@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).<br><br>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.<br><br>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.<br><br>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 &amp; 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 &amp; 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 &amp; 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 &amp; 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.<br><br>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.<br><br>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.<br><br>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 &amp; 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 &amp; 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 &amp; 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.<br><br>OBJECTIVE: To establish cardiovascular parameters as a common metric for cross-species translation of aerobic exercise impact.<br><br>METHOD: We evaluated aerobic exercise impact on heart rate (HR) in 21 early-stage PD subjects (Hoehn Yahr &#x2264;1.5) exercising in non-contact boxing training for &#x2265;3 months, &#x2265;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.<br><br>RESULTS: After completing aerobic exercise for &#x223c;30&#x200a;min, PD subjects had increased HR&#x223c;35% above baseline (&#x223c;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-na&#xef;ve PD subjects. In KO and age-matched wild-type (WT) rats, treadmill speeds of 8-10&#x200a;m/min increased HR up to 25% above baseline (&#x223c;67% maximum HR), with no further increases up to 16&#x200a;m/min. Exercised KO, but not WT, rats showed increased locomotor activity compared to an age-matched exercise-na&#xef;ve cohort at 5 months old.<br><br>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 &amp; 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.<br><br>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.<br><br>RESULTS: We trained Antilogic against a database of 18072 pictures of antibiograms. Overall agreement against the validation set reached 97% (16&#xa0;855/17&#xa0;281) regarding phenotypes. The severity rate of errors was also evaluated: 1.66% (287/17&#xa0;281) were major errors and 0.80% (136/17&#xa0;281) were very major errors. After implementation of uncertainty quantifications, the rate of errors decreased to 0.80% (114/13&#xa0;451) and 0.42% (51/13&#xa0;451) for major and very major errors respectively.<br><br>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.<br><br>METHODS: Binding of labeled, pre-formed A&#x3b2; 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 A&#x3b2; 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.<br><br>RESULTS: We demonstrated that higher TauO concentrations effectively outcompete A&#x3b2;O and become the prevailing synaptic-associated species. Conversely, high concentrations of A&#x3b2;O facilitate synaptic TauO recruitment. Immunofluorescence analyses of mouse primary cortical neurons confirmed differential synaptic binding dynamics of A&#x3b2;O and TauO. Moreover, in vivo experiments using old 3xTgAD mice ICV injected with either A&#x3b2;O or TauO fully supported these findings. Consistent with these observations, FASS-LTP analyses demonstrated that TauO-induced suppression of chemical LTP was exacerbated by A&#x3b2;O. Finally, predigestion with proteinase K abolished the ability of TauO to compete off A&#x3b2;O without affecting the ability of high A&#x3b2;O levels to increase synaptic TauO recruitment. Thus, unlike A&#x3b2;O, TauO effects on synaptosomes are hampered by the absence of protein substrate in the membrane.<br><br>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 &amp; 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&amp;nbsp;badius, Phellinus&amp;nbsp;resinaceus, and Phellinus&amp;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.<br><br>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 &amp; 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 &amp; 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 &amp; 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.<br><br>RESULTS: A BD Influx&#xae; 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&#x2122; BacLight&#x2122; 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.<br><br>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, I&#x110; 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 &amp; 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.<br><br>METHODS: 91 male and female macaques (rhesus and cynomolgus), ranging in age from 4&#xa0;years (adolescent) to 10&#xa0;years (adult) were required to increase their consumption of ethanol in 30-day increments: 0&#xa0;g/kg/day, followed by 0.5&#xa0;g/kg/day, 1.0&#xa0;g/kg/day, and, finally, 1.5&#xa0;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.<br><br>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.<br><br>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.<br><br>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.<br><br>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&#x200b;. 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.<br><br>CONCLUSIONS: We suggest a new coherent nomenclature for the genomes present&#x200b;. 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 &amp; 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 &amp; 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 &amp; Caring; Illness Experience &amp; Disease Pathology; Environment, Self &amp; Sustainability; Power, Rights &amp; 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 &amp; 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 &amp; 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 &amp; 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 &amp; Veldkamp or Cenchrus advena (Wipff &amp; 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 &amp; Jurberg, 1965 and P. coreodes Bergroth, 1911 and analysis of the reproductive isolating mechanisms.}, journal = {Parasites &amp; 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.<br><br>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.<br><br>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 &#x2640; &#xd7; P. coreodes &#x2642; died before oviposition, and the F1 hybrids of P. coreodes &#x2640; x P. tertius &#x2642; 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.<br><br>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 &amp; numerical data ; *Datasets as Topic ; Electronic Mail/*statistics &amp; numerical data ; Humans ; Social Media/*statistics &amp; 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 &amp; 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) &lt;br /&gt;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 &amp; 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 &amp; 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 &amp; 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.<br><br>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 &amp; 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 &amp; 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 &amp; 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 &amp; 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 &amp; development ; Ecosystem ; Environmental Monitoring/legislation &amp; jurisprudence/*methods ; Food Safety/*methods ; Government Publications as Topic ; Guidelines as Topic ; Pesticides/toxicity ; Plants, Genetically Modified/*growth &amp; 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).<br><br>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.<br><br>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.<br><br>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 &amp; 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 &amp; 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 &amp; 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 &amp; histology/*classification/*genetics ; Haplotypes/genetics ; Likelihood Functions ; Male ; Models, Theoretical ; *Phylogeny ; Species Specificity ; Tooth/anatomy &amp; 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 &amp; 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 &amp; 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 &amp; 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 &amp; Cribb, 1998), forming a poorly-supported clade with Proctotrema addisoni Searle, Cutmore &amp; 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.<br><br>STUDY DESIGN: In total, 11 healthy young pre-menopausal female participants (mean age: 24.4 &#xb1; 1.8 years, BMI: 22.1 &#xb1; 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 &#x223c;70 % maximum heart rate (mean: 133.4 &#xb1; 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 &#x3b1;-amylase activity were determined.<br><br>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 &#x3b1;-amylase secretion also increased in the Exercise procedure at S1 (p < 0.05), but concentrations returned to baseline levels at S2.<br><br>CONCLUSIONS: Moderate intensity exercise leads to an increase in &#x3b1;-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.<br><br>RESULTS: Questions have arisen regarding the utility of these markers e.g., ITS, BT and TEF1-&#x3b1; 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.<br><br>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.<br><br>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&#xa0;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.<br><br>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 &amp; 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 &amp; 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.<br><br>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&#x2009;=&#x2009;15) served for DNA extraction, while the other set (n&#x2009;=&#x2009;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.<br><br>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.<br><br>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 &amp; purification ; Cryptosporidium parvum/classification/genetics/isolation &amp; 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 &amp; control/*veterinary ; Haemonchus/immunology ; Plasma/immunology ; Retrospective Studies ; Serum/immunology ; Sheep ; Sheep Diseases/parasitology/*prevention &amp; control ; Vaccination/*veterinary ; Vaccines/administration &amp; 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.<br><br>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.<br><br>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.<br><br>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 &amp; 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 &amp; 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.<br><br>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&#xa0;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.<br><br>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 &amp; purification/metabolism ; Cell Fractionation/*methods ; Cell Wall/*chemistry ; Fungal Proteins/*isolation &amp; purification/metabolism ; Gases/*pharmacology ; Humans ; Microalgae/*chemistry/drug effects/growth &amp; 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 &amp; histology/*classification/genetics/isolation &amp; 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 &amp; Cribb, 2002 as Proenenterum allanwilliamsi (Bray &amp; Cribb, 2002) n. comb. and transfer of Koseiria huxleyi Bray &amp; Cribb, 2001 to a new genus as Enenterageitus huxleyi (Bray &amp; 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 &amp; 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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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 &amp; histology/classification ; Tooth/*anatomy &amp; 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 &amp; dosage/*toxicity ; Disease Models, Animal ; Female ; Herbicides/administration &amp; 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 &amp; 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 &amp; 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 &amp; 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 &amp; 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 &amp; histology/*classification/genetics ; Cytochromes b/genetics ; DNA/genetics ; Discriminant Analysis ; Ecosystem ; Evolution, Molecular ; Female ; Genetic Variation ; Male ; Molar/anatomy &amp; 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 &amp; 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 &amp; 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 &amp; 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, &#xc7; 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.<br><br>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.<br><br>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.<br><br>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, &#x141; 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.<br><br>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.<br><br>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.<br><br>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 &amp; 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.<br><br>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.<br><br>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.<br><br>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.<br><br>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, &#xc5; 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 &amp; 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 &amp; development/isolation &amp; 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 &amp; 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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>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&#xa0;is dated to late Miocene (ca. 8.7&#x2009;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.<br><br>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 &amp; purification ; *Biodiversity ; *Biological Evolution ; Environment ; Phylogeny ; Plankton/*isolation &amp; 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 &amp; German BMBF/International ; //TU Nachwuchsring/International ; }, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Baltic States ; Eukaryota/classification/genetics/*isolation &amp; purification ; Fresh Water/*chemistry/microbiology/parasitology ; Plankton/classification/genetics/*isolation &amp; 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 &amp; 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 &amp; purification ; Nontuberculous Mycobacteria/*genetics/isolation &amp; 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.<br><br>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.<br><br>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.<br><br>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 &amp; development/isolation &amp; purification ; Brazil ; Europe ; Norway ; Phylogeny ; Spores, Fungal/classification/genetics/growth &amp; development/isolation &amp; 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 &amp; dosage ; Cattle ; Congresses as Topic ; Israel ; *Mycobacterium bovis ; One Health ; Tuberculosis, Bovine/*prevention &amp; 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 hierarchic