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04 Mar 2024 at 01:58
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Bibliography on: Species Concept


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RJR: Recommended Bibliography 04 Mar 2024 at 01:58 Created: 

Species Concept

Wikipedia: The species problem is the set of questions that arises when biologists attempt to define what a species is. Such a definition is called a species concept; there are at least 26 recognized species concepts. A species concept that works well for sexually reproducing organisms such as birds is useless for species that reproduce asexually, such as bacteria. The scientific study of the species problem has been called microtaxonomy. One common, but sometimes difficult, question is how best to decide which species an organism belongs to, because reproductively isolated groups may not be readily recognizable, and cryptic species may be present. There is a continuum from reproductive isolation with no interbreeding, to panmixis, unlimited interbreeding. Populations can move forward or backwards along this continuum, at any point meeting the criteria for one or another species concept, and failing others. Many of the debates on species touch on philosophical issues, such as nominalism and realism, and on issues of language and cognition. The current meaning of the phrase "species problem" is quite different from what Charles Darwin and others meant by it during the 19th and early 20th centuries. For Darwin, the species problem was the question of how new species arose. Darwin was however one of the first people to question how well-defined species are, given that they constantly change.

Created with PubMed® Query: ( ("species concept"[tiab:~6] OR "species concepts"[tiab] OR "species problem") NOT "invasive species" ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2024-03-01

Dong Y, Zhang Q, Mao Y, et al (2024)

Control of two insect pests by expression of a mismatch corrected double-stranded RNA in plants.

Plant biotechnology journal [Epub ahead of print].

RNA interference (RNAi) has emerged as an efficient technology for pest control by silencing the essential genes of targeted insects. Owing to its nucleotide sequence-guided working mechanism, RNAi has a high degree of species-specificity without impacts on non-target organisms. However, as plants are inevitably under threat by two or more insect pests in nature, the species-specific mode of RNAi-based technology restricts its wide application for pest control. In this study, we artificially designed an intermediate dsRNA (iACT) targeting two β-Actin (ACT) genes of sap-sucking pests Bemisia tabaci and Myzus persicae by mutual correction of their mismatches. When expressing hairpin iACT (hpiACT) from tobacco nuclear genome, transgenic plants are well protected from both B. tabaci and M. persicae, either individually or simultaneously, as evidenced by reduced fecundity and suppressed ACT gene expression, whereas expression of hpRNA targeting BtACT or MpACT in transgenic tobacco plants could only confer specific resistance to either B. tabaci or M. persicae, respectively. In sum, our data provide a novel proof-of-concept that two different insect species could be simultaneously controlled by artificial synthesis of dsRNA with sequence optimization, which expands the range of transgenic RNAi methods for crop protection.

RevDate: 2024-02-29

Monecke S (2024)

Threatened chronotopes: can chronobiology help endangered species?.

Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology [Epub ahead of print].

Pittendrigh and Daan's 1976 article "Pacemaker structure: A clock for all seasons" marks the foundation of modern seasonal chronobiology. It proposed the internal coincidence model comprised of a Morning (M) and Evening (E) oscillator, which are coupled but synchronized separately by dawn and dusk. It has become an attractive model to explain the seasonal adaptation of circadian rhythms. Using the example of the European hamster, this article connects the classical entrainment concept to species decline and, ultimately, conservation concepts. Seasonality of this species is well studied and circannual rhythms have been described in at least 32 parameters. The European hamster is listed as critically endangered on the International Union for Conservation of Nature (IUCN) red list. Changes in the temporal structure of the environment (the chronotope) caused by climate change and light pollution might be responsible for the global decline. The article shows that classical chronobiological concepts such as the internal coincidence model (Pittendrigh and Daan Pittendrigh and Daan, J Comp Physiol [a] 106:333-355, 1976) are helpful to understand the (chronobiological) causes of the decline and can potentially support species conservation. Knowing the species' physiological limitations as well as its adaptation capacities can potentially prevent its extinction at a time when classical conservation concepts have reached their limits.

RevDate: 2024-02-23

Wang S, Jiang N, R Ma (2024)

Morphology and Phylogeny Reveal Three New Species of Cytospora Associated with Tree Cankers in China.

Journal of fungi (Basel, Switzerland), 10(2): pii:jof10020139.

Cytospora (Cytosporaceae, Diaporthales) is a fungal genus that usually inhabits plants as endophytes, saprobes, as well as pathogens. Species of this genus are characterized by possessing allantoid hyaline conidia and ascospores. Samples with typical Cytospora canker symptoms on Prunus davidiana, P. padus and Salix sp. were collected in Tibet and Xinjiang, China. Species were identified using both morphological and molecular approaches of combined loci of internal transcribed spacer region rDNA (ITS), the partial actin (act) region, RNA polymerase II second largest subunit (rpb2), the translation elongation factor 1-alpha (tef1) gene and the partial be-ta-tubulin (tub2) gene. Six isolates in the present study formed three distinct clades from previously known species. Cytospora hejingensis sp. nov. from Salix sp., C. jilongensis sp. nov. from P. davidiana and C. kunsensis from P. padus were proposed herein. The current study improves the understanding of species concept in Cytospora.

RevDate: 2024-02-20

Lukhtanov VA (2024)

Polytypic species concept and subspecies in the genomic era.

Proceedings of the National Academy of Sciences of the United States of America, 121(9):e2317038121.

RevDate: 2024-02-13

Koch Bach R, Murithi HM, Slocum CR, et al (2024)

Remarkably high ITS haplotype diversity of the fungal Select Agent Coniothyrium glycines discovered throughout its range in sub-Saharan Africa.

Phytopathology [Epub ahead of print].

Red leaf blotch of soybean, caused by the fungus Coniothyrium glycines, is a foliar disease characterized by blotching, necrosis, and defoliation, which has only been reported from Africa. The species is listed as a Select Agent by the Federal Select Agent Program due to its potentially devastating impacts to soybean production should it spread to the U.S. Despite its potential import, very few isolates are available for study. Herein, we obtained 96 new C. glycines isolates from six soybean-producing countries throughout sub-Saharan Africa. Along with 12 previously collected ones, we sequenced each at the internal transcribed spacer (ITS) region. Between all isolates, we identified a total of 28 single nucleotide polymorphisms and 23 haplotypes. One hypothesis to explain the tremendous diversity uncovered at the ITS-which is generally conserved within a species-is that our current species concept of C. glycines is too broad, and that there may be multiple species that cause RLB. Zambia contained the highest haplotype diversity, a significant fraction of which remains unsampled. Most haplotypes were specific to a single country, except for two, which were found in Zambia and either neighboring Mozambique or Zimbabwe. This geographic specificity indicates that the ITS region may be useful in identifying source populations or routes of transmission should this pathogen spread beyond Africa. The observed geographic partitioning of this pathogen is likely the result of millions of years of replication on little-studied native hosts, given that soybean has only been cultivated in Africa since the early 1900s.

RevDate: 2024-02-10

Maggisano V, Capriglione F, Mio C, et al (2024)

RNA Profile of Cell Bodies and Exosomes Released by Tumorigenic and Non-Tumorigenic Thyroid Cells.

International journal of molecular sciences, 25(3): pii:ijms25031407.

Tumor cells release exosomes, extracellular vesicle containing various bioactive molecules such as protein, DNA and RNA. The analysis of RNA molecules packaged in exosomes may provide new potential diagnostic or prognostic tumor biomarkers. The treatment of radioiodine-refractory aggressive thyroid cancer is still an unresolved clinical challenge, and the search for biomarkers that are detectable in early phase of the disease has become a fundamental goal for thyroid cancer research. By using transcriptome analysis, this study aimed to analyze the gene expression profiles of exosomes secreted by a non-tumorigenic thyroid cell line (Nthy-ori 3.1-exo) and a papillary thyroid cancer (TPC-1-exo) cell line, comparing them with those of cell bodies (Nthy-ori 3.1-cells and TPC-1-cells). A total of 9107 transcripts were identified as differentially expressed when comparing TPC-1-exo with TPC-1-cells and 5861 when comparing Nthy-ori 3.1-exo with Nthy-ori 3.1-cells. Among them, Sialic acid-binding immunoglobulin-like lectins 10 and 11 (SIGLEC10, SIGLEC11) and Keratin-associated protein 5 (KRTAP5-3) transcripts, genes known to be involved in cancer progression, turned out to be up-regulated only in TPC-1-exo. Gene ontology analysis revealed significantly enriched pathways, and only in TPC-1-exo were the differential expressed genes associated with an up-regulation in epigenetic processes. These findings provide a proof of concept that some mRNA species are specifically packaged in tumor-cell-derived exosomes and may constitute a starting point for the identification of new biomarkers for thyroid tumors.

RevDate: 2024-02-09

Smith JE, FP Gabbaï (2023)

Are Ar3SbCl2 Species Lewis Acidic? Exploration of the Concept and Pnictogen Bond Catalysis Using a Geometrically Constrained Example.

Organometallics, 42(3):240-245.

As part of our investigations into the Lewis acidic behavior of antimony derivatives, we have decided to study the properties of 5-phenyl-5,5-dichloro-λ[5]-dibenzostibole (1), a dichlorostiborane with an antimony atom confined to a five-membered heterocycle. Our work shows that the resulting geometrical constraints elevate the Lewis acidity of the antimony atom, as confirmed by the crystal structure of 1-THF and the solution study of the interaction of 1 with Ph3PO. The enhanced Lewis acidic properties of 1, which exceed those of simple dichlorostiboranes such as Ph3SbCl2, also become manifest in pnictogen bonding catalysis experiments involving the reductions of imines with Hantzsch ester. The influence of geometrical constraints in the chemistry of this compound is also supported by a computational activation strain analysis as well as by an energy decomposition analysis of a model Me3PO adduct.

RevDate: 2018-12-20
CmpDate: 2018-12-20

Gippoliti S, CP Groves (2018)

Overlooked mammal diversity and conservation priorities in Italy: Impacts of taxonomic neglect on a Biodiversity Hotspot in Europe.

Zootaxa, 4434(3):511-528 pii:zootaxa.4434.3.7.

For more than half a century, little taxonomic revisionary work has been directed towards extant European mammals so that the limits of most geographically widespread polytypic species remained scientifically untested. Occasionally, taxonomic changes have been proposed and several new species have been resurrected / discovered in the last decades mainly on the basis of genetic studies, often considered the only tool to establish objective species boundaries. Nevertheless, the precise details of species boundaries, subspecific variation and phylogenetic relationships remain unknown for several European mammal taxa. The inadequacies of outdated, incomplete taxonomic knowledge reach an extreme in southern Europe, and notably Italy, where cryptic species abound and specimen-based research is scanty. The state of mammalian taxonomic knowledge in Italy shows that Linnaean and Wallacean shortfalls are no means restricted to hyperdiverse, understudied tropics. They undermine our knowledge of temperate regions, with severe consequences for biodiversity conservation policies in Europe, where conservation assessments overlook significant endemic biodiversity. European mammalogy stands to benefit from an infusion of the tree-thinking philosophy that undergirds evolutionary theory and particularly phylogenetic methods systematics. Furthermore, it is important that taxonomic research be seen as a normal part of scientific advancement and of critical importance as the basis of a sound biodiversity conservation policy.

RevDate: 2024-02-04

Petrović K, Orzali L, Krsmanović S, et al (2024)

Genetic diversity and pathogenicity of the Fusarium species complex on soybean in Serbia.

Plant disease [Epub ahead of print].

Using morphological and cultural characteristics for identification, 36 Fusarium isolates were recovered from diseased roots, stems, and seeds of soybean from several localities throughout Vojvodina Province, Serbia, were identified as Fusarium spp. Based on molecular characterization, 12 Fusarium species were identified: F. acuminatum, F. avenaceum, F. commune, F. equiseti, F. graminearum, F. incarnatum, F. oxysporum, F. proliferatum, F. solani, F. sporotrichioides, F. subglutinans, and F. tricinctum. The EF-1α based-phylogeny grouped the isolates into 12 well-supported clades, but the polymorphisms among sequences in some clades suggested the use of the species complex concept: (1) FIESC - F. incarnatum and F. equiseti; (2) FOSC - F. oxysporum; (3) FSSC - F. solani; and (4) FAATSC - F. acuminatum, F. avenaceum and F. tricinctum. Pathogenicity tests showed that the most aggressive species causing soybean seed rot were F. sporotrichioides, F. graminearum, FIESC, and F. avenaceum. Furthermore, F. subglutinans, FSSC, and F. proliferatum, showed a high percentage of pathogenicity on soybean seeds (80-100%), while variability in pathogenicity occurred within isolates of F. tricinctum species has occurred variability in the virulence of different isolates. FOSC, F. commune and F. acuminatum had the lowest pathogenicity degree. To our knowledge, this is the first study of the characterization of Fusarium complex species on soybean in Serbia. This study provides valuable information about the structure composition of Fusarium complex species and pathogenicity that will be used in further research on soybean resistance to Fusarium-based diseases.

RevDate: 2024-02-03

Zhang N, Xue Z, Shi L, et al (2024)

Unveiling the Detailed Mechanism and Origins of Chemo-, Regio-, and Stereoselectivity of Rare-Earth Catalyzed Alternating Copolymerization of Polar and Nonpolar Olefins.

Inorganic chemistry [Epub ahead of print].

The direct copolymerization of polar and nonpolar olefins is of great interest and significance, as it is the most atom-economical and straightforward strategy for the synthesis of functional polyolefin materials. Despite considerable efforts, the precise control of monomer-sequence and their regio- and stereochemistry is full of challenges, and the related mechanistic origins are still in their infancy to date. Herein, the mechanistic studies on the model reaction of Sc-catalyzed co-syndiospecific alternating copolymerization of anisylpropylene (AP) and styrene were performed by DFT calculations. The results suggest that the subtle balance between electronic and steric factors plays an important role during monomer insertions, and a new amino-dissociated mechanism was proposed for AP insertion at chain initiation. AP insertion follows the 2,1-si-insertion pattern, which is mainly controlled by steric factors caused by the restricted MeO···Sc interaction. As for styrene insertion, it prefers the 2,1-re-insertion manner and its regio- and stereoselectivities are influenced by steric repulsions between the inserting styrene and the polymer chain or the ligand. More interestingly, it is found that the alternating monomer-sequence is mainly determined by the "steric matching" principle, which is quantitatively expressed by the buried volume of the metal center of the preinserted species. The concept of steric pocket has been successfully applied to explain the different performances of several catalysts and other alternating copolymerization reactions. The insightful mechanistic findings and the quantitative steric pocket model present here are expected to promote rational design of new rare-earth catalysts for developing regio-, stereo-, and sequence-controlled copolymerization of specific polar and nonpolar olefins.

RevDate: 2024-02-02

Campos LR, Trefflich S, Morais DA, et al (2024)

Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analysis.

Molecular biology and evolution pii:7596672 [Epub ahead of print].

Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key concept behind this strategy is that orthologous genes share ancestry to some extent. While reconstructing the history of a single gene is feasible with the existing computational resources, the reconstruction of entire biological systems remains challenging. Here we present Bridge, a new algorithm designed to infer the evolutionary root of orthologous genes in large-scale evolutionary analysis. The Bridge algorithm infers the evolutionary root of a given gene based on the distribution of its orthologs in a species tree. The Bridge algorithm is implemented in R and can be used either to assess genetic changes across the evolutionary history of orthologous groups or to infer the onset of specific traits in a biological system.

RevDate: 2024-02-01

Abad ZG, Burgess TI, Bourret T, et al (2023)

Phytophthora : taxonomic and phylogenetic revision of the genus.

Studies in mycology, 106:259-348.

Many members of the Oomycota genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of regulatory concern around the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for 20 species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani, P. honggalleglyana (Synonym: P. hydropathica), P. megakarya, P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. ×multiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated multigene phylogeny and molecular toolbox with seven genes (ITS rDNA, β-tub, COI, EF1α, HSP90, L10, and YPT1) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 species, are associated with the "IDphy: molecular and morphological identification of Phytophthora based on the types" online resource (https://idtools.org/tools/1056/index.cfm). The first version of the IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic molecular toolbox with seven genes that includes the two metabarcoding genes (ITS and COI) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora, widely considered one of the most important genera of plant pathogens. Taxonomic novelties: New species: Phytophthora cajani K.S. Amin, Baldev & F.J. Williams ex Abad, Phytophthora honggalleglyana Abad, Phytophthora megakarya Brasier & M.J. Griffin ex Abad, Phytophthora pisi Heyman ex Abad, Phytophthora pseudopolonica W.W. Li, W.X. Huai & W.X. Zhao ex Abad & Kasiborski; New combinations: Phytophthora ×multiformis (Brasier & S.A. Kirk) Abad, Phytophthora uniformis (Brasier & S.A. Kirk) Abad; Epitypifications (basionyms): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora inundata Brasier et al., Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Lectotypifications (basionym): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Neotypifications (basionym): Phloeophthora syringae Kleb., Phytophthora meadii McRae Citation: Abad ZG, Burgess TI, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl JC, Verkleij G, Broders K, Schena L, Redford AJ (2023). Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology 106: 259-348. doi: 10.3114/sim.2023.106.05.

RevDate: 2024-01-30

Horstmann M, Quarles CD, Happel S, et al (2024)

Quantification of [[99]Tc]TcO4[-] in urine by means of anion-exchange chromatography-aerosol desolvation nebulization-inductively coupled plasma-mass spectrometry.

Analytical and bioanalytical chemistry [Epub ahead of print].

To sensitively determine [99]Tc, a new method for internal quantification of its most common and stable species, [[99]Tc]Tc[Formula: see text], was developed. Anion-exchange chromatography (IC) was coupled to inductively coupled plasma-mass spectrometry (ICP-MS) and equipped with an aerosol desolvation system to provide enhanced detection power. Due to a lack of commercial Tc standards, an isotope dilution-like approach using a Ru spike and called isobaric dilution analysis (IBDA) was used for internal quantification of [99]Tc. This approach required knowledge of the sensitivities of [99]Ru and [99]Tc in ICP-MS. The latter was determined using an in-house prepared standard manufactured from decayed medical [99m]Tc-generator eluates. This standard was cleaned and preconcentrated using extraction chromatography with TEVA resin and quantified via total reflection X-ray fluorescence (TXRF) analysis. IC coupled to ICP-MS enabled to separate, detect and quantify [[99]Tc]Tc[Formula: see text] as most stable Tc species in complex environments, which was demonstrated in a proof of concept. We quantified this species in untreated and undiluted raw urine collected from a patient, who previously underwent scintigraphy with a [99m]Tc-tracer, and determined a concentration of 19.6 ± 0.5 ng L[-1]. The developed method has a high utility to characterize a range of Tc-based radiopharmaceuticals, to determine concentrations, purity, and degradation products in complex samples without the need to assess activity parameters of [99(m)]Tc.

RevDate: 2024-01-29

Angeler DG, HB Fried-Petersen (2024)

Parallels of quantum superposition in ecological models: from counterintuitive patterns to eco-evolutionary interpretations of cryptic species.

BMC ecology and evolution, 24(1):15.

BACKGROUND: Superposition, i.e. the ability of a particle (electron, photon) to occur in different states or positions simultaneously, is a hallmark in the subatomic world of quantum mechanics. Although counterintuitive at first sight, the quantum world has potential to inform macro-systems of people and nature. Using time series and spatial analysis of bird, phytoplankton and benthic invertebrate communities, this paper shows that superposition can occur analogously in redundancy analysis (RDA) frequently used by ecologists.

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

CONCLUSION: We suggest that such "quantum weirdness" in the models is reconcilable with classical ecosystems logic when the focus of research shifts from morphological species to cryptic species that consist of genetically and ecologically differentiated subpopulations. We support our argument with theoretical discussions of eco-evolutionary interpretations that should become testable once suitable data are available.

RevDate: 2024-01-26

Saccò M, Mammola S, Altermatt F, et al (2024)

Groundwater is a hidden global keystone ecosystem.

Global change biology, 30(1):e17066.

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.

RevDate: 2024-01-24

Cheng R, Luo A, Orr M, et al (2024)

Cryptic diversity begets challenges and opportunities in biodiversity research.

Integrative zoology [Epub ahead of print].

How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.

RevDate: 2024-01-23

Godarzi B, Chandler F, van der Linden A, et al (2024)

A species-independent lateral flow microarray immunoassay to detect WNV and USUV NS1-specific antibodies in serum.

One health (Amsterdam, Netherlands), 18:100668 pii:S2352-7714(23)00188-X.

Arboviruses such as West Nile Virus (WNV) and Usutu Virus (USUV) are emerging pathogens that circulate between mosquitoes and birds, occasionally spilling over into humans and horses. Current serological screening methods require access to a well-equipped laboratory and are not currently available for on-site analysis. As a proof of concept, we propose here a species-independent lateral flow microarray immunoassay (LMIA) able to quickly detect and distinguish between WNV Non-Structural 1 (NS1) and USUV NS1-specific antibodies. A double antigen approach was used to test sera collected from humans, horses, European jackdaws (Corvus monedula), and common blackbirds (Turdus merula). Optimization of the concentration of capture antigen spotted on the LMIA membrane and the amount of detection antigen conjugated to detector particles indicated that maximizing both parameters increased assay sensitivity. Upon screening of a larger serum panel, the optimized LMIA showed significantly higher spot intensity for a homologous binding event. Using a Receiver Operating Characteristics (ROC) curve, WNV NS1 LMIA results in humans, horses, and C. monedula showed good correlation when compared to "gold standard" WNV FRNT90. The most optimal derived sensitivity and specificity of the WNV NS1 LMIA relative to corresponding WNV FRNT90-confirmed sera were determined to be 96% and 86%, respectively. While further optimization is required, this study demonstrates the feasibility of developing a species-independent LMIA for on-site analysis of WNV, USUV, and other arboviruses. Such a tool would be useful for the on-site screening and monitoring of relevant species in more remote or low-income regions.

RevDate: 2024-01-18

Reschke K, Morozova OV, Dima B, et al (2022)

Phylogeny, taxonomy, and character evolution in Entoloma subgenus Nolanea.

Persoonia, 49:136-170.

Nolanea is a well-known and long-established subgenus of the genus Entoloma traditionally defined mainly by the mycenoid basidiocarps of the included species. Until now, revisions of this subgenus including molecular data exist only on a regional scale. In this study, the phylogeny of species of Nolanea is analysed based on multi-gene DNA sequences including data of specimens from all continents. New primers are designed for the mitochondrial small subunit and RPB2. The performance of the DNA loci in reconstructing the phylogeny in subg. Nolanea is evaluated. An ancestral state reconstruction is used to infer the character state evolution as well as the importance and reliability of morphological characters used to define subclades below subgeneric rank. Based on the results, seven sections are recognised in Nolanea: the sections Holoconiota, Infularia, Mammosa, Nolanea, Papillata, Staurospora, and the newly described sect. Elegantissima. A large phylogeny based on the fungal barcode rDNA ITS with numerous type sequences is used to evaluate current species concepts. Several names are revealed to be synonyms of older names. Four species new to science are described, namely E. altaicum, E. argillaceum, E. cornicolor, and E. incognitum. Lectotypes, epitypes or neotypes are designated for E. cetratum, E. clandestinum, E. conferendum, E. cuspidiferum, E. hebes, E. minutum, E. nitens, and E. rhodocylix. The re-evaluation of the limits of subg. Nolanea leads to an altered concept excluding species with distinct, lageniform cheilocystidia. The section Ameides is placed in subg. Leptonia. For several species formerly accommodated in Nolanea, but excluded now, viz., E. lepiotoides, E. rhombisporum, E. subelegans, and E. velenovskyi the taxonomic position remains unclear, because of the yet unresolved phylogeny of the whole genus Entoloma. Citation: Reschke K, Morozova OV, Dima B, et al. 2022. Phylogeny, taxonomy, and character evolution in Entoloma subgenus Nolanea. Persoonia 49: 136-170. https://doi.org/10.3767/persoonia.2022.49.04.

RevDate: 2024-01-17

Miller KB, Michat MC, N Ferreira (Jr) (2024)

Reclassification of Cybistrinae Sharp, 1880 in the Neotropical Region (Coleoptera, Adephaga, Dytiscidae), with description of new taxa.

ZooKeys, 1188:125-168.

The classification of the Neotropical Cybistrinae Sharp, 1880 (Coleoptera: Adephaga: Dytiscidae) is extensively revised based on a phylogenetic analysis of morphological features of the group. A new genus, Nilssondytesgen. nov. is described for a unique new species, Nilssondytesdiversussp. nov. from Venezuela. The New World genus, Megadytes Sharp, 1882, with several subgenera, was found to not be monophyletic. The type species of Megadytes, Dytiscuslatus Fabricius, 1801 and the species Cybisterparvus Trémouilles, 1984 were found to be monophyletic together, and phylogenetically more closely related to Cybister Curtis, 1827 than to other species assigned to Megadytes sensu stricto, which were found to also be monophyletic. The name Megadytes is here restricted to include only Megadyteslatus and Megadytesparvus. These two species assigned to this newly restricted genus concept are reviewed and diagnosed. A new genus, Metaxydytesgen. nov., is erected to include all the other species currently assigned to Megadytes sensu stricto. The current subgenus names assigned to Megadytes, Bifurcitus Brinck, 1945, Paramegadytes Trémouilles & Bachmann, 1980, and Trifurcitus Brinck, 1945, are elevated to genus rank since they are variously paraphyletic. The two species assigned to Cybister (Neocybister) Miller, Bergsten & Whiting, 2007, Cybister (Neocybister) festae Griffini, 1895, and Cybister (Neocybister) puncticollis (Brullé, 1837) re reviewed and diagnosed with the former redescribed and its type specimens considered for the first time since its description. Another evidently new species and possible new genus, Megadytes species, IR57 (Ribera et al. 2008), from Peru, is also characterized, but not formally treated because of lack of important data for the single, partial specimen. Diagnostic features are illustrated for the entire group.

RevDate: 2024-01-14

Hilburn BG, Janosik AM, CE Johnston (2023)

Incipient speciation in allopatric Etheostoma rupestre (Percidae: Etheostomatinae) lineages, with the description of three new subspecies.

Zootaxa, 5343(2):151-172.

In recent years, new species descriptions for the North American darters have proliferated. Most species concepts accepted by contemporary ichthyologists require that a valid species be both monophyletic and diagnoseable, yet many lineages exhibit modal or range differences in morphological characteristics without individuals being diagnosable. Such scenarios present difficulties with regards to proper taxonomic recognition of divergent lineages and often prohibit appropriate conservation action. Following the example of recent authors, we provide meristic, geometric morphometric, and pigmentation data to support the recognition of three subspecies of Etheostoma rupestre, a species endemic to the Mobile Basin. These morphological data cohere with previous genetic work for E. rupestre. The nominate subspecies Etheostoma rupetsre rupestre (Tsais Rock Darter) is endemic to the Tombigbee River and Black Warrior River watersheds in Alabama and Mississippi and is characterized by having lower numbers of lateral blotches, lower range and mean of lateral line scales, lower modal number of scales above the lateral line, and lower degrees of nape squamation than other subspecies. Etheostoma rupestre piersoni (Shamrock Darter), ssp. nov., is endemic to the Cahaba and Alabama River Watersheds in Alabama and is characterized by intermediate counts of lateral blotches and higher scale counts and nape squamation than E. r. rupestre. Etheostoma rupestre uphapeense (Jade Darter), ssp. nov., is restricted to several small, disjunct populations in the Coosa and Tallapoosa watersheds in Alabama, Georgia, and Tennessee. Etheostoma r. uphapeense is characterized by having a higher mean number of lateral blotches than both other subspecies and higher scale counts than E. r. rupestre. While E. r. rupestre and E. r. piersoni are widespread and abundant within their respective ranges, E. r. uphapeense has a disjunct range and is often uncommon where it occurs. Etheostoma r. uphapeense should be monitored where it occurs to discern population trends.

RevDate: 2024-01-14

Hoare RJB, Patrick BH, Buckley TR, et al (2023)

Wing pattern variation and DNA barcodes defy taxonomic splitting in the New Zealand Pimelea Looper Notoreas perornata (Walker) (Lepidoptera: Geometridae: Larentiinae): the importance of populations as conservation units.

Zootaxa, 5346(1):1-27.

The endemic Notoreas perornata (Walker, 1863) complex (Lepidoptera: Geometridae: Larentiinae) from the North Island and northern South Island of New Zealand is reviewed. Larvae feed on Pimelea spp. (Thymelaeaceae), frequently in highly fragmented and threatened shrubland habitats. Allopatric populations tend to differ in size and wing pattern characteristics, but not in genitalia; moreover extensive variation renders recognition of subspecies / allopatric species based on any species concept problematic. A mitochondrial DNA gene tree is not congruent with morphology and indicates rapid recent divergence that has not settled into diagnosable lineages. Based on our results, we synonymise Notoreas simplex Hudson, 1898 with N. perornata (Walker, 1863), and retain N. perornata as a single, highly diverse but monotypic species. All known populations are illustrated to display variation. For conservation purposes, we recommend the continued recognition within the species of 10 populations or groups of populations that appear to be on the way to diverging at subspecific level based on morphological and/or DNA data. The conservation status of all these populations is reviewed. One conservation unit, comprising the populations from Westland, has not been seen since 1998 and is feared possibly extinct.

RevDate: 2024-01-13

Martin JM, Leece AB, Baker SE, et al (2024)

A lineage perspective on hominin taxonomy and evolution.

Evolutionary anthropology [Epub ahead of print].

An uncritical reliance on the phylogenetic species concept has led paleoanthropologists to become increasingly typological in their delimitation of new species in the hominin fossil record. As a practical matter, this approach identifies species as diagnosably distinct groups of fossils that share a unique suite of morphological characters but, ontologically, a species is a metapopulation lineage segment that extends from initial divergence to eventual extinction or subsequent speciation. Working from first principles of species concept theory, it is clear that a reliance on morphological diagnosabilty will systematically overestimate species diversity in the fossil record; because morphology can evolve within a lineage segment, it follows that early and late populations of the same species can be diagnosably distinct from each other. We suggest that a combination of morphology and chronology provides a more robust test of the single-species null hypothesis than morphology alone.

RevDate: 2024-01-11

Cai ZY, NH Xia (2023)

A Novel Elucidation for Synflorescences of Chinese Bamboos.

Plants (Basel, Switzerland), 13(1):.

The objective of this work is to elucidate the flowering structures of Chinese bamboos applying the synflorescence concept. To keep in line with grasses, the bamboo synflorescence is defined as a whole culm or a whole branch terminating in an inflorescence. For the first time, the repetitive and fundamental unit of bamboo synflorescences is clearly identified and termed as the "basic flowering branch". The basic flowering branch could be considered as the most simplified synflorescence for a bamboo species. Applying the synflorescence concept, the pseudospikelet is interpreted as a sort of basic flowering branch rather than a spikelet. Consequently, the synflorescence development pattern is consistent throughout the whole family. This study also marks the first recognition of both pseudospikelets and true spikelet flowering branches within the same bamboo synflorescence, which is observed in the genera Brachystachyum, Semiarundinaria and Menstruocalamus.

RevDate: 2024-01-08

Torresani M, Rocchini D, Ceola G, et al (2024)

Grassland vertical height heterogeneity predicts flower and bee diversity: an UAV photogrammetric approach.

Scientific reports, 14(1):809.

The ecosystem services offered by pollinators are vital for supporting agriculture and ecosystem functioning, with bees standing out as especially valuable contributors among these insects. Threats such as habitat fragmentation, intensive agriculture, and climate change are contributing to the decline of natural bee populations. Remote sensing could be a useful tool to identify sites of high diversity before investing into more expensive field survey. In this study, the ability of Unoccupied Aerial Vehicles (UAV) images to estimate biodiversity at a local scale has been assessed while testing the concept of the Height Variation Hypothesis (HVH). This hypothesis states that the higher the vegetation height heterogeneity (HH) measured by remote sensing information, the higher the vegetation vertical complexity and the associated species diversity. In this study, the concept has been further developed to understand if vegetation HH can also be considered a proxy for bee diversity and abundance. We tested this approach in 30 grasslands in the South of the Netherlands, where an intensive field data campaign (collection of flower and bee diversity and abundance) was carried out in 2021, along with a UAV campaign (collection of true color-RGB-images at high spatial resolution). Canopy Height Models (CHM) of the grasslands were derived using the photogrammetry technique "Structure from Motion" (SfM) with horizontal resolution (spatial) of 10 cm, 25 cm, and 50 cm. The accuracy of the CHM derived from UAV photogrammetry was assessed by comparing them through linear regression against local CHM LiDAR (Light Detection and Ranging) data derived from an Airborne Laser Scanner campaign completed in 2020/2021, yielding an [Formula: see text] of 0.71. Subsequently, the HH assessed on the CHMs at the three spatial resolutions, using four different heterogeneity indices (Rao's Q, Coefficient of Variation, Berger-Parker index, and Simpson's D index), was correlated with the ground-based flower and bee diversity and bee abundance data. The Rao's Q index was the most effective heterogeneity index, reaching high correlations with the ground-based data (0.44 for flower diversity, 0.47 for bee diversity, and 0.34 for bee abundance). Interestingly, the correlations were not significantly influenced by the spatial resolution of the CHM derived from UAV photogrammetry. Our results suggest that vegetation height heterogeneity can be used as a proxy for large-scale, standardized, and cost-effective inference of flower diversity and habitat quality for bees.

RevDate: 2024-01-01

Cook CN, Redford KH, MW Schwartz (2023)

Species conservation in the era of genomic science.

Bioscience, 73(12):885-890 pii:biad098.

The exponential increase in the availability of genomic data, derived from sequencing thousands of loci or whole genomes, provides exciting new insights into the diversity of life. However, it can also challenge established species concepts and existing management regimes derived from these concepts. Genomic data can help inform decisions about how to manage genetic diversity, but policies that protect identified taxonomic entities can generate conflicting recommendations that create challenges for practitioners. We outline three dimensions of management concern that arise when facing new and potentially conflicting interpretations of genomic data: defining conservation entities, deciding how to manage diversity, and evaluating the risks and benefits of management actions. We highlight the often-underappreciated role of values in influencing management choices made by individuals, scientists, practitioners, the public, and other stakeholders. Such values influence choices through mechanisms such as the Rashomon effect, whereby management decisions are complicated by conflicting perceptions of the causes and consequences of the conservation problem. To illustrate how this might operate, we offer a hypothetical example of this effect for the interpretation of genomic data and its implications for conservation management. Such value-based decisions can be challenged by the rigidity of existing management regimes, making it difficult to achieve the necessary flexibility to match the changing biological understanding. We finish by recommending that both conservation geneticists and practitioners reflect on their respective values, responsibilities, and roles in building a more robust system of species management. This includes embracing the inclusion of stakeholders in decision-making because, as in many cases, there are not objectively defensible right or wrong decisions.

RevDate: 2023-12-28

Noble PJ, Seitz C, Lee SS, et al (2023)

Characterization of algal community composition and structure from the nearshore environment, Lake Tahoe (United States).

Frontiers in ecology and evolution, 10:1-16.

Periphyton assemblages from the nearshore environment of the west (California) side of Lake Tahoe, were analyzed to determine their taxonomic composition and community structure across habitats and seasons. Lake Tahoe is the second deepest lake in the US and an iconic oligotrophic subalpine lake with remarkable transparency. It has experienced offshore cultural eutrophication since the 1960s with observations of nuisance nearshore algal growth since the mid 2000s attributed to anthropogenic stressors. Samplings from November 2019-September 2020 provide useful snapshots against which older monitoring may be contextualized. A voucher flora, complete with descriptions, photo-documentation and referencing to species concepts employed, was created as a method of providing reproducible identification and enumeration of algal species, and more seamless reconciliation of detailed taxonomic data with future monitoring projects. The eulittoral zone (0-2 m) is seasonally dominated by elongate araphid (Synedra, Ulnaria) and stalked or entubed diatoms (Gomphonema, Cymbella, Encyonema). The sublittoral zone (>2 m) is dominated by a nitrogen-fixing Epithemia-cyanobacteria assemblage with less seasonal changes in dominance and composition that expanded to impinge on the 2 m depths of the eulittoral zone in the Fall. Sublittoral epipsammic samples, despite their proximity to rocks, had a very distinct diatom composition and high species dominance, similar to what was seen in the Fall eulittoral samples, with high numbers of Staurosirella chains and small biraphid diatoms. The deeper samples at 30 and 50 m contained high numbers of live Epithemia, and indicate a thriving sublittoral assemblage at these greater depths, but with less biomass. The 2019-20 data show many of the same diatom taxa observed in the 1970's and 1980's but with changes in species dominance. Notably, there was less of the green alga Mougeotia, when compared to the 1970's data, and a higher dominance by nitrogen fixing Epithemia in the sublittoral zone, persisting year-round. These new data show roughly double the algal species biodiversity that had been documented previously in the Lake Tahoe nearshore, and is largely attributed to the methods employed. Adopting these new methods in future monitoring efforts should improve harmonization of taxonomic data and help advance our knowledge of the contributions to nearshore cultural eutrophication.

RevDate: 2023-12-21

Harrington TC, Ferreira MA, Somasekhara YM, et al (2023)

An expanded concept of Ceratocystis manginecans and five new species in the Latin American Clade of Ceratocystis.

Mycologia [Epub ahead of print].

The genus Ceratocystis contains a number of emerging plant pathogens, mostly members of the Latin American Clade (LAC), in which there are several unresolved taxonomic controversies. Among the most important are Brazilian pathogens in the C. fimbriata complex, C. manginecans and C. eucalypticola. Representatives of C. manginecans and C. eucalypticola from India and China, respectively, were shown to be fully interfertile in laboratory matings, and hybrids between the putative species were identified on Punica in India. An Indian tester strain was sexually compatible with representatives of what has been considered C. fimbriata on numerous hosts across Brazil. In this revision of the LAC, the name C. fimbriata is restricted to the widely dispersed Ipomoea strain, and C. manginecans is recognized as a Brazilian species that is important on Mangifera, Eucalyptus, and many other crops. C. mangivora and C. mangicola are also considered synonyms of C. manginecans. Based on phylogenetics and mating studies, two other Brazilian species are recognized: C. atlantica, sp. nov., and C. alfenasii, sp. nov., each with wide host ranges. Three new Caribbean species are recognized based on phylogenetics and earlier inoculation studies: C. costaricensis, sp. nov., on Coffea, C. cubensis, sp. nov., on Spathodea, and C. xanthosomatis, sp. nov., on the vegetatively propagated aroids Xanthosoma and Syngonium. Some of the other Ceratocystis species were based primarily on unique internal transcribed spacer (ITS) rDNA sequences, but the unreliability of rDNA sequences was demonstrated when intraspecific crossing of isolates with differing ITS sequences generated single-ascospore progeny with intragenomic variation in ITS sequences and others with new ITS sequences. Species recognition in Ceratocystis should use phenotype, including intersterility tests, to help identify which lineages are species. Although some species remain under-studied, we recognize 16 species in the LAC, all believed to be native to Latin America, the Caribbean region, or eastern USA.

RevDate: 2023-12-17

Rodriguez Gutierrez G, Ortiz Perez A, S Palzer (2023)

Integrated, Selective, Simultaneous Multigas Sensing Based on Nondispersive Infrared Spectroscopy-Type Photoacoustic Spectroscopy.

ACS sensors [Epub ahead of print].

Most chemical sensing scenarios require the selective and simultaneous determination of the concentrations of multiple gas species. In order to enable large-scale monitoring, reliability, robustness, and the potential for integration and miniaturization are key parameters that next-generation sensing technologies must comply with. Due to their superior sensitivity and selectivity as compared to standard NDIR-type systems, photoacoustic NDIR-approaches offer a means for selective detection at much reduced system dimensions such that microintegration becomes feasible. This contribution presents an acoustic frequency multiplexing method to integrate sensing capabilities for the parallel analysis of multiple gases in a single device without loss in selectivity via sound frequency separation. The approach is demonstrated using mid-infrared light emitting diodes and a multigas photoacoustic detector to monitor some of the most important greenhouse gases: carbon dioxide and methane. The number of gas species the sensor concept is able to detect simultaneously can be expanded without increasing the size of the system or its complexity. Additionally, the results demonstrate that the integrated device features the same selectivity and sensitivity as the currently used single gas photoacoustic NDIR systems. Furthermore, the possibility of an extension to any number of gas species is argued.

RevDate: 2023-12-14

Zhu LR, Wang ZY, Luo JJ, et al (2023)

Mercury-Mediated Epitaxial Accumulation of Au Atoms for Stained Hydrogel-Improved On-Site Mercury Monitoring.

Analytical chemistry [Epub ahead of print].

Trivalent Au ions are easily reduced to be zerovalent atoms by coexisting reductant reagents, resulting in the subsequent accumulation of Au atoms and formation of plasmonic nanostructures. In the absence of stabilizers or presence of weak stabilizers, aggregative growth of Au nanoparticles (NPs) always occurs, and unregular multidimensional Au materials are consequently constructed. Herein, the addition of nanomole-level mercury ions can efficiently prevent the epitaxial accumulation of Au atoms, and separated Au NPs with mediated morphologies and superior plasmonic characteristics are obtained. Experimental results and theoretical simulation demonstrate the Hg-concentration-reliant formation of plasmonic nanostructures with their mediated sizes and shapes in the presence of weak reductants. Moreover, the sensitive plasmonic responses of reaction systems exhibit selectivity comparable to that of Hg species. As a concept of proof, polymeric carbon dots (CDs) were used as the initial reductant, and the reactions between trivalent Au and CDs were studies. Significantly, Hg atoms prevent the epitaxial accumulation of Au atoms, and plasmonic NPs with decreased sizes were in situ synthesized, corresponding to varied surface plasmonic resonance absorption performance of the CD-induced hybrids. Moreover, with the integration of sensing substrates of CD-doped hydrogels, superior response stabilities, analysis selectivity, and sensitivity of Hg[2+] ions were achieved on the basis of the mercury-mediated in situ chemical reactions between trivalent Au ions and reductant CDs. Consequently, a high-performance sensing strategy with the use of Au NP-staining hydrogels (nanostaining hydrogels) was exhibited. In addition to Hg sensing, the nanostaining hydrogels facilitated by doping of emerging materials and advanced chem/biostrategies can be developed as high-performance on-site monitoring routes to various pollutant species.

RevDate: 2023-12-09

Shentu J, Lu Y, Li Y, et al (2023)

Compact Combustion Mechanisms of Typical n-Alkanes Developed by the Minimized Reaction Network Method.

Molecules (Basel, Switzerland), 28(23): pii:molecules28237695.

The existing combustion kinetic modeling method which aims at developing phenomenological combustion mechanisms characterized by multiple reactions confronts several challenges, including the conflicts between computing resources and mechanism scales during numerical simulation, etc. In order to address these issues, the minimized reaction network method for complex combustion system modeling based on the principle of simultaneous chemical equilibrium is proposed, which is aimed to develop combustion mechanisms with minimal reaction steps under a limited number of species. The concept of mechanism resolution is proposed in this method, and the reaction network with minimal reaction steps under a given mechanism resolution is constructed so that the scale of mechanisms is compressed greatly. Meanwhile, distinguishing from other mechanisms, the reversible form of elementary reactions is adopted and the classical two-parameter (A, Ea) Arrhenius equation fits the rate constants. Typical n-alkanes including n-butane, n-heptane, n-octane, n-decane, n-dodecane and n-hexadecane were taken as examples to indicate the development process of mechanisms and systematic kinetic validations were carried out. Results show that this method leads to very compact mechanisms with satisfactory accuracy, and it eliminates the process of mechanism reduction and is beneficial for mechanism optimization. This method and the derived kinetic mechanisms are hoped to contribute to combustion engineering applications.

RevDate: 2023-12-05

Logan RK, Vaudo JJ, Wetherbee BM, et al (2023)

Seasonally mediated niche partitioning in a vertically compressed pelagic predator guild.

Proceedings. Biological sciences, 290(2012):20232291.

Niche partitioning among closely related, sympatric species is a fundamental concept in ecology, and its mechanisms are of broad interest for understanding ecosystem functioning and predicting the impacts of human-driven environmental change. However, identifying mechanisms by which top marine predators partition available resources has been especially challenging given the difficulty of quantifying resource use of large pelagic animals. In the eastern tropical Pacific (ETP), three large, highly mobile and ecologically similar pelagic predators (blue marlin (Makaira nigricans), black marlin (Istiompax indica) and sailfish (Istiophorus platypterus)) coexist in a vertically compressed habitat. To evaluate each species' ecological niche, we leveraged a decade of recreational fisheries data, multi-year satellite tracking with high-resolution dive data, and stable isotope analysis. Fishery interaction and telemetry-based three-dimensional seasonal utilization distributions suggested high spatial and temporal overlap among species; however, seasonal and diel variability in diving behaviour produced spatial partitioning, leading to low trophic overlap among species. Expanding oxygen minimum zones will reduce the available vertical habitat within predator guilds, likely leading to increases in interspecific competition. Thus, understanding the mechanisms of habitat partitioning among predators in the vertically compressed ETP can provide insight into how predators in other ocean regions may respond to vertically limited habitats.

RevDate: 2023-11-25

Li WJ, Li FF, Bai J, et al (2023)

Isolation and characterization of intestinal bacteria associated with cellulose degradation in grasshoppers (Orthoptera).

Journal of insect science (Online), 23(6):.

Insect gut bacteria play an essential role in the nutritional metabolism, growth, and development of insects. Grasshoppers (Orthoptera) are cellulose-rich plant-feeding pests. Although the biological potential of grasshopper gut microorganisms to assist cellulose decomposition is well established, microbial resources for efficient degradation of cellulose biomass are still scarce and need to be developed. In this study, we used selective media to isolate cellulose-degrading bacteria from the intestines of Atractomorpha sinensis, Trilophidia annulata, Sphingonotus mongolicus, and Calliptamus abbreviatus. Phylogenetic analysis based on the maximum likelihood method using 16S rDNA sequencing sequences to identify bacteria revealed the isolation of 11 strains belonging to 3 genera, including Klebsiella, Aeromonas, and Bacillus. The degradability of the isolates to cellulose was then determined by the DNS colorimetric method, and the results showed that Bacillus had the highest degradation rate. The elucidation of microbial cellulose degradation capacity in grasshoppers not only contributes to the understanding of multiple plant-insect-microbe interactions, but also provides a valuable microbial resource for solving the biomass conversion of cellulose species problem.

RevDate: 2023-11-21

Kuang X, Liu Y, Luo H, et al (2023)

Triggerable Prodrug Nanocoating Enables On-Demand Activation of Microbial and Small-Molecular Therapeutics for Combination Treatment.

Journal of the American Chemical Society [Epub ahead of print].

The synergy of living microbial and small-molecular therapeutics has been widely explored for treating a variety of diseases, while current combination strategies often suffer from low bioavailability, heterogeneous spatiotemporal distribution, and premature drug release. Here, the use of a triggerable prodrug nanocoating is reported to enable the on-demand activation of microbial and small-molecular therapeutics for combination treatment. As a proof-of-concept study, a reactive oxygen species-responsive aromatic thioacetal linker is employed to prepare cationic chitosan-drug conjugates, which can form a nanocoating on the surface of living bacteria via electrostatic interaction. Following administration, the wrapped bacteria can be prevented from in vivo insults by the shielding effect of the nanocoating and be co-delivered with the conjugated drug in a spatiotemporally synchronous manner. Upon reaching the lesion site, the upgraded reactive oxygen species trigger in situ cleavage of the thioacetal linker, resulting in the release of the conjugated drug and a linker-derived therapeutic cinnamaldehyde. Meanwhile, a charge reversal achieved by the generation of negatively charged thiolated chitosan induces the dissociation of the nanocoating, leading to synchronous release of the living bacteria. The adequate activation of the combined therapeutics at the lesion site exhibits superior synergistic treatment efficacy, as demonstrated by an in vivo assessment using a mouse model of colitis. This work presents an appealing approach to combine living microbial and small-molecular therapeutics for advanced therapy of diseases.

RevDate: 2023-11-20

Wang MZ, Wu J, Zhang SL, et al (2023)

Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity.

Cladistics : the international journal of the Willi Hennig Society [Epub ahead of print].

Species delimitation has long been a subject of controversy, and there are many alternative concepts and approaches used to define species in plants. The genus Amana (Liliaceae), known as "East Asian tulips" has a number of cryptic species and a huge genome size (1C = 21.48-57.35 pg). It also is intriguing how such a spring ephemeral genus thrives in subtropical areas. However, phylogenetic relationships and species delimitation within Amana are challenging. Here we included all species and 84 populations of Amana, which are collected throughout its distribution range. A variety of methods were used to clarify its species relationships based on a combination of morphological, ecological, genetic, evolutionary and phylogenetic species concepts. This evidence supports the recognition of at least 12 species in Amana. Moreover, we explored the complex evolutionary history within the genus and detected several historical hybridization and introgression events based on phylogenetic trees (transcriptomic and plastid), phylonetworks, admixture and ABBA-BABA analyses. Morphological traits have undergone parallel evolution in the genus. This spring ephemeral genus might have originated from a temperate region, yet finally thrives in subtropical areas, and three hypotheses about its adaptive evolution are proposed for future testing. In addition, we propose a new species, Amana polymorpha, from eastern Zhejiang Province, China. This research also demonstrates that molecular evidence at the genome level (such as transcriptomes) has greatly improved the accuracy and reasonability of species delimitation and taxon classification.

RevDate: 2023-11-14

Karnbrock SBH, M Alcarazo (2023)

Cooperation between p-Block Elements and Redox-Active Ligands: Stoichiometric and Catalytic Transformations.

Chemistry (Weinheim an der Bergstrasse, Germany) [Epub ahead of print].

The relevance acquired by redox-active ligands in modern catalysis stems from their facile delivery and acceptance of electrons, either to the metal they coordinate or directly to an incoming substrate that also binds the central metal. Doing that, they generate coordinated radicals and provide access to more than one spin state during the catalytic cycle. As consequence, the new reaction barriers get reduced when compared to similar processes that are restricted to a single spin surface. The principles that govern this genuine approach to catalyst design are well-established, and their implementation has allowed the development of synthetically useful catalytic transformations; however, the extension of the concept to species in which p-block elements take the role of central atoms remains largely underdeveloped. Through the discussion of the key achievements and recent progress, this Concept Article highlights this original approach to design (organo)catalysts, discloses the progress achieved, and also reveals the many shortcomings still existing in the field.

RevDate: 2023-11-14

Pezoa JE, Ramírez DA, Godoy CA, et al (2023)

A Spatial-Spectral Classification Method Based on Deep Learning for Controlling Pelagic Fish Landings in Chile.

Sensors (Basel, Switzerland), 23(21): pii:s23218909.

Fishing has provided mankind with a protein-rich source of food and labor, allowing for the development of an important industry, which has led to the overexploitation of most targeted fish species. The sustainable management of these natural resources requires effective control of fish landings and, therefore, an accurate calculation of fishing quotas. This work proposes a deep learning-based spatial-spectral method to classify five pelagic species of interest for the Chilean fishing industry, including the targeted Engraulis ringens, Merluccius gayi, and Strangomera bentincki and non-targeted Normanichthtys crockeri and Stromateus stellatus fish species. This proof-of-concept method is composed of two channels of a convolutional neural network (CNN) architecture that processes the Red-Green-Blue (RGB) images and the visible and near-infrared (VIS-NIR) reflectance spectra of each species. The classification results of the CNN model achieved over 94% in all performance metrics, outperforming other state-of-the-art techniques. These results support the potential use of the proposed method to automatically monitor fish landings and, therefore, ensure compliance with the established fishing quotas.

RevDate: 2023-11-08

Ferchiou S, Caza F, de Boissel PGJ, et al (2022)

Applying the concept of liquid biopsy to monitor the microbial biodiversity of marine coastal ecosystems.

ISME communications, 2(1):61.

Liquid biopsy (LB) is a concept that is rapidly gaining ground in the biomedical field. Its concept is largely based on the detection of circulating cell-free DNA (ccfDNA) fragments that are mostly released as small fragments following cell death in various tissues. A small percentage of these fragments are from foreign (nonself) tissues or organisms. In the present work, we applied this concept to mussels, a sentinel species known for its high filtration capacity of seawater. We exploited the capacity of mussels to be used as natural filters to capture environmental DNA fragments of different origins to provide information on the biodiversity of marine coastal ecosystems. Our results showed that hemolymph of mussels contains DNA fragments that varied considerably in size, ranging from 1 to 5 kb. Shotgun sequencing revealed that a significant amount of DNA fragments had a nonself microbial origin. Among these, we found DNA fragments derived from bacteria, archaea, and viruses, including viruses known to infect a variety of hosts that commonly populate coastal marine ecosystems. Taken together, our study shows that the concept of LB applied to mussels provides a rich and yet unexplored source of knowledge regarding the microbial biodiversity of a marine coastal ecosystem.

RevDate: 2023-11-04

Francischini DDS, MAZ Arruda (2023)

One-point calibration and matrix-matching concept for quantification of potentially toxic elements in wood by LA-ICP-MS.

Analytical and bioanalytical chemistry [Epub ahead of print].

The aim of this work is to evaluate two quantitative methods, based on the external calibration applied in laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analysis, known as (i) analytical curve and (ii) one-point calibration, using the concept of matrix matching to quantify three potentially toxic elements (PTEs) in wood samples. These can biologically register changes in the abiotic environment and be applied to monitoring climate change or environmental toxicity. In this case, standard sample preparation was evaluated to prepare the standard pellets using Pinus taeda species as a matrix-matching concept. Six pellets of P. taeda, with different Pb, Cd, and Ba concentrations, were prepared to build the analytical curve and one-point calibration strategies. The LA-ICP-MS parameters were optimised for [206]Pb, [208]Pb, [112]Cd, [114]Cd, [137]Ba, and [138]Ba isotope analysis in wood samples. The two calibration strategies provided 74-110% analytical recovery from certified reference materials and similar results to those obtained by ICP-MS through the acid digestion of environmental wood samples from São Paulo City (Brazil). This demonstrated the applicability of the one-point calibration strategy in quantifying PTEs in wood samples, which could be used with environmental analyses. Differences observed between the Ba isotope results obtained via LA-ICP-MS and ICP-MS quantification were related to sampling by LA-ICP-MS and the ICP-MS sample introduction, as well as to laser matrix and transport effects because of the difference between the wood species evaluated.

RevDate: 2023-11-02

Hübner J, Chemyreva VG, DG Notton (2023)

Taxonomic and nomenclatural notes on Geodiaprialongiceps Kieffer, 1911 (Hymenoptera, Diapriidae) and synonymy of the genus Geodiapria Kieffer, 1910.

ZooKeys, 1183:1-11.

This paper reviews the status of Geodiapria and its nominotypical and only included species G.longiceps. Geodiapria was previously understood to be very similar to, and doubtfully separated from the genus Basalys. We use integrative taxonomy (morphology, DNA-barcoding, phylogenetic tree building) to show that the valid name for what was G.longiceps Kieffer, 1911 is now Basalysrufocinctus (Kiefer, 1911) and that Geodiapria is consequently a junior synonym of Basalyssyn. nov. The following taxa are new synonyms of B.rufocinctus: Loxotropalongiceps Wasmann, 1909, syn. nov., G.longiceps Kieffer, 1911, syn. nov., L.rufosignata Kieffer, 1911, syn. nov. Basalysrufocinctus is newly reported from Corsica, Germany, Norway and Spain.

RevDate: 2023-10-28

Sakala J (2024)

Fossil Wood Analyses: Several Examples from Five Case Studies in the Area of Central and NW Bohemia, Czech Republic.

Methods in molecular biology (Clifton, N.J.), 2722:89-104.

In the area of the Central and NW Bohemia, Czech Republic, the fossil wood is quite abundant, found in different states of preservation and present from Paleozoic (Pennsylvanian), through Mesozoic (Upper Cretaceous), to Cenozoic (upper Eocene to lower Miocene). So, this small area is ideal to demonstrate various aspects of the fossil wood analyses, including anatomy (unifacial vs. bifacial cambium, formation of tyloses and its significance, early vs. late wood, unambiguity of scientific terminology, stem vs. root wood), taphonomy (completeness of fossil record, influence of environment on mode of preservation, influence of preservation on wood anatomy and preservation potential, discrepancy between the record of wood and other organs), systematics (stem vs. crown group, wide concept of fossil wood genera, "mosaic" species, wood of extinct plants), and palaeoclimatic reconstruction (definition of "wood type," subjective vs. objective methods). The majority of the studied woods were thin-sectioned following the standard techniques and observed with a compound light microscope.

RevDate: 2023-10-28

Chen P, Abeywickrama PD, Ji S, et al (2023)

Molecular Identification and Pathogenicity of Diaporthe eres and D. hongkongensis (Diaporthales, Ascomycota) Associated with Cherry Trunk Diseases in China.

Microorganisms, 11(10): pii:microorganisms11102400.

This study aimed to identify fungal species associated with trunk diseases of sweet cherries (Prunus avium) in several commercial cherry orchards in Beijing, Guizhou and Shandong provinces, China. In total, eighteen fungal strains that fitted well into the species concept of Diaporthe were isolated. Based on both morphological and multi-locus phylogenetic analyses of internal transcribed spacer region (ITS), beta-tubulin (tub-2), calmodulin (Cal) and translation elongation factor 1-α (tef1-α) sequencing data, fourteen isolates were identified as Diaporthe eres, while four isolates were classified as D. hongkongensis. Here, we report D. hongkongensis causing sweet cherry branch dieback disease and, further, we confirmed the host association of D. eres with sweet cherries in China. A pathogenicity assay revealed the ability of both D. eres and D. hongkongensis to cause shoot necrosis and stem lesions on Prunus avium cv. 'Brooks' (mean lesion lengths of 1.86 cm and 1.56 cm, respectively). The optimal temperature for the growth of both Diaporthe species was tested. The optimal growth temperature for D. hongkongensis was 30 °C, and the 25-28 °C temperatures were the most favorable for the growth of D. eres strains. This research advances the understanding of fungal trunk diseases in fruit crops, particularly gummosis and branch dieback disease in Chinese cherry orchards, and will aid growers in making decisions about cultural practices and disease management.

RevDate: 2023-10-27

Wang Y, Shi J, Wu Y, et al (2023)

Selection of Flagship Species and Their Use as Umbrellas in Bird Conservation: A Case Study in Lishui, Zhejiang Province, China.

Animals : an open access journal from MDPI, 13(11): pii:ani13111825.

The concept of flagship species is widely used in conservation biology. Flagship birds play a key role in raising conservation funds, increasing awareness of biodiversity conservation, and maintaining ecosystem services. This study selected flagship bird species in Lishui, Zhejiang Province, China, and assessed their conservation effectiveness and ability to serve as umbrella species. A regional bird survey program from 2019-2022 recorded 361 bird species in Lishui. This study constructed a framework of flagship species selection based on social, ecological, economic, and cultural criteria. The analytic hierarchy process-entropy weight method (AHP-EM) was used to rank the score of 361 bird species, and the MaxEnt model was used to analyze the suitable distribution areas of these species. Finally, 10 species, which covered the distribution sites of all 361 bird species, were selected as the flagship species of Lishui. The distribution areas covered all the nature reserves and the priority areas of biodiversity of Lishui, in which these 10 species can also serve as umbrella species to protect local biodiversity. The methodology and ideas in this study could provide insights into the application of conservation concepts at the local level, as well as suggest possible recommendations for local governments to select flagship species for conservation.

RevDate: 2023-10-21

Chen SP, Liu WT, Cheng FY, et al (2023)

Ozone containment through selective mitigation measures on precursors of volatile organic compounds.

The Science of the total environment pii:S0048-9697(23)06580-4 [Epub ahead of print].

Abatement of volatile organic compounds (VOCs) ozone reduction is usually carried out by reducing the total amount of VOCs without considering reactivity between different species. This study incorporates the concept of maximum incremental reactivity (MIR) and speciation profiles into the industrial emission inventory of Taiwan to target organic species from industrial sources with the greatest ozone formation potentials (OFPs). These high OFP sources/species are then mitigated to assess the O3 reduction amount (ΔO3) with Community Multiscale Air Quality (CMAQ) modeling under VOC-limited conditions. The objective is to minimize the number of target sources/species and their tonnage while achieving maximum O3 reduction. This approach is referred to as the Selective Precursor Mitigation (SPM). A case study of a high ozone episode (September 4-10, 2020) was chosen for illustration, during which a relatively stagnant atmospheric condition with minimal transboundary ozone occurred. A series of scenarios to target the highest OFP chemicals/industries for mitigation are compared for the achievable max. ΔO3, areas affected (area coverage), and reduction efficiency. For instance, by reducing the ten leading industry classes with the island's highest OFPs (OFPind), up to 19 % of max. 1-h ΔO3 can be expected. If, however, the same tonnage of VOCs as that of OFPind is distributed to all industries without considering the reactivity, called the overall mitigation (OM), comparable results to those of OFPind were found, but the number of sources needed to be managed with OM would increase by nearly three times (29,662 for OM vs. 11,981 for OFPind). Further reducing the management scale by only zooming in the ten highest OFP chemicals within the ten leading OFP industries (OFPsp) would result in relatively limited area coverage. Still, major ozone hot spots could be alleviated. Although the domain is set on the island of Taiwan, the SPM approach is universally applicable to other regions worldwide to gain the maximum ozone reduction effect at a minimized societal cost.

RevDate: 2023-10-20

Nordmann T, Wickenhagen S, Doležal M, et al (2023)

Bichromatic UV detection system for atomically-resolved imaging of ions.

The Review of scientific instruments, 94(6):.

We present a compact bichromatic imaging system, located outside of the vacuum chamber of a trapped ion apparatus that collects the fluorescence of 230.6 and 369.5 nm photons simultaneously on a shared electron-multiplying charge-coupled device (EMCCD) camera. The system contains two lens doublets, consisting of a sphere and an asphere. They provide a numerical aperture of 0.45 and 0.40 at 230.6 and 369.5 nm, respectively, and enable spatially resolved state detection with a large field of view of 300 μm for long 115In+/172Yb+ Coulomb crystals. Instead of diffraction-limited imaging for one wavelength, the focus in this system is on simultaneous single-ion resolved imaging of both species over a large field, with special attention to the deep UV wavelength (230.6 nm) and the low scattering rate of In+ ions. The introduced concept is applicable to other dual-species applications.

RevDate: 2023-10-18

Melekhin M, Potekhin A, Gentekaki E, et al (2023)

Paramecium (Oligohymenophorea, Ciliophora) diversity in Thailand sheds light on the genus biogeography and reveals new phylogenetic lineages.

The Journal of eukaryotic microbiology [Epub ahead of print].

Paramecium (Ciliophora, Oligohymenophorea) is a good model to study ciliate biogeography. Extensive sampling mainly in northern hemisphere has led to 16 valid morphological species description thus far. However, a majority of hard-to-reach regions, including South East Asia, are underinvestigated. Our study combined traditional morphological and molecular approaches to reveal the biodiversity of Paramecium in Thailand from more than 110 samples collected in 10 provinces. Representatives of seven morphological species were identified from our collection, including the rare species, such as P. gigas and P. jenningsi. Additionally, we detected five different sibling species of the P. aurelia complex, described a new cryptic species P. hiwatashii n. sp. phylogenetically related to P. caudatum, and discovered a potentially new genetic species of the P. bursaria species complex. We also documented a variety of bacterial cytoplasmic symbionts from at least nine monoclonal cultures of Paramecium.

RevDate: 2023-10-18

Ibarra-Chávez R, Haag AF, Dorado-Morales P, et al (2020)

Rebooting Synthetic Phage-Inducible Chromosomal Islands: One Method to Forge Them All.

Biodesign research, 2020:5783064.

Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in Saccharomyces cerevisiae based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from Staphylococcus aureus and Escherichia coli and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.

RevDate: 2023-10-16

Yong RQ, Martin SB, NJ Smit (2023)

A new species of Siphoderina Manter, 1934 (Digenea: Cryptogonimidae) infecting the Dory Snapper Lutjanus fulviflamma (Teleostei: Lutjanidae) from the east coast of South Africa.

Systematic parasitology [Epub ahead of print].

Parasitological assessment of marine fishes at Sodwana Bay in the iSimangaliso Marine Protected Area on the east coast of South Africa revealed a new species of cryptogonimid trematode infecting the pyloric caeca of the Dory Snapper, Lutjanus fulviflamma (Forsskål) (Lutjanidae). The new species is morphologically consistent with the concept of the large genus Siphoderina Manter, 1934; its phylogenetic position within this genus was validated through molecular sequencing of the ITS2 and partial 28S ribosomal DNA sub-regions. We name this species Siphoderina nana n. sp. and comment on the current state of understanding for this genus of cryptogonimids.

RevDate: 2023-10-16

Li F, Hou L, Liu W, et al (2023)

Carbon Vacancy-Enhanced Activity of Fe-N-C Single Atom Catalysts toward Luminol Chemiluminescence in the Absence of H2O2.

Analytical chemistry [Epub ahead of print].

The classic luminol-H2O2 chemiluminescence (CL) systems suffer from easy self-decomposition of H2O2 at room temperature, hindering the practical applications of the luminol-H2O2 CL system. In this work, unexpectedly, we found that the carbon vacancy-modified Fe-N-C single atom catalysts (VC-Fe-N-C SACs) can directly trigger a luminol solution to generate strong CL emission in the absence of H2O2. The Fe-based SACs were prepared through the conventional pyrolysis of zeolitic imidazolate frameworks. The massive carbon vacancies were readily introduced into Fe-N-C SACs through a tannic acid-etching process. Carbon vacancy significantly enhanced the catalytic activity of Fe-N-C SACs on the CL reaction of luminol-dissolved oxygen. The VC-Fe-N-C SACs performed a 13.4-fold CL enhancement compared with the classic luminol-Fe[2+] system. It was found that the introduction of a carbon vacancy could efficiently promote dissolved oxygen to convert to reactive oxygen species. As a proof of concept, the developed CL system was applied to detect alkaline phosphatase with a linear range of 0.005-1 U/L as well as a detection limit of 0.003 U/L. This work demonstrated that VC-Fe-N-C SAC is a highly efficient CL catalyst that can promote the analytic application of the luminol CL system.

RevDate: 2023-10-14

Boltenkov EV (2023)

Resolving the Puzzle of Iris maackii (Iridaceae): A Morphological Insight into Its Taxonomy.

Plants (Basel, Switzerland), 12(19): pii:plants12193349.

Since the early 20th century, Iris maackii (Iridaceae) has been considered a synonym of I. laevigata, a synonym of I. pseudacorus, or an accepted species. The current concept of I. maackii in the literature and databases is often applied to yellow-flowered plants with prominently veined rosette leaves, which are diagnostic features of I. pseudacorus growing in Northeast Asia. Therefore, the objective was to clarify the taxonomic identity of I. maackii. This study is based on a critical examination of the literature, on the observed morphological characters in the holotype of I. maackii, and on a morphological comparison of I. maackii with living plants of I. laevigata and I. pseudacorus. Additionally, a morphometric comparison of the seed characters was carried out to clarify the morphological distinction among I. maackii, I. laevigata, and I. pseudacorus. A careful study demonstrated that the rosette leaf texture and the morphology of the flowering stem, fruit, and seeds of I. maackii are identical to or within the variation range of I. laevigata. Thus, I. maackii is morphologically non-distinct from I. laevigata and should be recognized as a taxonomic synonym of the latter. An image of the holotype of I. maackii is provided along with detailed illustrations of I. laevigata and I. pseudacorus.

RevDate: 2023-10-11

Shukla I, Gaynor KM, Worm B, et al (2023)

The diversity of animals identified as keystone species.

Ecology and evolution, 13(10):e10561.

Although the keystone species concept was conceived of over 50 years ago, contemporary efforts to synthesize related literature have been limited. Our objective was to create a list of keystone animal species identified in the literature and to examine the variation in the traits of species and the ecosystem influences they elicit. We documented 230 species considered keystones. A clustering analysis classified them into five archetypes based on combinations of their taxonomic class, body size, trophic level, and role (consumers, modifiers, or prey). Although conservation and public perception of keystones primarily focuses on large vertebrate consumers, our analysis reveals that researchers have defined a wide diversity of keystone species, with large variation in associated ecosystem processes. Future research may confront ambiguity in the definition of keystone status, as well as clarify the type, abundance, and quality of data required to assign the term. Identifying keystones with increased rigor would not only enrich the literature but also inform intervention to safeguard threatened keystones and their associated influences on ecosystems.

RevDate: 2023-10-06

Carlisle JD, Keinath DA, Albeke SE, et al (2018)

Identifying Holes in the Greater Sage-Grouse Conservation Umbrella.

The Journal of wildlife management, 82(5):948-957.

The umbrella species concept, wherein multiple species are indirectly protected under the umbrella of a reserve created for one, is intended to enhance conservation efficiency. Although appealing in theory and common in practice, empirical tests of the concept have been scarce. We used a real-world, semi-protected reserve established to protect a high-profile umbrella species (greater sage-grouse [Centrocercus urophasianus]) to investigate 2 potential mechanisms underlying the concept's successful application: reserve size and species similarity. We estimated how much habitat protection the established reserve provided to 52 species of conservation concern associated with vegetation communities where greater sage-grouse occur. To illustrate the importance of reserve size, we compared the effectiveness of the established reserve to alternative greater sage-grouse reserves of various sizes and to simulated reserves of equal size but sited with no regard for greater sage-grouse. We further assessed whether key species' traits were associated with different levels of protection under the umbrella reserve. The established umbrella reserve protected 82% of the state's greater sage-grouse population and 0-63% of the habitat of the background species examined. The reserve outperformed equally sized, simulated reserves for only 12 of 52 background species. As expected, larger alternative reserves served as better umbrellas, but regardless of reserve size, not all species received equal protection. The established reserve was most effective at protecting the habitat of species that were most similar to the umbrella species (i.e., avian species, those highly associated with sagebrush plant communities, and those with widespread habitat). In contrast, the habitat of species with restricted distributions, particularly when combined with vegetation associations not closely matching the umbrella species, was not protected as well by the umbrella reserve. Such species require additional, targeted attention to achieve conservation objectives. Successful application of the umbrella species concept requires careful consideration of the characteristics of the umbrella species, the reserve delineated on its behalf, and the similarity of the umbrella species to its purported background species.

RevDate: 2023-10-06

Carlisle JD, Stewart DR, AD Chalfoun (2017)


Western North American naturalist, 77(4):450-463.

Conservation practitioners often rely on areas designed to protect species of greatest conservation priority to also conserve co-occurring species (i.e., the umbrella species concept). The extent to which vertebrate species may serve as suitable umbrellas for invertebrate species, however, has rarely been explored. Sage-grouse (Centrocercus spp.) have high conservation priority throughout much of the rangelands of western North America and are considered an umbrella species through which the conservation of entire rangeland ecosystems can be accomplished. Harvester ants are ecosystem engineers and play important roles in the maintenance and function of rangeland ecosystems. We compared indices of the abundance of western harvester ants (Pogonomyrmex occidentalis) and Greater Sage-Grouse (Centrocercus urophasianus) at 72 sites in central Wyoming, USA in 2012. The abundance of harvester ant mounds was best predicted by a regression model that included a combination of local habitat characteristics and the abundance of sage-grouse. When controlling for habitat-related factors, areas with higher abundances of sage-grouse pellets (an index of sage-grouse abundance and/or habitat use) had higher abundances of ant mounds than areas with lower abundances of sage-grouse pellets. The causal mechanism underlying this positive relationship between sage-grouse and ant mound abundance at the fine scale could be indirect (e.g., both species prefer similar environmental conditions) or direct (e.g., sage-grouse prefer areas with a high abundance of ant mounds because ants are an important prey item during certain life stages). We observed no relationship between a broad-scale index of breeding sage-grouse density and the abundance of ant mounds. We suspect that consideration of the non-breeding habitat of sage-grouse and finer-scale measures of sage-grouse abundance are critical to the utility of sage-grouse as an umbrella species for the conservation of harvester ants and their important role in rangeland ecosystems.

RevDate: 2023-10-05

Eggertson QA, Rintoul TL, CA Lévesque (2023)

Resolving the Globisporangium ultimum (Pythium ultimum) species complex.

Mycologia [Epub ahead of print].

The Globisporangium ultimum (formerly Pythium ultimum) species complex was previously composed of two morphological varieties: var. ultimum and var. sporangiiferum. Prior attempts to resolve this morphology-based species complex using molecular techniques have been inconclusive or conflicting. The increased availability of sequenced genomes and isolates identified as G. ultimum var. ultimum and var. sporangiiferum has allowed us to examine these relationships at a higher resolution and with a broader scope than previously possible. Using comparative genomics, we identified highly variable gene regions and designed primers for four new protein-coding genes for phylogenetics. These were then used alongside three known markers to generate a nuclear multigene genealogy of the species complex. From a collection of 163 isolates belonging to the target taxa, a subset of 29 was chosen to be included in this study (verified with nuclear rDNA internal transcribed spacer 1 [ITS1] and mitochondrial cytochrome c oxidase subunit 1 [cox1] sequences). Seventeen isolates of var. ultimum were selected to be representative of variations in genotype, morphology, and geographic collection location. The 12 isolates of var. sporangiiferum included all available specimens identified either morphologically (in previous studies) or through sequence similarity with ITS1 and cox1. Based on the fulfillment of reciprocal monophyly and observed genealogical concordance under the genealogical concordance phylogenetic species recognition, we determined that the Globisporangium ultimum species complex is composed of four genetically distinct species: Globisporangium ultimum, Globisporangium sporangiiferum, Globisporangium solveigiae, and Globisporangium bothae.

RevDate: 2023-09-30

Abachi H, Moallem M, Taghavi SM, et al (2023)

Garlic Bulb Decay and Soft Rot Caused by the Cross-Kingdom Pathogen Burkholderia gladioli.

Plant disease [Epub ahead of print].

In 2021, two Gram-negative bacterial strains were isolated from garlic (Allium sativum) bulbs showing decay and soft rot symptoms in central Iran. The bacterial strains were aggressively pathogenic on cactus, garlic, gladiolus, onion, potato, and saffron plants, and induced soft rot symptoms on carrot, cucumber, potato and radish discs. Furthermore, they were pathogenic on sporophore of cultivated and wild mushrooms. Phylogenetic analyses revealed that the bacterial strains belong to Burkholderia gladioli species. Garlic bulb rot caused by B. gladioli has rarely been reported in the literature. Historically, B. gladioli strains had been assigned to four pathovars i.e. B. gladioli pv. alliicola, B. gladioli pv. gladioli, B. gladioli pv. agaricicola, and B. gladioli pv. cocovenenans infecting onion, Gladiolus sp., mushrooms, and poisoning foods, respectively. Multilocus (i.e., 16S rRNA, atpD, gyrB, and lepA genes) sequence-based phylogenetic investigations including reference strains of B. gladioli pathovars showed that the two garlic strains belong to phylogenomic clade 2 of the species which includes the pathotype strain of B. gladioli pv. alliicola. Although the garlic strains were phylogenetically closely related to the B. gladioli pv. alliicola reference strains, they possessed pathogenicity characteristics that overlapped with three of the four historical pathovars including the ability to rot onion (pv. alliicola), gladiolus (pv. gladioli) and mushrooms (pv. agaricicola). Further, pathotype of each pathovar could infect the hosts of other pathovars, undermining the utility of pathovar concept in this species. Overall, using phenotypic pathovar-oriented assays to classify B. gladioli strains should be replaced by phylogenetic or phylogenomic analysis.

RevDate: 2023-09-28

Cortese-Krott MM (2023)

The Reactive Species Interactome in Red Blood Cells: Oxidants, Antioxidants, and Molecular Targets.

Antioxidants (Basel, Switzerland), 12(9): pii:antiox12091736.

Beyond their established role as oxygen carriers, red blood cells have recently been found to contribute to systemic NO and sulfide metabolism and act as potent circulating antioxidant cells. Emerging evidence indicates that reactive species derived from the metabolism of O2, NO, and H2S can interact with each other, potentially influencing common biological targets. These interactions have been encompassed in the concept of the reactive species interactome. This review explores the potential application of the concept of reactive species interactome to understand the redox physiology of RBCs. It specifically examines how reactive species are generated and detoxified, their interactions with each other, and their targets. Hemoglobin is a key player in the reactive species interactome within RBCs, given its abundance and fundamental role in O2/CO2 exchange, NO transport/metabolism, and sulfur species binding/production. Future research should focus on understanding how modulation of the reactive species interactome may regulate RBC biology, physiology, and their systemic effects.

RevDate: 2023-09-27

Jiménez-Gaona Y, Vivanco-Galván O, Cruz D, et al (2023)

Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota).

Journal of fungi (Basel, Switzerland), 9(9): pii:jof9090894.

BACKGROUND: The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella.

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

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

RESULTS AND CONCLUSIONS: The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.

RevDate: 2023-09-25

Wang Z, Kim W, Wang YW, et al (2023)

The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.

Frontiers in fungal biology, 4:1214537.

Advances in genomics and transcriptomics accompanying the rapid accumulation of omics data have provided new tools that have transformed and expanded the traditional concepts of model fungi. Evolutionary genomics and transcriptomics have flourished with the use of classical and newer fungal models that facilitate the study of diverse topics encompassing fungal biology and development. Technological advances have also created the opportunity to obtain and mine large datasets. One such continuously growing dataset is that of the Sordariomycetes, which exhibit a richness of species, ecological diversity, economic importance, and a profound research history on amenable models. Currently, 3,574 species of this class have been sequenced, comprising nearly one-third of the available ascomycete genomes. Among these genomes, multiple representatives of the model genera Fusarium, Neurospora, and Trichoderma are present. In this review, we examine recently published studies and data on the Sordariomycetes that have contributed novel insights to the field of fungal evolution via integrative analyses of the genetic, pathogenic, and other biological characteristics of the fungi. Some of these studies applied ancestral state analysis of gene expression among divergent lineages to infer regulatory network models, identify key genetic elements in fungal sexual development, and investigate the regulation of conidial germination and secondary metabolism. Such multispecies investigations address challenges in the study of fungal evolutionary genomics derived from studies that are often based on limited model genomes and that primarily focus on the aspects of biology driven by knowledge drawn from a few model species. Rapidly accumulating information and expanding capabilities for systems biological analysis of Big Data are setting the stage for the expansion of the concept of model systems from unitary taxonomic species/genera to inclusive clusters of well-studied models that can facilitate both the in-depth study of specific lineages and also investigation of trait diversity across lineages. The Sordariomycetes class, in particular, offers abundant omics data and a large and active global research community. As such, the Sordariomycetes can form a core omics clade, providing a blueprint for the expansion of our knowledge of evolution at the genomic scale in the exciting era of Big Data and artificial intelligence, and serving as a reference for the future analysis of different taxonomic levels within the fungal kingdom.

RevDate: 2023-09-20

Biswas R, Batista Da Rocha C, Bennick RA, et al (2023)

Water-Soluble Fullerene Monoderivatives for Biomedical Applications.

ChemMedChem [Epub ahead of print].

Monoderivatives of fullerenes functionalized with hydrophilic groups make them water soluble, while preserving the hydrophobic fullerene cage. This class of molecules have intriguing biomedical applications, including drug delivery, photodynamic therapy (PDT), antiviral and antimicrobial activity and reactive oxygen species (ROS)-scavenging abilities. In this Concept we discuss the synthesis and biomedical applications of water-soluble fullerene monoderivatives and their biological behavior based on their structures.

RevDate: 2023-09-18

Pollmann M, Kuhn D, König C, et al (2023)

New species based on the biological species concept within the complex of Lariophagus distinguendus (Hymenoptera, Chalcidoidea, Pteromalidae), a parasitoid of household pests.

Ecology and evolution, 13(9):e10524.

The pteromalid parasitoid Lariophagus distinguendus (Foerster) belongs to the Hymenoptera, a megadiverse insect order with high cryptic diversity. It attacks stored product pest beetles in human storage facilities. Recently, it has been shown to consist of two separate species. To further study its cryptic diversity, strains were collected to compare their relatedness using barcoding and nuclear genes. Nuclear genes identified two clusters which agree with the known two species, whereas the barcode fragment determined an additional third Clade. Total reproductive isolation (RI) according to the biological species concept (BSC) was investigated in crossing experiments within and between clusters using representative strains. Sexual isolation exists between all studied pairs, increasing from slight to strong with genetic distance. Postzygotic barriers mostly affected hybrid males, pointing to Haldane's rule. Hybrid females were only affected by unidirectional Spiroplasma-induced cytoplasmic incompatibility and behavioural sterility, each in one specific strain combination. RI was virtually absent between strains separated by up to 2.8% COI difference, but strong or complete in three pairs from one Clade each, separated by at least 7.2%. Apparently, each of these clusters represents one separate species according to the BSC, highlighting cryptic diversity in direct vicinity to humans. In addition, these results challenge the recent 'turbo-taxonomy' practice of using 2% COI differences to delimitate species, especially within parasitic Hymenoptera. The gradual increase in number and strength of reproductive barriers between strains with increasing genetic distance also sheds light on the emergence of barriers during the speciation process in L. distinguendus.

RevDate: 2023-09-14

Fowers BJ, Novak LF, Kiknadze NC, et al (2023)

Is the concept of personality capacious enough to incorporate virtues?.

Frontiers in psychology, 14:1232637.

We will consider four answers to the question about whether the concept of personality is capacious enough to incorporate virtues. The simplest is that the concept of personality encompasses all individual variations in persons. It follows from this answer that virtues would, as individual differences, be incorporated into personality. Unfortunately, definitions of personality do not always invoke such capaciousness, and, in practice, most scholars limit their work to the Big Five or HEXACO models, which do not incorporate virtues. The second answer is that the concept of personality incorporates all trait or dimension level variations across persons, with some exceptions, such as intelligence, attachment style, and psychopathy. Following this definition, virtues, as traits, would be incorporated into such a broad definition of personality. Unfortunately, the boundaries for inclusion and exclusion into personality are fuzzy in this case, and there is no extant definition of personality that solves this problem. The third answer is that personality traits and virtue traits are similar, but distinct concepts. This article presents conceptual and empirical arguments for this similarity in seeing traits as a higher order concept that includes the species of personality and the species of virtue. The fourth answer is that personality and virtue are unrelated. This answer is dismissed because there are many studies that indicate that they are correlated, and few advocate such a clear differentiation. The conclusion is that, pending conceptual and empirical results indicating otherwise, the genus-species relationship seems most fitting where traits are a genus, and personality and virtue are each a species within that genus.

RevDate: 2023-09-11

Thomas GWC, Hughes JJ, Kumon T, et al (2023)

The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats.

bioRxiv : the preprint server for biology pii:2023.08.28.555178.

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

RevDate: 2023-09-08

Mercogliano R, D Dongo (2023)

Fish welfare during slaughter: the European Council Regulation 1099/09 application.

Italian journal of food safety, 12(3):10926.

The Treaty of Lisbon states that animals are sentient beings. Fish species show physiological differences from terrestrial animals and are slaughtered and killed in a very different context. Many existing commercial killing methods expose fish to extensive suffering over a prolonged period of time, and some of the slaughtering practices they experience can cause pain and distress. This study highlights the limited feasibility of European Council Regulation 1099/09 requirements on welfare when killing cephalopods and crustaceans. Sentience is the animal's capacity to have positive (comfort, excitement) and negative (pain, anxiety, distress, or harm) feelings. Considerable evidence is now showing that the major commercial fish species, including cephalopods and crustaceans, possess complex neurological substrates supporting pain sensitivity and conscious experiences. In the legislation applied to scientific procedures, the concept of sentience in these species is important. Therefore, it would be appropriate to acknowledge current scientific evidence and establish reference criteria for fish welfare. For the welfare of fish species during slaughter, European Council Regulation 1099/09 applicability is limited. Fish welfare during slaughter is more than just an ethical problem. According to the One-Health approach, food safety should also include the concept of sentience for fish welfare. Pending studies that dispel all doubt, the precautionary principle of European Council Regulation 178/04 remains valid and should be applied to fish welfare.

RevDate: 2023-09-07

Ansari L, Asgari B, Zare R, et al (2023)

Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran.

International journal of systematic and evolutionary microbiology, 73(9):.

During a survey of species diversity of Penicillium and Talaromyces in sugarcane (Saccharum officinarum) rhizosphere in the Khuzestan province of Iran [1], 195 strains were examined, from which 187 belonged to Penicillium (11 species) and eight to Talaromyces (one species). In the present study, three strains of Penicillium belonging to section Exilicaulis series Restricta, identified as P. restrictum by Ansari et al. [1], were subjected to a phylogenetic study. The multilocus phylogeny of partial β-tubulin, calmodulin and RNA polymerase II second largest subunit genes enabled the recognition of one new phylogenetic species that is here formally described as Penicillium rhizophilum sp. nov. This species is phylogenetically distinct in series Restricta, but it does not show significant morphological differences from other species previously classified in the series. Therefore, we here placed bias on the phylogenetic species concept. The holotype of Penicillium rhizophilum sp. nov. is IRAN 18169F and the ex-type culture is LA30[T] (=IRAN 4042C[T]=CBS 149737[T]).

RevDate: 2023-08-31

Sen A, Ansari A, Swain A, et al (2023)

Probing the Origins of Puzzling Reactivity in Fe/Mn-Oxo/Hydroxo Species toward C-H Bonds: A DFT and Ab Initio Perspective.

Inorganic chemistry [Epub ahead of print].

Activation of C-H bonds using an earth-abundant metal catalyst is one of the top challenges of chemistry, where high-valent Mn/Fe-oxo(hydroxo) biomimic species play an important role. There are several open questions related to the comparative oxidative abilities of these species, and a unifying concept that could accommodate various factors influencing reactivity is lacking. To shed light on these open questions, here, we have used a combination of density functional theory (DFT) (B3LYP-D3/def2-TZVP) and ab initio (CASSCF/NEVPT2) calculations to study a series of high-valent metal-oxo species [M[n+]H3buea(O/OH)] (M = Mn and Fe, n = II to V; H3buea = tris[(N'-tert-butylureaylato)-N-ethylene)]aminato towards the activation of dihydroanthracene (DHA). The H-bonding network in the ligand architecture influences the ground state-excited state gap and brings several excited states of the same spin multiplicity closer in energy, which triggers reactivity via one of those excited states, reducing the kinetic barriers for the C-H bond activation and rationalizing several puzzling reactivity trends observed in various high-valent Mn/Fe-oxo(hydroxo) species.

RevDate: 2023-08-28

Génin F, Rambeloarivony H, Silvestro D, et al (2023)

Ontogeny and phylogeny of mating behaviour: social heteroch rony in primates.

Theoretical biology forum, 116(1-2):15-50.

Based on the Recognition Concept of species, the specific-mate contact model posits that mating systems develop as combinations of two fundamental courtship strategies that we interpret here in terms of behavioural heterochrony: territorial mate-attraction evolved as an effect of peramorphosis whereas group-living mate-seeking evolved as an effect of paedomorphosis. We tested this hypothesis on primates in a phylogenetic and paleo-climatic context. Our results suggest that primate promiscuity (both males and females are mate-seekers) evolved with group-living from ancestral pair-living monogamy (both males and females are mate-attractors) in the Palaeogene, as the result of a slowdown in growth (neoteny) caused by increased environmental predictability. A secondary return to territorial monogamy probably evolved as the result of accelerated growth driven by seasonality (acceleration). Polygamy evolved in the Neogene during periods of forest fragmentation and environmental unpredictability. Small monogamous ancestors evolved seasonal polyandry (female attraction) as an effect of truncated development (progenesis). Large promiscuous, neotenic ancestors evolved non-seasonal polygyny (male attraction) as an effect of prolonged development (hypermorphosis) in males. We conclude that social heterochrony offers alternative explanations for the coevolution of life history and mating be-haviour; and we discuss the implications of our model for human social evolution.

RevDate: 2023-08-26

Xesfyngi Y, Georgoutsou-Spyridonos M, Tripathy A, et al (2023)

A High-Performance Antibacterial Nanostructured ZnO Microfluidic Device for Controlled Bacterial Lysis and DNA Release.

Antibiotics (Basel, Switzerland), 12(8): pii:antibiotics12081276.

In this work, the antibacterial properties of nanostructured zinc oxide (ZnO) surfaces are explored by incorporating them as walls in a simple-to-fabricate microchannel device. Bacterial cell lysis is demonstrated and quantified in such a device, which functions due to the action of its nanostructured ZnO surfaces in contact with the working fluid. To shed light on the mechanism responsible for lysis, E. coli bacteria were incubated in zinc and nanostructured ZnO substrates, as well as the here-investigated ZnO-based microfluidic devices. The unprecedented killing efficiency of E. coli in nanostructured ZnO microchannels, effective after a 15 min incubation, paves the way for the implementation of such microfluidic chips in the disinfection of bacteria-containing solutions. In addition, the DNA release was confirmed by off-chip PCR and UV absorption measurements. The results indicate that the present nanostructured ZnO-based microfluidic chip can, under light, achieve partial inactivation of the released bacterial DNA via reactive oxygen species-mediated oxidative damage. The present device concept can find broader applications in cases where the presence of DNA in a sample is not desirable. Furthermore, the present microchannel device enables, in the dark, efficient release of bacterial DNA for downstream genomic DNA analysis. The demonstrated potential of this antibacterial device for tailored dual functionality in light/dark conditions is the main novel contribution of the present work.

RevDate: 2023-08-26

Jabin G, Joshi BD, Wang MS, et al (2023)

Mid-Pleistocene Transitions Forced Himalayan ibex to Evolve Independently after Split into an Allopatric Refugium.

Biology, 12(8): pii:biology12081097.

Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8-0.5 mya and c. 50-30 kya, with an intermediate large population expansion c. 0.2-0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale.

RevDate: 2023-08-16

Carrasco RA, KM Breen (2023)

Allostasis in Neuroendocrine Systems Controlling Reproduction.

Endocrinology pii:7243365 [Epub ahead of print].

Allostasis provides a supporting role to the homeostatic control of biological variables in mammalian species. While the concept of homeostasis is related to the control of variables within a set point or range that are essential to life, allostasis refers to systems that facilitate adaptation to challenges that the organism faces and the new requirements for survival. Essential for such adaptation is the role played by the brain in eliciting neural and neuroendocrine responses. Reproductive function is fundamental for the survival of species but is costly in energetic terms and requires a synchrony with an ever-changing environment. Thus, in many species reproductive function is blocked or delayed over immediate challenges. This review will cover the physiological systems and neuroendocrine pathways that supply allostatic control over reproductive neuroendocrine systems. Light, hypoxia, temperature, nutrition, psychosocial, and immune mediators influence the neuroendocrine control of reproductive functions through pathways that are confluent at the paraventricular nucleus; however, understanding of the integrative responses to these stimuli has not been clarified. Likely, the ultimate consequence of these allostatic mechanisms is the modification of kisspeptin and gonadotropin-releasing hormone neuronal activity, thus compromising reproduction function in the short term, while preserving species survivability.

RevDate: 2023-08-08

Weiss AS, Niedermeier LS, von Strempel A, et al (2023)

Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community.

Nature communications, 14(1):4780.

A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Using a synthetic gut bacterial community, we aimed to study the role of individual members in community assembly, identify putative keystone species and test their influence across different environments. Single-species dropout experiments reveal that bacterial strain relationships strongly vary not only in different regions of the murine gut, but also across several standard culture media. Mechanisms involved in environment-dependent keystone functions in vitro include exclusive access to polysaccharides as well as bacteriocin production. Further, Bacteroides caecimuris and Blautia coccoides are found to play keystone roles in gnotobiotic mice by impacting community composition, the metabolic landscape and inflammatory responses. In summary, the presented study highlights the strong interdependency between bacterial community ecology and the biotic and abiotic environment. These results question the concept of universally valid keystone species in the gastrointestinal ecosystem and underline the context-dependency of both, keystone functions and bacterial interaction networks.

RevDate: 2023-08-01

Wang XC, Zhuang WY, RL Zhao (2023)

Species Diversity of Helvella lacunosa Clade (Pezizales, Ascomycota) in China and Description of Sixteen New Species.

Journal of fungi (Basel, Switzerland), 9(7):.

Helvella lacunosa and its allies are widely distributed in the Northern Hemisphere and perform important functions in ecosystems. A comprehensive study on 101 collections of Helvella lacunosa, including those deposited in four Chinese fungaria or collected recently from 10 provinces, was conducted based on morphological and molecular characteristics. Phylogenies of "Helvella lacunosa clade" inferred from Hsp90, ITS, LSU, and TEF were reconstructed with 49 lineages recognized, of which 25 lineages occurred in China, and each represented an individual species. Sixteen new species were determined with detailed descriptions and illustrations. Two new Chinese records were reported. Species concepts and their distinctions in macro- and micro-features were discussed.

RevDate: 2023-07-26

Huang GJ, Li CW, Lee PY, et al (2023)

Electronic Preresonance Stimulated Raman Scattering Spectromicroscopy Using Multiple-Plate Continuum.

The journal of physical chemistry. B [Epub ahead of print].

Stimulated Raman scattering (SRS) spectromicroscopy is a powerful technique that enables label-free detection of chemical bonds with high specificity. However, the low Raman cross section due to typical far-electronic resonance excitation seriously restricts the sensitivity and undermines its application to bio-imaging. To address this bottleneck, the electronic preresonance (EPR) SRS technique has been developed to enhance the Raman signals by shifting the excitation frequency toward the molecular absorption. A fundamental weakness of the previous demonstration is the lack of dual-wavelength tunability, making EPR-SRS only applicable to a limited number of species in the proof-of-concept experiment. Here, we demonstrate the EPR-SRS spectromicroscopy using a multiple-plate continuum (MPC) light source able to examine a single vibration mode with independently adjustable pump and Stokes wavelengths. In our experiments, the C═C vibration mode of Alexa 635 is interrogated by continuously scanning the pump-to-absorption frequency detuning throughout the entire EPR region enabled by MPC. The results exhibit 150-fold SRS signal enhancement and good agreement with the Albrecht A-term preresonance model. Signal enhancement is also observed in EPR-SRS images of the whole Drosophila brain stained with Alexa 635. With the improved sensitivity and potential to implement hyperspectral measurement, we envision that MPC-EPR-SRS spectromicroscopy can bring the Raman techniques closer to a routine in bio-imaging.

RevDate: 2023-07-24

Cobo-Simón M, Hart R, H Ochman (2023)

Gene flow and species boundaries of the genus Salmonella.

mSystems [Epub ahead of print].

The genus Salmonella comprises two species, Salmonella bongori and Salmonella enterica, which are infectious to a wide variety of animal hosts. The diversity within S. enterica has been further partitioned into 6-10 subspecies based on such features as host range, geography, and most recently, genetic relatedness and phylogenetic affiliation. Although Salmonella pathogenicity is attributable to large numbers of acquired virulence factors, the extent of homologous exchange in the species at large is apparently constrained such that the species and subspecies form distinct clusters of strains. To explore the extent of gene flow within and among subspecies, and to ultimately define true biological species, we evaluated patterns of recombination in over 1,000 genomes currently assigned to the genus. Those Salmonella subspecies containing sufficient numbers of sequenced genomes to allow meaningful analysis-i.e., subsp. enterica and diarizonae-were found to be reproductively isolated from one another and from all other subspecies. Based on the configuration of genomic sequence divergence among subspecies, it is expected that each of the other Salmonella subspecies will also represent a biological species. Our findings argue against the application of prescribed nucleotide-identity thresholds to delineate bacterial species and contend that the Biological Species Concept should not be disregarded for bacteria, even those, like Salmonella, that demonstrate complex patterns of species and subspecies divergence. IMPORTANCE The Biological Species Concept (BSC), which defines species boundaries based on the capacity for gene exchange, is widely used to classify sexually reproducing eukaryotes but is generally thought to be inapplicable to bacteria due to their completely asexual mode of reproduction. We show that the genus Salmonella, whose thousands of described serovars were formerly considered to be strictly clonal, undergoes sufficient levels of homologous recombination to be assigned to species according to the BSC. Aside from the two recognized species, Salmonella enterica and Salmonella bongori, several (and likely all) of the subspecies within S. enterica are reproductively isolated from one another and should each be considered a separate biological species. These findings demonstrate that species barriers in bacteria can form despite high levels of nucleotide identity and that commonly applied thresholds of genomic sequence identity are not reliable indicators of bacterial species status.

RevDate: 2023-07-30

Tong S, Samet JM, Steffen W, et al (2023)

Solidarity for the Anthropocene.

Environmental research, 235:116716 pii:S0013-9351(23)01520-7 [Epub ahead of print].

Social solidarity is essential to large-scale collective action, but the need for solidarity has received little attention from scholars of Earth Systems, sustainability and public health. Now, the need for solidarity requires recognition. We have entered a new planetary epoch - the Anthropocene - in which human-induced global changes are occurring at an unprecedented scale. There are multiple health crises facing humanity - widening inequity, climate change, biodiversity loss, diminishing resources, persistent poverty, armed conflict, large-scale migration, and others. These global challenges are so far-reaching, and call for such extensive, large-scale action, that solidarity is a sine qua non for tackling these challenges. However, the heightened need for solidarity has received little attention in the context of the Anthropocene and, in particular, how it can be created and nurtured has been overlooked. In this commentary, we explore the concept of solidarity from inter-species, intra-generational and inter-generational perspectives. We also propose strategies to enhance solidarity in the Anthropocene.

RevDate: 2023-07-21
CmpDate: 2023-07-21

Lisboa TP, de Faria LV, de Oliveira WBV, et al (2023)

Cost-effective protocol to produce 3D-printed electrochemical devices using a 3D pen and lab-made filaments to ciprofloxacin sensing.

Mikrochimica acta, 190(8):310.

A novel conductive filament based on graphite (Gr) dispersed in polylactic acid polymer matrix (PLA) is described to produce 3D-electrochemical devices (Gr/PLA). This conductive filament was used to additively manufacture electrochemical sensors using the 3D pen. Thermogravimetric analysis confirmed that Gr was successfully incorporated into PLA, achieving a composite material (40:60% w/w, Gr and PLA, respectively), while Raman and scanning electron microscopy revealed the presence of defects and a high porosity on the electrode surface, which contributes to improved electrochemical performance. The 3D-printed Gr/PLA electrode provided a more favorable charge transfer (335 Ω) than the conventional glassy carbon (1277 Ω) and 3D-printed Proto-pasta® (3750 Ω) electrodes. As a proof of concept, the ciprofloxacin antibiotic, a species of multiple interest, was selected as a model molecule. Thus, a square wave voltammetry (SWV) method was proposed in the potential range + 0.9 to + 1.3 V (vs Ag|AgCl|KCl(sat)), which provided a wide linear working range (2 to 32 µmol L[-1]), 1.79 µmol L[-1] limit of detection (LOD), suitable precision (RSD < 7.9%), and recovery values from 94 to 109% when applied to pharmaceutical and milk samples. Additionally, the sensor is free from the interference of other antibiotics routinely employed in veterinary practices. This device is disposable, cost-effective, feasibly produced in financially limited laboratories, and consequently promising for evaluation of other antibiotic species in routine applications.

RevDate: 2023-08-06
CmpDate: 2023-08-03

Graves JL (Jr) (2023)

Favored Races in the Struggle for Life: Racism and the Speciation Concept.

Cold Spring Harbor perspectives in biology, 15(8): pii:cshperspect.a041454.

Evolutionary speciation, whether it be cladistic or phyletic, has always been associated with race concepts. Biological races are conceived as definable stages of divergence from a common ancestor. However, the species concept in Western science began within a special creationist framework. The sixteenth century European voyages of discovery resulted in special creationist schemes explaining the origin of the new peoples encountered. These were designed to provide the moral justification for their colonization and enslavement. By the seventeenth century, European naturalists were beginning to seriously question the meaning of the variation within the animals and plants they observed within the context of God's role in creation. By the middle of the nineteenth century, "the species question" was the most important intellectual enterprise within biology. Here I discuss how notions of speciation influenced and were influenced by conceptions of race within Homo sapiens.

RevDate: 2023-07-18

Bhat AH, Machado RAR, Abolafia J, et al (2023)

Multigene Sequence-Based and Phenotypic Characterization Reveals the Occurrence of a Novel Entomopathogenic Nematode Species, Steinernema anantnagense n. sp.

Journal of nematology, 55(1):20230029.

Three entomopathogenic nematode populations were isolated from agricultural fields in the Anantnag district of Jammu and Kashmir (India). Sequences of multiple gene regions and phenotypic features show that they are conspecific and represent a novel species. Molecular and morphological features provided evidence for placing the new species into the "Kushidai" clade. Within this clade, analysis of sequence data of the internal transcribed spacer (ITS) gene, the D2D3 region of the 28S rRNA gene, the mitochondrial cytochrome oxidase I (mtCOI) gene, and the mitochondrial 12S (mt12S) gene depicted the novel species as a distinctive entity closely related to Steinernema akhursti, S. kushidai, and S. populi. Phylogenetic analyses also show that the new species is a sister species to S. akhursti, and these two species are closely related to S. kushidai and S. populi. Additionally, the new species does not mate or produce fertile progeny with any of the closely related species, reinforcing its uniqueness from a biological species concept standpoint. The new species is further characterized by the third-stage infective juveniles with almost straight bodies (0.7-0.8 mm length), poorly developed stoma and pharynx, and conoid-elongate tail (49-66 µm) with hyaline posterior part. Adult females are characterized by short and conoid tails bearing a short mucron in the first generation and long conoid tails with thin mucron in the second generation. Adult males have ventrally curved spicules in both generations. Moreover, the first-generation male has rounded manubrium, fusiform gubernaculum, conoid and slightly ventrally curved tails with minute mucron, and the second generation has rhomboid manubrium anteriorly ventrad bent, and tails with long and robust mucron. The morphological, morphometrical, molecular, and phylogenetic analyses support the new species status of this nematode, which is hereby described as Steinernema anantnagense n. sp. The bacterial symbiont associated with S. anantnagense n. sp. represents a novel species, closely related to Xenorhabdus japonica. These findings shed light on the diversity of entomopathogenic nematodes and their symbiotic bacteria, providing valuable information for future studies in this field.

RevDate: 2023-07-16

Poorter L, Amissah L, Bongers F, et al (2023)

Successional theories.

Biological reviews of the Cambridge Philosophical Society [Epub ahead of print].

Succession is a fundamental concept in ecology because it indicates how species populations, communities, and ecosystems change over time on new substrate or after a disturbance. A mechanistic understanding of succession is needed to predict how ecosystems will respond to land-use change and to design effective ecosystem restoration strategies. Yet, despite a century of conceptual advances a comprehensive successional theory is lacking. Here we provide an overview of 19 successional theories ('models') and their key points, group them based on conceptual similarity, explain conceptual development in successional ideas and provide suggestions how to move forward. Four groups of models can be recognised. The first group (patch & plants) focuses on plants at the patch level and consists of three subgroups that originated in the early 20th century. One subgroup focuses on the processes (dispersal, establishment, and performance) that operate sequentially during succession. Another subgroup emphasises individualistic species responses during succession, and how this is driven by species traits. A last subgroup focuses on how vegetation structure and underlying demographic processes change during succession. A second group of models (ecosystems) provides a more holistic view of succession by considering the ecosystem, its biota, interactions, diversity, and ecosystem structure and processes. The third group (landscape) considers a larger spatial scale and includes the effect of the surrounding landscape matrix on succession as the distance to neighbouring vegetation patches determines the potential for seed dispersal, and the quality of the neighbouring patches determines the abundance and composition of seed sources and biotic dispersal vectors. A fourth group (socio-ecological systems) includes the human component by focusing on socio-ecological systems where management practices have long-lasting legacies on successional pathways and where regrowing vegetations deliver a range of ecosystem services to local and global stakeholders. The four groups of models differ in spatial scale (patch, landscape) or organisational level (plant species, ecosystem, socio-ecological system), increase in scale and scope, and reflect the increasingly broader perspective on succession over time. They coincide approximately with four periods that reflect the prevailing view of succession of that time, although all views still coexist. The four successional views are: succession of plants (from 1910 onwards) where succession was seen through the lens of species replacement; succession of communities and ecosystems (from 1965 onwards) when there was a more holistic view of succession; succession in landscapes (from 2000 onwards) when it was realised that the structure and composition of landscapes strongly impact successional pathways, and increased remote-sensing technology allowed for a better quantification of the landscape context; and succession with people (from 2015 onwards) when it was realised that people and societal drivers have strong effects on successional pathways, that ecosystem processes and services are important for human well-being, and that restoration is most successful when it is done by and for local people. Our review suggests that the hierarchical successional framework of Pickett is the best starting point to move forward as this framework already includes several factors, and because it is flexible, enabling application to different systems. The framework focuses mainly on species replacement and could be improved by focusing on succession occurring at different hierarchical scales (population, community, ecosystem, socio-ecological system), and by integrating it with more recent developments and other successional models: by considering different spatial scales (landscape, region), temporal scales (ecosystem processes occurring over centuries, and evolution), and by taking the effects of the surrounding landscape (landscape integrity and composition, the disperser community) and societal factors (previous and current land-use intensity) into account. Such a new, comprehensive framework could be tested using a combination of empirical research, experiments, process-based modelling and novel tools. Applying the framework to seres across broadscale environmental and disturbance gradients allows a better insight into what successional processes matter and under what conditions.

RevDate: 2023-07-12

Cannon CH, M Lerdau (2023)

Conservation should not make 'perfect' an enemy of 'good'.

RevDate: 2023-07-07
CmpDate: 2023-07-06

Flütsch S, Wiestner F, Butticaz L, et al (2023)

Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp.

BMC genomics, 24(1):375.

BACKGROUND: Vibrio spp. are a diverse group of ecologically important marine bacteria responsible for several foodborne outbreaks of gastroenteritis around the world. Their detection and characterization are moving away from conventional culture-based methods towards next generation sequencing (NGS)-based approaches. However, genomic methods are relative in nature and suffer from technical biases arising from library preparation and sequencing. Here, we introduce a quantitative NGS-based method that enables the quantitation of Vibrio spp. at the limit of quantification (LOQ) through artificial DNA standards and their absolute quantification via digital PCR (dPCR).

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

CONCLUSIONS: We significantly advance existing quantitative (meta)genomic methods by ensuring metrological traceability of NGS-based DNA quantification. Our method represents a useful tool for future metagenomic studies aiming at quantifying microbial DNA in an absolute manner. The inclusion of dPCR into sequencing-based methods supports the development of statistical approaches for the estimation of measurement uncertainties (MU) for NGS, which is still in its infancy.

RevDate: 2023-07-12

Johnson A, Miller EA, Weber B, et al (2023)

Evidence of host specificity in Lactobacillus johnsonii genomes and its influence on probiotic potential in poultry.

Poultry science, 102(9):102858 [Epub ahead of print].

To date, the selection of candidate strains for probiotic development in production animals has been largely based upon screens for desired phenotypic traits. However, increasing evidence indicates that the use of host-specific strains may be important, because coevolution with the animal host better prepares a bacterial strain to colonize and succeed in its respective host animal species. This concept was applied to Lactobacillus johnsonii in commercial poultry production because of its previous correlation with enhanced bird performance. Using 204 naturally isolated chicken- and turkey-source L. johnsonii, we demonstrate that there is a strong phylogenetic signal for coevolution with the animal host. These isolates differ phenotypically, even within host source, and these differences can be correlated with certain L. johnsonii phylogenetic clades. In commercial turkey poults, turkey-specific strains with strong in vitro phenotypes performed better early in life than strains lacking those phenotypes. A follow-up performance trial in broiler chickens demonstrated that chicken-specific strains result in better overall bird performance than nonchicken-specific strains. Collectively, this work provides evidence for the impact of host adaptation on a probiotic strain's potential. Furthermore, this top-down approach is useful for screening larger numbers of isolates for probiotic candidates.

RevDate: 2023-07-01

Han SL, Wang MM, Ma ZY, et al (2023)

Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus.

Studies in mycology, 104:87-148.

Fusarium species are important cereal pathogens that cause severe production losses to major cereal crops such as maize, rice, and wheat. However, the causal agents of Fusarium diseases on cereals have not been well documented because of the difficulty in species identification and the debates surrounding generic and species concepts. In this study, we used a citizen science initiative to investigate diseased cereal crops (maize, rice, wheat) from 250 locations, covering the major cereal-growing regions in China. A total of 2 020 Fusarium strains were isolated from 315 diseased samples. Employing multi-locus phylogeny and morphological features, the above strains were identified to 43 species, including eight novel species that are described in this paper. A world checklist of cereal-associated Fusarium species is provided, with 39 and 52 new records updated for the world and China, respectively. Notably, 56 % of samples collected in this study were observed to have co-infections of more than one Fusarium species, and the detailed associations are discussed. Following Koch's postulates, 18 species were first confirmed as pathogens of maize stalk rot in this study. Furthermore, a high-confidence species tree was constructed in this study based on 1 001 homologous loci of 228 assembled genomes (40 genomes were sequenced and provided in this study), which supported the "narrow" generic concept of Fusarium (= Gibberella). This study represents one of the most comprehensive surveys of cereal Fusarium diseases to date. It significantly improves our understanding of the global diversity and distribution of cereal-associated Fusarium species, as well as largely clarifies the phylogenetic relationships within the genus. Taxonomic novelties: New species: Fusarium erosum S.L. Han, M.M. Wang & L. Cai, Fusarium fecundum S.L. Han, M.M. Wang & L. Cai, Fusarium jinanense S.L. Han, M.M. Wang & L. Cai, Fusarium mianyangense S.L. Han, M.M. Wang & L. Cai, Fusarium nothincarnatum S.L. Han, M.M. Wang & L. Cai, Fusarium planum S.L. Han, M.M. Wang & L. Cai, Fusarium sanyaense S.L. Han, M.M. Wang & L. Cai, Fusarium weifangense S.L. Han, M.M. Wang & L. Cai. Citation: Han SL, Wang MM, Ma ZY, Raza M, Zhao P, Liang JM, Gao M, Li YJ, Wang JW, Hu DM, Cai L (2023). Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus. Studies in Mycology 104: 87-148. doi: 10.3114/sim.2022.104.02.

RevDate: 2023-07-01

Réblová M, Hernández-Restrepo M, Sklenář F, et al (2022)

Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys.

Studies in mycology, 103:87-212.

Chloridium is a little-studied group of soil- and wood-inhabiting dematiaceous hyphomycetes that share a rare mode of phialidic conidiogenesis on multiple loci. The genus has historically been divided into three morphological sections, i.e. Chloridium, Gongromeriza, and Psilobotrys. Sexual morphs have been placed in the widely perceived genus Chaetosphaeria, but unlike their asexual counterparts, they show little or no morphological variation. Recent molecular studies have expanded the generic concept to include species defined by a new set of morphological characters, such as the collar-like hyphae, setae, discrete phialides, and penicillately branched conidiophores. The study is based on the consilience of molecular species delimitation methods, phylogenetic analyses, ancestral state reconstruction, morphological hypotheses, and global biogeographic analyses. The multilocus phylogeny demonstrated that the classic concept of Chloridium is polyphyletic, and the original sections are not congeneric. Therefore, we abolish the existing classification and propose to restore the generic status of Gongromeriza and Psilobotrys. We present a new generic concept and define Chloridium as a monophyletic, polythetic genus comprising 37 species distributed in eight sections. In addition, of the taxa earlier referred to Gongromeriza, two have been redisposed to the new genus Gongromerizella. Analysis of published metabarcoding data showed that Chloridium is a common soil fungus representing a significant (0.3 %) proportion of sequence reads in environmental samples deposited in the GlobalFungi database. The analysis also showed that they are typically associated with forest habitats, and their distribution is strongly influenced by climate, which is confirmed by our data on their ability to grow at different temperatures. We demonstrated that Chloridium forms species-specific ranges of distribution, which is rarely documented for microscopic soil fungi. Our study shows the feasibility of using the GlobalFungi database to study the biogeography and ecology of fungi. Taxonomic novelties: New genus: Gongromerizella Réblová; New sections: Chloridium section Cryptogonytrichum Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Gonytrichopsis Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Metachloridium Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Volubilia Réblová, Hern.-Restr., M. Kolařík & F. Sklenar; New species: Chloridium bellum Réblová & Hern.-Restr., Chloridium biforme Réblová & Hern.-Restr., Chloridium detriticola Réblová & Hern.-Restr., Chloridium gamsii Réblová & Hern.-Restr., Chloridium guttiferum Réblová & Hern.-Restr., Chloridium moratum Réblová & Hern.-Restr., Chloridium peruense Réblová & Hern.-Restr., Chloridium novae-zelandiae Réblová & Hern.-Restr., Chloridium elongatum Réblová & Hern.-Restr., Chloridium volubile Réblová & Hern.-Restr.; New varieties: Chloridium bellum var. luteum Réblová & Hern.-Restr., Chloridium detriticola var. effusum Réblová & Hern.-Restr., Chloridium chloridioides var. convolutum Réblová & Hern.-Restr.; New combinations: Chloridium section Gonytrichum (Nees & T. Nees) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Mesobotrys (Sacc.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium section Pseudophialocephala (M.S. Calabon et al.) Réblová, Hern.-Restr., M. Kolařík & F. Sklenar, Chloridium simile (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium chloridioides (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium subglobosum (W. Gams & Hol.-Jech.) Réblová & Hern.-Restr., Chloridium fuscum (Corda) Réblová & Hern.-Restr., Chloridium ypsilosporum (Hol.-Jech.) Réblová & Hern.-Restr., Chloridium costaricense (G. Weber et al.) Réblová & Hern.-Restr., Chloridium cuneatum (N.G. Liu et al.) Réblová & Hern.-Restr., Fusichloridium cylindrosporum (W. Gams & Hol.-Jech.) Réblová, Gongromeriza myriocarpa (Fr.) Réblová, Gongromeriza pygmaea (P. Karst.) Réblová, Gongromerizella lignicola (F. Mangenot) Réblová, Gongromerizella pachytrachela (W. Gams & Hol.-Jech) Réblová, Gongromerizella pini (Crous & Akulov) Réblová; New name: Chloridium pellucidum Réblová & Hern.-Restr.; Epitypifications (basionyms): Chaetopsis fusca Corda, Gonytrichum caesium var. subglobosum W. Gams & Hol.-Jech.; Lectotypification (basionym): Gonytrichum caesium Nees & T. Nees. Citation: Réblová M, Hernández-Restrepo M, Sklenář F, Nekvindová J, Réblová K, Kolařík M (2022). Consolidation of Chloridium: new classification into eight sections with 37 species and reinstatement of the genera Gongromeriza and Psilobotrys. Studies in Mycology 103: 87-212. doi: 10.3114/sim.2022.103.04.

RevDate: 2023-06-17

Jiang Y, Wu R, Zhang W, et al (2023)

Construction of stable microbial consortia for effective biochemical synthesis.

Trends in biotechnology pii:S0167-7799(23)00155-5 [Epub ahead of print].

Microbial consortia can complete otherwise arduous tasks through the cooperation of multiple microbial species. This concept has been applied to produce commodity chemicals, natural products, and biofuels. However, metabolite incompatibility and growth competition can make the microbial composition unstable, and fluctuating microbial populations reduce the efficiency of chemical production. Thus, controlling the populations and regulating the complex interactions between different strains are challenges in constructing stable microbial consortia. This Review discusses advances in synthetic biology and metabolic engineering to control social interactions within microbial cocultures, including substrate separation, byproduct elimination, crossfeeding, and quorum-sensing circuit design. Additionally, this Review addresses interdisciplinary strategies to improve the stability of microbial consortia and provides design principles for microbial consortia to enhance chemical production.

RevDate: 2023-06-22
CmpDate: 2023-06-15

Gouvêa DY, I Brigandt (2023)

Against unifying homology concepts: Redirecting the debate.

Journal of morphology, 284(7):e21599.

The term "homology" is persistently polysemous, defying the expectation that extensive scientific research should yield semantic stability. A common response has been to seek a unification of various prominent definitions. This paper proposes an alternative strategy, based on the insight that scientific concepts function as tools for research: When analyzing various conceptualizations of homology, we should preserve those distinguishing features that support particular research goals. We illustrate the fruitfulness of our strategy by application to two cases. First, we revisit Lankester's celebrated evolutionary reappraisal of homology and argue that his analysis has been distorted by assimilation to modern agendas. His "homogeny" does not mean the same thing as modern evolutionary "homology," and his "homoplasy" is no mere antonym. Instead, Lankester uses both new terms to pose a question that remains strikingly relevant-how do mechanistic and historical causes of morphological resemblance interact? Second, we examine the puzzle of avian digit homology, which exemplifies disciplinary differences in homology conceptualization and assessment. Recent progress has been fueled by the development of new tools within the relevant disciplines (paleontology and developmental biology) and especially by increasing interdisciplinary cooperation. Conceptual unification has played very little role in this work, which instead seeks concrete evolutionary scenarios that integrate all the available evidence. Together these cases indicate the complex relationship between concepts and other tools in homology research.

RevDate: 2023-07-04
CmpDate: 2023-06-09

Kock A, Pheiffer W, Wepener V, et al (2023)

Using Confocal Microscopy and Pigment Analyses to Detect Adverse Insecticide Effects in non-target Freshwater Diatom species - a proof-of-concept Using Nitzschia palea.

Bulletin of environmental contamination and toxicology, 110(6):107.

The persistence of insecticides in aquatic environments is a cause of concern and to date hardly any studies have focused on the effects that DDT and deltamethrin have on non-target freshwater diatom communities. The application of diatoms in ecotoxicological studies is well acknowledged and therefore this study used laboratory bioassays to determine the effects that DDT and deltamethrin have on a monoculture of a diatom indicator species, Nitzschia palea. The insecticides affected the morphology of chloroplasts at all exposure concentrations. These effects were a maximum reduction in chlorophyll concentrations (4.8% and 2.3%), cell viability (51% and 42%), and increases in cell deformities (3.6% and 1.6%) following exposure to DDT and deltamethrin respectively. Based on the results we propose that methods, such as confocal microscopy, chlorophyll-α analysis and cell deformities are useful tools in assessing the effects of insecticides on diatoms.

RevDate: 2023-05-31

Cocquyt C, D Verschuren (2023)

Checklist of the diatoms (Bacillariophyta) from Lake Naivasha, Kenya, with some historical notes.

PhytoKeys, 224:101-174.

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.

RevDate: 2023-05-28

Amézquita A, Mazariegos-H LA, Cañaveral S, et al (2023)

Species richness under a vertebral stripe: integrative taxonomy uncovers three additional species of Pholidobolus lizards (Sauria, Squamata, Gymnophthalmidae) from the north-western Colombian Andes.

ZooKeys, 1141:119-148.

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.

RevDate: 2023-05-25

Eilertsen HC, Strømholt J, Bergum JS, et al (2023)

Mass Cultivation of Microalgae: II. A Large Species Pulsing Blue Light Concept.

Biotech (Basel (Switzerland)), 12(2):.

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.

RevDate: 2023-05-23

Raclariu-Manolică AC, Mauvisseau Q, HJ de Boer (2023)

Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations.

Frontiers in pharmacology, 14:1179099.

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.

RevDate: 2023-06-19
CmpDate: 2023-06-19

Pacheco MA, AA Escalante (2023)

Origin and diversity of malaria parasites and other Haemosporida.

Trends in parasitology, 39(7):501-516.

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.

RevDate: 2023-06-19
CmpDate: 2023-06-19

Li M, Li H, Zhang X, et al (2023)

Mechanistic Insight into Anion-Binding Catalytic Living Cationic Polymerization.

Angewandte Chemie (International ed. in English), 62(26):e202303237.

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.

RevDate: 2023-05-17
CmpDate: 2023-05-17

Temraleeva AD, EA Portnaya (2023)

Morphological and Molecular Genetic Analyses of the Genus Vischeria (Eustigmatophyceae, Ochrophyta) in the Algal Collection of Soil Science Institute.

Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections, 508(1):20-31.

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.

RevDate: 2023-05-14

Iwamoto Y, Degawa Y, T Nakayama (2023)

Re-examination of a rare protosteloid amoeba Schizoplasmodiopsis micropunctata, and the revision of Tychosporium (Cavosteliida, Variosea, Amoebozoa).

Mycoscience, 64(2):63-68.

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.

RevDate: 2023-05-08
CmpDate: 2023-05-08

Jeanroy F, Demontrond F, Vidal FX, et al (2023)

Deciphering dynamic combinatorial libraries of glycoclusters with miniaturized weak affinity chromatography coupled with mass spectrometry (nano-FAC-MS).

Analytica chimica acta, 1261:341227.

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.

RevDate: 2023-05-07

Nascimento Brito V, Lana Alves J, Sírio Araújo K, et al (2023)

Endophytic Trichoderma species from rubber trees native to the Brazilian Amazon, including four new species.

Frontiers in microbiology, 14:1095199.

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.

RevDate: 2023-04-25

Ballego-Campos I, Bonifácio SKV, LCS Assis (2023)

A unified view of homology.

Cladistics : the international journal of the Willi Hennig Society [Epub ahead of print].

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.

RevDate: 2023-04-25

Shibata S, Y Hirooka (2022)

Taxonomy and phylogeny of Exobasidium pentasporium causing witches' broom of Rhododendron species.

Mycoscience, 63(6):247-253.

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.

RevDate: 2023-06-27
CmpDate: 2023-06-20

Liberles DA (2023)

A Genomic Conceptualization of Species.

Journal of molecular evolution, 91(4):379-381.

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.

RevDate: 2023-04-24
CmpDate: 2023-04-18

Bangal P, H Sridhar (2023)

Revisiting the 'nuclear species' concept: do we really know what we think we know?.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 378(1878):20220108.

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'.

RevDate: 2023-05-27
CmpDate: 2023-04-17

De León ME, Wilson HS, Jospin G, et al (2023)

Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives.

Microbial genomics, 9(4):.

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.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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The complex idea of “species” has evolved over time, yet its meaning is far from resolved. This comprehensive work takes a fresh look at an idea central to the field of biology by tracing its history from antiquity to today. John S. Wilkins explores the essentialist view, a staple of logic from Plato and Aristotle through the Middle Ages to fairly recent times, and considers the idea of species in natural history―a concept often connected to reproduction. Tracing “generative conceptions” of species back through Darwin to Epicurus, Wilkins provides a new perspective on the relationship between philosophical and biological approaches to this concept. He also reviews the array of current definitions. Species is a benchmark exploration and clarification of a concept fundamental to the past, present, and future of the natural sciences.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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