs can be humanized, with a mixed donor and recipient cell population similar to the chimerism seen in long surviving allografts or even with complete leukocyte replacement. Pilot experiments in rodents suggest that organs from fully xenogeneic chimeras can be made into xenogeneic targets that are no more provocative of complement activation than allografts when they are transplanted into the donor bone marrow species. Although the validity of this concept of organ xenograft preparation is only at the pilot stage of verification, there is reason to suspect that the complement trigger of humoral rejection can be thereby disarmed. If this can be accomplished, independent evidence suggests that cellular rejection can be controlled with conventional T-cell directed immunosuppression, perhaps even with surprising ease. The potential subtle liability of synthetic products of xenogeneic parenchymal cells is not yet known.}, } @article {pmid7595923, year = {1994}, author = {Jacobson, LS and Clark, IA}, title = {The pathophysiology of canine babesiosis: new approaches to an old puzzle.}, journal = {Journal of the South African Veterinary Association}, volume = {65}, number = {3}, pages = {134-145}, pmid = {7595923}, issn = {1019-9128}, mesh = {Anemia/etiology/veterinary ; Animals ; Babesiosis/complications/*physiopathology ; *Dog Diseases/physiopathology ; Dogs ; Multiple Organ Failure/etiology/veterinary ; Pulmonary Edema/etiology/veterinary ; Renal Insufficiency/etiology/veterinary ; Thrombocytopenia/etiology/veterinary ; }, abstract = {The haemoprotozoan parasite, Babesia canis, is the cause of an economically important and potentially life-threatening disease of dogs in South Africa, the pathophysiology of which is incompletely understood. Available literature is reviewed, with emphasis on the pathophysiology of the anaemia and complications of babesiosis. The remainder of the review explores the possibility that pathophysiological mechanisms currently being investigated in human malaria and bovine babesiosis (in which, as in canine babesiosis, an intra-erythrocytic parasite causes multi-systemic pathology) might also be active in B. canis infections. The entity referred to as the multiple organ dysfunction syndrome is discussed as a proposed mechanism within which apparently unrelated aspects of babesiosis form a predictable pattern. The molecular mediators of multiple organ dysfunction, including cytokines, nitric oxide and free oxygen radicals, are generated by host tissues, and are now under active study to help elucidate the pathophysiology of malaria. The similarities between the manifestations of different diseases in different host species can be explained by the concept that the disease process is largely mediated by these molecules, generated by the host in response to the parasite, rather than arising directly from the parasite itself. The current direction of malaria research provides a basis for future research into the pathophysiology of canine babesiosis.}, } @article {pmid7898951, year = {1994}, author = {Bradley, DJ}, title = {Watson, Swellengrebel and species sanitation: environmental and ecological aspects.}, journal = {Parassitologia}, volume = {36}, number = {1-2}, pages = {137-147}, pmid = {7898951}, issn = {0048-2951}, mesh = {Ecology ; Environment ; History, 19th Century ; History, 20th Century ; Humans ; Indonesia ; Malaria/*history/prevention & control ; Malaysia ; Mosquito Control/*history ; }, abstract = {Following the discovery of mosquito transmission of malaria, the theory and practice of malaria control by general and selective removal of specific vector populations resulted particularly from Malcolm Watson's empirical work in peninsular Malaysia, first in the urban and peri-urban areas of Klang and Port Swettenham and subsequently in the rural rubber plantations, and from the work of N.H. Swellengrebel in nearby Indonesia on the taxonomy, ecology and control of anophelines. They developed the concept of species sanitation: the selective modification of the environment to render a particular anopheline of no importance as a vector in a particular situation. The lack of progress along these lines in India at that time is contrasted with that in south-east Asia. The extension of species sanitation and related concepts to other geographical areas and to other vector-borne disease situations is outlined.}, } @article {pmid7972357, year = {1994}, author = {O'Donnell, AG and Goodfellow, M and Hawksworth, DL}, title = {Theoretical and practical aspects of the quantification of biodiversity among microorganisms.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {345}, number = {1311}, pages = {65-73}, doi = {10.1098/rstb.1994.0087}, pmid = {7972357}, issn = {0962-8436}, mesh = {*Bacteria/genetics ; *Conservation of Natural Resources ; Ecology ; *Fungi/genetics ; Sequence Analysis, RNA ; }, abstract = {The quantification of biodiversity among microorganisms has to address both theoretical and practical aspects. Species concepts are often at variance with those applied in macroorganisms, and satisfactory concepts suitable for general use in bacteria and fungi have yet to be formulated. Molecular approaches have not yet provided a universal solution to this key issue. Quantification in habitats such as soil is difficult as isolation procedures yield only a small and skewed selection of the microorganisms present. Indices of taxonomic or phylogenetic diversity have potential in the quantification of microbial diversity at a range of ranks, but the non-equivalence of ranks and representatives of the taxa detected have to be addressed. Chemical and molecular methods have immense potential in the quantification of microbial diversity in environmental samples; 16S rRNA has shown particular promise with bacteria, but as yet the fungi lack a universal probe. A greater awareness of the limitations of existing approaches and methodologies used by microbiologists is needed, but significant progress can be anticipated as new technologies are developed and become more widely adopted.}, } @article {pmid8021607, year = {1994}, author = {Gerna, G and Steele, AD and Hoshino, Y and Sereno, M and Garcia, D and Sarasini, A and Flores, J}, title = {A comparison of the VP7 gene sequences of human and bovine rotaviruses.}, journal = {The Journal of general virology}, volume = {75 (Pt 7)}, number = {}, pages = {1781-1784}, doi = {10.1099/0022-1317-75-7-1781}, pmid = {8021607}, issn = {0022-1317}, mesh = {Amino Acid Sequence ; Animals ; Antibodies, Monoclonal ; *Antigens, Viral ; Capsid/chemistry/*genetics ; *Capsid Proteins ; Cattle ; Child ; Conserved Sequence ; Diarrhea/microbiology ; Finland ; Genes, Viral/*genetics ; Humans ; Italy ; Molecular Sequence Data ; Neutralization Tests ; Rotavirus/chemistry/classification/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; United Kingdom ; Viral Structural Proteins/*genetics ; }, abstract = {The sequences of the gene encoding VP7 (the major outer capsid protein) from one bovine and three human rotavirus strains were determined because of their unusual VP7 specificities. Two of the human strains (PA 169 and PA 151) had VP7 serotype 6 specificity whereas the two other strains, recovered from a child (HAL 1166) and a calf (678) belonged to VP7 serotype 8. The serotype 8 strains exhibited a high degree of sequence conservation when compared with each other and with other serotype 8 strains previously sequenced. The serotype 6 human strains shared a greater degree of sequence similarity with previously reported serotype 6 bovine strains than with other rotavirus serotypes; however the degree of sequence similarity among PA 169, PA 151 and the bovine strains was lower than had been previously reported for strains belonging to the same serotype. The demonstration of rotavirus serotypes that are shared between human and animal species supports the concept that interspecies transmission occurs and may play a role in rotavirus evolution.}, } @article {pmid8031731, year = {1994}, author = {Emmans, GC}, title = {Effective energy: a concept of energy utilization applied across species.}, journal = {The British journal of nutrition}, volume = {71}, number = {6}, pages = {801-821}, doi = {10.1079/bjn19940188}, pmid = {8031731}, issn = {0007-1145}, mesh = {*Animal Nutritional Physiological Phenomena ; Animals ; Cattle ; Chickens/*metabolism ; Dietary Fats/metabolism ; Energy Intake/*physiology ; *Energy Metabolism ; Feces/chemistry ; Lipid Metabolism ; Mammals/*metabolism ; Models, Biological ; Nitrogen/urine ; Proteins/metabolism ; Ruminants/metabolism ; Swine ; }, abstract = {An energy system is described in which, in both single-stomached and ruminant animals, the heat increment of feeding is considered to be linearly related to five measurable quantities. For both kinds of animals three of the quantities, with their heat increments in parentheses, are urinary N (wu; kJ/g), faecal organic matter (wd; kJ/g) and positive protein retention (wp; kJ/g). In ruminants the other two, with their heat increments in parentheses, are CH4 energy (wm; kJ/kJ) and positive lipid retention (w1; kJ/g); in single-stomached animals they are positive lipid retention from feed lipid (wII; kJ/g), and positive lipid retention not from feed lipid (wI; kJ/g). Data from suitable experiments on steers, pigs and chickens were used to test the system and to estimate wu 29.2, wd 3.80, wp 36.5, wm 0.616, wI 16.4 and wII 4.4. The values for wu, wd, wm and (wI - wII) allow an energy scale, called effective energy, to be defined for both single-stomached animals and ruminants. On this energy scale the values of wp and wI, together with the heats of combustion of protein and lipid of 23.8 and 39.6 kJ/g respectively, allow the energy requirement to be expressed as (MH + 50PR + 56LR) for both kinds of animal, where PR and LR are the rates of positive protein and lipid retention (g/d), and MH is the maintenance heat production (kJ/d) which can be estimated as 0.96 of the fasting heat production. The effective energy (EE) yielded to a ruminant animal by a feed ingredient can be estimated as EE (MJ/kg organic matter) = 1.15ME - 3.84 - 4.67DCP, where ME is the metabolizable energy value (MJ/kg organic matter) and DCP is the digested crude protein content (kg/kg organic matter) with both measured at maintenance. Alternatively, EE can be estimated as EE (MJ/kg) = GE (d - 0.228) - 4.67DCP, where GE is the gross energy (MJ/kg) and d is the energy digestibility (MJ/MJ) also measured at maintenance. The EE yielded to a single-stomached animal can be estimated as EE (kJ/g) = 1.17ME - 4.2CP - 2.44, where ME (kJ/g) is measured at, or corrected to, zero N-retention and CP (g/g) is the crude protein (N x 6.25) content of the feed ingredient. The system is simpler for ruminants, and more accurate for both kinds of animal, than those now in use. As effective energy values can be tabulated for ingredients, and are additive to the extent that ME values are additive, they can be used to formulate diets using linear programming.}, } @article {pmid8023332, year = {1994}, author = {Januszkiewicz, AJ and Mayorga, MA}, title = {Nitrogen dioxide-induced acute lung injury in sheep.}, journal = {Toxicology}, volume = {89}, number = {3}, pages = {279-300}, doi = {10.1016/0300-483x(94)90101-5}, pmid = {8023332}, issn = {0300-483X}, mesh = {Administration, Inhalation ; Animals ; Bronchoalveolar Lavage Fluid ; Dose-Response Relationship, Drug ; Female ; Lung/drug effects/physiology ; Lung Diseases/blood/*chemically induced ; Mouth Breathing ; Nitrogen Dioxide/blood/*toxicity ; Nose/physiology ; Pulmonary Circulation/drug effects ; Respiration ; Sheep ; }, abstract = {Lung mechanics, hemodynamics and blood chemistries were assessed in sheep (Ovis aries) before, and up to 24 h following, a 15-20 min exposure to either air (control) or approximately 500 ppm nitrogen dioxide (NO2). Histopathologic examinations of lung tissues were performed 24 h after exposure. Nose-only and lung-only routes of exposure were compared for effects on NO2 pathogenesis. Bronchoalveolar lavage fluids from air- and NO2-exposed sheep were analyzed for biochemical and cellular signs of NO2 insult. The influence of breathing pattern on NO2 dose was also assessed. Five hundred ppm NO2 exposure of intubated sheep (lung-only exposure) was marked by a statistically significant, albeit small, blood methemoglobin increase. The exposure induced an immediate tidal volume decrease, and an increase in both breathing rate and inspired minute ventilation. Pulmonary function, indexed by lung resistance and dynamic lung compliance, progressively deteriorated after exposure. Maximal lung resistance and dynamic lung compliance changes occurred at 24 h post exposure, concomitant with arterial hypoxemia. Bronchoalveolar lavage fluid epithelial cell number and total protein were significantly increased while macrophage number was significantly decreased within the 24 h post-exposure period. Histopathologic examination of lung tissue 24 h after NO2 revealed patchy edema, mild hemorrhage and polymorphonuclear and mononuclear leukocyte infiltration. The NO2 toxicologic profile was significantly attenuated when sheep were exposed to the gas through a face mask (nose-only exposure). Respiratory pattern was not significantly altered, lung mechanics changes were minimal, hypoxemia did not occur, and pathologic evidence of exudation was not apparent in nose-only, NO2-exposed sheep. The qualitative responses of this large animal species to high-level NO2 supports the concept of size dependent species sensitivity to NO2. In addition, when inspired minute ventilation was used as a dose-determinant, a linear relationship between NO2 dose and lung resistance was found. The importance of these findings, NO2 dose-determinants, and the utility of sheep as a large animal inhalation model are discussed.}, } @article {pmid21236812, year = {1994}, author = {Cohan, FM}, title = {Genetic exchange and evolutionary divergence in prokaryotes.}, journal = {Trends in ecology & evolution}, volume = {9}, number = {5}, pages = {175-180}, doi = {10.1016/0169-5347(94)90081-7}, pmid = {21236812}, issn = {0169-5347}, abstract = {Recent work shows that genetic exchange in prokaryotes is less frequent but more promiscuous than that in eukaryotes. As a result, genetic exchange plays very different roles in determining the patterns of evolutionary divergence in these major groups. Because sexual isolation is not a prerequisite for divergence in the prokaryotic world, the biological species concept is not appropriate for bacteria. However, there is a species concept that may apply universally.}, } @article {pmid7994108, year = {1994}, author = {Amato, G and Gatesy, J}, title = {PCR assays of variable nucleotide sites for identification of conservation units.}, journal = {EXS}, volume = {69}, number = {}, pages = {215-226}, doi = {10.1007/978-3-0348-7527-1_12}, pmid = {7994108}, issn = {1023-294X}, mesh = {Alligators and Crocodiles/*genetics ; Animals ; Conservation of Natural Resources/*methods ; DNA Primers/genetics ; Polymerase Chain Reaction/*methods ; }, abstract = {A number of authors have recently suggested that the best approach for identifying units of conservation is to follow a systematics model of character analysis (Amato, 1991; Cracraft, 1991; Vogler and DeSalle, 1994). This approach necessitates the use of an operational, typological, evolutionary species concept. The use of the phylogenetic species concept has the utility and philosophical logic appropriate for this task. Additionally, there is a large body of literature that uses this framework, along with a parsimony based character analysis to identify patterns of phylogeny (Cracraft, 1983; Nelson and Platnick, 1981; Nixon and Wheeler, 1990). While we advocate this approach, we recognize that one of its limiting factors is sample size. We propose that by selective direct sequencing plus rapid sampling of variable target characters by polymerase chain reaction (PCR) assays of specific sites, sufficiently large numbers of individuals can be accurately, inexpensively, and quickly surveyed for diagnostic characters. This procedure is demonstrated by a survey of variable nucleotide sites in the Caiman crocodilus complex.}, } @article {pmid7976007, year = {1994}, author = {Künzle, H}, title = {Somatovisceral projections from spinal cord and dorsal column nuclei to the thalamus in hedgehog tenrecs.}, journal = {Somatosensory & motor research}, volume = {11}, number = {2}, pages = {131-148}, doi = {10.3109/08990229409028866}, pmid = {7976007}, issn = {0899-0220}, mesh = {Afferent Pathways/anatomy & histology ; Animals ; Ganglia, Spinal/*anatomy & histology ; Geniculate Bodies/anatomy & histology ; Hedgehogs/anatomy & histology ; Inferior Colliculi/anatomy & histology ; Nerve Fibers/ultrastructure ; Prosencephalon/anatomy & histology ; Sensory Receptor Cells/*anatomy & histology ; Somatosensory Cortex/*anatomy & histology ; Species Specificity ; Spinal Cord/*anatomy & histology ; Spinothalamic Tracts/anatomy & histology ; Thalamic Nuclei/*anatomy & histology ; Viscera/*innervation ; }, abstract = {In order first to overcome the difficulties in understanding the increasing amount of information available regarding the mammalian somatosensory thalamus, and then to correlate the findings among different species and integrate them into a general concept of thalamic organization, the present study investigated the spinothalamic and medial lemniscal projections in Madagascan hedgehog tenrecs (Echinops telfairi and Setifer setosus). Tracer substances were injected into the dorsal column nuclei and into spinal segments at various levels; additional injections were made into the inferior colliculus. The ascending somesthetic projections were to predominantly contralateral posterolateral target areas, and were almost mirror-like on both sides to intralaminar and medial thalamic nuclei. The densest and most extensive projections, originating mainly from the high cervical spinal cord and the dorsal column nuclei, reached the posterolateral thalamus caudal to the lateral geniculate nucleus. This region was difficult to subdivide cytoarchitecturally; nevertheless, on the basis of its labeling pattern, several subdivisions could be described and preliminary named. Some of them compared tentatively with the internal portion of the medial geniculate nucleus (GM) and the ventral posterior nuclear complex (VPC) in more differentiated mammals. The most prominent subdivision, however, located subjacent to the lateral surface of the brainstem, was shown to receive additional fibers from the inferior colliculus. This region might be considered a further subdivision of GM, VPC, a perigeniculate area, and/or a region of its own not comparable at present, with thalamic regions in other mammals. On the other hand, it may also be a remnant of the hypothetical, diffuse multimodal region from which GM and VPC have possibly evolved.(ABSTRACT TRUNCATED AT 250 WORDS)}, } @article {pmid7957724, year = {1994}, author = {Torte, MP and Courjon, JH and Flandrin, JM and Magnin, M and Magenes, G}, title = {Anatomical segregation of different adaptative processes within the vestibulocerebellum of the cat.}, journal = {Experimental brain research}, volume = {99}, number = {3}, pages = {441-454}, pmid = {7957724}, issn = {0014-4819}, mesh = {Adaptation, Physiological/*physiology ; Animals ; Cats ; Cerebellum/*anatomy & histology/*physiology ; Electric Stimulation ; Eye Movements/physiology ; Habituation, Psychophysiologic/physiology ; Neuronal Plasticity/physiology ; Nystagmus, Optokinetic/physiology ; Photic Stimulation ; Reflex, Vestibulo-Ocular/physiology ; Uvula/physiology ; Vestibule, Labyrinth/*anatomy & histology/*physiology ; }, abstract = {Bilateral surgical lesions of the flocculus or the nodulo-uvular lobes were performed in the cat. Effects of these lesions on optokinetic and optokinetic afternystagmus OKAN), vestibulo-ocular reflex (VOR), visual suppression, and adaptation and habituation of VOR were studied using an identical experimental protocol. After flocculectomy, all these functions were impaired, except for habituation. Long-term postoperative recordings only revealed a recovery of the suppression of VOR, suggesting a limited contribution of the flocculus to this function. After nodulo-uvulectomy, only habituation and OKAN were modified. When the lesion was restricted to part of the uvula, OKAN duration was decreased. For other lesions involving the uvula together with the nodulus and/or the lobules VII-VIII,OKAN duration was increased. Habituation was lost after destruction of the nodulo-uvular lobes. When this latter structure was damaged, the retention component of habituation was selectively impaired, sparing the acquisition. Additional lesions outside the vestibulocerebellum appeared necessary to suppress the two components. Comparison of results obtained after flocculectomy and after nodulouvulectomy confirms and extends to non-primate species the concept of a "differential control" of adaptation and habituation by distinct vestibulocerebellar structures.}, } @article {pmid7569043, year = {1994}, author = {Holland, MK and Jackson, RJ}, title = {Virus-vectored immunocontraception for control of wild rabbits: identification of target antigens and construction of recombinant viruses.}, journal = {Reproduction, fertility, and development}, volume = {6}, number = {5}, pages = {631-642}, doi = {10.1071/rd9940631}, pmid = {7569043}, issn = {1031-3613}, mesh = {Animals ; Antigens/*genetics ; Australia ; *Contraception, Immunologic ; Female ; *Genetic Vectors ; Male ; Oocytes/immunology ; *Pest Control ; Poxviridae/genetics ; *Rabbits ; Spermatozoa/immunology ; Viruses/*genetics ; }, abstract = {The need to control animal populations arises in many situations in the world from a variety of motives. Present control strategies are almost universally based on lethal procedures. Increasingly, there is dissatisfaction with such approaches from many different perspectives. In response to these concerns, the concept of controlling populations of pest species through control of their fertility has been mooted. Successful examples of this approach exist in cases of small, discrete pest populations but application of this to a widely distributed species over a broad geographical area has not yet been achieved. In this article, we report on a new approach to fertility control, virus-vectored immunocontraception, and discuss its applicability to control of wild rabbit populations. Particular emphasis is placed on the strategy for selection of a target molecule capable of inducing an immunocontraceptive response and on how the gene encoding such a molecule might be engineered into the myxoma virus for distribution into the population. The fact that the procedures for antigen identification and the viral engineering methods used are, to varying extents, generic means that the broad principles of this approach are applicable in other species.}, } @article {pmid7909261, year = {1993}, author = {Vogler, AP and Knisley, CB and Glueck, SB and Hill, JM and Desalle, R}, title = {Using molecular and ecological data to diagnose endangered populations of the puritan tiger beetle Cicindela puritana.}, journal = {Molecular ecology}, volume = {2}, number = {6}, pages = {375-383}, doi = {10.1111/j.1365-294x.1993.tb00030.x}, pmid = {7909261}, issn = {0962-1083}, mesh = {Animals ; Base Sequence ; Coleoptera/classification/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Ecology ; Haplotypes ; Maryland ; Molecular Sequence Data ; New England ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Population Density ; Sequence Analysis, DNA ; }, abstract = {Populations of the puritan tiger beetle Cicindela puritana in the eastern United States were found to be highly threatened at the Connecticut River, whereas several large populations on the western shore and newly discovered populations on the eastern shore of the Chesapeake Bay appeared to be less endangered. We assessed if the disjunct C. puritana subgroups are genetically distinct and therefore should be treated as separate units for conservation purposes. A total of 13 individuals from the Connecticut River and 27 individuals from the Chesapeake Bay were each analysed by sequencing of up to 837 base pairs of mitochondrial DNA per individual. Five different haplotypes could be distinguished. In a phylogenetic analysis of these DNA sequences that included four related Cicindela species as out-groups, haplotypes from the Chesapeake Bay represent a distinct clade. The conservation status of these populations was evaluated using a phylogenetic approach based on cladistic analysis and the framework of the phylogenetic species concept. According to this analysis, beetles from the Connecticut River and the Chesapeake Bay have to be considered as independent units. Populations from the eastern and western shore of Chesapeake Bay are not split in more than one unit using the same criteria, although they exhibited some degree of genetic subdivision. The results from the mtDNA analysis were corroborated by ecological parameters in that the Chesapeake Bay populations can be distinguished from all congeners by their different habitat association.}, } @article {pmid15335669, year = {1993}, author = {Vázquez, JA and de la Fuente, L and Berron, S and O'Rourke, M and Smith, NH and Zhou, J and Spratt, BG}, title = {Ecological separation and genetic isolation of Neisseria gonorrhoeae and Neisseria meningitidis.}, journal = {Current biology : CB}, volume = {3}, number = {9}, pages = {567-572}, doi = {10.1016/0960-9822(93)90001-5}, pmid = {15335669}, issn = {0960-9822}, abstract = {BACKGROUND: Classifying bacteria into species is problematic. Most microbiologists consider species to be groups of isolates that share some arbitrary degree of relatedness of biochemical or molecular (such as DNA sequence) features and that, ideally, are clearly delineated from all other groups of isolates. The main problem in applying to bacteria a biological concept of species based on the ability or inability of their genes to recombine, is that recombination appears to be rare in bacteria in nature, as indicated by the strong linkage disequilibrium between alleles found in most bacterial populations. However, there are some naturally transformable bacteria in which assortative recombination appears to be so frequent that alleles are in, or close to, linkage equilibrium. For these recombining populations a biological concept of species might be applicable.

RESULTS: Populations of Neisseria gonorrhoeae and Neisseria meningitidis from Spain were analysed by multilocus enzyme electrophoresis. The data indicate that assortative recombination occurs frequently within populations, but not between populations. Similarly, the sequences of two house-keeping genes show no evidence of intragenic recombination between N. gonorrhoeae and N. meningitidis.

CONCLUSIONS: N. gonorrhoeae and N. meningitidis represent extremely closely related 'sexual' populations that appear to be genetically isolated in nature, and thus conform to the biological concept of species. The extreme uniformity of N. gonorrhoeae house-keeping genes suggests that this species may have arisen recently as a clone of N. meningitidis that could colonize the genital tract. Ecological isolation - of populations that can colonize the genital tract from those that can colonize the nasopharynx - may have been an important component in speciation, leading to a lower frequency of recombination between species than within species.}, } @article {pmid8263964, year = {1993}, author = {Moffat, MP and Karmazyn, M}, title = {Protective effects of the potent Na/H exchange inhibitor methylisobutyl amiloride against post-ischemic contractile dysfunction in rat and guinea-pig hearts.}, journal = {Journal of molecular and cellular cardiology}, volume = {25}, number = {8}, pages = {959-971}, doi = {10.1006/jmcc.1993.1108}, pmid = {8263964}, issn = {0022-2828}, mesh = {Adenine Nucleotides/metabolism ; Amiloride/*analogs & derivatives/pharmacology/therapeutic use ; Animals ; Creatine Kinase/metabolism ; Glycogen/metabolism ; Guinea Pigs ; Heart/*drug effects ; Heart Rate/drug effects ; Hydrogen-Ion Concentration ; In Vitro Techniques ; Ion Transport/drug effects ; Lactates/metabolism ; Male ; Myocardial Contraction/*drug effects ; Myocardial Ischemia/drug therapy/metabolism/*physiopathology ; Myocardial Reperfusion Injury/*drug therapy ; Myocardium/metabolism ; Phosphocreatine/metabolism ; Rats ; Rats, Sprague-Dawley ; Sodium-Hydrogen Exchangers/antagonists & inhibitors ; }, abstract = {We studied the effects of the potent Na/H exchange inhibitor methylisobutyl amiloride (MIA, 1 microM) on post-ischemic ventricular recovery and energy metabolic status in spontaneously contracting, isolated rat and guinea-pig hearts subjected to 45 min zero-flow ischemia followed by reperfusion. For both species, MIA was added either 15 min prior to ischemia and was present throughout reperfusion or was added at the time of reperfusion only. In control rat hearts, force recovery after 30 min of reperfusion was 25.6 +/- 6.0% of the pre-ischemic value whereas in hearts pre-treated with MIA recovery was enhanced to 55.4 +/- 9% (P < 0.05). Elevation of resting tension during the first 20 min of reperfusion was also significantly reduced by MIA pre-treatment. When MIA was added at the time of reperfusion only, recovery was generally lower than that seen with MIA pre-treatment although significantly higher values were seen through much of the reperfusion period. In rat hearts, MIA reduced the time required for return to sustained contractile recovery particularly in those hearts where the drug was added prior to ischemia (control, 11.4 +/- 2.7 min; MIA, 2.6 +/- 0.5 min, P < 0.05). Similar effects of MIA pre-treatment were seen in guinea-pig hearts in terms of contractile recovery, time to recovery and reduction in resting tension although MIA addition at the time of reperfusion was without beneficial effect either on the magnitude of contractile recovery or time required for restoration of function. In guinea-pig hearts, recovery of function was accompanied by substantial bradycardia. However, maintenance of ventricular rate through electrical pacing exerted no significant influence on the protective effects of MIA pre-treatment. There was no effect of MIA on energy metabolites in reperfused rat hearts or paced guinea-pig hearts, although in spontaneously contracting guinea-pig hearts improved recovery of function was associated with significantly higher levels of high energy phosphates. No effects of tissue metabolites were seen in ischemic non-reperfused hearts irrespective of treatment. The protective effects of MIA were not related to diminished release of creatine kinase during reperfusion. Our results demonstrate marked protective effects of MIA, on the reperfused rat and guinea-pig myocardium. These studies also demonstrate, for the first time, that the effects of amiloride analogues are not species specific and further support the concept that Na/H exchange inhibition may represent an effective therapeutic approach for the protection of reperfused cardiac tissue.}, } @article {pmid7692471, year = {1993}, author = {Hildebrand, M}, title = {Bioactivation of eptaloprost in animals and man.}, journal = {Prostaglandins}, volume = {46}, number = {2}, pages = {177-189}, doi = {10.1016/0090-6980(93)90043-7}, pmid = {7692471}, issn = {0090-6980}, mesh = {Absorption ; Aged ; Animals ; Biotransformation ; Epoprostenol/analogs & derivatives/blood ; Feces ; Female ; Half-Life ; Humans ; Iloprost/*analogs & derivatives/blood/pharmacokinetics/urine ; Kinetics ; Macaca fascicularis ; Male ; Middle Aged ; Rats ; Rats, Wistar ; Species Specificity ; Tritium ; }, abstract = {Eptaloprost is a novel concept PGI2-mimetic, which is designed to be activated to the pharmacologically potent cicaprost via beta-oxidation. By pro-drug formation advantages in terms of sustained delivery of prostacyclin-mimetic activity were envisaged. The active metabolite is known to be metabolically stable and highly pharmacologically potent. In the present set of experiments the pharmacokinetics of eptaloprost was studied in rat, monkey and man by i.v. and ig administration of tritiated compound. Eptaloprost was completely and rapidly absorbed in all three species. Peak plasma levels of the parent compound were observed within 30 min postdose. Total clearance of the pro-drug accounted for 170, 62 and 66 ml/min/kg in rat, monkey and man. Disposition of eptaloprost exhibited half-lives of 0.1 to 0.5 h and mean residence times accounted for 0.15, 0.4 and 0.6 h in the three species. The active metabolite cicaprost was present in the central compartment with a slight delay as compared to eptaloprost. Its peak plasma levels were found within 0.25 to 0.5 h postdose. Disposition of radiolabel in plasma and 3H-excretion with the urine and feces was determined by the pharmacokinetic behaviour of cicaprost. In rats excretion was mainly biliary while monkeys and man excreted almost unchanged cicaprost in equal portions with urine and feces. Half-lives of renal excretion were in the range of terminal half-lives in the central compartment. Neither in animals nor in man eptaloprost administration resulted in an advantageous systemic profile of cicaprost. On the contrary the bioavailable dose fraction of cicaprost was lower as compared to cicaprost administration. A delay or an extension of cicaprost plasma levels was not observed. The present pharmacokinetic data of eptaloprost studied in three species demonstrated that a pro-drug concept based on simple beta-oxidative bioactivation could be successfully realized for a special PGI2-mimetic. An advantage resulting from oral pro-drug administration as compared to direct treatment with the active metabolite could not be shown. For long-lasting plasma levels of cicaprost a chemically determined retardation might require a more sophisticated pro-drug concept or alternatively pharmaceutical technology is required.}, } @article {pmid8100678, year = {1993}, author = {Bryant, C}, title = {Molecular variation in Trichinella.}, journal = {Acta tropica}, volume = {53}, number = {3-4}, pages = {319-330}, doi = {10.1016/0001-706x(93)90037-c}, pmid = {8100678}, issn = {0001-706X}, mesh = {Animals ; Genetic Variation/*genetics ; Humans ; Isoenzymes/genetics ; Trichinella/enzymology/*genetics ; Trichinellosis/epidemiology/immunology ; }, abstract = {The taxonomic status of variants within the genus Trichinella is problematical. Some authors recognise no fewer than four species (Trichinella spiralis, T. pseudospiralis, T. nativa and T. nelsoni), others regard T. nativa and T. nelsoni as strains of T. spiralis (T. spiralis var nativa or sylvatica), while others consider the genus to be monospecific, with a variety of more or less well defined isolates. Much of the current evidence adduced to support these various positions is similar to that used pre-1983. It derives from studies of the incidence of Trichinella infections in wild and in domestic animals, comparisons of infectivity of different isolates in laboratory animals and studies of immunity. However, it has become clear that infectivity and epidemiological studies are unreliable tools for discriminating between isolates of Trichinella and it has been shown that differences in the elicitation of immune responses are as much a function of the host as of the parasite. The introduction of monoclonal antibody technology has, however, permitted the identification of specific antigens in different isolates. The information is as yet scant, and one antigen does not a species make. Isozyme analysis provides some support for separating the various isolates of Trichinella into distinct groups, but cannot of itself shed light on the species problem until certain conditions are met. These conditions are difficult to achieve even in organisms abundantly available and without the baggage of the parasitic habit. Isozyme analysis is probably best used to support the newer studies of genomic DNA. Recent analyses of DNA by restriction endonucleases and dot-blot hybridisation techniques show ample promise of insights into speciation, and a new technique for amplifying the DNA from a single larva by the polymerase chain reaction offers exciting prospects. However, the position yet remains as stated in the first section of this abstract.}, } @article {pmid8436615, year = {1993}, author = {Corbett, RJ and Laptook, AR and Garcia, D and Ruley, JI}, title = {Energy reserves and utilization rates in developing brain measured in vivo by 31P and 1H nuclear magnetic resonance spectroscopy.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {13}, number = {2}, pages = {235-246}, doi = {10.1038/jcbfm.1993.29}, pmid = {8436615}, issn = {0271-678X}, support = {5P41-PR02584/PR/OCPHP CDC HHS/United States ; BRSG 2 S07 RR 07175-13/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn ; Brain/*growth & development/*metabolism ; Brain Ischemia/*metabolism/physiopathology ; Energy Metabolism ; Glucose/metabolism ; Lactates/metabolism ; Lactic Acid ; *Magnetic Resonance Spectroscopy ; Phosphocreatine/metabolism ; Swine ; }, abstract = {Age-related changes in cerebral energy utilization were examined in swine, a species whose maximal rate of development is known to occur in the perinatal period. Interleaved in vivo 31P and 1H nuclear magnetic resonance spectroscopy was used to measure the rates of change in cerebral concentrations of phosphocreatine (PCr), nucleoside triphosphates, and lactate following complete ischemia, induced via cardiac arrest, in a total of 19 newborn, 10-day-old, and 1-month-old piglets. Preischemic concentrations of these three metabolites plus glucose and glycogen were determined in a separate experiment on 12 piglets whose brains were funnel-frozen in situ. The rate constants for the PCr and ATP decline and lactate increase were determined by nonlinear regression fits to the experimental data, assuming first-order kinetics. The rate constants and preischemic metabolite concentrations were used to calculate the initial flux of high-energy phosphate equivalents (approximately P), which was used as an estimate of cerebral energy utilization at the point when ischemia was initiated. Cerebral energy utilization equaled 6.5 +/- 1.9, 9.5 +/- 3.2, and 15.1 +/- 3.2 mumol approximately P/g/min in newborn, 10-day-old, and 1-month-old piglets, respectively. Within each age group the energy utilization rate was not altered by hyperglycemia-induced increases in cerebral energy reserves, but during hypoglycemia cerebral energy utilization rates decrease. The slope of approximately P versus time decreased with the duration of ischemia, indicating that cerebral energy utilization rates decrease after the first few minutes of ischemia. Newborn piglets had higher cerebral energy utilization rates compared with literature values for newborn rats and mice. This is consistent with the concept that newborns from a species with a perinatal stage of maximal growth and development will have higher cerebral energy demands compared with newborns from a species such as rodents, whose maximal growth occurs postnatally. However, this conclusion remains tentative because literature cerebral utilization rates estimated from the initial slope of approximately P-versus-time plots tend to underestimate the true rate, since the assumption of continued linearity may not be valid for the interval chosen.}, } @article {pmid8095776, year = {1993}, author = {Wang, J and Lin, Y and Eremenko, AV and Kurochkin, IN and Mineyeva, MF}, title = {Affinity biosensors based on preconcentration/voltammetric analysis. Detection of phenothiazine drugs at Langmuir-Blodgett films of tyrosine hydroxylase.}, journal = {Analytical chemistry}, volume = {65}, number = {5}, pages = {513-516}, doi = {10.1021/ac00053a005}, pmid = {8095776}, issn = {0003-2700}, mesh = {*Biosensing Techniques ; Oxidation-Reduction ; Phenothiazines/*analysis ; Sensitivity and Specificity ; Tyrosine 3-Monooxygenase/*chemistry ; }, abstract = {A new route for operating affinity biosensors based on the voltammetric monitoring of the accumulated guest (analyte) is described. High sensitivity and selectivity accrue from the coupling of the specific receptor binding process and the inherent sensitivity of the preconcentration/pulse-voltammetric scheme. The redox (measurement) process results in dissociation of the receptor-guest complex, thus allowing multiple analytical determinations. The receptor layer also serves as an effective barrier that excludes interfering species. The new concept of preconcentration/voltammetric affinity biosensors is illustrated in connection with the detection of phenothiazine drugs using Langmuir-Blodgett films of their receptor, the enzyme tyrosine hydroxylase. The effect of various experimental variables upon the sensor performance is described.}, } @article {pmid8441831, year = {1993}, author = {Zbinden, G}, title = {The concept of multispecies testing in industrial toxicology.}, journal = {Regulatory toxicology and pharmacology : RTP}, volume = {17}, number = {1}, pages = {85-94}, doi = {10.1006/rtph.1993.1009}, pmid = {8441831}, issn = {0273-2300}, mesh = {Animals ; Animals, Laboratory ; Dogs ; *Drug-Related Side Effects and Adverse Reactions ; History, 20th Century ; Humans ; Rats ; Species Specificity ; Toxicology/history/*standards ; United States ; United States Food and Drug Administration ; }, abstract = {The multispecies approach in toxicity testing was originally motivated by the frequent findings of species differences in responsiveness to the pharmacological and acute toxic effects of chemicals. When the guidelines for repeated-dose toxicity experiments were developed in the early 1940s, the concept of using several species of animals was automatically included without careful scientific validation. In response to demands from the U.S. Food and Drug Administration and other national and international regulatory bodies, the protocols for acute and repeated-dose toxicity testing became highly formalized, and the requirement to conduct all studies in a rodent and a nonrodent species was established. With time, most guidelines also specified the species that had to be used, and the most common recommendation was to use the rat as the rodent and the dog as the nonrodent. In recent years, many reasons for differences in responsiveness of various animal species and man to the toxic effects of chemicals have been identified. This knowledge is now used extensively to assess contradictory findings in routine safety studies in the rodent and the nonrodent species. It is often possible to identify the species that appears to be more predictive for man than the other, and risk assessment for man is then based mainly on the findings in the more representative species. Since contrary toxicological findings in rodents and nonrodents occur frequently, one could propose to perform detailed scientific investigations prior to the selection of the species for toxicological investigations, as it has already been suggested by the working group of the European Society for the Study of Drug Toxicology in 1965 and is still an option mentioned in the currently valid EEC drug safety guidelines of 1983. For practical reasons such early investigations of biological properties and pharmacokinetic and metabolic characteristics of test chemicals in various laboratory animal species are hardly ever done prior to the initiation of safety studies. However, techniques are now developed with which species selection for toxicity testing can be made on the basis of rational scientific investigations.}, } @article {pmid11652252, year = {1993}, author = {Bekoff, M and Gruen, L}, title = {Animal welfare and individual characteristics: a conversation against speciesism.}, journal = {Ethics & behavior}, volume = {3}, number = {2}, pages = {163-175}, doi = {10.1207/s15327019eb0302_2}, pmid = {11652252}, issn = {1050-8422}, mesh = {Animal Experimentation ; *Animal Rights ; Animal Welfare ; Animals ; Communication ; Homicide ; Humans ; Individuality ; Moral Obligations ; Pain ; Personhood ; Self Concept ; Social Responsibility ; Stress, Psychological ; Wounds and Injuries ; }, abstract = {It seems impossible for a human being not to have some point of view concerning nonhuman animal (hereafter animal) welfare. Many people make decisions about how humans are permitted to treat animals using speciesist criteria, basing their decisions on an individual's species membership rather than on that animal's individual characteristics. Although speciesism provides a convenient way for making difficult decisions about who should be used in different types of research, we argue that such decisions should rely on an analysis of individual characteristics and should not be based merely on species membership. We do not argue that the concept of species is never useful or important. To make our points, we present a conversation among a skeptic, an agnostic, and a proponent of the view that our moral obligations to an animal must be based on an analysis of that individual's characteristics. In the course of the discussion, concepts such as personhood, consciousness, cognitive ability, harm, and pain are presented, because one's understanding of these concepts informs his or her ethical decisions about the use of animals by humans.}, } @article {pmid8094009, year = {1993}, author = {Molina, FI and Shen, P and Jong, SC}, title = {Validation of the species concept in the genus Dekkera by restriction analysis of genes coding for rRNA.}, journal = {International journal of systematic bacteriology}, volume = {43}, number = {1}, pages = {32-35}, doi = {10.1099/00207713-43-1-32}, pmid = {8094009}, issn = {0020-7713}, mesh = {Base Sequence ; DNA, Fungal/genetics ; *Genes, Fungal ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/*genetics/metabolism ; Species Specificity ; Yeasts/*classification/*genetics ; }, abstract = {The gene coding for the small-subunit rRNA of 11 type strains belonging to the genus Dekkera and its anamorph, Brettanomyces, was amplified by using the polymerase chain reaction and subjected to digestion with a series of restriction endonucleases. Similarity coefficients were calculated from the number of shared and unique fragments, and a cluster analysis yielded four distinct groups with the following ascosporogenous states: Dekkera anomala, Dekkera bruxellensis, Dekkera custersiana, and Dekkera naardenensis. Results correlate with evidence from isoenzyme electrophoresis and DNA homology analysis. They also confirm previously reported anamorph-teleomorph connections and recently proposed synonymies within the genus.}, } @article {pmid15463618, year = {1992}, author = {Lymbery, AJ}, title = {Interbreeding, monophyly and the genetic yardstick: species concepts in parasites.}, journal = {Parasitology today (Personal ed.)}, volume = {8}, number = {6}, pages = {208-211}, doi = {10.1016/0169-4758(92)90266-5}, pmid = {15463618}, issn = {0169-4758}, abstract = {The biological species concept defines species on the criterion of interbreeding. This may not be applicable to many parasites that are capable of self-fertilization and asexual reproduction. In this review, Alan Lymbery explores alternative concepts that may be applied to recognize species in such groups, using the cestode genus Echinococcus as an example. Two conclusions can be drawn. First, that the applicability of the biological species concept should not be dismissed without some knowledge o f the frequency of interbreeding in natural populations. Second, that where interbreeding is absent or rare, species should be delimited on the basis o f both monophyletic origin and genetic distinctness.}, } @article {pmid15463609, year = {1992}, author = {Bastien, P and Blaineau, C and Pages, M}, title = {Leishmania: sex, lies and karyotype.}, journal = {Parasitology today (Personal ed.)}, volume = {8}, number = {5}, pages = {174-177}, doi = {10.1016/0169-4758(92)90016-u}, pmid = {15463609}, issn = {0169-4758}, abstract = {The exploration of the genome of the tryponosomotid protozoan Leishmania has been difficult until recently owing to a number of obstacles, not least our ignorance of the ploidy and of the number of chromosomes (as in many other protozoa, the latter do not condense during mitosis), the uncertainty of the species concept in these allegedly asexual protozoa and the absence of classical genetic studies. Here, Patrick Bastien, Christine Bloineou and Michel Pages discuss the advances in this field brought about by the advent of molecular biology and its techniques, with on emphasis on ploidy and genetic exchange. In particular, they discuss the data from pulsed field gel electrophoresis (PFGE). When coupled with DNA restriction analysis, PFGE constitutes a powerful tool for the direct examination o f chromosomes of protozoa.}, } @article {pmid17744718, year = {1992}, author = {Grant, PR and Grant, BR}, title = {Hybridization of bird species.}, journal = {Science (New York, N.Y.)}, volume = {256}, number = {5054}, pages = {193-197}, doi = {10.1126/science.256.5054.193}, pmid = {17744718}, issn = {0036-8075}, abstract = {Hybridization, the interbreeding of species, provides favorable conditions for major and rapid evolution to occur. In birds it is widespread. Approximately one in ten species is known to hybridize, and the true global incidence is likely to be much higher. A longitudinal study of Darwin's finch populations on a Galápagos island shows that hybrids exhibit higher fitness than the parental species over several years. Hybrids may be at an occasional disadvantage for ecological rather than genetic reasons in this climatically fluctuating environment. Hybridization presents challenges to the reconstruction of phylogenies, formulation of biological species concepts and definitions, and the practice of biological conservation.}, } @article {pmid24202518, year = {1992}, author = {Gallais, A}, title = {Analysis of variance components of testcross progenies in an autotetraploid species and consequences for recurrent selection with a tester.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {83}, number = {3}, pages = {353-359}, pmid = {24202518}, issn = {0040-5752}, abstract = {For autotetraploid species the development of the concept of test value (value in testcross) leads to a simple description of the variance among testcross progenies. When defining directly genetic effects at the level of the value of the progenies, there is no contribution of triand tetragenic interactions. To estimate additive and dominance variances it is only necessary to have the population of progenies structured in half-sib or full-sib families; it is then possible to determine the presence of epistasis using a two-way mating design. When the theory of recurrent selection is applied dominance variance can be neglected for the prediction of genetic advance in one cycle as well for the development of combined selection when progenies are structured in families. The results are similar to those for diploids with two-locus epistasis. The more efficient scheme consists of the development of pair-crossing in off-season generations (for intercrossing) and simultaneous crossing of each plant to the tester. In comparison to the classical scheme, the relative efficiency of such a scheme is 41%. The use of combined selection will further increase this superiority.}, } @article {pmid21235932, year = {1992}, author = {Baum, D}, title = {Phylogenetic species concepts.}, journal = {Trends in ecology & evolution}, volume = {7}, number = {1}, pages = {1-2}, doi = {10.1016/0169-5347(92)90187-G}, pmid = {21235932}, issn = {0169-5347}, } @article {pmid24258591, year = {1991}, author = {Frérot, B and Foster, SP}, title = {Sex pheromone evidence for two distinct taxa withinGraphania mutans (Walker).}, journal = {Journal of chemical ecology}, volume = {17}, number = {11}, pages = {2077-2093}, pmid = {24258591}, issn = {0098-0331}, abstract = {The sex pheromones of two populations ofGraphania mutans (Walker) were analyzed. Females from an Auckland population produced (Z)-9-tetradecenol (Z9-14∶OH), (Z)-9-tetradecenyl acetate (Z9-14∶OAc), (Z)-7-tetradecenol (Z7-14∶OH) and (Z)-7-tetradecenyl acetate (Z7-14∶OAc), while females from a Lincoln population produced these four compounds and a large amount of (Z)-9-tetradecenal (Z9-14∶Ald). Significant differences, paralleling the difference between females, were observed when the responses of males of both populations to the above and other related compounds were tested by electroantennogram, field-trapping, and wind-tunnel bioassays. The most distinct difference was observed in the wind tunnel. Males from both taxa flew upwind and touched pheromone sources containing sex pheromone extract of females of their own taxon, but either did not initiate upwind flight or arrested upwind flight shortly after taking flight in response to extract from females of the other taxon. The difference between the pheromone systems of the two populations is probably due to the presence and importance of Z9-14∶Ald in the pheromone blend of the Lincoln population. Thus the addition of a relatively large amount of Z9-14∶Aid to a four-component pheromone blend (i.e., Z9-14∶OH, Z9-14∶OAc, Z7-14∶OH, andZ7-14∶OAc) attractive to Auckland males completely suppressed trap catches of male G.Mutans in Auckland but large numbers of males were caught at both Lincoln and Nelson in traps baited with this five-component blend. In wind-tunnel studies, the addition of even small (1% of amount of Z9-14∶OH) amounts ofZ9-14∶Ald to the four-component blend resulted in a significantly greater proportion of Auckland males arresting upwind flight than to the four-com ponent blend. It is suggested that these two populations of G. nations represent distinct sibling species within the described concept.}, } @article {pmid23196188, year = {1990}, author = {Giannì, A and Piras, L}, title = {Autoecological and molecular approach to the species problem in the Euplotes vannus-crassus-minuta group (Ciliophora, Hypotrichida).}, journal = {European journal of protistology}, volume = {26}, number = {2}, pages = {142-148}, doi = {10.1016/S0932-4739(11)80108-2}, pmid = {23196188}, issn = {0932-4739}, abstract = {The long standing species problem in the Euplotes vannus-crassus-minuta group is addressed here by means of restriction enzyme rDNA maps and salinity and temperature tolerance tests performed on several strains of these morphospecies (i.e. morphologically identified species). The rationale in collecting such data (which add to others existing in literature) is to provide a broad data base to allow a multi-integrated approach to the problem at hand. The autoecological parameters considered and the rDNA maps proved to be different in the three morphospecies. Both recent literature and our data suggest the existence of E. vannus, E. crassus and E. minuta as separate evolutionary entities. Conceptual and practical implications of our findings are discussed.}, } @article {pmid2635595, year = {1989}, author = {Xu, PS}, title = {[The species problem in medicinal plant studies].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {14}, number = {12}, pages = {707-10, 761}, pmid = {2635595}, issn = {1001-5302}, mesh = {Pharmacognosy/*classification ; Plants, Medicinal/*classification ; Species Specificity ; }, abstract = {The present paper made a brief introduction to the two current major species concepts and the various types of "species" existent in nature. The author emphatically pointed out that in any case species are heterogeneous instead of homogeneous. Thus pharmacognostists should not be content with mere identification of the scientific names of plants, but are obligated to find out the intraspecific variations associated with pharmacognostic identification and to bring to light the regularities of formation, accumulation and dynamic changes of secondary metabolic products for medical use.}, } @article {pmid2635158, year = {1989}, author = {Adams, M and Andrews, RH and Robinson, B and Christy, P and Baverstock, PR and Dobson, PJ and Blackler, SJ}, title = {A genetic approach to species criteria in the amoeba genus Naegleria using allozyme electrophoresis.}, journal = {International journal for parasitology}, volume = {19}, number = {8}, pages = {823-834}, doi = {10.1016/0020-7519(89)90107-0}, pmid = {2635158}, issn = {0020-7519}, mesh = {Alleles ; Animals ; Electrophoresis, Cellulose Acetate ; *Genetic Variation ; Isoenzymes/*analysis ; Naegleria/*classification/enzymology/genetics ; Phylogeny ; }, abstract = {The present study employs allozyme electrophoresis to characterize and inter-relate 61 isolates of Naegleria. Diploidy was confirmed, with heterozygotes observed at 29 of the 33 loci established and in all but two isolates. With a single exception, isolates clustered at two levels of similarity, either below 21% or above 52%. It is argued that such a major discontinuity provides a sound biological basis for a species concept in Naegleria. On this basis the present species-level taxonomy does not reflect the genetic diversity of the genus. The study recognized 18 genetic groups of species rank. The subspecies N. australiensis italica deserves specific rank; additional thermophilic species not closely related to N. fowleri and N. lovaniensis are recognized; and N. gruberi as currently conceived is a complex of 10 species, at least five of which are represented in the formal culture collections. Most species are genetically too different for relationships to be elucidated by allozyme electrophoresis, supporting the view that some of the times of divergence within the genus are extremely ancient.}, } @article {pmid2517768, year = {1989}, author = {Samovar, AG}, title = {[The search for the sexual process or its equivalents in the Trypanosomatidae].}, journal = {Tsitologiia}, volume = {31}, number = {12}, pages = {1403-1422}, pmid = {2517768}, issn = {0041-3771}, mesh = {Animals ; Drug Resistance ; Genetic Markers ; Isoenzymes/analysis ; Methods ; Reproduction/physiology ; Trypanosomatina/cytology/drug effects/genetics/*physiology ; }, abstract = {Literary evidence on searching for the sexual process in the life cycles of the trypanosomatids are reviewed. Based on the data provided, a; conclusion is made that the stable well-accepted viewpoint on the absence of any genetic exchanges in these flagellates is to be rejected. However, forms and mechanisms of the discovered phenomena are investigated insignificantly. The results reported in the number of publications suggest the presence of the sexual process, at least, in Trypanosoma brucei. But the existence of other forms of genetic exchanges, both in this and in other species, is also possible. The species problem in the trypanosomatids is discussed.}, } @article {pmid2482330, year = {1989}, author = {Paterson, RR and Bridge, PD and Crosswaite, MJ and Hawksworth, DL}, title = {A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. III. An evaluation of pectinase and amylase isoenzymes for species characterization.}, journal = {Journal of general microbiology}, volume = {135}, number = {11}, pages = {2979-2991}, doi = {10.1099/00221287-135-11-2979}, pmid = {2482330}, issn = {0022-1287}, mesh = {Amylases/*analysis ; Cluster Analysis ; Glycoside Hydrolases/*analysis ; Isoenzymes/*analysis ; Penicillium/classification/*enzymology/genetics ; Polygalacturonase/*analysis ; Species Specificity ; }, abstract = {Polyacrylamide gel electrophoresis of extracellular pectinase and amylase isozymes of 170 mainly terverticillate Penicillium strains was undertaken. The data were coded and subjected to numerical analysis. Variation in intensity of isozymes was observed in repeat analyses of some strains, although most were consistent. Variation was also observed between some representative strains of species. P. viridicatum was more variable than P. brevicompactum and P. hordei for intensity of pectinase activity. There was a correlation between the grouping of the strains on the basis of the isozymes and the species concepts only in some cases. The method proved useful for the identification of strains producing intense activity which provided clear patterns, for example, P. brevicompactum and P. chrysogenum and to a lesser extent P. solitum var. crustosum and P. hordei. The method was also exclusionary in that some species were restricted to a particular cluster or subcluster. Amylase patterns confirmed that strains referred to as single species are not all homogeneous genetically, and that some strains are not simply haploid homokaryons. The genetic heterogeneity of the strains explains some of the problems in the systematics of the terverticillate penicillia.}, } @article {pmid2803757, year = {1989}, author = {Björklind, A and Ringertz, S and Kronvall, G}, title = {Types of interpretive errors in susceptibility testing. Zone breakpoints for norfloxacin disk diffusion testing.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {97}, number = {10}, pages = {941-948}, doi = {10.1111/j.1699-0463.1989.tb00502.x}, pmid = {2803757}, issn = {0903-4641}, mesh = {*Microbial Sensitivity Tests ; Norfloxacin/*pharmacology ; Regression Analysis ; }, abstract = {A total of 548 strains of the eleven most common urinary tract pathogens were investigated for possible errors in norfloxacin susceptibility tests comparing MIC determinations with disk diffusion assays. Most strains were found to be sensitive with MIC-90 values below 1.0 for the Enterobacteriaceae while the classical nalidixic acid resistant species, the gram-positive bacteria and Pseudomonas aeruginosa, were less susceptible to norfloxacin with MIC-90 above 1.0 mg/l. MIC-values close to interpretive MIC-limits were recorded for S. faecalis and S. agalactiae using the recommendations of the national Committee for Clinical Laboratory Standards (NCCLS) (susceptible, S less than or equal to 4.0) and for P. aeruginosa and S. aureus using the Swedish Reference Group for Antibiotics (SRGA) standards (S less than or equal to 1.0). Susceptibility interpretations for these species showed a lack of accuracy consistent with methodological problems of reproducibility, an error called type I. The changes in the MIC-limits required for these strains to correct the error would be S less than or equal to 4 for P. aeruginosa and S. aureus, S less than or equal to 8 for S. agalactiae and S less than or equal to 0.5 for S. faecalis. A type II error, occurring when a bacterial species shows a regression line different from the regular line, was also identified for S. saprophyticus. The use of breakpoints derived from single strains regression analysis corrected this error and also reduced the frequency of similar misinterpretations in other species. The term "species-specific MIC-limits" should be introduced along with the established concept of "species-specific interpretive zone breakpoints" to allow for the correction of type I interpretive errors. Type II errors can be corrected by using species-specific interpretive breakpoints, either issued by reference laboratories or derived by calculations from single-strain regression analysis in the individual laboratory.}, } @article {pmid16666689, year = {1989}, author = {Jenkins, CL}, title = {Effects of the Phosphoenolpyruvate Carboxylase Inhibitor 3,3-Dichloro-2-(Dihydroxyphosphinoylmethyl)propenoate on Photosynthesis: C(4) Selectivity and Studies on C(4) Photosynthesis.}, journal = {Plant physiology}, volume = {89}, number = {4}, pages = {1231-1237}, pmid = {16666689}, issn = {0032-0889}, abstract = {The effect of 3,3-dichloro-2-(dihydroxyphosphinoylmethyl)-propenoate (DCDP), an analog of phosphoenolpyruvate (PEP), on PEP carboxylase activity in crude leaf extracts and on photosynthesis of excised leaves was examined. DCDP is an effective inhibitor of PEP carboxylase from Zea mays or Panicum miliaceum; 50% inhibition was obtained at 70 or 350 micromolar, respectively, in the presence of 1 millimolar PEP and 1 millimolar HCO(3) (-). When fed to leaf sections via the transpiration stream, DCDP at 1 millimolar strongly inhibited photosynthesis in C(4) species (79-98% inhibition for a range of seven C(4) species), but only moderately in C(3) species (12-46% for four C(3) species), suggesting different mechanisms of inhibition for each photosynthetic type. The response of P. miliaceum (C(4)) net photosynthesis to intercellular pCO(2) showed that carboxylation efficiency, as well as the CO(2) saturated rate, are lowered in the presence of DCDP and supported the view that carboxylation efficiency in C(4) species is directly related to PEP carboxylase activity. A fivefold increase in intercellular pCO(2) over that occurring in P. miliaceum under normal photosynthesis conditions only increased net photosynthesis rate in the presence of 1 millimolar DCDP from zero to about 5% of the maximal uninhibited rate. Therefore, it seems unlikely that direct fixation of atmospheric CO(2) by the bundle sheath cells makes any significant contribution to photosynthetic CO(2) assimilation in C(4) species. The results support the concept that C(4)-selective herbicides may be developed based on inhibitors of C(4) pathway reactions.}, } @article {pmid2647059, year = {1989}, author = {Van Regenmortel, MH}, title = {Applying the species concept to plant viruses.}, journal = {Archives of virology}, volume = {104}, number = {1-2}, pages = {1-17}, pmid = {2647059}, issn = {0304-8608}, mesh = {Phylogeny ; Plant Viruses/*classification ; Species Specificity ; }, abstract = {Plant virologists who maintain that the concept of species cannot be applied to viruses argue their case in terms of an obsolete concept of biological species defined by gene pools and reproductive isolation and applicable only to sexually reproducing organisms. In fact, various species concepts have been used by biologists and some of them are applicable to asexual organisms. The rationale for applying the species concept in virology is that viruses are biological entities and not chemicals: they possess genes, replicate, specialize, evolve and occupy specific ecological niches. The following definition is proposed: a virus species is a polythetic class of viruses constituting a replicating lineage and occupying a particular ecological niche. Such a definition of the species category does not and cannot provide a list of diagnostic properties for recognizing members of a particular virus species. It should also be stressed that a single property such as an arbitrary level of genome homology or the extent of serological relationship always fails to establish membership in a polythetic class. A binomial system of nomenclature is advocated in which the vernacular English name of the plant virus is adopted as the species name and the group name is assimilated to the level of genus. Adoption of this system would ensure that a universal classification system based on the classical categories of species, genus, and family becomes possible for all viruses.}, } @article {pmid2619506, year = {1989}, author = {Kuryłowicz, W and Gyllenberg, HG}, title = {Problems in taxonomy of streptomycetes.}, journal = {Archivum immunologiae et therapiae experimentalis}, volume = {37}, number = {1-2}, pages = {235-249}, pmid = {2619506}, issn = {0004-069X}, mesh = {Streptomyces/*classification ; }, abstract = {The bacterial species concept has different bearings. It is used to define "natural" entities with low intra-group variation, but also to serve more subjective purposes. One of problems in Streptomyces taxonomy is that it applies the species concept in both ways, i.e. both to clarify natural relationships and to protect potential (bio)technological inventions. The latter usage has introduced a streptomycetal "technospecies" which may require definition and description in other terms and by other tools than the "nomentaxospecies" which represent a more objective approach to Streptomyces taxonomy. Genetic engineering creates "man-made" microorganisms which are characterized by completely different sets of criteria as compared to their natural counterparts, which may imply needs for different taxonomies for both kinds of organisms. However, since they may occur side by side in one environment both "man-made" and "natural" streptomycetes have to be identified and classified by the same methods and tools, but in such a way which allows their separation.}, } @article {pmid2491624, year = {1989}, author = {Zhou, ZZ and Zheng, Y and Steenstra, R and Hickey, WF and Teuscher, C}, title = {Actively-induced experimental allergic orchitis (EAO) in Lewis/NCR rats: sequential histo- and immunopathologic analysis.}, journal = {Autoimmunity}, volume = {3}, number = {2}, pages = {125-134}, doi = {10.3109/08916938909019961}, pmid = {2491624}, issn = {0891-6934}, support = {HD-06274/HD/NICHD NIH HHS/United States ; HD-21100/HD/NICHD NIH HHS/United States ; HD-21926/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Autoimmune Diseases/etiology/*immunology/pathology ; Histocompatibility Antigens Class II/metabolism ; Immunohistochemistry ; Infertility, Male/etiology ; Male ; Orchitis/etiology/*immunology/pathology ; Rats ; Rats, Inbred Lew ; Time Factors ; }, abstract = {Active experimental allergic orchitis (EAO) was induced in Lewis/NCr rats by immunization with homologous rat testicular homogenate. Groups of animals were studied sequentially at five day intervals for histopathologic signs of disease. Inflammatory lesions were first observed in the ductus efferentes as early as 5 days following immunization. Immunohistochemical analysis of the testes, rete testis, ductus efferentes and caput, corpus and cauda epididymis of immunized rats on day five revealed that only the ductus efferentes exhibited a significant increase in the number of interstitial cells expressing Ia antigens (MRC OX-6) as well as CD4 (W3/25) positive helper/inducer T lymphocytes, CD8 (MRC OX-8) positive cytotoxic T lymphocytes and/or natural killer cells and macrophages (MRC OX-42). Increased staining for Ia antigens was also associated with both the vascular and ductal epithelial cells whereas cells within the lumen of the ducts were consistently negative for Ia antigen expression. In contrast, there was no detectable increase in the level of expression of rat MHC class I antigens (MRC OX-18) by any of the cells of the ductus efferentes. Similarly, there was no increase in the number of MAR 18.5 and/or MRC OX-12 positive B lymphocytes. By day 15, autoimmune epididymitis was observed in the cauda and corpus epididymis with the caput becoming involved by day 20. In the testes, the first histopathologic changes observed were scattered inflammatory infiltrates on day 15 and scattered foci of aspermatogenesis on day 20. Inflammatory lesions were first seen in the rete testis and the seminiferous tubules on day 25-30 with maximal involvement occurring on day 35-40. Early inflammatory lesions in the seminiferous tubules were characterized by peritubular and/or interstitial mixed cellular infiltrates. Later lesions included granuloma formation and necrosis. Autoimmune vasitis was not seen in any of the animals studied. Control rats immunized with rat liver homogenate plus adjuvants or adjuvants alone did not exhibit any of the histopathologic lesions described above. The observed results, when compared to those of previous studies examining the sequential histo- and immunopathology of active EAO in the guinea pig and mouse, support the concept that: 1) significant species specificity may exist with regard to regional differences in susceptibility to autoimmune attack within the male reproductive tract and 2) that such differences correlate with early maximal expression of Ia by cells within the male reproductive tract.}, } @article {pmid2466367, year = {1989}, author = {Yogev, D and Levisohn, S and Razin, S}, title = {Genetic and antigenic relatedness between Mycoplasma gallisepticum and Mycoplasma synoviae.}, journal = {Veterinary microbiology}, volume = {19}, number = {1}, pages = {75-84}, doi = {10.1016/0378-1135(89)90092-8}, pmid = {2466367}, issn = {0378-1135}, mesh = {Animals ; Antigens, Bacterial/analysis/*genetics ; Blotting, Southern ; Blotting, Western ; Cross Reactions ; DNA Probes ; DNA, Bacterial/*genetics ; Deoxyribonuclease EcoRI ; Epitopes/analysis/genetics ; Mycoplasma/*genetics/immunology ; Nucleic Acid Hybridization ; Poultry ; RNA, Ribosomal/genetics ; }, abstract = {The two avian pathogens Mycoplasma gallisepticum and Mycoplasma synoviae were found, by Southern blot hybridization of their digested DNAs, to share genomic nucleotide sequences additional to those of the highly conserved ribosomal RNA genes. The assumption that some of the shared sequences encode for antigens or epitopes common to both mycoplasmas was supported by Western immunoblot analysis of cell proteins of one mycoplasma with specific antiserum to the other mycoplasma. Interestingly, the band patterns of reactive antigens were different for some of the M. gallisepticum strains, supporting the concept that the species is genotypically variable. The results of the present study may explain the cross-reactivity of the two mycoplasmas noted previously in a variety of routine serological tests.}, } @article {pmid2853685, year = {1988}, author = {Tanaka, M and Grossniklaus, U and Herr, W and Hernandez, N}, title = {Activation of the U2 snRNA promoter by the octamer motif defines a new class of RNA polymerase II enhancer elements.}, journal = {Genes & development}, volume = {2}, number = {12B}, pages = {1764-1778}, doi = {10.1101/gad.2.12b.1764}, pmid = {2853685}, issn = {0890-9369}, support = {R01 GM38810-01/GM/NIGMS NIH HHS/United States ; }, mesh = {B-Lymphocytes ; DNA-Binding Proteins ; *Enhancer Elements, Genetic ; Fungal Proteins/genetics ; Globins/genetics ; HeLa Cells ; Humans ; Models, Genetic ; Plasmids ; *Promoter Regions, Genetic ; RNA Polymerase II/*genetics ; RNA, Small Nuclear/*genetics ; *Saccharomyces cerevisiae Proteins ; Simian virus 40/genetics ; Simplexvirus/genetics ; Transcription Factors/genetics ; Transfection ; Viral Proteins/genetics ; }, abstract = {The recent discovery that the activation domains of transcriptional activators (e.g., GAL4) from a number of species are interchangeable has led to the concept of a general mechanism for activation of RNA polymerase II genes. We have examined the different activities of the SV40 octamer motif ATGCAAAG in B cells and in HeLa cells in the context of either the beta-globin promoter, a TATA-box-containing mRNA promoter, or the U2 snRNA promoter, which contains a snRNA-specific proximal element. In the context of the beta-globin promoter, the octamer motif is a B-cell-specific enhancer element, whereas it is a ubiquitous enhancer element for the U2 snRNA promoter. The U2 promoter is unique in that it is not activated by enhancer elements that activate the beta-globin promoter, and a hybrid U2 promoter containing the upstream activating sequence UASG is not stimulated by a yeast GAL4 trans-activator. Together, these observations suggest that in the context of the U2 promoter, the octamer motif defines a new class of RNA polymerase II enhancer elements, which bind transcription factors that trans-activate gene expression by a different mechanism than the general mechanism mentioned above. These results are discussed in light of the possibility that the ubiquitous octamer binding protein Oct-1 and the B-cell-specific octamer binding protein Oct-2 are involved in the activation of the U2 and beta-globin promoters, respectively.}, } @article {pmid2849425, year = {1988}, author = {Marc, S and Leiber, D and Harbon, S}, title = {Fluoroaluminates mimic muscarinic- and oxytocin-receptor-mediated generation of inositol phosphates and contraction in the intact guinea-pig myometrium. Role for a pertussis/cholera-toxin-insensitive G protein.}, journal = {The Biochemical journal}, volume = {255}, number = {2}, pages = {705-713}, pmid = {2849425}, issn = {0264-6021}, mesh = {Adenylate Cyclase Toxin ; Aluminum/*pharmacology ; Aluminum Chloride ; *Aluminum Compounds ; Animals ; Atropine/pharmacology ; Carbachol/pharmacology ; Chlorides/pharmacology ; Cyclic AMP/metabolism ; Endometrium/drug effects ; Female ; Fluorides/*pharmacology ; GTP-Binding Proteins/metabolism ; Guinea Pigs ; Inositol Phosphates/*metabolism ; Myometrium/*metabolism ; Pertussis Toxin ; Receptors, Angiotensin/*metabolism ; Receptors, Muscarinic/*metabolism ; Receptors, Oxytocin ; Sodium Fluoride/pharmacology ; Sugar Phosphates/*metabolism ; Uterine Contraction/drug effects ; Virulence Factors, Bordetella/pharmacology ; }, abstract = {1. In the intact guinea-pig myometrium, carbachol and oxytocin stimulated a specific receptor-mediated phospholipase C activation, catalysing the breakdown of PtdIns(4,5)P2 with the sequential generation of InsP3, InsP2 and InsP. Stimulation of muscarinic receptors also triggered an inhibition of cyclic AMP accumulation caused by prostacyclin. 2. NaF plus AlCl3 mimicked the effects of carbachol and oxytocin by inducing, in a dose-dependent manner, the generation of all three inositol phosphates as well as uterine contractions. AlCl3 enhanced the fluoride effect, supporting the concept that A1F4- was the active species. Under similar conditions, fluoroaluminates activated the guanine nucleotide regulatory protein Gi, reproducing the inhibitory effect of carbachol on cyclic AMP concentrations. 3. Both carbachol- and oxytocin-mediated increases in inositol phosphates, as well as contractions, were insensitive to pertussis toxin, under conditions where the expression of Gi was totally prevented. Cholera toxin, which activates Gs and enhances cyclic AMP accumulation, failed to affect basal or oxytocin-evoked inositol phosphate generation, but induced a slight, though consistent, attenuation of the muscarinic inositol phosphate response, which was similarly evoked by forskolin. 4. The data provide evidence that, in the myometrium, (a) a G protein mediates the generation of inositol phosphates and the Ca2+-dependent contractile event, (b) the relevant G protein that most probably couples muscarinic and oxytocin receptors to phospholipase C is different from Gi and Gs, the proteins that couple receptors to adenylate cyclase, and (c) cyclic AMP does not seem to control the phosphoinositide cycle, but rather exerts a negative regulation at the muscarinic-receptor level.}, } @article {pmid2460241, year = {1988}, author = {Viebahn, C and Lane, EB and Ramaekers, FC}, title = {Keratin and vimentin expression in early organogenesis of the rabbit embryo.}, journal = {Cell and tissue research}, volume = {253}, number = {3}, pages = {553-562}, pmid = {2460241}, issn = {0302-766X}, mesh = {Animals ; Female ; Immunohistochemistry ; Keratins/*immunology/physiology ; Pregnancy ; Rabbits/*embryology ; Vimentin/*immunology/physiology ; }, abstract = {The expression of vimentin and keratins is analysed in the early postimplantation embryo of the rabbit at 11 days post conceptionem (d.p.c.) using a panel of monoclonal antibodies specific for single intermediate filament polypeptides (keratins 7, 8, 18, 19 and vimentin) and a "pan-epithelial" monoclonal keratin antibody. Electrophoretic separation of cytoskeletal preparations obtained from embryonic tissues, in combination with immunoblotting of the resulting polypeptide bands, demonstrates the presence of the rabbit equivalents of human keratins 8, 18, and vimentin in 11-day-old rabbit embryonic tissues. Immunohistochemical staining shows that several embryonic epithelia such as notochord, surface ectoderm, primitive intestinal tube, and mesonephric duct, express keratins, while others (neural tube, dermomyotome) express vimentin, and a third group (coelomic epithelia) can express both. Similarly, of the mesenchymal tissues sclerotomal mesenchyme expresses vimentin, while somatopleuric mesenchyme (abdominal wall) expresses keratins, and splanchnopleuric mesenchyme (dorsal mesentery) expresses both keratins and vimentin. While these results are in accordance with most results of keratin and vimentin expression in embryos of other species, they stand against the common concept of keratin and vimentin specificity in adult vertebrate tissues. Furthermore, keratin and vimentin are not expressed in accordance with germ layer origin of tissues in the mammalian embryo; rather the expression of these proteins seems to be related to cellular function during embryonic development.}, } @article {pmid3396001, year = {1988}, author = {Keizer, HG and van Rijn, J and Pinedo, HM and Joenje, H}, title = {Effect of endogenous glutathione, superoxide dismutases, catalase, and glutathione peroxidase on adriamycin tolerance of Chinese hamster ovary cells.}, journal = {Cancer research}, volume = {48}, number = {16}, pages = {4493-4497}, pmid = {3396001}, issn = {0008-5472}, mesh = {Animals ; Catalase/*physiology ; Cell Survival/drug effects ; Cells, Cultured ; Cricetinae ; Doxorubicin/*pharmacology ; Drug Resistance ; Glutathione/*physiology ; Glutathione Peroxidase/*physiology ; Superoxide Dismutase/*physiology ; }, abstract = {Based on the concept that activated oxygen species are causally involved in Adriamycin toxicity, endogenous antioxidant defenses are expected to be important determinants of cellular Adriamycin tolerance. We have tested this prediction by making use of an oxygen-resistant variant subline of Chinese hamster ovary cells (CHOr), which is characterized by increased levels of glutathione, copper- and zinc-containing superoxide dismutase, manganese-containing superoxide dismutase, catalase, and glutathione peroxidase. The levels of antioxidant defenses in wild-type CHO (CHOs) cells were within the range reported for human tumor cell lines, except for catalase, which was comparatively high. Oxygen-tolerant CHOr cells, which contained 4.3-fold more catalase activity than CHOs cells, were proportionally more resistant to H2O2, indicating that catalase activity in wild-type CHOs cells was still limiting H2O2 tolerance. The Adriamycin sensitivity of CHOs cells was compared to that of CHOr cells by clonogenic cell survival. After correcting for differential drug uptake in CHOs and CHOr cells, no significant difference in Adriamycin sensitivity could be detected. Furthermore, drug-induced cyanide-resistant oxygen consumption and electron spin resonance data indicated that both cell strains were equally efficient in reducing Adriamycin to its semiquinone radical and in generating activated oxygen species through oxidation-reduction cycling. These results indicate that Adriamycin tolerance of wild-type CHO cells, as determined by clonogenic cell survival, is not limited by endogenous glutathione, copper- and zinc-containing superoxide dismutase, manganese-containing superoxide dismutase, catalase, or glutathione peroxidase.}, } @article {pmid3419630, year = {1988}, author = {Stevens, BR and Fernandez, A and Sumners, C and Hearing, L}, title = {Neonatal rat brain astroglial dipeptidyl peptidase II activity regulation by cations and anions.}, journal = {Neuroscience letters}, volume = {89}, number = {3}, pages = {319-322}, doi = {10.1016/0304-3940(88)90546-0}, pmid = {3419630}, issn = {0304-3940}, support = {DK-38715/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn/anatomy & histology/*metabolism ; Anions/*pharmacology ; Astrocytes/*enzymology ; Brain/cytology/*enzymology ; Cations/*pharmacology ; Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/antagonists & inhibitors/*metabolism ; Osmolar Concentration ; Rats ; Rats, Inbred Strains ; Sulfur Oxides/pharmacology ; }, abstract = {Astrocytic glial cells from neonatal rat brains were grown in primary culture. Dipeptidyl peptidase II (DPP-II) enzyme activity was measured in cells disrupted by nonionic detergent. The rate of enzyme activity was measured in the presence of various ions, under isosmotic conditions adjusted using mannitol and NaCl. DPP-II activity was not affected by the candidate metal co-factors (2 mM) Co2+, Mg2+, and Mn2+, nor by the metal chelators EDTA and o-phenanthroline. However, selected cations (50 mM Cl- salts) significantly inhibited DPP-II activity compared to Na+ control; the relative inhibition ranking was Rb+ less than K+ less than Zn2+ less than Hg2+. Many test anions (50 mM Na+ salts) also inhibited DPP-II activity compared to Cl- control: SO4(2-) less than NO3- less than F- less than SO3(2-). Surprisingly, the anion S2O3(2-) was the only test agent which strongly stimulated activity. The data are consistent with the concept that specific ion species interact with the glial DPP-II enzyme to affect catalytic activity.}, } @article {pmid3410627, year = {1988}, author = {Lindstedt, SL and Wells, DJ and Jones, JH and Hoppeler, H and Thronson, HA}, title = {Limitations to aerobic performance in mammals: interaction of structure and demand.}, journal = {International journal of sports medicine}, volume = {9}, number = {3}, pages = {210-217}, doi = {10.1055/s-2007-1025008}, pmid = {3410627}, issn = {0172-4622}, mesh = {Animals ; Humans ; Mammals/anatomy & histology/*physiology ; Muscles/anatomy & histology/physiology ; *Oxygen Consumption ; Physical Exertion ; *Respiratory Physiological Phenomena ; Respiratory System/anatomy & histology ; }, abstract = {In this paper we have explored the linked series of structures that collectively comprise the respiratory system. In examining each of these structural resistors, some seem to be primarily fixed, for example, the trachea, while others must be primarily variable or adaptable, for example, the cardiovascular system. Those structures that are truly variable will not be maintained with structural capacity in excess of their functional demand. As a consequence, these structures are the ones that may most often appear to be limiting O2 uptake. However, we question under which in vivo circumstances the most plastic steps in the cascade of resistances will impart the single-step limitation to O2 uptake. When reviewed in this context, available experimental evidence suggests that among the most athletic animals (those with the greatest weight-specific VO2), the respiratory resistors are likely tuned rather than dominated by a single-step limitation. Skeletal muscle must set the demand for O2 in exercising animals; hence, the relationship between total skeletal muscle mitochondria and maximum O2 consumption is quantitatively consistent, spanning broad differences in body size and aerobic capacity. Those respiratory structures that are primarily nonadaptable must be built with enough "excess structure" to accommodate potential adaptation in an animal's aerobic capacity during its lifetime. Consequently, the least aerobic animals will always appear to experience a limitation to VO2max in one of the most plastic or adaptable structures. We suggest that the adaptable structures upstream to the muscle mitochondria are built and maintained at a cost-benefit maximum ("structural efficiency") in all species. This differs from the concept of optimal structural design or symmorphosis.}, } @article {pmid3049233, year = {1988}, author = {Vorontsov, NN}, title = {[Macromutation and evolution: the fixation of Goldschmidt's macromutations as species and genus traits. Hairlessness mutations in mammals].}, journal = {Genetika}, volume = {24}, number = {6}, pages = {1081-1088}, pmid = {3049233}, issn = {0016-6758}, mesh = {Animals ; Animals, Domestic ; Animals, Laboratory ; Animals, Wild ; *Biological Evolution ; *Hair ; Mammals/*genetics ; *Mutation ; Rats ; Species Specificity ; }, abstract = {A brief survey of the development of concepts on the role of macromutations in evolution is given. Contrary to Iu. A. Filipchenko (1926, 1927), who introduced the "micro- and macromutation" terms and believed that regularities of macroevolution could not be reduced to microevolutionary processes, the majority of "synthetists" explained any form of evolution by changes in allele frequencies. From the studies of Drosophila homoeotic mutants R. Goldschmidt (1940) developed the concept of "hopeful monsters" and their role in macroevolution. However, the homoeotic mutants are of drastically reduced viability, which allows the gradualists to reject Goldschmidt's ideas. The distribution of hairlessness mutations (hairless, nude etc.) with the monogenic pattern of inheritance in mammals was studied. Hairless mutants are known in Peromyscus, Mus musculus, Rattus rattus, R. norvegicus, Canis familiaris, Ovis aries. Hairlessness as norm is found in 53 among contemporaneous 1037 mammalian genera. Part of these cases (hairlessness in all Cetacea and Sirenia) may be explained in terms of both macromutations and obligatory gradualism. There is no doubt as to the macromutational origin of hairlessness in the bat Cheiromeles and the rodent Heterocephalus (Bathyergidae); the genera systematically and ecologically close to these have normal pelage. It is quite possible that hairlessness of walrus (Odobenus) has the same origin. The appearance and fixation of single Goldschmidt's macromutation cannot yet be considered as a macroevolutionary process, though the possibility of fixation of a macromutation in nature as a species and genus character contradicts strongly the concept of obligatory gradualism of evolution.}, } @article {pmid2466654, year = {1988}, author = {Kilias, H and Gelfi, C and Righetti, PG}, title = {Isoenzyme analysis of lichen algae in immobilized pH gradients.}, journal = {Electrophoresis}, volume = {9}, number = {4}, pages = {187-191}, doi = {10.1002/elps.1150090407}, pmid = {2466654}, issn = {0173-0835}, mesh = {Ampholyte Mixtures ; Chlorophyta/*analysis ; Hydrogen-Ion Concentration ; Isoelectric Focusing ; Isoenzymes/*analysis ; Lichens/*analysis ; Species Specificity ; Staining and Labeling ; }, abstract = {A base for a modern species' concept of chlorococcal algae can be obtained not by morphological analysis, but by biochemical characters, e.g. isoenzyme banding patterns. From isolated lichen algae of the genus Trebouxia de Puymaly a set of five such enzymes has been studied by isoelectric focusing in immobilized pH gradients (IPG): phosphoglucomutase, phosphoglucose isomerase, malate dehydrogenase, mannitol dehydrogenase and leucine aminopeptidase. The first four are resolved into isoforms in a pH 4-7 IPG interval, while the last one is analyzed in an IPG pH 3.5-5 span. The patterns are specific for distinct populations, inter- and intraspecifically varying in dependence from their geographical distribution or the lichen species from which they have been isolated. Their limited heterogeneity (one to four isoforms) suggests that they are the products of specific genes rather than artefacts of the extraction procedure or the IPG analysis. Sharp isozyme patterns can only be obtained in a mixed-bed, carrier-ampholyte (CA)-IPG gel and by anodic application, suggesting that the recently proposed mechanism of hydrophobic protein-IPG matrix interaction (Electrophoresis, 1987, 8, 62-70) is fully operative here. As an additional mechanism, it is proposed that, in some cases, CA might simply act, when added to an IPG gel, by buffering, in the transient state, the sample zone before the protein migrates from the liquid phase into the IPG matrix.}, } @article {pmid3193098, year = {1988}, author = {Baimai, V and Harbach, RE and Sukowati, S}, title = {Cytogenetic evidence for two species within the current concept of the malaria vector Anopheles leucosphyrus in Southeast Asia.}, journal = {Journal of the American Mosquito Control Association}, volume = {4}, number = {1}, pages = {44-50}, pmid = {3193098}, issn = {8756-971X}, mesh = {Animals ; Anopheles/*genetics/microbiology ; Asia, Southeastern ; Chromosomes ; Female ; Hybridization, Genetic ; Insect Vectors/*microbiology ; Karyotyping ; Malaria/*transmission ; Male ; }, abstract = {Karyotypes and crossing relationships were investigated for three allopatric populations of Anopheles leucosphyrus in Southeast Asia: South Kalimantan, Sumatra and Thailand. The mitotic karyotypes of these populations were similar to those previously observed in other species of the An. leucosphyrus group. Populations from Thailand and South Kalimantan exhibited telocentric and subtelocentric sex chromosomes, respectively, with a distinctive band of intercalary heterochromatin in the X chromosome. Strikingly different submetacentric X and Y chromosomes were observed in the population from Sumatra, and it seems likely that the evolution of these chromosomes occurred through the acquisition of constitutive heterochromatin. Sterile F1 males were observed in crosses between the Sumatra population and the populations from South Kalimantan and Thailand. No genetic incompatibility was observed in crosses between the latter two populations. We believe that the present concept of An. leucosphyrus includes two allopatric species, one inhabiting Borneo, West Malaysia and southern Thailand and one confined to Sumatra.}, } @article {pmid3364886, year = {1988}, author = {McNeill, TH and Koek, LL and Brown, SA and Rafols, JA}, title = {Age-related changes in the nigrostriatal system.}, journal = {Annals of the New York Academy of Sciences}, volume = {515}, number = {}, pages = {239-248}, doi = {10.1111/j.1749-6632.1988.tb32992.x}, pmid = {3364886}, issn = {0077-8923}, support = {AG00300/AG/NIA NIH HHS/United States ; AG03254/AG/NIA NIH HHS/United States ; AG05445/AG/NIA NIH HHS/United States ; }, mesh = {Aging/*physiology ; Animals ; Corpus Striatum/cytology/*physiology/ultrastructure ; Dendrites/ultrastructure ; Neurons/classification/ultrastructure ; Substantia Nigra/*physiology ; }, abstract = {These data support the view that the rate at which an organism ages is a summation of factors throughout life. While some cells seem to remain stable or even grow with age, others show significant regression. In this regard, different populations of striatal neurons show unique and different patterns of growth and development with advancing age. While aspiny II neurons show peak growth by 10 months of age, aspiny I and medium spiny I cells do not reach a growth peak until much later in life. In addition, our data support the notion that the occurrence and severity of structural changes in the aged brain are not distributed homogeneously and that many of the so-called "age-related" changes that were once generalized to the entire brain are brain-region, cell-type, and species specific. Furthermore, our data reinforces the concept that the correlation of structure and function is central to the analysis of an aging population because considerable differences may be found in data based on functionally impaired and unimpaired groups.}, } @article {pmid3269168, year = {1988}, author = {Pringle, KC}, title = {A reassessment of pregnancy staging.}, journal = {Fetal therapy}, volume = {3}, number = {3}, pages = {173-184}, doi = {10.1159/000263352}, pmid = {3269168}, issn = {0257-2788}, mesh = {*Embryonic and Fetal Development ; Female ; Humans ; Pregnancy/*physiology ; }, abstract = {A system of staging pregnancy that is directly related to normal development is proposed to replace the currently used 'trimester' system. If accepted, this concept of staging could be applied across species without the likelihood of a grossly incorrect assessment of the stage of development. In contrast to this, the division of a pregnancy into trimesters is based upon an accident of mathematics and bears no relationship to human development. The proposal is to divide pregnancy into three stages, termed 'horizons'. First is the 'embryonic horizon' from fertilisation until the end of the 8th week from fertilisation, i.e., 10 weeks from the first day of the last menstrual period (LMP). The 'early fetal horizon' extends from the end of the embryonic phase to the 25th week of gestation (i.e., 25 weeks from the first day of the LMP). This horizon is divided into the 'primitive phase' (up to the 15th week of gestation) and the 'transitional phase' (from the 15th to the 25th week of gestation). The 'late fetal horizon' extends from 25 weeks to beyond term and is divided into the 'premature phase' (from 25 weeks to 36 weeks of gestation), the 'mature phase' (36 weeks to term) and the 'post-mature phase' which extends from term to about 45 weeks of gestation. The importance of this phase is the fact that perinatal morbidity and mortality is proportional to the length of time the gestation continues beyond maturity. It must be stressed that the terms 'horizon' and 'phase' are intentionally imprecise. This is to emphasise that human development is a continuum and not a series of steps.}, } @article {pmid3143688, year = {1988}, author = {Milne, RG}, title = {Species concept should not be universally applied to virus taxonomy--but what to do instead?.}, journal = {Intervirology}, volume = {29}, number = {5}, pages = {254-259}, doi = {10.1159/000150053}, pmid = {3143688}, issn = {0300-5526}, mesh = {Plant Viruses/*classification ; Recombination, Genetic ; Viruses/*classification/genetics ; }, } @article {pmid3305361, year = {1987}, author = {Whipp, SC}, title = {Protease degradation of Escherichia coli heat-stable, mouse-negative, pig-positive enterotoxin.}, journal = {Infection and immunity}, volume = {55}, number = {9}, pages = {2057-2060}, pmid = {3305361}, issn = {0019-9567}, mesh = {Animals ; Bacterial Toxins/*metabolism ; Enterotoxins/*metabolism ; Escherichia coli/*pathogenicity ; Escherichia coli Proteins ; Intestines/microbiology/physiology ; Peptide Hydrolases/*metabolism ; Swine ; Trypsin Inhibitors/pharmacology ; Water-Electrolyte Balance ; }, abstract = {Enterotoxigenic Escherichia coli produces three enterotoxins: heat-labile toxin, a mouse-positive heat-stable toxin, and a mouse-negative heat-stable toxin (STb). The only species in which a response to STb has been documented is the pig, and this response is inconsistent. When STb was placed in 60 ligated jejunal segments (loops) in six pigs, a positive response (net secretion) was observed in only 40 loops. In contrast, when the jejunal lumen was pre-rinsed with 50 ml of saline, the same STb preparation induced net secretion in 60 of 60 loops. STb did not induce secretion in rinsed loops when jejunal luminal washings were collected and mixed with STb in vitro. The anti-STb activity of jejunal luminal washings was filterable through 0.45-micron-pore-size filters, was destroyed by heating at 100 degrees C for 15 min, and was blocked by soybean trypsin inhibitor. STb was inactivated when incubated with trypsin in vitro for 60 min at 37 degrees C. It is concluded that STb is susceptible to trypsin degradation and that variable amounts of trypsin-like activity in swine jejuna are responsible for inconsistent responses to STb in jejunal loops of swine. These results also suggest that the concept of species specificity of the STb response should be reexamined.}, } @article {pmid3039849, year = {1987}, author = {Keller, R and Silbert, JE and Furthmayr, H and Madri, JA}, title = {Aortic endothelial cell proteoheparan sulfate. I. Isolation and characterization of plasmamembrane-associated and extracellular species.}, journal = {The American journal of pathology}, volume = {128}, number = {2}, pages = {286-298}, pmid = {3039849}, issn = {0002-9440}, support = {AM-30556/AM/NIADDK NIH HHS/United States ; AM-30601/AM/NIADDK NIH HHS/United States ; HL-28373/HL/NHLBI NIH HHS/United States ; }, mesh = {5'-Nucleotidase ; Amino Acids/analysis ; Animals ; Aorta/analysis ; Cattle ; Cell Membrane/analysis ; Cells, Cultured ; Chondroitin Sulfate Proteoglycans/analysis/biosynthesis/*isolation & purification ; Chromatography, Ion Exchange ; Endothelium/*analysis ; Extracellular Matrix/*analysis ; Glycosaminoglycans/*isolation & purification ; Heparan Sulfate Proteoglycans ; Heparitin Sulfate/analysis/biosynthesis/*isolation & purification ; Molecular Weight ; Nucleotidases/analysis ; Proteoglycans/*isolation & purification ; }, abstract = {Proteoheparan sulfate biosynthesis was studied in cultured bovine aortic endothelial cells by means of pulse and pulse-chase experiments and subcellular fractionations. Three proteoheparan sulfate species were found in the medium. The major species, which the authors have called HS I, appeared in the medium only after an initial lag period and was also found associated with the plasma membrane. The other two (HS II and HS III) appeared in small amounts in the medium at early time points. At later times these were not readily observed because the large amounts of HS I present in the medium. The major medium species, HS I, appeared to be composed of approximately four heparan sulfate chains of approximately 35,000 daltons and a core protein of approximately 55,000 daltons apparent molecular weight. HS I appeared to be homogeneous by gel filtration on Sepharose CL 2B and 6B and elution from DEAE Sephacel, electrophoresis on Nu-Sieve agarose, and CsCl density centrifugation. After digestion with heparinase the core protein appeared to be homogeneous by S-200 Sephacel chromatography. HS I was also found associated with plasma membrane fractions of the cultured bovine aortic endothelial cells, and antisera raised against it stained epithelial and endothelial cells in patterns consistent with a cell surface localization. Of the other two species found in the medium, one (HS II) also appeared to be a component of the cell layer. This species appeared to contain approximately four heparan sulfate chains of approximately 20,000 daltons apparent molecular weight. Antisera raised against a similar molecule produced by HR 9 cell cultures stained basement membranes intensely, supporting the subcellular matrix localization of this molecule. The third species (HS III) was detected in culture medium only and apparently contained two heparan sulfate chains of approximately 20,000 daltons apparent molecular weight. These results support the concept of multiple endothelial cell proteoheparan sulfate species which exhibit differences in structure and localization and possibly diverse specialized functions.}, } @article {pmid3660945, year = {1987}, author = {Kuznetsov, VD}, title = {[Parallelism in the hereditary variability and population concept of species in representative prokaryotes].}, journal = {Zhurnal obshchei biologii}, volume = {48}, number = {4}, pages = {466-476}, pmid = {3660945}, issn = {0044-4596}, mesh = {Actinomycetales/classification/*genetics/metabolism ; DNA, Bacterial/genetics ; *Genetic Variation ; Mutation ; Nucleic Acid Hybridization ; Selection, Genetic ; }, } @article {pmid3105590, year = {1987}, author = {Swendsen, CL and Chilton, FH and O'Flaherty, JT and Surles, JR and Piantadosi, C and Waite, M and Wykle, RL}, title = {Human neutrophils incorporate arachidonic acid and saturated fatty acids into separate molecular species of phospholipids.}, journal = {Biochimica et biophysica acta}, volume = {919}, number = {1}, pages = {79-89}, doi = {10.1016/0005-2760(87)90220-7}, pmid = {3105590}, issn = {0006-3002}, support = {AI-17287/AI/NIAID NIH HHS/United States ; HL-26818/HL/NHLBI NIH HHS/United States ; HL-27799/HL/NHLBI NIH HHS/United States ; }, mesh = {Arachidonic Acid ; Arachidonic Acids/*blood ; Carbon Radioisotopes ; Humans ; Neutrophils/*metabolism ; Palmitic Acid ; Palmitic Acids/*blood ; Phospholipids/biosynthesis/*blood ; Stearic Acids/*blood ; Tritium ; }, abstract = {The incorporation of radiolabeled arachidonic acid and saturated fatty acids into choline-linked phosphoglycerides (PC) of rabbit and human neutrophils was investigated by resolving the individual molecular species by reversed-phase high performance liquid chromatography. PC from neutrophils incubated with a mixture of [3H]arachidonic acid and [14C]stearic or [14C]palmitic acid contains both radiolabels; however, double labeling of individual molecular species is minimal. After labeling for 2 h, the [3H]arachidonate is distributed almost equally between diacyl and 1-O-alkyl-2-acyl species, but it is incorporated into diacyl species containing unlabeled stearate or palmitate at the sn-1 position. In contrast, labeled saturated fatty acids are incorporated only into diacyl species and contain predominantly oleate and linoleate at the sn-2 position. Labeled linoleate is not incorporated into ether-linked species, but is found in the same species as labeled stearate. The findings suggest that mechanisms exist in neutrophils for specific shunting of exogenous arachidonic acid into certain phospholipid molecular species and support the concept that the 1-O-alkyl-2-arachidonoyl species may be a functionally segregated pool of arachidonic acid within the PC of neutrophils.}, } @article {pmid3036062, year = {1987}, author = {Cockcroft, S and Taylor, JA}, title = {Fluoroaluminates mimic guanosine 5'-[gamma-thio]triphosphate in activating the polyphosphoinositide phosphodiesterase of hepatocyte membranes. Role for the guanine nucleotide regulatory protein Gp in signal transduction.}, journal = {The Biochemical journal}, volume = {241}, number = {2}, pages = {409-414}, pmid = {3036062}, issn = {0264-6021}, mesh = {Aluminum/*pharmacology ; Aluminum Chloride ; *Aluminum Compounds ; Animals ; Cell Membrane/drug effects/enzymology ; Chlorides/*pharmacology ; Enzyme Activation/drug effects ; GTP-Binding Proteins/*metabolism ; Guanosine 5'-O-(3-Thiotriphosphate) ; Guanosine Triphosphate/analogs & derivatives/pharmacology ; In Vitro Techniques ; Liver/drug effects/*enzymology ; Phosphoinositide Phospholipase C ; Phosphoric Diester Hydrolases/*metabolism ; Rats ; Sodium Fluoride/*pharmacology ; Thionucleotides/pharmacology ; }, abstract = {Fluoride and guanosine 5'-[gamma-thio]triphosphate (GTP gamma S) both activate the hepatocyte membrane polyphosphoinositide phosphodiesterase (PPI-pde) in a concentration-dependent manner. AlCl3 enhances the fluoride effect, supporting the concept that [A1F4]- is the active species. Analysis of the products of inositol lipid hydrolysis demonstrate that phosphatidylinositol bisphosphate is the major lipid to be hydrolysed. Guanosine 5'-[beta-thio]diphosphate (GDP beta S) is an inhibitor of activation of PPI-pde by both fluoride and GTP gamma S. These observations suggest that the guanine nucleotide regulatory protein (termed Gp) bears a structural resemblance to the well-characterized G-proteins of the adenylate cyclase system and the cyclic GMP phosphodiesterase system in phototransduction.}, } @article {pmid17778636, year = {1987}, author = {Phelan, PL and Baker, TC}, title = {Evolution of male pheromones in moths: reproductive isolation through sexual selection?.}, journal = {Science (New York, N.Y.)}, volume = {235}, number = {4785}, pages = {205-207}, doi = {10.1126/science.235.4785.205}, pmid = {17778636}, issn = {0036-8075}, abstract = {Central to our understanding of the species concept is knowledge of the nature and evolution of reproductive isolating mechanisms. The once widely accepted model of Dobzhansky, which holds that isolation evolves through selection against hybrids of differentially adapted populations, is now largely rejected. This rejection is due to both theoretical difficulties and a paucity of examples of the predicted pattern of reproductive character displacement. From a survey of five families of Lepidoptera, entailing more than 800 species, evidence is given that male courtship pheromones have evolved within the context of sexual isolation as an adaptive response to mating mistakes between differentially adapted populations; however, distinct from the natural selection model of Dobzhansky, this report suggests the mechanism for change to be sexual selection.}, } @article {pmid3324304, year = {1987}, author = {Midtvedt, T}, title = {Intestinal bacteria and rheumatic disease.}, journal = {Scandinavian journal of rheumatology. Supplement}, volume = {64}, number = {}, pages = {49-54}, doi = {10.3109/03009748709096721}, pmid = {3324304}, issn = {0301-3847}, mesh = {Animals ; Arthritis, Experimental/etiology ; Arthritis, Rheumatoid/*etiology ; *Bacterial Infections ; Germ-Free Life ; Humans ; Intestines/*microbiology ; Phagocytosis ; Rats ; Synovial Membrane/physiology ; }, abstract = {The striking clinical and pathological similarities between certain naturally occurring infectious diseases in animal species and those of some human rheumatic diseases, such as rheumatoid arthritis (RA), have stimulated the search for a microbial etiology of the latter syndrome. A long series of microbial species, including aerobic and anaerobic intestinal bacteria, mycoplasma and several viruses have been put into focus. Most often, however, an initially positive report has been followed by several reports denying an etiological role of the microbial species in focus. However, the concept of a microbial trigger in the etiology and symptomatology of RA is still a subject of intense debate. Recent results have indicated a reversed effect of gram-positive vs. gram-negative intestinal bacteria on adjuvant-induced arthritis in germfree rats and microbial peptidoglycans have been shown to play a major role in this experimental model. It has been shown that the intestinal flora may include bacteria containing antigenic determinant(s) cross-reacting with some markers within the HLA-system. The intestinal flora may also influence upon several digestive and absorptive functions and thereby acting upon parameters of importance in the development of rheumatic disease.}, } @article {pmid3113991, year = {1987}, author = {Arking, R}, title = {Successful selection for increased longevity in Drosophila: analysis of the survival data and presentation of a hypothesis on the genetic regulation of longevity.}, journal = {Experimental gerontology}, volume = {22}, number = {3}, pages = {199-220}, doi = {10.1016/0531-5565(87)90040-4}, pmid = {3113991}, issn = {0531-5565}, support = {AG 01812/AG/NIA NIH HHS/United States ; }, mesh = {Aging/*genetics/physiology ; Animals ; Drosophila melanogaster/*genetics/physiology ; Female ; *Longevity ; Models, Biological ; Reproduction ; Selection, Genetic ; }, abstract = {Long lived strains of Drosophila melanogaster have been generated via 25 generations of artificial selection. The mean and the maximum lifespans have been increased both absolutely as well as relative to the controls. The mean lifespan of the selected line now exceeds the maximum lifespan of the controls. The data shows that this increase is entirely accounted for by a genetically based delay in the onset of senescence. Identification and analysis of biomarker data involving reproductive functions supports this interpretation and leads to a suggestion of the processes involved in the lifespan extension. This increase in the duration of the pre-senescent period is under both genetic and environmental control. Senescence itself is not under genetic control and appears to occur stochastically. Selection for decreased longevity was unsuccessful, supporting the concept of a minimum species specific lifespan. A testable hypothesis regarding the biphasic mode of gene regulation of senescence is presented in which a gene-environment interaction takes place in larval life that results in a temporal reprogramming of other, presumably structural, genes which act in adult life at a time prior to the onset of senescence.}, } @article {pmid17816502, year = {1986}, author = {Lewin, R}, title = {Recognizing Ancestors Is a Species Problem: An anthropologist argues that the number of hominid species in the fossil record has probably been underestimated.}, journal = {Science (New York, N.Y.)}, volume = {234}, number = {4783}, pages = {1500}, doi = {10.1126/science.234.4783.1500}, pmid = {17816502}, issn = {0036-8075}, } @article {pmid15462747, year = {1986}, author = {Williams, RB}, title = {Hapantotypes: a possible solution to some problems of parasite nomenclature.}, journal = {Parasitology today (Personal ed.)}, volume = {2}, number = {11}, pages = {314-316}, doi = {10.1016/0169-4758(86)90128-6}, pmid = {15462747}, issn = {0169-4758}, abstract = {Parasites usually have several morphologically distinct stages in their life cycles. Some infect different host species at different stages of their development, and many are distinguished partly by the lesions caused in their hosts. Molecular techniques, seeking to clarify host-parasite relationships, often attempt definition o f species or subspecies in terms of enzyme profiles, DNA 'finger-prints', or other subcellulor characteristics. So, under the International Code of Zoological Nomenclature, what carries the species name? Which 'specimen' represents the unique name-bearing reference for a specific name? The problem is particularly daunting for parasitologists. In this article, Ray Williams discusses the idea that instead of a single 'type specimen', a suite of specimens - the hapontotype - representing several stages in the life cycle of a species would be a more useful concept.}, } @article {pmid2953127, year = {1986}, author = {Wolburg, H and Neuhaus, J and Mack, A}, title = {The glio-axonal interaction and the problem of regeneration of axons in the central nervous system--concept and perspectives.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {41}, number = {11-12}, pages = {1147-1155}, pmid = {2953127}, issn = {0939-5075}, mesh = {Animals ; Astrocytes/*physiology/ultrastructure ; Axons/*physiology/ultrastructure ; Brain/*physiology/ultrastructure ; *Nerve Regeneration ; Neuroglia/*physiology/ultrastructure ; Spinal Cord/*physiology ; }, abstract = {Lesion of the central nervous system in man is generally believed to be incurable. However, in the last time evidence accumulated that axonal growth occurs after a lesion if the growing neurites encounter a permissive environment. Since astrocytes play a considerable role as environmental factor in the CNS, the astrocytes from regenerative as well as from non-regenerative species were compared. The concept proposed here postulates that interactions between astrocytes and axons are of basic significance for fiber regeneration and have changed qualitatively during phylogeny: in lower vertebrates astrocytes guide growing and regenerating axons; in higher vertebrates including man the glioaxonal interactions were possibly deteriorated by the appearance of new compounds in the astrocytic membrane.}, } @article {pmid2444635, year = {1986}, author = {Rowat, JS and Squier, CA}, title = {Rates of epithelial cell proliferation in the oral mucosa and skin of the tamarin monkey (Saguinus fuscicollis).}, journal = {Journal of dental research}, volume = {65}, number = {11}, pages = {1326-1331}, doi = {10.1177/00220345860650110901}, pmid = {2444635}, issn = {0022-0345}, support = {BRS 6 2 SO7 RR05313/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Cell Division ; Epithelial Cells ; Female ; Keratins ; Male ; Metaphase ; Mitosis ; Mouth Mucosa/*cytology ; Saguinus ; Skin/*cytology ; Time Factors ; }, abstract = {Epithelial cell proliferation was determined in skin and various regions of the oral cavity of the tamarin monkey and was expressed by means of two mitotic indices: the number of metaphases per mm of epithelial surface, and the number of metaphases per mm basement membrane. A significant correlation was obtained between the rank ordering of the different regions according to each index. Generally, the non-keratinized tissues of the oral cavity had mitotic rates higher than those of the keratinized oral regions, with the epidermis having the lowest value. The mitotic index also correlated significantly with epithelial thickness, with the thicker regions showing a higher rate of proliferation. These results represent the first comprehensive set of values for a primate and are in general agreement with data obtained from non-primate species; the values support the concept that the oral lining tissue turns over more rapidly than does the masticatory mucosa (Bhaskar, 1980).}, } @article {pmid3641023, year = {1986}, author = {Sarkin, TL}, title = {The origin and evolution of vertebrate pattern and form--a theory of vertebrate development by preformation based on the genetic molecular shape.}, journal = {Medical hypotheses}, volume = {21}, number = {1}, pages = {1-41}, doi = {10.1016/0306-9877(86)90061-7}, pmid = {3641023}, issn = {0306-9877}, mesh = {Animals ; *Biological Evolution ; DNA/*genetics ; DNA, Superhelical/genetics ; Extremities/embryology ; Models, Anatomic ; *Models, Biological ; Models, Genetic ; Nucleic Acid Conformation ; Thorax/embryology ; Vertebrates/*embryology/genetics ; }, abstract = {A new hypothesis is presented to explain the origin of vertebrate form and the guiding mechanism by which embryological development occurs. The hypothesis is based on the observation which is demonstrated, that both vertebrate form and embryological development follow a pattern which correlates with the shapes formed by a spiral as it unfolds. The fact that the DNA molecule which carries the genetic information for embryological development, also has a helical structure, has suggested the hypothesis, that vertebrate form and its development are related to the molecular shape of the genetic material. A theoretical vertebrate genetic molecular structure is proposed and it is demonstrated how this structure by "unfolding", as growth occurs, (the mechanism for which is suggested) provides an accurate prepattern and a template for vertebrate embryological development and vertebrate form. Evolutionary implications follow, which question the Neo-Darwinian synthesis. These are firstly, that the vertebrate pattern is not the result of random genetic variations and natural selection, but owes its origin to a spiral pattern, possibly that of DNA. Secondly, that progressive changes occurring in the shape of the genetic molecule provide an explanation and a mechanism for the evolution of species; a concept which is demonstrated.}, } @article {pmid3736033, year = {1986}, author = {Weinstein, ES and Benson, DW and Fry, DE}, title = {Subpopulations of human heart mitochondria.}, journal = {The Journal of surgical research}, volume = {40}, number = {5}, pages = {495-498}, doi = {10.1016/0022-4804(86)90221-0}, pmid = {3736033}, issn = {0022-4804}, mesh = {Adenosine Diphosphate/metabolism ; Aged ; Female ; Glutamates/metabolism ; Humans ; Male ; Middle Aged ; Mitochondria, Heart/*classification/metabolism ; Oxygen Consumption ; Papillary Muscles/ultrastructure ; Polarography ; Proteins/metabolism ; Succinates/metabolism ; }, abstract = {Anatomically and biochemically distinct populations of cardiac mitochondria have been isolated from a number of animal species. The physiologic differences between subsarcolemmal (SS) and interfibrillar (IF) mitochondria, coupled with their different location within the cytomatrix, have led to speculation about possible specificities of function within the myocardial cell. To date, these two mitochondrial subpopulations have not been demonstrated in human cardiac tissue. Subsarcolemmal and interfibrillar cardiac mitochondria were isolated from papillary muscle removed from five patients undergoing mitral valve replacement surgery. Mitochondrial respiratory activity was determined polarographically. IF mitochondria had significantly higher state 3 (ADP-dependent) rates of respiration then SS mitochondria (116.7 +/- 7.1 versus 86.5 +/- 8.3 ng atoms or oxygen per minute per milligram mitochondrial protein; P less than 0.05 [mean +/- SE]). These data agree with similar studies performed in other animal species and support the concept of distinct subpopulations of mitochondria within the human myocardial cell.}, } @article {pmid3957805, year = {1986}, author = {Huston, JE and Rector, BS and Ellis, WC and Allen, ML}, title = {Dynamics of digestion in cattle, sheep, goats and deer.}, journal = {Journal of animal science}, volume = {62}, number = {1}, pages = {208-215}, doi = {10.2527/jas1986.621208x}, pmid = {3957805}, issn = {0021-8812}, mesh = {Animal Feed ; Animals ; Cattle/*physiology ; Deer/*physiology ; Digestion ; Goats/*physiology ; Sheep/*physiology ; Species Specificity ; Stomach, Ruminant/physiology ; }, abstract = {Four experiments were conducted to study factors affecting digestibility of forages in cattle, sheep, goats and white-tailed deer. In a series of digestion trials (Exp. 1), the dry matter digestibility of a moderately high fiber diet was greater in cattle than in deer. Digestibilities of the diet in sheep and goats were intermediate and not different from either extreme. In a second series of trials (Exp. 2), relative organic matter digestibilities were for goats more than sheep more than deer. However, in Exp. 2, intake in goats was very low and digestibility appeared to be positively related to retention time and inversely related to turnover rate. Results of three trials (Exp. 3) suggested that rate of digestion was related more to diet than to the animal species consuming the diet. In grazing animals (Exp. 4), goats digested a smaller percentage of consumed material than either cows or sheep during three of four seasons even though diets were of similar in vitro digestibility. This difference was related to a faster turnover and shorter retention time in goats. These data support the concept that there are species differences in gastrointestinal dynamics which may be which may be important determinants of adaptability to grazing conditions.}, } @article {pmid3942502, year = {1986}, author = {Rotstein, OD and Pruett, TL and Sorenson, JJ and Fiegel, VD and Nelson, RD and Simmons, RL}, title = {A Bacteroides by-product inhibits human polymorphonuclear leukocyte function.}, journal = {Archives of surgery (Chicago, Ill. : 1960)}, volume = {121}, number = {1}, pages = {82-88}, doi = {10.1001/archsurg.1986.01400010096012}, pmid = {3942502}, issn = {0004-0010}, support = {AI 14302/AI/NIAID NIH HHS/United States ; AI 21475/AI/NIAID NIH HHS/United States ; }, mesh = {Bacterial Toxins/biosynthesis/*pharmacology ; Bacteroides/growth & development/*metabolism ; Bacteroides fragilis/growth & development ; Cell Movement/drug effects ; Chemotaxis, Leukocyte/*drug effects ; Culture Media/pharmacology ; Exotoxins/*pharmacology ; Humans ; Hydrogen-Ion Concentration ; Neutrophils/*physiology ; }, abstract = {We have previously demonstrated that Bacteroides fragilis enhanced Escherichia coli-induced lethality in the rat fibrin-clot peritonitis model. As a possible mechanism for this phenomenon, it was hypothesized that B fragilis inhibited host defense mechanisms, allowing the E coli to flourish and kill the animal. Culture filtrates of three Bacteroides species were tested in vitro for their effect on human polymorphonuclear leukocyte (PMN) chemotaxis and random migration. Two of these, B fragilis and Bacteroides distasonis, impaired PMN migration. The other, Bacteroides thetaiotaomicron, caused variable inhibition of neutrophil chemotaxis. The ability of the culture filtrates to inhibit neutrophil function appeared to depend on two factors: (1) adequate growth of the Bacteroides culture, permitting production of the leukotoxic factor, and (2) reduction of the culture pH to a level at which the putative toxin could exert its effect. Further studies revealed that the factor was heat stable, had a molecular weight less than 500, and that its effect on PMNs was only partially reversed by multiple washings. This supports the concept that Bacteroides species may contribute to the pathogenicity of mixed infections by producing a factor that inhibits host neutrophil function.}, } @article {pmid4094459, year = {1985}, author = {Bernstein, H and Byerly, HC and Hopf, FA and Michod, RE}, title = {Sex and the emergence of species.}, journal = {Journal of theoretical biology}, volume = {117}, number = {4}, pages = {665-690}, doi = {10.1016/s0022-5193(85)80246-0}, pmid = {4094459}, issn = {0022-5193}, support = {1 K04 HD00583/HD/NICHD NIH HHS/United States ; GM27219/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; Female ; Male ; Reproduction ; *Sex ; Sexual Behavior, Animal ; }, abstract = {We argue that the existence of species as distinct and relatively homogeneous groupings of individuals is a consequence of the nonlinear dynamics inherent in sexual reproduction. This approach provides an answer to two interrelated problems which Darwin posed and tried to solve. Why are there missing links (i.e. gaps) between species in habitat space, and why are there missing links between species in time as evidenced in the fossil record? A crucial difference between outcrossing sexual organisms (i.e. organisms in which mating is between different individuals) and obligate selfers or parthenogens lies in the dynamic of the underlying replication process. Replication is a linear function of density for obligate selfers or parthenogens but nonlinear for outcrossing sexuals. The non-linearity stems from the simple fact that with outcrossing, two individuals must come together to mate. We argue that this fact leads to density dependent fitness (per capita rate of increase) with an intrinsic disadvantage of low population density. This cost of rarity results in a distribution of distinct species. By establishing the causal connections in evolution between outcrossing sex and the very existence of species as distinct collections of organisms, our account lends theoretical support to a unitary concept of species with interbreeding as the fundamental defining property.}, } @article {pmid3004048, year = {1985}, author = {Edberg, SC}, title = {Principles of nucleic acid hybridization and comparison with monoclonal antibody technology for the diagnosis of infectious diseases.}, journal = {The Yale journal of biology and medicine}, volume = {58}, number = {5}, pages = {425-442}, pmid = {3004048}, issn = {0044-0086}, mesh = {Antibodies, Monoclonal ; Bacteria/genetics ; Bacterial Infections/*diagnosis/microbiology ; Clinical Laboratory Techniques ; Cloning, Molecular ; DNA Restriction Enzymes ; Humans ; Nucleic Acid Hybridization ; Plasmids ; Species Specificity ; Virus Diseases/*diagnosis ; Viruses/genetics ; }, abstract = {Until the 1980s the diagnosis of specific etiologic agents of infectious diseases rested with their isolation in vitro and identification by analysis of their phenotypic characteristics. In the 1970s the concept of a microbial species evolved from phenotypic analysis to nucleic acid homology. Currently, nucleic acid sequences specific for a given species are being isolated and amplified and utilized not only to identify the pathogen after it has been grown in vitro but also elucidate it directly in biological material. The procedures for making nucleic acid hybridization probes are analogous to the generation of monoclonal antibody tests. Currently, research and development are centered in choosing the particular nucleic acid to analyze, establishing the most efficient vector system for amplifying the nucleic acid, generating an efficient means of selecting the particular nucleic acid fragment specific for the microorganism, and in measuring the hybridization reaction. While immunological techniques have been utilized in the clinical laboratory for over thirty years, the means of detecting nucleic acid hybridization reactions are just beginning to be usable in the clinical diagnostic laboratory. Much of nucleic acid hybridization research is proprietary, and a particular challenge is to develop a means whereby information can be used for the progress of science as a whole when generated by private ownership.}, } @article {pmid3940013, year = {1985}, author = {Murant, AF}, title = {Taxonomy and nomenclature of viruses.}, journal = {Microbiological sciences}, volume = {2}, number = {7}, pages = {218-220}, pmid = {3940013}, issn = {0265-1351}, mesh = {Plant Viruses/*classification/genetics ; Terminology as Topic ; }, abstract = {In his article The species concept in plant virology Milne1 describes the CMI/AAB Descriptions of Plant Viruses2 as providing the 'creeping barrage' (for the 'anti-species' views of many plant virologists and others) in the seemingly unending trench warfare over virus taxonomy and nomenclature. As an editor since 1970 (with BD Harrison) of this continuing series, I am moved to fire a few additional shots in support of Milne's thesis.}, } @article {pmid4018074, year = {1985}, author = {Yajko, DM and Hadley, WK}, title = {Support of the single species concept for Streptococcus milleri by DNA hybridization data.}, journal = {European journal of clinical microbiology}, volume = {4}, number = {3}, pages = {355-356}, pmid = {4018074}, issn = {0722-2211}, mesh = {*DNA, Bacterial ; *Nucleic Acid Hybridization ; Streptococcus/*classification ; }, } @article {pmid4055310, year = {1985}, author = {Milne, RG}, title = {Alternatives to the species concept for virus taxonomy.}, journal = {Intervirology}, volume = {24}, number = {2}, pages = {94-98}, doi = {10.1159/000149624}, pmid = {4055310}, issn = {0300-5526}, mesh = {Genes, Viral ; RNA Viruses/classification ; Species Specificity ; Terminology as Topic ; Viruses/*classification/genetics ; }, abstract = {The species concept seems to be inescapably based on the occurrence, in a population, of regular genetic interchange which leads to the formation of common gene pools and on the presence of barriers to interchange which distinguish one gene pool from another. Present knowledge indicates that some types of viruses (e.g. Orthomyxoviridae, Reoviridae) may exchange genes and have a gene-pool population structure; application of the species concept here is legitimate and likely to be feasible in practice. However, it seems that other types of viruses (e.g., tobamoviruses, tombusviruses) do not indulge in regular gene exchange and that common gene pools, distinct from each other, do not occur. Rather, there is clonal multiplication, accumulation of variants, and a fanwise radiation of types with little or no genetic exchange across the rays of the fan. Here, the species concept cannot usefully be applied at either the theoretical or the practical level. If viruses within some major groups are not amenable to being classified and named as species, it follows that attempts to apply the species concept to all viruses should be abandoned. An alternative system that can embrace all cases is already used by plant virologists and merits careful examination by others. Adoption of a 'nonspecies' general approach need not exclude the proposition that in some instances virus species do exist and can be identified and named, as special subsets of the general case. If we cease to aim for the universal pigeonholing of viruses into genera and species, binomial latinized names lose their chief justification.(ABSTRACT TRUNCATED AT 250 WORDS)}, } @article {pmid4055309, year = {1985}, author = {Bishop, DH}, title = {The genetic basis for describing viruses as species.}, journal = {Intervirology}, volume = {24}, number = {2}, pages = {79-93}, doi = {10.1159/000149623}, pmid = {4055309}, issn = {0300-5526}, mesh = {Bunyaviridae/*classification/genetics ; DNA Replication ; Genetic Complementation Test ; RNA, Messenger/genetics ; RNA, Viral/genetics ; Serotyping ; Species Specificity ; Transcription, Genetic ; Virus Replication ; }, abstract = {The basis for the taxonomic definition of viruses or other species eventually has to be genetic. Since the beginning of the taxonomical considerations of organisms, the criterion that individuals can be grouped together on the basis of genetic compatibilities has been adopted as the guiding principle for describing a species. Although the genetic tests for grouping and distinguishing viruses may be different, the principle behind the species concept can still be applied. Also, the very existence of virus heredity and invokes the concept of speciation.}, } @article {pmid4055308, year = {1985}, author = {Kingsbury, DW}, title = {Species classification problems in virus taxonomy.}, journal = {Intervirology}, volume = {24}, number = {2}, pages = {62-70}, doi = {10.1159/000149621}, pmid = {4055308}, issn = {0300-5526}, mesh = {Adenoviridae/classification ; Adenoviruses, Human/classification ; Animals ; Humans ; Orthomyxoviridae/classification ; Plant Viruses/classification ; Reproduction ; Species Specificity ; Viruses/*classification ; }, abstract = {Although the species is the fundamental unit of taxonomy, virologists only recently have begun to classify virus species in a systematic way under the leadership of the International Committee on Taxonomy of Viruses. Progress has been slow and uneven for several reasons: (i) Attempts to sort species are hampered even when the distinction between classification and nomenclature is blurred. Classifying is based on observation and involves deductive reasoning, whereas naming can be as arbitrary as desired, even to the point of dispensing with the traditional Latin binomial form. (ii) Some virologists deny the possibility of applying the species concept to asexual organisms, such as viruses. Those persons are influenced by an obsolete definition of biological species which rests on observed or inferred barriers to sexual reproduction. (iii) New taxonomic tools, such as mathematical (numerical) taxonomy, might be applied profitably to virus classification, but are unfamiliar to many virologists.}, } @article {pmid3965709, year = {1985}, author = {Marhevka, VC and Ebner, NA and Sehon, RD and Hanna, PE}, title = {Mechanism-based inactivation of N-arylhydroxamic acid N,O-acyltransferase by 7-substituted-N-hydroxy-2-acetamidofluorenes.}, journal = {Journal of medicinal chemistry}, volume = {28}, number = {1}, pages = {18-24}, doi = {10.1021/jm00379a005}, pmid = {3965709}, issn = {0022-2623}, support = {CA-24427/CA/NCI NIH HHS/United States ; }, mesh = {2-Acetylaminofluorene/*analogs & derivatives ; *Acetyltransferases ; Acyltransferases/*antagonists & inhibitors ; Animals ; Cricetinae ; Cysteine/pharmacology ; Glutathione/pharmacology ; Hydroxyacetylaminofluorene/*analogs & derivatives/pharmacology ; Liver/enzymology ; Male ; Mathematics ; Mesocricetus ; Molecular Weight ; Structure-Activity Relationship ; }, abstract = {N-Arylhydroxamic acid N,O-acyltransferase (AHAT) catalyzes the transfer of the N-acetyl group from N-arylhydroxamic acids to arylamines. In the absence of an arylamine acceptor, AHAT catalyzes the conversion of N-arylhydroxamic acids to reactive electrophilic intermediates that become irreversibly bound to cellular nucleophiles, including those present on AHAT itself. As part of an investigation of the AHAT-catalyzed bioactivation process, a series of 7-substituted analogues of N-hydroxy-2-acetamidofluorene (1) was synthesized and evaluated in vitro as substrates and inactivators of a partially purified hamster hepatic AHAT preparation. All of the compounds functioned as acetyl donors in the AHAT-catalyzed transacetylation of 4-aminoazobenzene (AAB) and all of them were inactivators of AHAT. The inactivation process exhibited apparent first-order kinetics, and the 7-methoxy compound exhibited the largest inactivation rate constant. Quantitative structure-activity analysis provided support for the concept that positively charged species are involved in the inactivation of AHAT by this series of compounds. Results of experiments in which nucleophilic trapping agents such as glutathione, cysteine, methionine, guanosine phosphate, and tRNA were included in incubation mixtures with AHAT and the N-arylhydroxamic acids indicated that electrophiles which diffuse away from the enzyme active site participate in the inactivation process.}, } @article {pmid3940002, year = {1985}, author = {Lachance, MA}, title = {Current views on the yeast species.}, journal = {Microbiological sciences}, volume = {2}, number = {4}, pages = {122-126}, pmid = {3940002}, issn = {0265-1351}, mesh = {Animals ; Yeasts/*classification ; }, abstract = {The application of the biological species concept to the delineation of yeast species is becoming a reality. Studies centred on heterothallic Pichia and related species, and on homothallic species of Kluyveromyces have facilitated a better understanding of the concept of 'yeast species'.}, } @article {pmid3840465, year = {1985}, author = {Harrison, BD}, title = {Usefulness and limitations of the species concept for plant viruses.}, journal = {Intervirology}, volume = {24}, number = {2}, pages = {71-78}, doi = {10.1159/000149622}, pmid = {3840465}, issn = {0300-5526}, mesh = {Cloning, Molecular ; DNA/analysis ; Genetic Variation ; Plant Viruses/*classification/genetics ; RNA, Viral/genetics ; Species Specificity ; }, abstract = {Continuing concerns among virologists are what range of isolates is covered by one virus name and whether such names relate to categories broadly equivalent to biological species of higher organisms. In the potyviruses, tobamoviruses, and probably other groups of plant viruses with monopartite RNA genomes, exchange of genetic information among isolates is not known to occur; our ability to delineate separate viruses apparently depends on the extent to which biological fitness involves several correlated changes in the genomes of variant clones. Although some such correlated changes are found where viruses infect different plant families, intergrading forms occur in many instances where the host ranges of variants overlap. In plant viruses with multipartite RNA or DNA genomes, the extent of gene pools can be assessed from the ability of isolates to form pseudo-recombinants by reassortment of their genome parts. In the nepoviruses, clusters of virus strains sharing a gene pool resemble, but seem more sharply delimited than, the clusters based on nucleotide sequence homology or serological specificity. In the tobraviruses gene pools do not coincide with serological groupings, and in the geminiviruses biologically very distinct entities have much genome homology and are closely related serologically. The biological species concept seems inappropriate or impractical for many plant viruses, and a more flexible and pragmatic approach to assigning virus isolates to nameable categories is advocated.}, } @article {pmid6152473, year = {1984}, author = {Bolli, R and Fisher, DJ and Taylor, AA and Young, JB and Miller, RR}, title = {Effect of alpha-adrenergic blockade on arrhythmias induced by acute myocardial ischemia and reperfusion in the dog.}, journal = {Journal of molecular and cellular cardiology}, volume = {16}, number = {12}, pages = {1101-1117}, doi = {10.1016/s0022-2828(84)80037-1}, pmid = {6152473}, issn = {0022-2828}, support = {RR-00350/RR/NCRR NIH HHS/United States ; }, mesh = {Adrenergic alpha-Antagonists/*pharmacology ; Animals ; Arrhythmias, Cardiac/*drug therapy ; Blood Pressure/drug effects ; Carbon Dioxide/metabolism ; Coronary Circulation/*drug effects ; Coronary Disease/*complications ; Dogs ; Dose-Response Relationship, Drug ; Female ; Heart Rate/drug effects ; Male ; Myocardial Infarction/complications ; Phentolamine/pharmacology ; Prazosin/blood/pharmacology ; Propranolol/blood/pharmacology ; Receptors, Adrenergic, alpha/*drug effects ; Regional Blood Flow/drug effects ; }, abstract = {Studies in cats suggest alpha-adrenergic contributions to arrhythmias during myocardial ischemia and reperfusion. The validity of this concept in other species, however, remains uncertain. Thus, 106 chloralose-anesthetized open-chest dogs undergoing a 25 min coronary artery occlusion followed by reperfusion received saline (n = 52), prazosin (1 mg/kg, n = 26), phentolamine (5 mg/kg, n = 18), or phentolamine (same dose) + propranolol (1 mg/kg, n = 10). Alpha-blockade was confirmed by alpha-agonist dose-response studies. In phentolamine-treated dogs, arterial pressure and heart rate were kept constant to prevent exacerbation of ischemia. Control and treated groups were comparable with respect to variables known to affect arrhythmias, such as size of occluded and reperfused vascular beds, coronary collateral flow, severity of ischemia estimated from intramyocardial CO2 tension, and peak reactive hyperemia. During coronary occlusion, the number of single premature ventricular complexes was reduced by phentolamine (P less than 0.01), but not by prazosin or phentolamine + propranolol; no treatment affected the total number of couplets, ventricular tachycardia episodes and ventricular ectopic complexes, or the incidence of ventricular tachycardia and ventricular fibrillation. During coronary reperfusion, arrhythmias did not differ in control and treated groups. Thus, selective alpha 1-(prazosin), nonselective alpha 1- and alpha 2-(phentolamine), and combined alpha- and beta-blockade (phentolamine + propranolol) failed to attenuate complex arrhythmias induced by acute myocardial ischemia and reperfusion. Alpha-adrenergic mechanisms appear unimportant in the genesis of these arrhythmias in the canine model.}, } @article {pmid6444122, year = {1984}, author = {Onions, AH and Bridge, PD and Paterson, RR}, title = {Problems and prospects for the taxonomy of Penicillium.}, journal = {Microbiological sciences}, volume = {1}, number = {8}, pages = {185-189}, pmid = {6444122}, issn = {0265-1351}, mesh = {Multivariate Analysis ; Penicillium/*classification/cytology/metabolism ; Terminology as Topic ; }, abstract = {Classification of the economically important sections of the genus Penicillium requires clarification as species concepts based primarily on morphology differ. A multidisciplinary study using physiological characters, biochemistry of metabolites, ultrastructure, and traditional morphology has been initiated. The results will be subjected to cluster analysis techniques.}, } @article {pmid6444112, year = {1984}, author = {Milne, RG}, title = {The species problem in plant virology.}, journal = {Microbiological sciences}, volume = {1}, number = {5}, pages = {113-117}, pmid = {6444112}, issn = {0265-1351}, mesh = {Methods ; Plant Viruses/*classification ; Species Specificity ; Terminology as Topic ; }, abstract = {The systems currently used to classify and name viruses are discussed. It is concluded that, while the family-genus-species system is widely used for many viruses, the virus group-virus system used for plant viruses has a sounder theoretical basis and is easier to use. Its universal adoption should be considered. For plant viruses, the English vernacular name and the group name could form the basis of a binomial nomenclature.}, } @article {pmid6738294, year = {1984}, author = {Hunt, GE and Beilharz, GR and Storlien, LH and Johnson, GF and Kuchel, PW}, title = {Plasma and erythrocyte choline concentrations in rats following chronic treatment with lithium or choline.}, journal = {Life sciences}, volume = {34}, number = {19}, pages = {1853-1859}, doi = {10.1016/0024-3205(84)90679-9}, pmid = {6738294}, issn = {0024-3205}, mesh = {Animals ; Choline/*blood/pharmacology ; Erythrocytes/*metabolism ; Glutathione/blood ; Glycine/blood ; Lithium/*pharmacology ; Magnetic Resonance Spectroscopy ; Male ; Rats ; Rats, Inbred Strains ; }, abstract = {Rats were given daily injections of choline, lithium or lithium plus choline for either 11 or 18 days and red cell choline, glycine and glutathione levels were measured using proton nuclear magnetic resonance spectroscopy. In addition, plasma choline, plasma lithium and red cell lithium levels were measured 4 hr after the last dosage. Choline (1 mmol/kg) alone increased plasma but not red cell choline concentrations. Lithium (0.94 mmol/kg) elevated red cell choline levels but did not affect plasma choline concentrations. In contrast, red cell choline levels were not elevated in rats treated with a higher dose of lithium (1.88 mmol/kg). When choline was given in addition to the lower dose of lithium, a similar accumulation of red cell choline was observed suggesting that the lithium-induced choline accumulation was not enhanced by a greater availability of free choline. No differences were detected in red cell glycine or glutathione levels between any of the treatment groups. Therefore, lithium produced a specific (dose-dependent) accumulation of choline in rat erythrocytes. However, the 100% increase observed in rats was not as marked as the increased red cell choline levels reported in patients maintained on lithium (8 to 10-fold). This discrepancy supports the concept that species differences exist in red cell choline transport or metabolism.}, } @article {pmid6607141, year = {1984}, author = {Raphael, L and Tom, BH}, title = {Liposome facilitated xenogeneic approach for studying human colon cancer immunity: carrier and adjuvant effect of liposomes.}, journal = {Clinical and experimental immunology}, volume = {55}, number = {1}, pages = {1-13}, pmid = {6607141}, issn = {0009-9104}, support = {5-KO4 CA00579/CA/NCI NIH HHS/United States ; CA24024/CA/NCI NIH HHS/United States ; GM0742/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adjuvants, Immunologic ; Animals ; Antigens, Neoplasm/*immunology ; Antigens, Surface/*immunology ; Cell Line ; Colonic Neoplasms/*immunology ; Cytotoxicity, Immunologic ; Dose-Response Relationship, Immunologic ; Female ; Humans ; Immunity, Cellular ; Liposomes/*immunology ; Mice ; Mice, Inbred BALB C ; Phenotype ; Phospholipids ; Spleen/immunology ; T-Lymphocytes/immunology ; }, abstract = {Liposomes prepared with human LS174T colon tumour cell membranes induce specific primary xenogeneic immune responses in BALB/c splenocytes in vitro. Characterization of the adjuvant role of these liposomes was accomplished by determining the effect on immune induction of several modifications on the liposomal carrier. The results showed that the carrier effect of liposomes was mediated primarily by tumour antigens exposed on the outer surface. Trypsin treatment of the liposomes eliminated 95% of the surface protein and significantly (P less than 0.05) reduced the ability of liposomes to induce cytotoxic splenocytes. The generation of cytolytic activity with liposomes was dose-dependent, with a 10 micrograms protein threshold and a maximal response at 100 micrograms. 'Rigid' liposomes were shown to be significantly (P less than 0.05) more efficacious than fluid liposomes in inducing cytotoxicity. In addition, the data indicate that the xenogeneic cell-mediated immunity exhibits identical classes of effector cells as found in murine-murine reactions. Lymphocytes bearing the THY-1, Lyt-1 and Lyt-2 surface markers were necessary for immune induction. The role of Lyt-123 subpopulation was suggested by the inability to achieve normal cytolytic levels by reconstitution with Lyt-1 plus Lyt-2 cells. Adherent cells were, as expected, necessary for the generation of primary immunity. Indeed, the interaction of I-A+ adherent cells with liposomes for at least 8 h was required to generate subsequent maximal T cell cytotoxic activity. The phenotype of the cytotoxic effector cell was Thy-1+, Lyt-2+, and I-Ad-. If this were an allo-or syngeneic, and not a xenogeneic system, this study would be of less interest. However, when coupled with the known molecular homologies between murine and human lymphocyte antigens, these results suggest that the concept of cross species major histocompatibility complex (MHC) restriction is tenable. Thus the liposome is not only an effective antigen carrier, but also a functional adjuvant for in vitro induced cell-mediated immunity.}, } @article {pmid6397143, year = {1984}, author = {Samson, RA and Gams, W}, title = {The taxonomic situation in the hyphomycete genera Penicillium, Aspergillus and Fusarium.}, journal = {Antonie van Leeuwenhoek}, volume = {50}, number = {5-6}, pages = {815-824}, pmid = {6397143}, issn = {0003-6072}, mesh = {Aspergillus/*classification ; Fusarium/*classification/cytology ; Penicillium/*classification/cytology/metabolism/physiology ; Spores, Fungal ; Terminology as Topic ; }, abstract = {Classification of species in the three genera Penicillium, Aspergillus and Fusarium is in a state of change. Criteria used are reviewed; possible stabilization of nomenclature is envisaged. Proper typification of recognized species is necessary. In Penicillium and Aspergillus some species known mainly from fermented food are considered as domesticated versions of other, wild species. In Penicillium a further standardization of conditions of cultivation and careful description of micromorphology are necessary, before the species concepts of different laboratories can be reconciled. Secondary metabolites (mycotoxins, pigments) prove to support taxonomic conclusions reached by morphological work. In Aspergillus the taxonomic situation is simpler than in Penicillium, but typification is not yet sufficiently settled. For some well-known species older names were recently unearthed. In Fusarium the taxonomic views of different laboratories are becoming more similar, but much work on type specimens and neotypification of other species is still required. More genetic evidence is necessary to decide about specific or varietal rank in critical cases.}, } @article {pmid6141904, year = {1984}, author = {Sugita, O and Sawada, Y and Sugiyama, Y and Iga, T and Hanano, M}, title = {Kinetic analysis of tolbutamide-sulfonamide interaction in rabbits based on clearance concept. Prediction of species difference from in vitro plasma protein binding and metabolism.}, journal = {Drug metabolism and disposition: the biological fate of chemicals}, volume = {12}, number = {1}, pages = {131-138}, pmid = {6141904}, issn = {0090-9556}, mesh = {Animals ; Blood Proteins/*metabolism ; Drug Interactions ; Hydroxylation ; In Vitro Techniques ; Kinetics ; Male ; Metabolic Clearance Rate ; Microsomes, Liver/metabolism ; Protein Binding ; Rabbits ; Species Specificity ; Sulfonamides/*pharmacology ; Tolbutamide/*metabolism ; }, abstract = {The interaction between tolbutamide (TB) and sulfonamide (SA) in rabbits was quantitatively investigated by both in vivo and in vitro experiments, and the mechanisms of species difference between rabbits and rats were analyzed by comparing the two total body clearances (CLtot) obtained from in vivo and in vitro studies. The sulfonamides used were sulfaphenazole (SP) and sulfadimethoxine (SDM). In vivo CLtot of TB was changed little by SA in rabbits, which was contrary to the phenomenon seen in rats, i.e. CLtot was markedly decreased by SA in rats (Sugita et al., Biochem. Pharmacol., 30, 3347, 1981). The total body clearance defined as CL in vitro tot.pred was predicted for TB in the presence and absence of SA by the equation: CL in vitro tot.pred congruent to fB CL in vitro int, where fB is the blood-free fraction and CL in vitro int is the hepatic intrinsic clearance of unbound drug obtained from in vitro experiments using liver microsomal fraction. A comparatively good agreement was observed between the two CLtot obtained from in vivo and in vitro data. The analysis in rabbits based on these in vitro experiments showed that the small gross changes of in vivo CLtot induced by SA were due to the compensative changes of two factors, i.e. fB and CL in vitro int which in the presence of SA were approximately 200 and 50% of the control, respectively. However, in rats, the marked decrease of in vivo CLtot induced by SA was explained by the greater degree of the decrease in CL in vitro int than that of the increase in fB.(ABSTRACT TRUNCATED AT 250 WORDS)}, } @article {pmid6626555, year = {1983}, author = {Barden, JA and Wu, CS and Dos Remedios, CG}, title = {Actin monomer conformation under polymerizing conditions studied by proton nuclear magnetic resonance and circular dichroism spectroscopy.}, journal = {Biochimica et biophysica acta}, volume = {748}, number = {2}, pages = {230-235}, doi = {10.1016/0167-4838(83)90299-6}, pmid = {6626555}, issn = {0006-3002}, support = {GM-10880/GM/NIGMS NIH HHS/United States ; }, mesh = {Actins/*metabolism ; Animals ; Circular Dichroism ; Macromolecular Substances ; Magnetic Resonance Spectroscopy ; Muscles/metabolism ; Protein Conformation ; Rabbits ; }, abstract = {Skeletal muscle actin above a critical concentration polymerizes in physiological concentrations of KCl. Earlier studies have concluded that evidence exists for a monomeric species of actin with a conformation distinct from that of G-actin. Re-investigations of these earlier studies, however, have cast doubt on the concept of a new monomeric actin species. In this study we have adopted two methods, high-resolution proton nuclear magnetic resonance and near ultraviolet circular dichroism spectroscopy, to investigate the existence or otherwise of the putative monomer conformation variously called F-monomer, G-actin or KCl-monomer. For proton nuclear magnetic resonance spectroscopy, unmodified actin maintained below its critical concentration as well as higher concentrations of two chemically modified, unpolymerizable actin samples were studied in the absence and presence of KCl. No difference was found in the environment of even a single proton within the entire actin structure. For circular dichroism we studied actin maintained below its critical polymerization concentration and found very little change in ellipticities when KCl was added to the G-actin solution. We therefore conclude that there is no species of actin monomer with a conformation distinct from that of G-actin.}, } @article {pmid6658439, year = {1983}, author = {Chen, SX}, title = {Species concept and taxonomic principles.}, journal = {Scientia Sinica. Series B, Chemical, biological, agricultural, medical & earth sciences}, volume = {26}, number = {10}, pages = {1037-1045}, pmid = {6658439}, issn = {0253-5823}, mesh = {Animals ; Biological Evolution ; *Classification ; Humans ; Models, Biological ; }, abstract = {Based on the species concept of changing versus unchanging, the present work deals with the following two problems: First, why would the taxonomic system reflect evolutionary history? Second, how is this effected? Species are changing in the sense that each species has its own characteristics and there is no complete identity between any two species. On the other hand, species are unchanging and each one conserves a set of ancestral characters which allocates its taxonomic position, and this is the reason why the taxonomic system reflects evolutionary history. The taxonomic system is constructed to reflect evolutionary history mainly through the process of character analysis. Combining the viewpoints of cladistics and evolutionary systematics, the writer proposes six rules for character analysis which will provide the basis for analyzing evolutionary history.}, } @article {pmid6577245, year = {1983}, author = {Galili, U}, title = {Glucocorticoid induced cytolysis of human normal and malignant lymphocytes.}, journal = {Journal of steroid biochemistry}, volume = {19}, number = {1B}, pages = {483-490}, doi = {10.1016/0022-4731(83)90207-8}, pmid = {6577245}, issn = {0022-4731}, mesh = {Arthritis, Rheumatoid/*immunology ; Cell Survival/drug effects ; Cytotoxicity, Immunologic/*drug effects ; Female ; Fetus ; Glucocorticoids/*pharmacology ; Humans ; Hydrocortisone/pharmacology ; Infectious Mononucleosis/*immunology ; Leukemia/*immunology ; Leukemia, Lymphoid/immunology ; Leukemia, Myeloid/immunology ; Leukemia, Myeloid, Acute/immunology ; Lymph Nodes/immunology ; Lymphocytes/drug effects/*immunology ; Mitochondrial Swelling/drug effects ; Pregnancy ; Thymus Gland/immunology ; }, abstract = {Contrary to the general concept that man is a "glucocorticoid resistant species" this work demonstrates distinct human lymphoid subsets which are readily lysed in vitro by upper physiological and pharmacological concentrations of cortisol. These populations include the thymocyte precursor cells, i.e. prothymocytes, and immunoactivated T lymphocytes. Chronic lymphocytic leukemia cells and malignant cells from part of the acute lymphoblastic leukemia patients were also found to be highly sensitive to the in vitro cortisol induced lysis. The leukemic cells from all acute and chronic myeloid leukemias and from some acute lymphoblastic leukemia patients were found to be completely resistant to cortisol-induced lysis, even at the super pharmacological levels of the hormone. The lysis of the sensitive cell populations was specifically induced by glucocorticoids but not by other steroid hormones. Studies of the cytolic process showed high-affinity binding of the cortisol molecule to specific cytoplasmic receptor, and implied induction of "autolytic protein" synthesis. It is suggested that the observed in vitro cortisol-induced lysis accounts for part of the clinical effects of glucocorticoids. Furthermore this phenomenon may reflect a normal regulatory mechanism exerted by the corticoadrenal hormones on the immune system.}, } @article {pmid6342732, year = {1983}, author = {Kurup, VP and Piechura, JE and Ting, EY and Orlowski, JA}, title = {Immunochemical characterization of Nocardia asteroides antigens: support for a single species concept.}, journal = {Canadian journal of microbiology}, volume = {29}, number = {4}, pages = {425-432}, doi = {10.1139/m83-069}, pmid = {6342732}, issn = {0008-4166}, support = {HL 15389/HL/NHLBI NIH HHS/United States ; }, mesh = {Antigens, Bacterial/*analysis ; Cross Reactions ; Humans ; Immunoelectrophoresis, Two-Dimensional ; Molecular Weight ; Nocardia Infections/diagnosis ; Nocardia asteroides/*immunology ; Serologic Tests ; }, abstract = {Nocardia asteroides strains are highly heterogeneous. They show morphological, physiological, and immunological differences. In a previous study, we delineated seven immunotypes of N. asteroides. In the present study, we compared the culture filtrate antigens of these immunotypes by antigen-antibody crossed-immunoelectrophoresis and by rocket electrophoresis. We have also compared the antigen preparations by two-dimensional electrophoresis. While unique components constitute the major portion of the components, the results indicate that similar components are present in the culture filtrates of all strains. This finding supports the view of retaining all the immunotypes in the species Nocardia asteroides rather than designating different species such as N. farcinica and N. sebivorans.}, } @article {pmid6306784, year = {1983}, author = {Dubois-Prévost, R}, title = {[Psychological dimension of manducation].}, journal = {La semaine des hopitaux : organe fonde par l'Association d'enseignement medical des hopitaux de Paris}, volume = {59}, number = {12}, pages = {855-860}, pmid = {6306784}, mesh = {Animals ; Biological Evolution ; Child Development/*physiology ; *Drinking ; *Eating ; Humans ; Infant ; Infant, Newborn ; Mammals ; Mastication ; Salivation ; Sucking Behavior ; Taste ; Tooth Eruption ; }, abstract = {Manducation designates all the actions involved in drinking and eating. Thus manducation consists mainly of sucking, retaining and chewing food, salivary secretion, buccofacial somatesthesia, gustation, in some part olfaction, and finally swallowing: consequently an intricate combination of sensorial and both motor and secretory actuating functions, controlled and coordinated by upper neuromuscular functions. In addressing the multiplicity and complexity of rhinencephalic manifestations, which involve conjointly memorizing processes, feeding, sexual and olfactive functions, socioemotional behaviour, and the concept of individual and species preservation, the author has tried to define the psychological dimension of manducation. This viewpoint, which springs from evolution, leads to the discussion of the connexions and operative differences between the ancient rhinencephalic brain and the recent cortical one. The author has attempted to avoid psychological concepts in order to study psychical phenomena.}, } @article {pmid6221330, year = {1983}, author = {Pocidalo, JJ and Blayo, MC and Castaing, M}, title = {[Relations between acid-base equilibrium and body temperature. Physiological concepts and practical applications].}, journal = {Presse medicale (Paris, France : 1983)}, volume = {12}, number = {6}, pages = {355-360}, pmid = {6221330}, issn = {0755-4982}, mesh = {*Acid-Base Equilibrium ; Animals ; Blood Physiological Phenomena ; *Body Temperature ; Coronary Artery Bypass ; Dogs ; Erythrocytes/physiology ; Extracellular Space/physiology ; Humans ; Hydrogen-Ion Concentration ; Hypothermia, Induced ; Intracellular Fluid/physiology ; Plasma/physiology ; Temperature ; }, abstract = {In 1975 H. Rahn put forward a new concept of hydrogen ions regulation which explains acid-base regulation in relation to body temperature and applies to all animal species. At the root of this concept is the finding that maintenance of intracellular neutrality is governed by water dissociation and regulated by imidazole-rich protein buffers. The pH of the extracellular fluid, which receives acid by-products of cell activity, is kept higher than that of the intracellular fluid (relative alkalinity). The difference between extracellular pH and neutrality is constant for each species and ranges from 0.6 to 0.8 pH units. It is unaffected by changes in temperature, and the total CO2 content of extracellular fluid remains constant. The authors were able to confirm the value of this new concept in man by experimental studies of in vitro and in vivo blood of patients undergoing aorto-coronary bypass under controlled hypothermia. They draw the following practical conclusions: (1) in subjects under moderate or deep hypothermia for surgical purposes, the acid-base status can be controlled and the extracellular pH adjusted by ensuring intracellular neutrality; this is done by keeping PCO 2 at such a level that the arterial blood pH measured at 37 degrees C remains around 7.40; (2) the problem of correcting acid-base values (pH-PCO 2) according to body temperature is solved simply by using pH and PCO 2 values measured at 37 degrees C and interpreting them, as usual, in terms of metabolic or respiratory acidosis or alkalosis.}, } @article {pmid6629702, year = {1983}, author = {Gorman, BM}, title = {On the evolution of orbiviruses.}, journal = {Intervirology}, volume = {20}, number = {2-3}, pages = {169-180}, doi = {10.1159/000149388}, pmid = {6629702}, issn = {0300-5526}, mesh = {*Biological Evolution ; Electrophoresis, Polyacrylamide Gel ; Microscopy, Electron ; Recombination, Genetic ; Reoviridae/*classification/genetics ; Serotyping ; }, abstract = {The genomes of orbiviruses consist of 10 segments of double-stranded RNA. In cells simultaneously infected with two or more related viruses, recombinants are derived by independent reassortment of parental genes. The process is analogous to sexual reproduction in higher organisms and provides a mechanism for generating extensive diversity within this group of viruses. This genetic diversity can be explained by reference to modern concepts of the structure of natural populations of organisms. A species in the phylogenetic sense is the largest aggregate of individual organisms that evolves as a unit. The biological species concept stresses the community gene pool and reproductive isolation. The orbiviruses are now classified into 13 distinct serological groups, but confusion exists in defining species. Classification by reference to concepts of evolutionary species would define genetically interacting groups, estimate the extent of diversity within these groups, and establish phylogenetic relationships between species.}, } @article {pmid17246077, year = {1982}, author = {Quiros, CF}, title = {Tetrasomic segregation for multiple alleles in alfalfa.}, journal = {Genetics}, volume = {101}, number = {1}, pages = {117-127}, pmid = {17246077}, issn = {0016-6731}, abstract = {Evidence of tetrasomic inheritance in alfalfa, Medicago sativa L. and M. falcata L., for multiple codominant alleles at three isozymic loci is reported in this study. The locus Prx-1 governing anodal peroxidase and the loci Lap-1 and Lap-2 governing anodal leucine-aminopeptidase were studied by starch gel electrophoresis in seedling root tissue or seeds. The progenies from several di-, tri- or tetra-allelic plants belong to the species M. sativa and M. falcata and their hybrids were studied for the segregation of the three genes. In all cases, tetrasomic inheritance of chromosomal-type segregation was observed. In another progeny resulting from the crossing of two plants involving four different alleles at locus Lap-2, tetrasomic segregation with the possible occurrence of double reduction was observed. This study presents direct evidence of autotetraploidy and the existence of tetra-allelic loci in alfalfa. It also supports the concept that the species M. sativa and M. falcata are genetically close enough to be considered biotypes of a common species.}, } @article {pmid7125284, year = {1982}, author = {Eichler, W}, title = {[Head lice problems. I. Taxonomic position of Pediculus capitis].}, journal = {Angewandte Parasitologie}, volume = {23}, number = {2}, pages = {102-109}, pmid = {7125284}, issn = {0003-3162}, mesh = {Animals ; Biological Evolution ; Host-Parasite Interactions ; Insect Vectors ; Pediculus/*classification/physiology ; }, abstract = {The recognition of the head louse and the body louse being two different species is not quite new. This view is also supported by the author as can be seen in several publications. It is based on the biological species concept of the so-called new systematics. But even quite a few contributors doing research in the field of lice still ignore this concept. Therefore, the author emphasizes all "biological" species criteria referring to modern epidemiological research done in the last decades. Considering all these facts and contemporary evolutionary theory the author concludes that the two forms should be recognized as good species. The different subspecies of the head louse described as such are listed.}, } @article {pmid7123049, year = {1982}, author = {Davis, RE and Lee, IM}, title = {Comparative properties of spiroplasmas and emerging taxonomic concepts: a proposal.}, journal = {Reviews of infectious diseases}, volume = {4 Suppl}, number = {}, pages = {S122-8}, doi = {10.1093/clinids/4.supplement_1.s122}, pmid = {7123049}, issn = {0162-0886}, mesh = {Bacterial Proteins/analysis ; Cytosine/analysis ; DNA, Bacterial/analysis ; Electrophoresis, Polyacrylamide Gel ; Guanine/analysis ; Molecular Weight ; Nucleic Acid Conformation ; Nucleic Acid Hybridization ; Serotyping ; Spiroplasma/*classification ; }, abstract = {The major serogroups and distinct subgroups of spiroplasmas seem to represent distinct species. The scheme of classification into these groups was initially based on serologic properties and later supported by the results of studies of DNA-DNA homology and polyacrylamide gel electrophoretic analyses of cellular proteins. Because separate subgroups within the same major serogroup cross-react in growth inhibition tests and other serologic tests, a taxonomic scheme is proposed which implies that certain major criteria for species differentiation within the genus Mycoplasma cannot be appropriately applied to the genus Spiroplasma without modification. Nevertheless, the grouping scheme and proposed speciation satisfy requirements for a species concept that is utilitarian and operational and consistent with recommendations by the International Committee on Systematic Bacteriology, Subcommittee on the Taxonomy of Mollicutes.}, } @article {pmid6120950, year = {1982}, author = {Rapoport, B and Takai, NA and Filetti, S}, title = {Evidence for species specificity in the interaction between thyrotropin and thyroid-stimulating immunoglobulin and their receptor in thyroid tissue.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {54}, number = {5}, pages = {1059-1062}, doi = {10.1210/jcem-54-5-1059}, pmid = {6120950}, issn = {0021-972X}, support = {AM-00500/AM/NIADDK NIH HHS/United States ; AM-19289/AM/NIADDK NIH HHS/United States ; }, mesh = {Animals ; Cells, Cultured ; Cyclic AMP/metabolism ; Dogs ; Humans ; Immunoglobulin G/*metabolism ; Immunoglobulins, Thyroid-Stimulating ; In Vitro Techniques ; Receptors, Cell Surface/*metabolism ; Receptors, Thyrotropin ; Species Specificity ; Thyroid Gland/*metabolism ; Thyrotropin/*metabolism ; }, abstract = {The cAMP response in cultured human and dog thyroid cells was used to examine the relationship between human TSH, nonprimate TSH, and thyroid-stimulating immunoglobulin (TSI) bioactivity in human and nonhuman thyroid tissue. The bovine TSH (bTSH) to human TSH potency ratio was approximately 6-fold greater in dog than in human thyroid cells. Relative bioactivity of bTSH and TSI aslo differed in these cell types. Thus, four TSI samples produced approximately 6-fold greater stimulation relative to bTSH in human thyroid than in dog thyroid cells. It is discussed why these data suggest that the TSH receptor as well as TSH and TSI display species specificity as defined by the classical concept of this term.}, } @article {pmid7082201, year = {1982}, author = {Kochubeĭ, NM}, title = {[Ultimobranchial cysts in goitrous thyroids of sheep at high altitude].}, journal = {Arkhiv patologii}, volume = {44}, number = {4}, pages = {57-60}, pmid = {7082201}, issn = {0004-1955}, mesh = {*Altitude ; Animals ; Cysts/pathology/*veterinary ; Goiter/pathology/*veterinary ; Male ; Sheep ; Sheep Diseases/*pathology ; Thyroid Diseases/pathology/*veterinary ; *Ultimobranchial Body/pathology ; }, abstract = {Histomorphology of ultimobranchial cysts of thyroid glands of sheep is presented. The average incidence of cysts in sheep was 17.3%. The cysts have some characteristic features indicating their ultimobranchial origin: the presence of inhomogeneous "foamy" colloid staining positively for glycosaminoglycans, heteromorphism of the cells lining the internal surface of the cysts, and the presence of ciliary cells among them. The detection of ultimobranchial cysts in sheep with strumous thyroid glands not only extends the concept of the species appurtenance of these formations but also indicates the possibility of frequent occurrence of ultimobranchial cysts in hyperplastic processes of strumous and neoplastic nature which is of great diagnostic and prognostic significance.}, } @article {pmid6765100, year = {1982}, author = {Robert, F}, title = {[Hippocrates, Plato and Aristotle and the concept of genus and species].}, journal = {History and philosophy of the life sciences}, volume = {4}, number = {2}, pages = {173-201}, pmid = {6765100}, issn = {0391-9714}, mesh = {*Classification ; Greece, Ancient ; History, Ancient ; Philosophy, Medical ; Zoology/*history ; }, } @article {pmid7221565, year = {1981}, author = {Shiraishi, Y and Matsui, S and Sandberg, AA}, title = {Normalization by cell fusion of sister chromatid exchange in Bloom syndrome lymphocytes.}, journal = {Science (New York, N.Y.)}, volume = {212}, number = {4496}, pages = {820-822}, doi = {10.1126/science.7221565}, pmid = {7221565}, issn = {0036-8075}, support = {CA-14555/CA/NCI NIH HHS/United States ; }, mesh = {Cell Fusion ; Cells, Cultured ; *Crossing Over, Genetic ; Humans ; Hybrid Cells/physiology ; Photosensitivity Disorders/*genetics ; *Sister Chromatid Exchange ; Syndrome ; Telangiectasis/*genetics ; }, abstract = {Fusion of fresh lymphocytes from a Bloom syndrome (BS) patient with those of normal subjects or a BS heterozygote resulted in complete normalization of the frequency of sister chromatid exchanges in the chromosomes of BS cells. This normalization took place by the first mitosis in hybrid cells. In contrast, cultivation of BS lymphocytes with those of normal subjects or the BS heterozygote had no effect on sister chromatid exchanges. The cell fusion experiments suggest that the normalization on the sister chromatid exchanges. The cell fusion experiments suggest that the normalization of the sister chromatid exchange frequencies in BS cells can be achieved by factors conserved in the cells of various mammalian species. These findings are compatible with the concept that BS is a recessive genetic mutation at regulatory levels of the DNA repair function.}, } @article {pmid7274681, year = {1981}, author = {Economos, AC}, title = {Beyond rate of living.}, journal = {Gerontology}, volume = {27}, number = {5}, pages = {258-265}, doi = {10.1159/000212481}, pmid = {7274681}, issn = {0304-324X}, support = {1R01 AG02087/AG/NIA NIH HHS/United States ; }, mesh = {*Aging ; Animals ; Growth ; Life Expectancy ; Mammals/*physiology ; *Metabolism ; Selection, Genetic ; }, abstract = {The validity of the rate of living theory of aging in mammals has been seriously questioned over the last two decades because it does not account for the life span of many mammalian species. However, though this concept is an oversimplification and inapplicable in general, this does not mean that aging is unrelated to cellular metabolic processes. In general agreement with previous discussions, it can be stated that the rate of aging is proportional to the difference between the rate of cellular entropy production (which is by necessity roughly proportional to the rate of cellular biochemical processes and thus specific metabolic rate) and the cellular "counterentropic' mechanisms (such as cellular repair, antioxidant protection, etc.). These counterentropic mechanisms may have evolved to a different degree in some mammals. This could be effected indirectly by natural selection of certain traits, particularly those expressed in differences in the rates of embryonic and postnatal development. These rates, relatively to basal metabolic rate, determine a species' rate of becoming, which is proposed to be a predictor of mammalian life span. Data from 22 species, from shrew to elephant, with representatives from the main mammalian orders (including many exceptions to the rate of living concept), agree with this hypothesis. A mechanism underlying such natural selection, proposed elsewhere, is based on differential selection pressures among orders for which the different life-styles (particularly with respect to the birth of young) are responsible.}, } @article {pmid7441200, year = {1980}, author = {Davison, FD and Mackenzie, DW and Owen, RJ}, title = {Deoxyribonucleic acid base compositions of dermatophytes.}, journal = {Journal of general microbiology}, volume = {118}, number = {2}, pages = {465-470}, doi = {10.1099/00221287-118-2-465}, pmid = {7441200}, issn = {0022-1287}, mesh = {Arthrodermataceae/*analysis ; Base Composition ; Centrifugation, Density Gradient ; Cytosine/analysis ; *DNA, Fungal ; DNA, Satellite ; Guanine/analysis ; }, abstract = {DNA was extracted and purified from 55 dermatophyte isolates representing 34 species of Trichophyton, Microsporum and Epidermophyton. The base compositions of the chromosomal DNA were determined by CsCl density gradient centrifugation and were found to be in the narrow range of 48.7 to 50.3 mol % G + C. A satellite DNA component assumed to be of mitochondrial origin was present in most strains, with a G + C content ranging from 14.7 to 30.8 mol % G + C. Heterogeneity in microscopic and colonial characteristics was not reflected in differences in the mean G + C content of the chromosomal DNAs. Strains varied in the G + C contents of satelite DNA, but these did not correlate with traditional species concepts.}, } @article {pmid7436403, year = {1980}, author = {Johannsen, E}, title = {Hybridization studies within the genus Kluyveromyces van der Walt emend. van der Walt.}, journal = {Antonie van Leeuwenhoek}, volume = {46}, number = {2}, pages = {177-189}, pmid = {7436403}, issn = {0003-6072}, mesh = {Ascomycota/*classification ; Crosses, Genetic ; Culture Media ; *Hybridization, Genetic ; Lactose/metabolism ; Maltose/metabolism ; Mutation ; Recombination, Genetic ; Saccharomycetales/*classification/genetics/metabolism ; }, abstract = {Hybridization studies based on the prototrophic selection technique, involving the use of auxotrophic mutants of strains of all accepted species of the genus Kluyveromyces, are reported. Two main groups of mutally interfertile taxa were established withinthe genus. the first group comprises Kluyveromyces bulgaricus, K. cicerisporus, K. dobzhanskii, K. drosophilarus, K. fragilis, K. lactis; K. marxianus, K. phaseolosporus, K. vanudenii and K. wileenii. The second group consists of K. doazhanskii, K. drosophilarum, K. lactis, K. vanudenii and K. wickerhamii. Hybrids were also detected in crosses involving K. drosophilarum and K. waltii as well as K. marxianus and K. thermotolerans. In terms of the concept of the biological species and in compliance with requirements of the International Code of Botanical Nomenclature, taxa which hybridize with K. marxianus and form fertile recombinants at frequencies observed in intraspecific crosses, are accepted as varieties of K. marxianus.}, } @article {pmid24310481, year = {1979}, author = {Gustafsson, A}, title = {Linnaeus' Peloria: The history of a monster.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {54}, number = {6}, pages = {241-248}, pmid = {24310481}, issn = {0040-5752}, abstract = {The so-called Peloria case has been discussed repeatedly in world literature since the discovery of the five-spurred Linaria in 1742 and its description by Linnaeus in 1744. In 1742 a young Uppsala botanist found a peculiar specimen of the common toad-flax (now named Linaria vulgaris L.) on an island in the Stockholm archipelago. The plant, which had spread vegetatively, possessed five spurs instead of one spur, a characteristic of the common toad-flax. The material was presented to Linnaeus, who became quite excited. The finding was contrary to his concept that genera and species had universally arisen through an act of original creation and remained unchanged since then. In a famous thesis of 1744, Linnaeus called the deviating plant 'Peloria', Greek for 'monster'. The case of pelorism was discussed later on by a great number of famous writers and scientists including, for example, Goethe, Darwin, Naudin, De Vries and Stubbe. Parallel types were found in numerous species of other genera and families. Such aberrant forms are caused by spontaneous mutation. The history, mode of origin, morphology, inheritance and distribution of different Peloria mutants are discussed in the paper.}, } @article {pmid17747043, year = {1979}, author = {Weiss, MJ and Levy, DP}, title = {Sperm in "parhenogenetic" freshwater gastrotrichs.}, journal = {Science (New York, N.Y.)}, volume = {205}, number = {4403}, pages = {302-303}, doi = {10.1126/science.205.4403.302}, pmid = {17747043}, issn = {0036-8075}, abstract = {Freshwater members of the phylum Gastrotricha have been considered obligate parthenogens. In Lepidodermelia squammata, the species for which there is most evidence for parthenogenesis, sperm have been discovered. This finding will necessitate reexamination of the nature of sexuality and life cycles and of the concept of "species" in freshwater gastrotrichs.}, } @article {pmid17757999, year = {1979}, author = {Levin, DA}, title = {The nature of plant species.}, journal = {Science (New York, N.Y.)}, volume = {204}, number = {4391}, pages = {381-384}, doi = {10.1126/science.204.4391.381}, pmid = {17757999}, issn = {0036-8075}, abstract = {The species concept is a central tenet of biological diversity. Attempts to describe diversity have led to empirical concepts of species based on assumptions found wanting for plants. Plant species lack reality, cohesion, independence, and simple evolutionary or ecological roles. The concept of species for plant taxonomists and evolutionists can only serve as a tool for characterizing diversity in a mentally satisfying way. Diversity is idiosyncratic. ft is impossible to reconcile idiosyncrasy with preconceived ideas of diversity. The search for hidden likenesses is unlikely to yield a unifying species concept. The concept that is most operational and utilitarian for plants is a mental abstraction which orders clusters of diversity in multidimensional character space.}, } @article {pmid24309904, year = {1978}, author = {Hoffmann, P and Esser, K}, title = {Genetics of speciation in the basidiomycetous genus Polyporus.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {53}, number = {6}, pages = {273-282}, pmid = {24309904}, issn = {0040-5752}, abstract = {The wood rotting basidiomycete Polyporus (subgenus Leucopori Quel.) was chosen in order to investigate by genetic parameters the validity of the classical species concept based on typological characters.Species deliminations in this genus are derived from morphological characters and depend mainly on the size of hymenial pores. They were compared with those assigned from mating relations between 26 races of different geographic origin.All races could unequivocally be grouped into three separate entities corresponding with the typological species P. arcularius, P. brumalis and P. ciliatus on the basis of the following results: 1. As expected, the basic breeding system in Polyporus is the tetrapolar mechanism of homogenic incompatibility controlled by multiple alleles of the mating type factors A and B. 2. All intraspecific combinations were fertile. A conspicuous barrage formed in those crosses where dikaryotization and fruiting were impaired. This barrage is characterized by a clear zone, about 1-2 mm wide, free of aerial hyphae and reduced hyphal density in the growth medium. The delay observed in the onset of the sexual cycle was caused by retarded fusion of hyphae and blocked exchange of nuclei despite a compatible combination of the mating types. 3. Using two races of P. ciliatus as an example, it was revealed that barrage formation is started by the specific interaction of three independent genes (bi (+)/bi = barrage initiation, bfI 1/bfI 2 and bfII 1/bfII 2 = barrage formation) in a way characteristic for systems of heterogenic incompatibility: barrage formation requires the presence of the allele bi (+) in at least one mating partner additional to a heterogeneity in both bf-genes. 4. Interspecific combinations were sterile. There is no hyphal fusion between the mating partners and because of the mutual repulsion a sharp line formed in the area of contact that was designated as border line. Its formation is independent of mating type or nuclear status of the confronted mycelia. The good correspondence of the species limits derived from morphological and genetic data indicates the applicability and validity of both the typological and the biological species concept. The latter, however, proved superior in compensating the variability of morphological characters, at least in higher fungi.The bearing of our results and other known control mechanisms of the sexual cycle on the definition of the category 'species' are integrated in a proposed modification of the biological species concept: populations (races) belong to different species when the failure to interbreed and to produce viable offspring is not caused by genetic parameters operating in completion of the sexual cycle.}, } @article {pmid20174286, year = {1977}, author = {Measures, RM}, title = {PROBE: a new technique for measuring the density profile of a specific constituent using counterpropagating laser pulses.}, journal = {Applied optics}, volume = {16}, number = {11}, pages = {3016-3026}, doi = {10.1364/AO.16.003016}, pmid = {20174286}, issn = {1559-128X}, abstract = {A new approach at attaining density measurements of a specific constituent with spatial resolution using two counterpropagating laser pulses is proposed. This PROBE (Profile Resolution Obtained By Excitation) concept involves exciting the species of interest with one pulse then probing the wake of excited atoms or molecules with a second laser pulse. The lifetime of the excited state, in terms of the time for the laser pulse to cross the region of interest, turns out to be an important parameter in specifying the form of the relation needed to ascertain the profile of the species under investigation. This new technique could find application in several areas, range from remote atmospheric pollution monitoring in the ir to trace species profile evaluation within plasma or chemical reactors.}, } @article {pmid11610171, year = {1977}, author = {Voous, KH}, title = {The concept of species in retrospect and perspective.}, journal = {Janus; revue internationale de l'histoire des sciences, de la medecine, de la pharmacie, et de la technique}, volume = {64}, number = {}, pages = {109-118}, pmid = {11610171}, issn = {0021-4264}, mesh = {Biology/*history ; History, Ancient ; History, Early Modern 1451-1600 ; History, Medieval ; History, Modern 1601- ; }, } @article {pmid17731083, year = {1976}, author = {Abele, LG}, title = {Comparative species richness in fluctuating and constant environments: coral-associated decapod crustaceans.}, journal = {Science (New York, N.Y.)}, volume = {192}, number = {4238}, pages = {461-463}, doi = {10.1126/science.192.4238.461}, pmid = {17731083}, issn = {0036-8075}, abstract = {The number of decapod species associated with the coral Pocillopora damicornis is compared between two regions on the Pacific coast of Panama which are of the same geologic age but differ in environmental characteristics. The relationship between number of species and coral head size does not differ between the two regions but species composition among coral heads is more variable in the fluctuating environment. Thus there are more species (55 compared to 37) associated with corals in the fluctuating environment than in the constant environment. These data impugn the concept that environmental constancy increases species richness. They support the hypothesis that species equilibrium within habitats is maintained by measurable ecological factors-in this case, the effects of a natural physical disturbance.}, } @article {pmid5004743, year = {1971}, author = {Tsukamura, M}, title = {Some considerations on classification of Mycobacteria. Definition of bacterial species by introduction of the concept of "hypothetical median or mean organism".}, journal = {The Japanese journal of tuberculosis and chest diseases}, volume = {17}, number = {1}, pages = {18-30}, pmid = {5004743}, issn = {0021-5279}, mesh = {Mycobacterium/*classification ; Mycobacterium bovis/classification ; Mycobacterium tuberculosis/classification ; Statistics as Topic ; }, } @article {pmid5772252, year = {1969}, author = {Lemke, PA}, title = {A reevaluation of homothallism, heterothallism and the species concept in Sistotrema brinkmanni.}, journal = {Mycologia}, volume = {60}, number = {1}, pages = {57-76}, pmid = {5772252}, issn = {0027-5514}, mesh = {*Basidiomycota/classification/growth & development ; Culture Media ; Genetics ; Mutation ; Species Specificity ; Spores/growth & development ; }, } @article {pmid5746159, year = {1968}, author = {Iablokov-Khnzorian, SM}, title = {[Concept of species].}, journal = {Zhurnal obshchei biologii}, volume = {29}, number = {6}, pages = {645-657}, pmid = {5746159}, issn = {0044-4596}, mesh = {*Classification ; *Zoology ; }, } @article {pmid5611024, year = {1967}, author = {El-Ani, AS}, title = {Life cycle and variation of Prototheca wickerhamii.}, journal = {Science (New York, N.Y.)}, volume = {156}, number = {3781}, pages = {1501-1503}, doi = {10.1126/science.156.3781.1501}, pmid = {5611024}, issn = {0036-8075}, mesh = {Culture Media ; Eukaryota/classification/*growth & development ; Fungi/classification/*growth & development ; *Genetic Variation ; Genetics, Microbial ; Mutation ; Spores ; }, abstract = {Prototheca wickerhamii is a yeastlike organism that resembles the green alga Chlorella. Nuclear division in coordination with cytoplasmic cleavage gives rise to uninucleate cytoplasmic segments, each of which acquires a delicate cell wall and develops into an autospore. The autospores in this species are spherical; but in a variant that presumably arose as a result of spontaneous mutation, the cytoplasmic cleavage is irregular, and the resultant autospores are ovoid to bacillary. When these variant autospores grow, they swell and round up before the nuclear division begins, producing spherical cells like those seen in wild-type cultures. In view of the fact that species concept in the genus is based on size and shape of cells, the variation limits in these morphological characteristics have significant bearing on species classification.}, } @article {pmid5906595, year = {1966}, author = {Targow, AM}, title = {Studies on atopic skin-test reactions. II. Fallacies that underlie the concept that fungi contain species-specific allergens.}, journal = {Annals of allergy}, volume = {24}, number = {3}, pages = {120-127}, pmid = {5906595}, issn = {0003-4738}, mesh = {*Allergens ; Asthma/*immunology ; *Fungi ; Humans ; Rhinitis, Allergic, Seasonal/*immunology ; *Skin Tests ; *Species Specificity ; }, } @article {pmid14255699, year = {1965}, author = {PRIDHAM, TG and LYONS, AJ}, title = {FURTHER TAXONOMIC STUDIES ON STRAIGHT TO FLEXUOUS STREPTOMYCETES.}, journal = {Journal of bacteriology}, volume = {89}, number = {2}, pages = {331-342}, pmid = {14255699}, issn = {0021-9193}, mesh = {*Cell Wall ; *Classification ; *Color ; *Research ; *Spores ; *Spores, Bacterial ; *Streptomyces ; *Streptomyces griseus ; }, abstract = {Pridham, Thomas G. (Northern Regional Research Laboratory, Peoria, Ill.), and Allister J. Lyons. Further taxonomic studies on straight to flexuous streptomycetes. J. Bacteriol. 89:331-342. 1965.-The best way to handle streptomycete classification, nomenclature, and identification is through application of a genus-species-subspecies concept. To establish a species, principal criteria are morphology of chains of spores and nature of spore-wall surfaces. Subspecies can be differentiated one from another by other criteria, such as chromogenicity, colors of sporulating aerial mycelium and of vegetative mycelium, carbon-utilization patterns, and assessment of qualitative production of antibiotics and sensitivity and resistance to antibacterial antibiotics. A literature study and laboratory studies of some strains suggested that streptomycetes with straight chains of spores could easily be differentiated from those with flexuous chains of spores. An intensive study of about 75 holotype and potential neotype strains indicated that such a differentiation is difficult to accomplish with confidence. Only 19 of the strains had straight chains of spores. These strains are considered, at this time, to be members of the species Streptomyces venezuelae Ehrlich et al. Forty-two of the strains had flexuous chains of spores and were assigned to the species Streptomyces griseus (Krainsky) Waksman and Henrici. Six of the strains had unusual spore-chain morphology. Classic taxonomic procedures allowed the separation of all the strains into a number of categories. The results suggest that more precise information on relationships of strains and qualitative antibiotic production will allow clarification of their sub-specific status. Consideration of the results obtained with strains having aberrant morphology allows some speculation on ranges of variations in morphology that might be encountered with the streptomycetes.}, } @article {pmid14255686, year = {1965}, author = {FRIEDMAN, S and DELEY, J}, title = {"GENETIC SPECIES" CONCEPT IN XANTHOMONAS.}, journal = {Journal of bacteriology}, volume = {89}, number = {1}, pages = {95-100}, pmid = {14255686}, issn = {0021-9193}, mesh = {*Centrifugation ; *DNA ; *DNA, Bacterial ; *Deuterium ; *Hybridization, Genetic ; *Metabolism ; *Molecular Weight ; *Nucleic Acid Hybridization ; *Research ; *Species Specificity ; *Xanthomonas ; }, abstract = {Friedman, S. (State University, Ghent, Belgium), and J. De Ley. "Genetic species" concept in Xanthomonas. J. Bacteriol. 89:95-100. 1965.-Deuterated, N(15)-labeled deoxyribonucleic acid (DNA) from Xanthomonas pelargonii forms distinct hybrids with ordinary DNA from X. hederae, X. juglandis, and X. carotae. Hybridization is less pronounced with X. phaseoli and X. begoniae. There is evidence that some hybridization occurs with X. vesicatoria, X. campestris, and X. tamarindi. These results favor the concept of a "genetic species," rather than a division of the genus into many separate species based almost entirely on phytopathogenic host specificity.}, } @article {pmid14219057, year = {1964}, author = {DELEY, J and FRIEDMAN, S}, title = {DEOXYRIBONUCLEIC ACID HYBRIDS OF ACETIC ACID BACTERIA.}, journal = {Journal of bacteriology}, volume = {88}, number = {4}, pages = {937-945}, pmid = {14219057}, issn = {0021-9193}, mesh = {*Acetic Acid ; *Acetobacter ; *Bacteria ; *Base Composition ; *DNA ; *DNA, Bacterial ; *Hybridization, Genetic ; *Nucleic Acid Hybridization ; *Research ; }, abstract = {De Ley, J. (State University, Ghent, Belgium), and S. Friedman. Deoxyribonucleic acid hybrids of acetic acid bacteria. J. Bacteriol. 88:937-945. 1964.-Deuterated N(15)-labeled deoxyribonucleic acid (DNA) from Acetobacter aceti (mesoxydans 4) forms hybrids with ordinary DNA from other species of this genus (A. xylinum, A. pasteurianus, A. estunensis, and possibly A. xylinoides) when the guanine plus cytosine base composition does not vary by more than 1 to 2%. Beyond this limit (A. aceti Ch31 and A. muciparus 5) no hybrids are formed. The hybrids are apparently derived from an asymmetrical part of the compositional distribution. The results lend strength to the concept of a genetic species rather than to a division of a genus into sharply separated species, based on small phenotypic differences. Taxonomic implications are discussed.}, } @article {pmid4157725, year = {1964}, author = {De Ley, J and Friedman, S}, title = {[Desoxyribonucleic acid hybrids and the bacterial species concept].}, journal = {Archives internationales de physiologie et de biochimie}, volume = {72}, number = {4}, pages = {681-683}, pmid = {4157725}, issn = {0003-9799}, mesh = {Acetobacter/*classification/*metabolism ; Biochemical Phenomena ; Biochemistry ; DNA/*biosynthesis ; Genetics ; In Vitro Techniques ; Ultracentrifugation ; }, } @article {pmid14206507, year = {1964}, author = {HAYASHI, K}, title = {[ON A NEW CONCEPT OF "CENTER SPECIES" AND A CLASSIFICATION BASED ON THE CROSS-RELATIONSHIP OF MICROORGANISMS].}, journal = {Nihon saikingaku zasshi. Japanese journal of bacteriology}, volume = {19}, number = {}, pages = {175-180}, pmid = {14206507}, issn = {0021-4930}, mesh = {*Bacteria ; *Classification ; *Gram-Positive Cocci ; *Sarcina ; *Staphylococcus ; }, } @article {pmid13763754, year = {1960}, author = {LOVE, A}, title = {Species concept and taxonomy--a prelude.}, journal = {Revue canadienne de biologie}, volume = {19}, number = {}, pages = {216-218}, pmid = {13763754}, issn = {0035-0915}, mesh = {*Biological Evolution ; }, } @article {pmid13750107, year = {1960}, author = {SENN, HA}, title = {The species concept and taxonomy--summary.}, journal = {Revue canadienne de biologie}, volume = {19}, number = {}, pages = {320-325}, pmid = {13750107}, issn = {0035-0915}, mesh = {*Biological Evolution ; }, } @article {pmid13707891, year = {1960}, author = {GRANT, WF}, title = {The categories of classical and experimental taxonomy and the species concept.}, journal = {Revue canadienne de biologie}, volume = {19}, number = {}, pages = {241-262}, pmid = {13707891}, issn = {0035-0915}, mesh = {*Biological Evolution ; }, } @article {pmid13688306, year = {1960}, author = {BEAUDRY, JR}, title = {The species concept: its evolution and present status.}, journal = {Revue canadienne de biologie}, volume = {19}, number = {}, pages = {219-240}, pmid = {13688306}, issn = {0035-0915}, mesh = {*Biological Evolution ; }, } @article {pmid13810304, year = {1960}, author = {CIFERRI, R}, title = {The concept of species from superior to inferior plants.}, journal = {Mycopathologia et mycologia applicata}, volume = {13}, number = {}, pages = {81-92}, doi = {10.1007/BF02155504}, pmid = {13810304}, issn = {0027-5530}, mesh = {*Microbiology ; *Plants ; }, } @article {pmid13566160, year = {1958}, author = {ANDREWES, CH and SNEATH, PH}, title = {The species concept among viruses.}, journal = {Nature}, volume = {182}, number = {4627}, pages = {12-14}, doi = {10.1038/182012a0}, pmid = {13566160}, issn = {0028-0836}, mesh = {*Viruses ; }, } @article {pmid13509324, year = {1958}, author = {THIBAULT, P}, title = {[Concept of Shigella species].}, journal = {Annales de l'Institut Pasteur}, volume = {94}, number = {2}, pages = {213-8; discussion 219-23}, pmid = {13509324}, issn = {0020-2444}, mesh = {*Shigella ; }, } @article {pmid13509323, year = {1958}, author = {LE MINOR, L}, title = {[Concept of Salmonella species].}, journal = {Annales de l'Institut Pasteur}, volume = {94}, number = {2}, pages = {207-212}, pmid = {13509323}, issn = {0020-2444}, mesh = {*Salmonella ; }, } @article {pmid13509322, year = {1958}, author = {RENOUX, G}, title = {[Concept of species in the genus Brucella].}, journal = {Annales de l'Institut Pasteur}, volume = {94}, number = {2}, pages = {179-206}, pmid = {13509322}, issn = {0020-2444}, mesh = {*Brucella ; }, } @article {pmid13509321, year = {1958}, author = {SCHAEFFER, P}, title = {[Concept of species after recent research of bacterial genetics].}, journal = {Annales de l'Institut Pasteur}, volume = {94}, number = {2}, pages = {167-178}, pmid = {13509321}, issn = {0020-2444}, mesh = {*Bacteria ; *Research ; }, } @article {pmid13509320, year = {1958}, author = {VENDRELY, R}, title = {[Concept of species in the light of recent biochemical data & the L cycle].}, journal = {Annales de l'Institut Pasteur}, volume = {94}, number = {2}, pages = {142-166}, pmid = {13509320}, issn = {0020-2444}, mesh = {*Bacteria ; DNA/*metabolism ; *Light ; }, } @article {pmid13412619, year = {1957}, author = {WAKSMAN, SA}, title = {Species concept among the actinomycetes with special reference to the genus Streptomyces.}, journal = {Bacteriological reviews}, volume = {21}, number = {1}, pages = {1-29}, doi = {10.1128/br.21.1.1-29.1957}, pmid = {13412619}, issn = {0005-3678}, mesh = {*Actinobacteria ; *Actinomyces ; *Fungi ; *Streptomyces ; }, } @article {pmid13443835, year = {1957}, author = {DINGER, JE}, title = {[The concept of species in bacteriology].}, journal = {Acta Leidensia}, volume = {26}, number = {}, pages = {65-73}, pmid = {13443835}, issn = {0065-1362}, mesh = {*Bacteriology ; }, } @article {pmid13229217, year = {1954}, author = {THOM, C}, title = {The evolution of species concepts in Aspergillus and Penicillium.}, journal = {Annals of the New York Academy of Sciences}, volume = {60}, number = {1}, pages = {24-34}, doi = {10.1111/j.1749-6632.1954.tb39995.x}, pmid = {13229217}, issn = {0077-8923}, mesh = {*Aspergillus ; *Biological Evolution ; *Penicillium ; }, } @article {pmid13010234, year = {1952}, author = {CONRAD-MARTIUS, H}, title = {[The species problem through natural philosophical examination].}, journal = {Experientia}, volume = {8}, number = {10}, pages = {400-404}, doi = {10.1007/BF02176210}, pmid = {13010234}, issn = {0014-4754}, mesh = {*Biological Evolution ; *Zoology ; }, } @article {pmid15396753, year = {1949}, author = {BURMA, BH and MAYR, E}, title = {The species concept.}, journal = {Evolution; international journal of organic evolution}, volume = {3}, number = {4}, pages = {369-373}, doi = {10.1111/j.1558-5646.1949.tb00037.x}, pmid = {15396753}, issn = {0014-3820}, mesh = {Humans ; *Species Specificity ; }, } @article {pmid18880602, year = {1948}, author = {MANSFELD, R}, title = {[About the concept of species in systematic botany].}, journal = {Biologisches Zentralblatt}, volume = {67}, number = {7-8}, pages = {320-331}, pmid = {18880602}, issn = {0006-3304}, mesh = {*Botany ; }, } @article {pmid21001007, year = {1945}, author = {KURSANOV, LI}, title = {Concept of species in its application to the lower plants.}, journal = {Mikrobiologiia}, volume = {14}, number = {4}, pages = {210-214}, pmid = {21001007}, issn = {0026-3656}, mesh = {*Plants ; *Species Specificity ; }, } @article {pmid1285065, year = {1992}, author = {Miller, CC and Fayrer-Hosken, RA and Timmons, TM and Lee, VH and Caudle, AB and Dunbar, BS}, title = {Characterization of equine zona pellucida glycoproteins by polyacrylamide gel electrophoresis and immunological techniques.}, journal = {Journal of reproduction and fertility}, volume = {96}, number = {2}, pages = {815-825}, doi = {10.1530/jrf.0.0960815}, pmid = {1285065}, issn = {0022-4251}, mesh = {Animals ; Antigens/*chemistry/immunology/isolation & purification ; Cross Reactions ; *Egg Proteins ; Electrophoresis, Gel, Two-Dimensional ; Electrophoresis, Polyacrylamide Gel ; Epitopes/analysis ; Horses/immunology/*physiology ; Hot Temperature ; Immunoblotting ; Membrane Glycoproteins/*chemistry/immunology/isolation & purification ; Molecular Weight ; *Receptors, Cell Surface ; Silver Staining ; Solubility ; Zona Pellucida Glycoproteins ; }, abstract = {This study was designed to explore the composition of the equine zona pellucida (EZP) by one- and two-dimensional polyacrylamide gel electrophoresis (1D- and 2D-PAGE), silver staining and immunoblotting techniques. Antral follicles palpable on frozen-thawed equine ovaries were aspirated with a needle and syringe, and the resultant follicular fluid, cellular material and oocytes were pooled. Oocytes were placed in Petri dishes, moved by narrow-bore pipette to droplets of phosphate-buffered saline (PBS) and mechanically cleaned of cumulus cells. The EZP from these collected oocytes was solubilized, and then analysed by 1D- and 2D-PAGE. Silver stained 2D-PAGE of the EZP revealed the presence of three EZP glycoprotein families of apparent molecular mass ranges of 93-120 kDa, 73-90 kDa and 45-80 kDa. Immunoblot analysis of EZP glycoproteins resolved by 2D-PAGE using rabbit antisera against pig zonae pellucidae (R alpha HSPZ) confirmed the presence of three EZP glycoprotein families and established the existence of common epitopes between equine and porcine ZP glycoproteins. Further immunodetection using 2D-PAGE-separated glycoproteins illustrated that the 45-80 kDa family is recognized by the monoclonal antibody R5, developed against the porcine ZP glycoprotein of molecular mass 55-120 kDa. Guinea-pig antiserum against endo-beta-galactosidase-treated rabbit ZP 55 kDa glycoprotein (R55K), which specifically recognizes the rabbit ZP glycoprotein with the lowest molecular mass, also recognized the EZP 45-80 kDa glycoprotein family. Guinea-pig polyclonal antisera developed against total heat-solubilized rabbit ZP (GP alpha HSRZ) recognized the 73-90 kDa EZP glycoprotein family exclusively. After heat solubilization and treatment of EZP with endo-beta-galactosidase to remove polylactosaminoglycans, silver stained 1D-PAGE again demonstrated the presence of three glycoproteins with apparent molecular masses of 60, 75 and 90 kDa. The partially deglycosylated 60 kDa equine glycoprotein is recognized on immunoblot by the monoclonal antibody R5; the 75 kDa EZP glycoprotein is recognized by GP alpha HSRZ; and all three EZP glycoproteins separated by 1D-PAGE are recognized by R alpha HSPZ. These data add further support to the concept of cross-species zona pellucida glycoprotein antigenicity.}, } @article {pmid1360380, year = {1992}, author = {Ritschel, WA and Vachharajani, NN and Johnson, RD and Hussain, AS}, title = {The allometric approach for interspecies scaling of pharmacokinetic parameters.}, journal = {Comparative biochemistry and physiology. C, Comparative pharmacology and toxicology}, volume = {103}, number = {2}, pages = {249-253}, doi = {10.1016/0742-8413(92)90003-p}, pmid = {1360380}, issn = {0742-8413}, mesh = {Animals ; Body Weight ; Humans ; Life Expectancy ; Organ Size ; *Pharmacokinetics ; Species Specificity ; }, abstract = {A long standing problem in pharmacokinetics and toxicology is the extrapolation and correlation between results obtained in different animal species and man. Animal data may be scaled-up to predict PPs in man using the allometric approach. The allometric approach is empirical, but easy, and is based on the fact that the underlying physiological processes such as blood flow, heartbeat duration, breath duration etc. are essentially physical and related to B. This approach is generally applicable to compounds that are essentially renally excreted. For substances that are highly extracted by the liver, Cltot is a function of the LBF among various species. Based on the concept of neoteny, use of brain weight affords a more correct approach to the scaling of Cl(int) of low extraction ratio drugs. By using the invariant pharmacokinetic time, the superficial differences in concentration-time profiles due to chronological time among different species are removed. Finally, as Boxenbaum (1984) has said "parameters to be scaled, independent variables, and the mathematical relationships used in the scaling process are all at the discretion of the investigator. There are no proper or improper approaches; the only limitations are those imposed by the investigator."}, } @article {pmid1328477, year = {1992}, author = {Van Ranst, M and Kaplan, JB and Burk, RD}, title = {Phylogenetic classification of human papillomaviruses: correlation with clinical manifestations.}, journal = {The Journal of general virology}, volume = {73 (Pt 10)}, number = {}, pages = {2653-2660}, doi = {10.1099/0022-1317-73-10-2653}, pmid = {1328477}, issn = {0022-1317}, support = {5P30CA13330/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Amino Acid Sequence ; DNA, Viral/genetics ; Humans ; Molecular Sequence Data ; Oncogene Proteins, Viral/classification/*genetics ; Open Reading Frames ; Organ Specificity ; Papillomaviridae/*classification/genetics/pathogenicity ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Tumor Virus Infections/genetics/*pathology ; Viral Proteins/classification/*genetics ; }, abstract = {Human papillomaviruses (HPVs) are a heterogeneous group of small dsDNA viruses which cause a variety of proliferative epithelial lesions at specific anatomical sites. Although more than 65 different virus types have been cloned and characterized, no uniform classification system exists. In order to classify HPV DNA types, phylogenetic trees were constructed based on nucleotide sequence alignments using parsimony and distance matrix algorithms. The resulting phylogenetic trees provide a classification of the HPVs into specific groups encompassing the known tissue tropism and oncogenic potential of each HPV type. The implications of a phylogenetic taxonomy on the diagnostic detection of HPVs and the concept of different HPV species are discussed.}, } @article {pmid1571021, year = {1992}, author = {Ackermann, HW and DuBow, MS and Jarvis, AW and Jones, LA and Krylov, VN and Maniloff, J and Rocourt, J and Safferman, RS and Schneider, J and Seldin, L}, title = {The species concept and its application to tailed phages.}, journal = {Archives of virology}, volume = {124}, number = {1-2}, pages = {69-82}, pmid = {1571021}, issn = {0304-8608}, mesh = {Bacteriophages/*classification/genetics/immunology/ultrastructure ; Classification/*methods ; Nucleic Acid Hybridization ; Sequence Homology, Nucleic Acid ; Serotyping ; Species Specificity ; Virology/*methods ; }, abstract = {A recently proposed polythetic definition of virus species appears easily applicable to bacteriophages. Criteria for classification of tailed phages are evaluated. Morphology, DNA homology, and serology are the most important criteria for delineation of species, but no single criterion is satisfactory. Dot-blot hybridization and seroneutralization may suggest false relationships by detecting common sequences in the DNA of otherwise unrelated phages. Species of tailed phages can be defined by a combination of morphology and DNA homology or serology. A procedure for identification of novel phages is outlined. Phage names should include elements of host names.}, } @article {pmid1658185, year = {1991}, author = {Swallow, CJ and Grinstein, S and Sudsbury, RA and Rotstein, OD}, title = {Nitric oxide derived from L-arginine impairs cytoplasmic pH regulation by vacuolar-type H+ ATPases in peritoneal macrophages.}, journal = {The Journal of experimental medicine}, volume = {174}, number = {5}, pages = {1009-1021}, pmid = {1658185}, issn = {0022-1007}, mesh = {*Acid-Base Equilibrium ; Animals ; Arginine/analogs & derivatives/metabolism/*pharmacology ; Bicarbonates/metabolism ; Cyclic AMP/physiology ; Cyclic GMP/physiology ; Cytoplasm/metabolism ; Female ; Hydrogen-Ion Concentration ; In Vitro Techniques ; Lipopolysaccharides ; Macrophages/drug effects/*metabolism ; Mice ; Nitric Oxide/*pharmacology ; Peritoneal Cavity/cytology ; Proton-Translocating ATPases/antagonists & inhibitors/*physiology ; Sodium/metabolism ; Vacuoles/*enzymology ; omega-N-Methylarginine ; }, abstract = {The ability of macrophages (Møs) to function within an acidic environment has been shown to depend on cytoplasmic pH (pHi) regulation by vacuolar-type H+ ATPases. Møs metabolize L-arginine via an oxidative pathway that generates nitric oxide, nitrate, and nitrite. Since each of these products could potentially inhibit vacuolar-type H+ ATPases, we investigated the effect of L-arginine metabolism on Mø pHi regulation in thioglycolate-elicited murine peritoneal Møs. H+ ATPase-mediated pHi recovery from an imposed cytoplasmic acid load was measured fluorometrically. When Møs were incubated with L-arginine (0.25-2.0 mM), their rate of pHi recovery declined progressively from 2 to 6 h of incubation. By contrast, the recovery rate of cells incubated in arginine-free medium remained stable over the same period. The impairment of pHi recovery was specific for L-arginine, and was blocked competitively by NG-monomethyl-L-arginine, demonstrating its dependence on L-arginine metabolism. In addition, the inhibition of pHi recovery was enhanced by lipopolysaccharide, an agent known to stimulate L-arginine metabolism by Møs. Scavenging the L-arginine metabolite nitric oxide with either ferrous sulphate or ferrous myoglobin prevented the inhibition of pHi recovery, implying that L-arginine-derived nitric oxide was the species responsible for the inhibition. This concept was supported by the finding of elevated nitrite levels in the supernatant of cells incubated in L-arginine. Furthermore, incubation of Møs with sodium nitroprusside mimicked the L-arginine-dependent inhibition of H+ ATPase activity. Treatment with the cyclic GMP analogue, 8-bromoguanosine 3':5'-cyclic monophosphate, similarly impaired Mø pHi recovery, suggesting that a nitric oxide-stimulated elevation of cyclic GMP may contribute to the L-arginine-dependent inhibition of pHi regulation.}, } @article {pmid1779919, year = {1991}, author = {Aboitiz, F}, title = {Lineage selection and the capacity to evolve.}, journal = {Medical hypotheses}, volume = {36}, number = {2}, pages = {155-156}, doi = {10.1016/0306-9877(91)90260-6}, pmid = {1779919}, issn = {0306-9877}, mesh = {Animals ; *Biological Evolution ; Models, Genetic ; Mutation ; *Selection, Genetic ; }, abstract = {The capacity of genetic recombination is an unusual adaptive trait since it is based on the capacity to produce evolutionary change rather than on the capacity to produce better performing individuals. The evolution of this character has been considered to be a case of group or species selection. Alternatively, I introduce a new concept, lineage selection, to account for the evolution of this trait.}, } @article {pmid1782293, year = {1991}, author = {Fang, JS and Jagiello, GM}, title = {Unique state of sexual dimorphism of crossing-over in diplotene spermatocytes and oocytes of Mesocricetus brandti, a species with neonatal oogenesis.}, journal = {Biology of reproduction}, volume = {45}, number = {3}, pages = {447-454}, doi = {10.1095/biolreprod45.3.447}, pmid = {1782293}, issn = {0006-3363}, mesh = {Animals ; Animals, Newborn/*physiology ; Cricetinae ; *Crossing Over, Genetic ; Female ; Male ; Meiosis ; Mesocricetus ; Oocytes/*ultrastructure ; *Oogenesis ; *Sex Characteristics ; Spermatozoa/*ultrastructure ; }, abstract = {Sexual dimorphism of recombination has been held by classic genetic theory to disfavor the heterogametic sex. Assessment of chiasma frequencies at the diplotene stage of meiosis has been used as a valid measure of this concept and in many species has revealed, as expected, an increased frequency in female vs. male germ cells. Mesocricetus brandti, a species currently used in investigations of gonadal regression, photoperiods, and hibernation, was found by this measure to be an exception to this rule, with an average of 29.81 chiasmata in spermatocytes and 23.16 in oocytes. Sites of crossing-over unique to each sex were also detected. Oogenesis occurs in this species as a postnatal phenomenon and is suggested as a possible critical factor for the exceptional recombinant behavior.}, } @article {pmid1943153, year = {1991}, author = {Sereno, MI}, title = {Four analogies between biological and cultural/linguistic evolution.}, journal = {Journal of theoretical biology}, volume = {151}, number = {4}, pages = {467-507}, doi = {10.1016/s0022-5193(05)80366-2}, pmid = {1943153}, issn = {0022-5193}, mesh = {*Biological Evolution ; Cell Physiological Phenomena ; *Culture ; Genes/physiology ; Humans ; *Linguistics ; Models, Biological ; }, abstract = {The intricate phenomena of biology on the one hand, and language and culture on the other, have inspired many writers to draw analogies between these two evolutionary systems. These analogies can be divided into four principal types: species/language, organism/concept, genes/culture, and cell/person. Here, it is argued that the last analogy--between cells and persons--is the most profound in several respects, and, more importantly, can be used to generate a number of empirical predictions. In the first half of the paper, the four analogies are each evaluated after briefly describing criteria for a good predictive analogy. In the second half of the paper, the cell/person analogy and predictions deriving from it are explored in detail.}, } @article {pmid1831948, year = {1991}, author = {Zaĭdenov, AM and Morozov, AA and Kostiukovskiĭ, VM and Gurleva, GG and Brudnyĭ, RA and Kalashnikov, IA and Blagorodova, NS and Nagornaia, AF and Kutishevskaia, EF and Kucheriavaia, IE}, title = {[Pseudotuberculosis in the Krasnodar Territory. The clinico-epidemiological characteristics of its morbidity and the biological properties of its strains].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {4}, pages = {26-28}, pmid = {1831948}, issn = {0372-9311}, mesh = {Antibodies, Bacterial/blood ; Camping ; Child ; Disease Outbreaks/*statistics & numerical data ; Disease Reservoirs ; Food Microbiology ; Health Resorts ; Humans ; Russia/epidemiology ; Seasons ; Yersinia pseudotuberculosis/immunology/*isolation & purification ; Yersinia pseudotuberculosis Infections/*epidemiology/etiology/microbiology ; }, abstract = {Group cases of pseudotuberculosis, first registered at health-restoring institutions of the health resort of Gelendzhik (the Krasnodar Territory), are described. The etiology of these cases of the disease was established on the basis of clinico-epidemiological data, specific seroconversion in 66% of the examined patients and the isolation of Yersinia pseudotuberculosis strains from the feces of four patients. The combination of signs observed in the isolated strains, viz. the presence of plasmids with molecular weights of 75 and 45 MD, resistance to bactericidal factors of normal human serum and autoagglutination in cell culture medium, made it possible to consider these strains to be virulent. The cases of infection were probably caused by the use of fresh cabbage salad. The study of 3,128 rodents caught in the Krasnodar Territory, including those caught in the area of the health resort, resulted in the isolation of 105 Y. enterocolitica strains and strains of 5 other Yersinia species, but not Y. pseudotuberculosis strains. The concept on the saprozoonotic nature of pseudotuberculosis was substantiated.}, } @article {pmid1958131, year = {1991}, author = {Van Regenmortel, MH and Maniloff, J and Calisher, C}, title = {The concept of virus species.}, journal = {Archives of virology}, volume = {120}, number = {3-4}, pages = {313-314}, pmid = {1958131}, issn = {0304-8608}, mesh = {Terminology as Topic ; Viruses/*classification ; }, } @article {pmid1912947, year = {1991}, author = {Baulieu, EE}, title = {Neurosteroids: a new function in the brain.}, journal = {Biology of the cell}, volume = {71}, number = {1-2}, pages = {3-10}, doi = {10.1016/0248-4900(91)90045-o}, pmid = {1912947}, issn = {0248-4900}, mesh = {Animals ; Brain/*metabolism ; Humans ; Molecular Structure ; Steroids/*metabolism ; }, abstract = {"Neurosteroids" accumulate in the central nervous system independently of supply by peripheral endocrine glands. Dehydroepiandrosterone (DHA) and pregnenolone (delta 5P) were first found in the rat brain. Then, a steroid biosynthetic pathway was demonstrated in oligodendrocytes, mostly by enzyme immunocytochemistry and biochemical studies in primary cultures of glial cells, where the formation, from appropriate radioactive precursors, of delta 5P, delta 5-pregn-3 beta, 20 alpha-diol (20 alpha-DH delta 5P), progesterone (P), 5 alpha-pregnane-3,20-dione (5 alpha-DHP) and 3 alpha-hydroxy-5 alpha-pregnane-20-one (3 alpha, 5 alpha-THP), as well as estrogen-induced nuclear progesterone receptor (PR) was observed. Several biological effects of neurosteroids have been observed, such as electrical stimulation of neurones, involvement in behaviorial activities, modulation of GABAA-receptor (GABAA-R) function (potentiated by 3 alpha, 5 alpha-THP and its 21-hydroxyderivative, antagonized by delta 5P- and DHA-sulfates) and growth/differentiation of glial cells in vitro. Preliminary findings suggest that the neurosteroid concept applies to all mammalian species, including man. Further investigations should assess the pathophysiological significance of the synthesis of neurosteroids and decipher their mechanisms of action via nuclear and membrane receptors.}, } @article {pmid1856360, year = {1991}, author = {Sapunov, VB}, title = {[The concept of "species--ecological mates" and some obscure points in the evolution of the family of hominids].}, journal = {Izvestiia Akademii nauk SSSR. Seriia biologicheskaia}, volume = {}, number = {1}, pages = {152-156}, pmid = {1856360}, issn = {0002-3329}, mesh = {Animals ; *Biological Evolution ; Ecology ; Hominidae/*classification ; Humans ; Species Specificity ; }, abstract = {Species-ecological twins are the related species that inhabit the same habitats. Both micro- and macroevolution proceeds faster in a system with two such species than in a single species. The hypothesis that evolution of hominids was accelerated by the existence of twin species has been proposed. Species of the Australopithecus genus were twin species for Homo habilis and H. erectus. Both paleontological and cryptozoological data indicate that H. sapiens also has a complimentary species. Small population of the twin species may still exist in obscure parts of the Earth.}, } @article {pmid2132434, year = {1990}, author = {de Zulueta, J}, title = {Forty years of malaria eradication in Sardinia. A new appraisal of a great enterprise.}, journal = {Parassitologia}, volume = {32}, number = {2}, pages = {231-236}, pmid = {2132434}, issn = {0048-2951}, mesh = {Animals ; Anopheles/parasitology ; Foundations ; History, 20th Century ; History, Ancient ; Humans ; Insect Vectors ; Italy/epidemiology ; Malaria/epidemiology/history/mortality/*prevention & control ; Mosquito Control/*history ; Plasmodium falciparum ; Prevalence ; United Nations ; }, abstract = {The campaign against malaria in Sardinia carried out by the Ente Regionale per la Lotta Anti-Anofelica in Sardegna (ERLAAS), appears today as one of the greatest efforts against malaria since the discovery of its aetiology and mode of transmission. The disease was eradicated without achieving the eradication of the vector, Anopheles labranchiae, the main objective of the campaign. This species eradication failure had been at first attributed to the indigenous character of A. labranchiae and its long standing in the island. A more recent analysis, based on paleoclimatological information, makes virtually impossible the presence of A. labranchiae during the last (Würm) glacial period and indicates a comparatively recent introduction of the species in the island. It was the absence of A. atroparvus, with which it has usually to compete in Southern Europe, what permitted the wide distribution of A. labrianchiae in the island. Four decades after the events the concept of species eradication as an anti-malaria weapon appears as basically wrong, the results of Sardinia as well as those obtained in the Italian mainland having demonstrated that the eradication of the vector was not required for the successful eradication of the disease.}, } @article {pmid1695478, year = {1990}, author = {Sheahan, K and O'Brien, MJ and Burke, B and Dervan, PA and O'Keane, JC and Gottlieb, LS and Zamcheck, N}, title = {Differential reactivities of carcinoembryonic antigen (CEA) and CEA-related monoclonal and polyclonal antibodies in common epithelial malignancies.}, journal = {American journal of clinical pathology}, volume = {94}, number = {2}, pages = {157-164}, doi = {10.1093/ajcp/94.2.157}, pmid = {1695478}, issn = {0002-9173}, mesh = {*Antibodies, Monoclonal ; Antibodies, Neoplasm/*immunology ; Carcinoembryonic Antigen/*immunology ; Carcinoma/immunology/*pathology ; Epitopes/immunology ; Female ; Humans ; Immunoenzyme Techniques ; Male ; Neoplasm Metastasis ; }, abstract = {To evaluate the role of carcinoembryonic antigen (CEA) in solving problems of tumor histogenesis in surgical pathology, monoclonal antibodies to four distinct epitopes of CEA (E-Z-EM) were applied to paraffin sections of 303 epithelial neoplasms from multiple sites. Two epitopes were CEA specific (D14 and B7.1), one was shared with nonspecific cross-reacting antigen (NCA) (B7.8), and the fourth (B18) was common to CEA, NCA, and biliary glycoprotein antigen (BGP). A sample of the tumors (n = 110) was also stained with a polyclonal anti-CEA (DAKO). Gastrointestinal adenocarcinomas, including esophageal and gastric (n = 19), small intestinal (n = 8), colorectal (n = 56), biliary tract (n = 8), and pancreatic adenocarcinomas (n = 14), were consistently positive with all five antibodies. Other predominantly gland-forming carcinomas tested, comprising lung (n = 22), ovary (n = 18), and endometrium (n = 12), were either invariably negative with all five antibodies (endometrial adenocarcinoma, non-mucinous ovarian adenocarcinoma) or demonstrated selective and variable positivity (lung: D14, 50%; ovarian mucinous: D14, 50%). Among large polygonal cell carcinomas (hepatocellular carcinoma, renal cell carcinoma, melanoma, and adrenal carcinoma), only hepatomas stained positively, showing a distinctive canalicular staining pattern with the B18 (BGP epitope) (55%) and polyclonal antibody (50%). In the small polygonal cell carcinoma category, true CEA positivity was rare in breast (D14, 10% and B7.1, 14%) and never seen in prostatic carcinomas and carcinoid tumors. A subset of these breast (8 of 42), prostate (4 of 22), and carcinoids (4 of 7) showed exclusive positivity for the B18 antibody (NCA/BGP epitope). Ovarian serous papillary carcinomas (n = 14), papillary carcinomas of thyroid (n = 12), transitional cell carcinomas of the bladder (n = 11), and mesotheliomas (n = 3) were negative with all monoclonal antibodies. Metastatic carcinomas (n = 74) showed a similar pattern of reactivity to primary tumors. The authors conclude that CEA immunostaining may assist in identifying the histogenesis of epithelial tumors in several morphologic categories; that differential reactivities of the CEA monoclonal antibody panel exceed those of the polyclonal antibody; and that the discriminating power of the monoclonal panel is related to whether (1) CEA is or is not produced or (2) NCA or BGP is produced without concomitant CEA production. There is little evidence to support a concept of site-specific CEA species.}, } @article {pmid1695661, year = {1990}, author = {Berger, P and Klieber, R and Panmoung, W and Madersbacher, S and Wolf, H and Wick, G}, title = {Monoclonal antibodies against the free subunits of human chorionic gonadotrophin.}, journal = {The Journal of endocrinology}, volume = {125}, number = {2}, pages = {301-309}, doi = {10.1677/joe.0.1250301}, pmid = {1695661}, issn = {0022-0795}, mesh = {Antibodies, Monoclonal/*immunology ; Chorionic Gonadotropin/analysis/*immunology ; Chorionic Gonadotropin, beta Subunit, Human ; Enzyme-Linked Immunosorbent Assay ; Epitopes/immunology ; Glycoprotein Hormones, alpha Subunit/analysis/immunology ; Humans ; Immunoenzyme Techniques ; Peptide Fragments/analysis/immunology ; Radioimmunoassay ; }, abstract = {Discordant results on body fluid levels of human chorionic gonadotrophin (hCG) free alpha- and beta-subunits under physiological and pathophysiological conditions, prompted us to raise a total of 260 monoclonal antibodies (MCA) against free hCG-alpha, free hCG-beta, holo-hCG, human follicle-stimulating hormone and bovine luteinizing hormone; 153 MCA recognizing the human alpha-subunit and 28 reacting with hCG-beta were extensively analysed for their intra- and inter-species cross-reactivity with homologous hormones, and for the compatibility of epitopes recognized by them. The immunological topography of free hCG-alpha and free hCG-beta was resolved by these MCA, and epitope maps were designed. Six antigenic determinants on the free alpha-chain (alpha 1-alpha 6), clustered in three spatially distinct domains, and seven epitopes on the surface of free hCG-beta (beta 1-beta 7), could be distinguished. Strikingly, three alpha-chain epitopes (alpha 4, alpha 5 and alpha 6) were shared between various species, which is in contradiction to the concept of immunological species-specificity of alpha-subunits. Three determinants were found to be present only on the free subunits but not on holo-hCG (alpha 6, beta 6 and beta 7), and only two determinants (beta 1 and beta 7) were hormone-specific for hCG. Based on this information, an immunoenzymometric assay for the free alpha-subunit of human glycoprotein hormones was established, with a sensitivity of 1.3 pg/well and a cross-reactivity with holo-hCG of less than 0.005%.(ABSTRACT TRUNCATED AT 250 WORDS)}, } @article {pmid2331796, year = {1990}, author = {Morey, AL and Carlile, S}, title = {Auditory brainstem of the ferret: maturation of the brainstem auditory evoked response.}, journal = {Brain research. Developmental brain research}, volume = {52}, number = {1-2}, pages = {279-288}, doi = {10.1016/0165-3806(90)90246-u}, pmid = {2331796}, issn = {0165-3806}, mesh = {Acoustic Stimulation ; Aging/*physiology ; Animals ; Auditory Pathways/*physiology ; Auditory Threshold ; Brain Stem/growth & development/*physiology ; Carnivora/*physiology ; Evoked Potentials ; Female ; Ferrets/growth & development/*physiology ; Male ; Reaction Time/physiology ; }, abstract = {A longitudinal study of developmental changes in the brainstem auditory evoked response (BAER) was made on 19 ferrets between postnatal days 25 (P25) and 50. Responses to free-field click stimuli were recorded from anaesthetized animals, and compared with data obtained from 8 adult ferrets. A reproducible BAER was first recordable on P27, although the response onset was generally later in smaller animals. BAER onset preceded eye opening, which started on P32. Adult-like thresholds were observed in all animals by P40, but the age at which they were attained was also dependent on size. The BAER in the adult ferret consists of 4 main vertex-positive peaks occurring in the first 5 ms following transient acoustic stimulation. In the youngest animals the presence of an additional peak (between II and III) and the slurring of peaks III and IV were consistent features. The individual peaks undergo an asymmetrical pattern of development, with mean peak I latency attaining an adult value at P40, while mean peak IV latency is still 115% of the mean adult value at that age. BAERs could routinely be recorded using high stimulus presentation rates (greater than 40/s), though an increase in absolute and interpeak latencies occurred, the extent of which decreased with age. The pattern of BAER development in the ferret is compared with that in other species, and the concept of the 'silent period' (period between conception and onset of hearing) as a standard unit of auditory development is introduced.}, } @article {pmid2272775, year = {1990}, author = {Van Regenmortel, MH}, title = {Virus species, a much overlooked but essential concept in virus classification.}, journal = {Intervirology}, volume = {31}, number = {5}, pages = {241-254}, doi = {10.1159/000150159}, pmid = {2272775}, issn = {0300-5526}, mesh = {Plant Viruses/*classification ; Terminology as Topic ; Viruses/*classification ; }, } @article {pmid2167260, year = {1990}, author = {Shuter, SL and Davies, MJ and Garlick, PB and Hearse, DJ and Slater, TF}, title = {Studies on the effects of antioxidants and inhibitors of radical generation on free radical production in the reperfused rat heart using electron spin resonance spectroscopy.}, journal = {Free radical research communications}, volume = {9}, number = {3-6}, pages = {223-232}, doi = {10.3109/10715769009145680}, pmid = {2167260}, issn = {8755-0199}, support = {R01-HL 372780/HL/NHLBI NIH HHS/United States ; }, mesh = {Allopurinol/pharmacology ; Animals ; Antioxidants/*pharmacology ; Catalase/pharmacology ; Deferoxamine/pharmacology ; Electron Spin Resonance Spectroscopy ; *Free Radicals ; In Vitro Techniques ; Male ; Myocardial Reperfusion Injury/*metabolism ; Rats ; Rats, Inbred Strains ; Superoxide Dismutase/pharmacology ; }, abstract = {Reperfusion of the heart after a period of ischaemia can precipitate ventricular arrhythmias and lead to an exacerbation of tissue injury. Direct evidence to suggest the involvement of free radicals has been obtained using electron spin resonance (esr) spectroscopy and the spin trap N-tert. butyl-alpha-phenyl nitrone (PBN). In the present study, we have used esr spectroscopy and PBN to examine the individual effects of superoxide dismutase (SOD), catalase, allopurinol or desferal on radical production in the isolated, reperfused rat heart. A burst of radical production was observed in the control group during the first 5 minutes of reperfusion; the peak occurred during the first minute, when signal intensity had increased by almost 300%, but returned to the baseline by 15 minutes of reperfusion. The esr signals were consistent with the trapping of either alkoxyl or carbon-centered radicals (aN = 13.6 and aH = 1.56 G). In the desferal-treated group, a burst of radical production was observed during the first five minutes of reperfusion; this was maximal during the second minute, when signal intensity had increased by almost 200%, but had returned to the baseline value by 30 minutes of reperfusion. In the SOD-treated group, a burst of radical production was observed during the first 10 minutes of reperfusion; signal intensity was maximal during the tenth minute of reperfusion, when signal intensity had increased by almost 200%, but had returned to the baseline value by 30 minutes of reperfusion. In the allopurinol- and catalase-treated groups, no significant burst of radical production could be detected. These data further support the concept that cytotoxic, oxygen-derived species are formed upon reperfusion and that hydrogen peroxide and/or hydroxyl radicals, are likely to be involved.}, } @article {pmid2092335, year = {1990}, author = {Rheinberger, HJ}, title = {[Buffon: time, change and history].}, journal = {History and philosophy of the life sciences}, volume = {12}, number = {2}, pages = {203-223}, pmid = {2092335}, issn = {0391-9714}, mesh = {Animals ; *Biological Evolution ; France ; History, 18th Century ; Humans ; Life Style ; *Philosophy/history ; Social Change ; Time ; }, abstract = {There is a longstanding and ongoing controversy about whether Buffon is to be regarded as a forerunner of evolutionism in the eighteenth century, or even as one of the founders of transformistic biology. There are good reasons to deny this claim. There are good reasons even to deny that the question which is going to be answered negatively is of particular importance. The present paper addresses the issue from a different angle. It analyzes the concept of time operative in the natural history writings of Buffon, and it delineates the articulation of the concepts of time, change, and history with its organizing impact on Buffon's discourse on earth and organisms. It is argued that although with his species concept Buffon tries to introduce the classical notion of a physical system into biology, in order to do so, he has to subvert it by an element of time. This guides him in considering various aspects of organic change, but by itself does not lead to a general perspective of transformation. On the other hand, in his Epoques de la nature, Buffon introduces a general law of geological change, thus arriving at something which could be called a physically intelligible history. The conquest of natural history by physics, in one and the same movement, leads to a subversion of physical geology by history, and prevents biology from becoming evolutionistic in the sense in which the nineteenth century understands this term.}, } @article {pmid1968651, year = {1990}, author = {Savic, IR and Nevo, E}, title = {The Spalacidae: evolutionary history, speciation and population biology.}, journal = {Progress in clinical and biological research}, volume = {335}, number = {}, pages = {129-153}, pmid = {1968651}, issn = {0361-7742}, mesh = {Animals ; *Biological Evolution ; Chromosomes ; Genetic Variation ; Karyotyping ; Paleontology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Population ; Rodentia/*genetics ; }, abstract = {The evolutionary history of Spalacidae is reviewed taxonomically, paleontologically and neontologically. We focused selectively on taxonomy, biogeography, paleontology and evolutionary origins, chromosomal evolution, population biology and the species concept in Spalacidae. We concluded that the taxonomy of Spalacidae needs a modern revision based on chromosome and molecular-genetic data, beside that of morphology, physiology and behavior. The subterranean Spalacidae originated probably from a muroid-cricetoid stock in Asia Minor or vicinity, in Upper Oligocene times and adaptively radiated underground in the Balkans, steppic Russia and Middle East, extending into North Africa. The major important evolutionary feature in peripatric or allopatric speciation and adaptive radiation was karyotypic evolution, primarily through Robertsonian changes. More than 30 karyotypes (2n = 38-62; NF = 72-124) earlier represented by 8 classical species, occur primarily allopatrically or parapatrically, with only marginal sympatry, across the Eastern Mediterranean range of the family. Most karyotypes represent biospecies adapted at multiple organizational levels to their different ecologies. A short overview is presented on population biology and life history parameters of the Spalacidae which result in K-selected, "equilibrium species". Speciation in action and adaptive radiation embracing molecular and organismal adptations to the subterranean unique ecotope and to four different climatic regimes, have been multidisciplinarily studied in the Israeli Spalax ehrenbergi superspecies.}, } @article {pmid554549, year = {1979}, author = {Giorgio, A}, title = {[New classification of bacterium (author's transl)].}, journal = {Annali Sclavo; rivista di microbiologia e di immunologia}, volume = {21}, number = {6}, pages = {743-769}, pmid = {554549}, mesh = {Bacteria/*classification/cytology ; Bacterial Physiological Phenomena ; Terminology as Topic ; }, abstract = {The Author proposes a new classification of bacterium. It has been drawn up with the acquisitions of these last years regarding morfological, physiological and ecological characteristics and genetics of bacterium. It is also based on a new biological concept of the species, which is valid both for the "procarioti" and for the "eucarioti". Such a new concept, in time, makes a really new natural classification of the bacterium possible. Therefore the classification proposed here does not want to be nor must it be considered complete. It has been formed to be dynamic, capable that is of being modified as knowledge progresses.}, } @article {pmid289785, year = {1979}, author = {Kenney, RM and Condon, W and Ganjam, VK and Channing, C}, title = {Morphological and biochemical correlates of equine ovarian follicles as a function of their state of viability or atresia.}, journal = {Journal of reproduction and fertility. Supplement}, volume = {}, number = {27}, pages = {163-171}, pmid = {289785}, issn = {0449-3087}, mesh = {Androgens/metabolism ; Animals ; Chorionic Gonadotropin/metabolism ; Estrogens/metabolism ; Estrus ; Extracellular Space/physiology ; Female ; Horses/*physiology ; Ovarian Follicle/*cytology/physiology ; *Ovulation ; Pregnancy ; Progesterone/metabolism ; Prostaglandins F/metabolism ; }, abstract = {The histological features and hormonal content of follicular fluid of antral follicles during oestrus were correlated. As a result it was possible to characterize several categories of viable and atretic follicles. A seemingly important stage in maturation appeared to be at 3 cm in diameter since follicular oestrogens and androgens underwent a 3-fold increase in concentration at that size. Evidence was obtained to suggest that oestrogens are anti-atretogenic. However, a drop in oestrogens was not the cause of atresia since degeneration commenced when levels were high. Contrary to the concept that androgens are atretogenic in some species, it was also evident that elevated androgens did not precipitate spontaneous atresia. Theca epithelioid cells not only underwent histological luteinization in viable follicles as they matured toward ovulation but occasionally in atretic follicles as well. Elevated prostaglandin F levels were associated with follicles in the transitory states of either luteinization or atresia. Granulosa cells of viable follicles only were capable of specifically binding hCG. It was not determined whether loss of binding capacity or atresia occurred first. Follicular atresia in the mare appears to be a gradual process of which the initiating cause remains unknown.}, } @article {pmid714145, year = {1978}, author = {Samson, RA and van der Lustgraaf, B}, title = {Aspergillus penicilloides and Eurotium halophilicum in association with house-dust mites.}, journal = {Mycopathologia}, volume = {64}, number = {1}, pages = {13-16}, pmid = {714145}, issn = {0301-486X}, mesh = {*Air Microbiology ; Animals ; Ascomycota/classification/*isolation & purification ; Aspergillus/classification/*isolation & purification ; *Dust ; Mites/*microbiology ; }, abstract = {Aspergillus penicilloides Speg., Eurotium halophilicum Christensen et al. and other xerophilic fungi were isolated from house dust. The isolates of E. halophilicum are described and compared with the type strain of this species. A. penicilloides appeared to be rather common. The species concept of this species is broadened to accomodate some variable forms with different colony characters and conidophore structures. The role of both species is discussed in connection with house-dust mites, house-dust allergy and skin diseases.}, } @article {pmid79606, year = {1978}, author = {Perlmutter, RM and Hansburg, D and Briles, DE and Nicolotti, RA and Davie, JM}, title = {Subclass restriction of murine anti-carbohydrate antibodies.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {121}, number = {2}, pages = {566-572}, pmid = {79606}, issn = {0022-1767}, mesh = {Animals ; *Antibodies, Bacterial ; Antibody Specificity ; Carbohydrates/*immunology ; Cattle ; Immunoglobulin G ; Mice ; Mice, Inbred A ; Mice, Inbred AKR ; Mice, Inbred BALB C ; Radioimmunoassay ; Streptococcus/*immunology ; gamma-Globulins/immunology ; }, abstract = {Examination of the subclass distribution of murine antibodies directed against groups A and C streptococcal carbohydrate, alpha-(1 leads to 3) dextran and phosphocholine yields the surprising observation that these carbohydrate antigens stimulate IgG responses largely restricted to the rare IgG3 subclass. This subclass restriction is particularly impressive in light of the low circulating levels of IgG3 in nonimmune mouse serum and the failure of a variety of other antigens including proteins and aromatic haptens to stimulate IgG3 antibody production. Attempts to alter the subclass restriction of antibodies with carbohydrate specificity by immunization with carbohydrate-coupled protein have been unsuccessful and indicate that immunoregulation of subclass expression probably occurs at the level of the antibody forming (B) cell. It is therefore conceivable that VH regions of murine immunoglobulins may be restricted to particular IgG subclasses. A similar type of subclass restriction has been reported in human and rat anti-carbohydrate antibodies. This recruitment of a minor immunoglobulin isotype by carbohydrate antigens in several species further supports the concept of immunoregulation at the level of subclass, and suggests that these and other mammals may share a structurally similar isotype with perhaps a common evolutionary origin.}, } @article {pmid104037, year = {1978}, author = {Goldsmid, JM and Rogers, S}, title = {A parasitological study on the chacma baboon (Papio ursinus) from the Northern Transvaal.}, journal = {Journal of the South African Veterinary Association}, volume = {49}, number = {2}, pages = {109-111}, pmid = {104037}, issn = {1019-9128}, mesh = {Animals ; Eukaryota ; Haplorhini ; Helminths ; Papio/*parasitology ; Parasite Egg Count/methods ; }, abstract = {Baboons imported into Rhodesia from the Northern Transvaal proved to be heavily infected with intestinal protozoa and helminths. In fact, six protozoan species, one cestode and eight nematode species were recorded. A new concept in "identification graphs" is included in the paper which allows one to read off directly the species of strongyle eggs being passed by baboons in Southern Africa based upon length and breadth measurements of the eggs. Treatment of Balantidium coli and nematode infections of baboons is discussed as is the implication of some of these intestinal parasite infections in terms of potential human infection under natural conditions.}, } @article {pmid677375, year = {1978}, author = {Green, CA and Gordon, DH and Lyons, NF}, title = {Biological species in Praomys (Mastomys) natalensis (Smith), a rodent carrier of Lassa virus and bubonic plague in Africa.}, journal = {The American journal of tropical medicine and hygiene}, volume = {27}, number = {3}, pages = {627-629}, doi = {10.4269/ajtmh.1978.27.627}, pmid = {677375}, issn = {0002-9637}, mesh = {Animals ; *Arenaviridae ; Female ; Hemoglobins/analysis ; *Lassa virus ; Male ; Rats/classification/genetics/*microbiology ; *Yersinia pestis ; Zimbabwe ; }, abstract = {Plague has been known from countries surrounding Rhodesia from as early as 1935, but was first reported from Rhodesia in 1974. Part of our investigation of the complex ecosystem involving Yersinia pestis is critical assessment of the evolutionary status of natural populations belonging to formal, taxonomic species of implicated rodents. We present data on chromosomal and hemoglobin variation in sympatric populations and laboratory produced hybrids that give unequivocal evidence for at least two biologicql species in the taxon Praomys (Mastomys) natalensis. We argue for the usefulness of the biological species concept as a basis for any ecological investigation into pathogen biology.}, } @article {pmid637368, year = {1978}, author = {MacNair, MR and Parker, GA}, title = {Models of parent-offspring conflict. II. Promiscuity.}, journal = {Animal behaviour}, volume = {26}, number = {1}, pages = {111-122}, doi = {10.1016/0003-3472(78)90010-6}, pmid = {637368}, issn = {0003-3472}, mesh = {Alleles ; Animals ; *Breeding ; Female ; *Gene Frequency ; Genes, Dominant ; Genes, Recessive ; *Genetics, Population ; Male ; Paternal Behavior ; Species Specificity ; }, abstract = {The population genetics of Trivers (1974) concept of parent-offspring is examined for species in which the effects of the conflict are felt by future half-sibs, as in promiscuous mating systems in which the male shows no parental care. Whether or not a rare conflictor gene will spread in a non-conflictor population depends on f(m) greater than (m + 1)/(0.5m + 1.5) for a dominant gene, and on f(m) greater than 1/4(7 + 3) for a recessive gene; f(m) is the fitness gained by a conflictor relative to a non-conflictor offspring [f(m) greater than 1], and m is the amount of parental investment taken by a conflictor relative to m = 1 for a non-conflictor. The ESS value for conflict (mo) in promiscuous species with zero male parental care has mo = f(mo)/4[df(mo)/dmo]. However, where the male maintains the same harem for several breeding seasons, or where there is promiscuity but both sexes contribute equally to parental care, conditions for conflict are equivalent to monogamy.}, } @article {pmid564357, year = {1978}, author = {Morin, LP and Fleming, AS}, title = {Variation of food intake and body weight with estrous cycle, ovariectomy, and estradiol benzoate treatment in hamsters (Mesocricetus auratus).}, journal = {Journal of comparative and physiological psychology}, volume = {92}, number = {1}, pages = {1-6}, doi = {10.1037/h0077435}, pmid = {564357}, issn = {0021-9940}, mesh = {Animals ; *Body Weight/drug effects ; *Castration ; Cricetinae ; Estradiol/*pharmacology ; *Estrus ; *Feeding Behavior/drug effects ; Female ; Humans ; Pregnancy ; Time Factors ; }, abstract = {Food intake and body weight of hamsters fluctuated systematically with the estrous cycle. Food intake and body weight were lowest when elevated endogenous estrogen levels were expected. Ovariectomized hamsters gained a significant amount of body weight compared with sham-operated animals. Replacement therapy with estradioal benzoate reduced the body weight and food intake of ovariectomized animals relative to oil-injected, ovariectomized control animals. The results are compared with similar data from rats and support the concept that in females of both species estradiol operates to regulate food intake and body weight.}, } @article {pmid107689, year = {1978}, author = {Reed, ES}, title = {Darwin's evolutionary philosophy: the laws of change.}, journal = {Acta biotheoretica}, volume = {27}, number = {3-4}, pages = {201-235}, pmid = {107689}, issn = {0001-5342}, mesh = {*Biological Evolution ; England ; History, 19th Century ; Humans ; Metaphysics ; Methods ; }, abstract = {The philosophical or metaphysical architecture of Darwin's theory of evolution by natural selection is analyzed and discussed. It is argued that natural selection was for Darwin a paradigmatic case of a natural law of change -- an exemplar of what Ghiselin (1969) has called selective retention laws. These selective retention laws lie at the basis of Darwin's revolutionary world view. In this essay special attention is paid to the consequences for Darwin's concept of species of his selective retention laws. Although Darwin himself explicity supported a variety of nominalism, implicit in the theory of natural selection is a solution to the dispute between nominalism and realism. It is argued that, although implicit, this view plays a very important role in Darwin's theory of natural selection as the means for the origin of species. It is in the context of these selective retention laws and their philosophical implications that Darwin's method is appraised in the light of recent criticisms, and the conclusion drawn that he successfully treated some philosophical problems by approaching them through natural history. Following this an outline of natural selection theory is presented in which all these philosophical issues are highlighted.}, } @article {pmid903426, year = {1977}, author = {Hughes, HC}, title = {Anatomical and neurobehavioral investigations concerning the thalamo-cortical organization of the rat's visual system.}, journal = {The Journal of comparative neurology}, volume = {175}, number = {3}, pages = {311-336}, doi = {10.1002/cne.901750306}, pmid = {903426}, issn = {0021-9967}, mesh = {Afferent Pathways/cytology/physiology ; Animals ; Form Perception/*physiology ; Geniculate Bodies/cytology ; Male ; Pattern Recognition, Visual/*physiology ; Rats ; Thalamus/cytology/*physiology ; Visual Cortex/cytology/*physiology ; }, abstract = {The organization of thalamic afferents to the rat's visual cortex was investigated autoradiographically and through the retrograde transport of horseradish peroxidase (HRP) following infections into striate and peristriate cortex. The results revealed that Nucleus lateralis posterior (NLP) projects to a large peristriate cortical field that includes areas 18A, 7, and the anterior portion of area 18, and to a circumscribed temporal area corresponding to Krieg's ('46a,b) area 20. The dorsal lateral geniculate nucleus (LGNd) was shown to project to two spatially discontinuous cortical areas. The largest geniculate receiving area is partially coextensive with Krieg's area 17, but an extension of this projection posterior and medial to the striate cortex was found. In addition, a geniculate projection to a restricted field located in the lateral peristriate cortex was identified. Concurrent investigations were designed to assess the pattern discrimination abilities of rats prepared with striate cortical ablations, lesions in NLP and combined striate-cortical and thalamic ablations. Comparison of these animals with normal control subjects revealed that the striate cortex in the rat (as in the cat [Doty, '71; Sprague et al., '77] and the tree shrew [Killackey and Diamond, '71; Ware et al., '74]) is not necessary for successful pattern discrimination, and that the geniculo-striate and NLP-extra-striate projection systems are both involved in mediating the visual discriminative abilities of the rat. The results add species generality to the concept that the central connections to the visual cortex are characterized by parallel-conducting thalamic channels and contribute to the growing number of demonstrations that the extra-striate cortex and associated thalamic cell groups contribute significantly to the process of visual-pattern recognition.}, } @article {pmid896482, year = {1977}, author = {Gross, HJ and Domdey, H and Sänger, HL}, title = {Comparative oligonucleotide fingerprints of three plant viroids.}, journal = {Nucleic acids research}, volume = {4}, number = {6}, pages = {2021-2028}, pmid = {896482}, issn = {0305-1048}, mesh = {Oligonucleotides/*analysis ; Oligoribonucleotides/*analysis ; *Plant Viruses ; *RNA, Viral ; Species Specificity ; }, abstract = {5' Phosphorylation in vitro with gamma-32P-ATP and T4 phage induced polynucleotide kinase was used to obtain RNAase A and RNAase T1 fingerprints of three plant viroids: Potato spindle tuber viroid from tomato (PSTV-tom), chrysanthemum stunt viroid from cineraria (ChSV-cin) and citrus exocortis viroid from Gynura aurantiaca (CEV-gyn). These three viroids differ significantly from each other as judged from their oligonucleotide patterns. This supports the concept of individual viroid species.}, } @article {pmid833542, year = {1977}, author = {Bodel, PT and Nichols, BA and Bainton, DF}, title = {Appearance of peroxidase reactivity within the rough endoplasmic reticulum of blood monocytes after surface adherence.}, journal = {The Journal of experimental medicine}, volume = {145}, number = {2}, pages = {264-274}, pmid = {833542}, issn = {0022-1007}, mesh = {Animals ; *Cell Adhesion ; Cell Differentiation ; Endoplasmic Reticulum/enzymology ; Humans ; Macrophages/enzymology ; Monocytes/*enzymology/physiology/ultrastructure ; Peroxidases/*metabolism ; Rats ; }, abstract = {Rabbit blood monocytes, which contain no cytochemically demonstrable peroxidase, develop peroxidatic activity in the RER and perinuclear cisternae within 2 h after adherence to serum- or fibrin-coated surfaces. A similar reactivity appears in surface-adherent human and rat blood monocytes. In both localization and characteristics, this enzyme reactivity in monocytes resembles that normally seen in the resident peritoneal macrophages of the rabbit, as well as in several types of tissue macrophages in other species. Thus this observation supports the concept, presently based on the kinetic data of other investigators, that blood monocytes are the precursors of such cells. Moreover, the appearance of new enzyme activity after adherence may reflect alterations in cellular metabolism resulting from plasma membrane:surface interactions.}, } @article {pmid140452, year = {1976}, author = {Devriese, LA and Oeding, P}, title = {Characteristics of Staphylococcus aureus strains isolated from different animal species.}, journal = {Research in veterinary science}, volume = {21}, number = {3}, pages = {284-291}, pmid = {140452}, issn = {0034-5288}, mesh = {Animals ; Bacteriophage Typing ; Cattle/microbiology ; Cell Wall/immunology ; Columbidae/microbiology ; Fibrinolysin/biosynthesis ; Hemolysin Proteins/biosynthesis ; Humans ; Poultry/microbiology ; Sheep/microbiology ; Staphylococcus aureus/*classification/immunology/metabolism ; }, abstract = {Staphylococcus aureus strains originating from humans, cows, poultry, pigs, dogs and pigeons were characterised according to the biotyping scheme of Hájek and Marsálek (1971). All strains obtained from poultry, dogs and pigeons and the majority of bovine, human and porcine strains were classifiable as belonging to different biotypes. Two types were found to be present among poultry strains isolated in Europe and Japan. The porcine strains formed a heterogenic collection. One biotype predominated in the other host species. The characteristic S aureus wall teichoic acid (beta-N-acetylglucosaminyl ribitol teichoic acid) was present in nearly all poultry and pig strains. Strains from dogs and pigeons were found to present several properties which were not in agreement with the species description given for S aureus. They did not produce acetoin from glucose and their capacity to produce acid from mannitol in anaerobic conditions was very weak or absent. They were often negative in the clumping factor (slide coagulase) test and usually did not produce hyaluronidase. The production of acid from glucose in anaerobic conditions was slower and less intensive in these strains than in the S aureus strains from other origins. The results of this study support the concept of subdividing the species S aureus into biotypes or ecotypes.}, } @article {pmid797713, year = {1976}, author = {Sohn, D}, title = {Two concepts of adaptation: Darwin's and psychology's.}, journal = {Journal of the history of the behavioral sciences}, volume = {12}, number = {4}, pages = {367-375}, doi = {10.1002/1520-6696(197610)12:4<367::aid-jhbs2300120408>3.0.co;2-e}, pmid = {797713}, issn = {0022-5061}, mesh = {*Adaptation, Biological ; *Adaptation, Psychological ; Animals ; History, 19th Century ; History, 20th Century ; Humans ; Psychology/*history ; United States ; }, abstract = {The paper takes issue with the traditional view of Darwin's influence on psychology; namely, that it is he who passed on to psychology the concept of individual adaptation. Three arguments are presented: a) that Darwin, qua scientist, was only interested in species adaptation, an entirely different concept from that of individual adaptation, b) that Darwin's writings on individual adaptation are so unexceptional that it is inconceivable that psychologists should have been influenced by them and c) that the two concepts are logically incompatible since species adaptation presupposes a strict hereditary determinism, while individual adaptation conceives of the organism either as free and undetermined or else as determined by the environment.}, } @article {pmid983329, year = {1976}, author = {Monchenko, VI and Tavolzhanova, TI}, title = {[Concept of biological species in relation to the systematics of cyclopes (Crustacea, Cyclopidae)].}, journal = {Zhurnal obshchei biologii}, volume = {37}, number = {4}, pages = {563-574}, pmid = {983329}, issn = {0044-4596}, mesh = {Animals ; Crustacea/*classification ; Female ; Male ; }, } @article {pmid1250842, year = {1976}, author = {Kabara, JJ and Riggin, RM and Kissinger, PT}, title = {Abnormal levels of urinary catecholamines in dystrophic mice and hamsters.}, journal = {Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine (New York, N.Y.)}, volume = {151}, number = {1}, pages = {168-172}, doi = {10.3181/00379727-151-39167}, pmid = {1250842}, issn = {0037-9727}, mesh = {Animals ; Catecholamines/analysis/*urine ; Chromatography, Ion Exchange ; Cricetinae ; Dihydroxyphenylalanine/urine ; Dopamine/urine ; Electrochemistry ; Epinephrine/urine ; Mice ; Muscular Dystrophy, Animal/*urine ; Norepinephrine/urine ; }, abstract = {Twenty-four-hour urine was collected from normal and dystrophic mice and hamsters for catecholamine determinations. A new method of analysis was used whereby 3,4-dihydroxyphenylalanine (DOPA), dopamine (DA), norepinephrine (NE), and epinephrine (E) were measured simultaneously. The procedure is based on a combination of liquid-solid extraction, cation exchange chromatography, and controlled potential electrochemistry. The results of these experiments indicated that while DA levels were similar in both normal and pathological animal urine, DOPA levels decreased slightly in the dystrophic mouse but not the hamster, and NE and E levels in dystrophic groups were two and four times greater than normal in both species. The data supports the concept of biochemical alterations in tissue other than muscle. While not necessarily supportive to catecholamine abnormality as the primary cause of muscular dystrophy, the present data cast doubt that this disease is a primary muscle disease.}, } @article {pmid1087561, year = {1976}, author = {Lemmel, EM and Botzenhardt, U}, title = {[Immunosuppressive treatment of rheumatic diseases. Experimental bases of a rational concept of therapeutic approach (author's transl)].}, journal = {Arzneimittel-Forschung}, volume = {26}, number = {7}, pages = {1281-1295}, pmid = {1087561}, issn = {0004-4172}, mesh = {Animals ; Antibody Formation/drug effects ; Autoimmune Diseases ; Cell Division/drug effects ; Cell Survival/drug effects ; Cyclophosphamide/pharmacology ; Immunosuppressive Agents/*pharmacology ; Lupus Erythematosus, Systemic/drug therapy ; Lymphocytes/cytology/*drug effects/immunology ; Mercaptopurine/pharmacology ; Mice ; Mice, Inbred NZB ; Rabbits ; Rheumatic Diseases/*drug therapy/immunology ; Species Specificity ; }, abstract = {For treatment of diseases such as rheumatoid arthritis or systemic lupus erythematodes, which are initiated or sustained by immune-pathological mechanisms, various "immunosuppressive" drugs are used. There are conflicting data as to the benefit of this type of therapy. In this paper it is attempted to define a base for a more differentiated application of available drugs, since the present therapeutic approach seems rather empiric or is deducted from analogy to selected animal experiments. The investigations presented focus primarily on the behaviour of the small and medium lymphocytes of the organism, the adopted carriers of immunological (as well as autoimmune) reactivity, under conventional conditions (and under the influence of suitable drugs) as a biological supposition for the activity of "immunosuppressives". In rabbits, and mice, number and rate of proliferation of lymphoid cells is determined in untreated controls and animals treated with 6-mercaptopurine (6-MP) and cyclophosphamide (Cy), two immunosuppressive agents representing different types of pharmacological action. The elucidation why in rabbits both substances are equally immunosuppressive, whereas in mice only Cy has significant immunosuppressive activity, yields the base for a therapeutic concept of clinical immunosuppression. This species dependent activity of 6-MP can be explained by different proliferation kinetics of lymphoid cells in mouse and rabbit. Lymphocytes of the rabbit, compared to those of mice, are short-lived and have a distinctly higher proliferation rate. Thus, 6-MP, as an antiproliferative agent, leads, in the rabbit (under long-term as well as single-dose therapy) to a significant reduction of the number of small lymphocytes, whereas it reduces the long-lived lymphocytes of the mouse only marginally, thus explaining the good immunosuppressive potency in the rabbit and failure in the mouse. Cy leads, in both species, to a marked reduction of small lymphocytes and affects the long-lived cells of the mouse as well, resulting in high immunosuppressive potency in both species. In the NZB mouse, a well-fitting model of human lupus erythomatodes, Cy is successful in prophylaxis and therapy. A similar therapeutic effect cannot be obtained with 6-MP. Neither of the two groups of substances revealed selective activity on circulating T- or B-cells. According to the literature available, lymphocytes in humans are predominantly long-lived, too. Accordingly, Cy possesses a good immunosuppressive potency in man, too. Its therapeutic success is paralleled by a reduction of small lymphocytes. In conclusion, a true basic immunosuppressive therapy of autoimmune diseases in humans will primarily be possible by aid of substances which act through a cytotoxic mechanism and are thus able to affect even the long-lived human lymphocytes. In contrast, a substance acting purely through interference with certain steps of cell proliferation will predominantly remain restricted to an antiphlogistic use.}, } @article {pmid1041693, year = {1975}, author = {Small, E}, title = {American law and the species problem in Cannabis: science and semantics.}, journal = {Bulletin on narcotics}, volume = {27}, number = {3}, pages = {1-20}, pmid = {1041693}, issn = {0007-523X}, mesh = {Botany ; Cannabis/*classification/history ; History, 19th Century ; History, 20th Century ; Legislation, Drug ; *Terminology as Topic ; United States ; }, } @article {pmid804499, year = {1975}, author = {Keefer, DA and Stumpf, WE}, title = {Atlas of estrogen-concentrating cells in the central nervous system of the squirrel monkey.}, journal = {The Journal of comparative neurology}, volume = {160}, number = {4}, pages = {419-441}, doi = {10.1002/cne.901600402}, pmid = {804499}, issn = {0021-9967}, mesh = {Amygdala/metabolism ; Animals ; Atlases as Topic ; Brain/*metabolism ; Brain Mapping ; Castration ; Cerebral Cortex/metabolism ; Diencephalon/metabolism ; Estradiol/*metabolism ; Female ; Haplorhini/*metabolism ; Hypothalamus/metabolism ; Mesencephalon/metabolism ; Neurons/*metabolism ; Rats ; Saimiri/*metabolism ; Species Specificity ; Spinal Cord/metabolism ; Telencephalon/metabolism ; Tritium ; Uterus/metabolism ; }, abstract = {Estrogen is concentrated within cellular nuclei in discrete regions of the monkey brain 30 and 60 minutes following intravenous injection of [3H] estradiol. Chromatographic data is provided to suggest that most of the localized estrogen is in the form of estradiol with lesser amounts of estrone and estriol. Three "major" areas of estrogen accumulation include: (1) preopticostrial accumulation: n. preopticus medialis--n. interstitialis striae terminalis, (2) basal hypothalamic accumulation: n. infundibularis--n. ventromedialis--n. premammillaris ventralis, and (3) the amygdaloid accumulation. Several "minor" areas of estrogen accumulation include the tuberculum olfactorium, insulae Calleja, n. triangularis septi, a. hypothalamica anterior, n. anterior hypothalami, n. paraventricularis, n. supraopticus, n. periventricularis and the substantia grisea centralis. The neocortex, rhombencephalon and spinal cord are essentially unlabeled. The major areas of accumulation are similar in several other mammalian and avian species while these, and some minor areas of accumulation, have been shown in neuroanatomical studies to be interconnected by several pathways, especially the stria terminalis. Lesion, implant, stimulation, recording and morphometric studies, in several species, support the concept that this arrangement provides a neuroanatomical substrate which would allow the integration of the various facets of the neuroendocrine reproductive response.}, } @article {pmid164939, year = {1975}, author = {Miller, RW and Macdowall, FD}, title = {The tiron free radical as a sensitive indicator of chloroplastic photoautoxidation.}, journal = {Biochimica et biophysica acta}, volume = {387}, number = {1}, pages = {176-187}, doi = {10.1016/0005-2728(75)90062-6}, pmid = {164939}, issn = {0006-3002}, mesh = {Benzenesulfonates/*metabolism ; Chloroplasts/*metabolism/ultrastructure ; Electron Spin Resonance Spectroscopy ; Free Radicals ; Kinetics ; Light ; Oxidation-Reduction ; Oxygen Consumption ; *Photophosphorylation ; Plants ; Quinones ; Superoxide Dismutase/metabolism ; Triticum ; }, abstract = {Wheat chloroplasts photochemically reduced molecular oxygen, as a Hill oxidant in the Mehler reaction, to superoxide anion which then oxidized added 1,2-dihydroxybenzene-3,5-disulfonate to its semiquinone, a comparatively stable free radical at pH 7. The last mentioned reaction was rapid in aqueous solution, but the rate of formation of 1,2-dihydroxybenzene-3,5-disulfonate semiquinone by the chloroplast system was calculated as T1 of 0.6 s. The Mehler reaction, or more specifically the univalent reduction of oxygen by Photosystem I, was rate-limiting so that the 1,2-dihydroxybenzene-3,5-disulfonate seniquinone was a useful spin probe for superoxide anion production at room temperature. The ESR signal of 1,2-dihydroxybenzene-3,5-disulfonate semiquinone was proportional to its steady state concentration and decayed in the dark with a T1/2 of 5-6 s. This oxygen-dependent signal was enhanced by mediation of chloroplastic oxygen reduction through methyl viologen. The superoxide anion scavengers ascorbate and L-epinephrine competitively obscured 1,2-dihydroxybenzene-3,5-disulfonate semiquinone formation, butadded superoxide dismutase was not as effective in this role. Partial inhibition by superoxide dismutase was achieved only by preincubation of Photosystem I enriched particles with ten times the endogenous concentration of superoxide dismutase. This and the persistence of a small amount of a 1,2-dihydroxybenzene-3,5-disulfonate (Tiron) oxidizing species in the dark supports the concept of Tiron accessibility but not the superoxide dismutase accessibility of superoxide anion bound in its formative enzyme complex. Benzoquinone and naphthoquinone disulfonate also reacted with superoxide anion, and supported both the Hill reaction and the Mehler reaction as final oxidants of both water and superoxide anion.}, } @article {pmid1240300, year = {1975}, author = {Hayashi, E}, title = {[The concept of Center Species and deduction and verification of new species using its classification system].}, journal = {Nihon saikingaku zasshi. Japanese journal of bacteriology}, volume = {30}, number = {1}, pages = {60-61}, pmid = {1240300}, issn = {0021-4930}, mesh = {Bacteria/*classification ; }, }