Acknowledging more biodiversity without more species

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(40)

Published: Sept. 25, 2023

Delimiting and naming biodiversity is a vital step toward wildlife conservation research. However, species delimitation must be consistent across biota so that the limited resources available for nature protection can spent effectively objectively. To date, newly discovered lineages typically are either left undescribed thus remain unprotected or being erroneously proposed as new despite mixed evidence completed speciation, in turn contributing to emerging problem of taxonomic inflation. Inspired by recent conceptual methodological progress, we propose standardized workflow combines phylogenetic hybrid zone analyses genomic datasets (“genomic taxonomy”), which phylogeographic do not freely admix ranked species, while those have remained fully genetically compatible subspecies. In both cases, encourage their formal naming, diagnosis, description promote social awareness biodiversity. The use loci throughout genome overcomes unreliability widely used barcoding genes when patterns complex, evaluation divergence reproductive isolation unifies long-opposed concepts lineage biological species. We suggest shift assessments from single level (species) two-level hierarchy (species subspecies) will lead more balanced perception intraspecific interspecific diversity valued adequately protected.

Language: Английский

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Species delimitation 4.0: integrative taxonomy meets artificial intelligence

Trends in Ecology & Evolution, Journal Year: 2024, Volume and Issue: 39(8), P. 771 - 784

Published: June 6, 2024

Although species are central units for biological research, recent findings in genomics raising awareness that what we call can be ill-founded entities due to solely morphology-based, regional descriptions. This particularly applies groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology ecology, etc.) become apparent: different favored concepts, lack universal characters/markers, missing appropriate analytical tools processes, and highly subjective ranking fusion datasets. Now, combined with artificial intelligence under a unified concept enable automated feature learning data integration, thus reduce subjectivity delimitation. approach will likely accelerate revising unraveling eukaryotic biodiversity.

Language: Английский

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Medicinal plants meet modern biodiversity science

Current Biology, Journal Year: 2024, Volume and Issue: 34(4), P. R158 - R173

Published: Feb. 1, 2024

Plants have been an essential source of human medicine for millennia. In this review, we argue that a holistic, interdisciplinary approach to the study medicinal plants combines methods and insights from three key disciplines - evolutionary ecology, molecular biology/biochemistry, ethnopharmacology is poised facilitate new breakthroughs in science, including pharmacological discoveries rapid advancements health well-being. Such research leverages data spanning space, time, species associated with plant evolution, genomics, metabolomic trait diversity, all which build heavily on traditional Indigenous knowledge. contrasts sharply most well-funded successful during last half-century, which, despite notable advancements, has greatly oversimplified dynamic relationships between humans, kept hidden larger narratives about these relationships, overlooked potentially important into life-saving medicines. We suggest people should be viewed as partners whose relationship involves complicated poorly explored set (socio-)ecological interactions not only domestication but also commensalisms mutualisms. short, are just chemical factories extraction exploitation. Rather, they may symbiotic shaped modern societies, improved health, extended lifespans.

Language: Английский

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Next‐generation species delimitation and taxonomy: Implications for biogeography

Journal of Biogeography, Journal Year: 2024, Volume and Issue: 51(9), P. 1709 - 1722

Published: Feb. 13, 2024

Abstract An accurate species‐level taxonomy is paramount for biogeographical research, and conversely, data are of importance species delimitation. We here review recent developments future perspectives direct relevance biogeographers. The understanding that independently evolving segments population‐level lineages, the rise integrative approaches to delimit such advent high‐throughput sequencing have considerably renewed discipline taxonomy. Using genome‐scale molecular datasets, extent admixture across hybrid zones can now be effectively assessed evolutionary independence lineages inferred, leading more reliable comparable delimitation criteria. Substantially divergent but admixing phylogeographical conveniently named as subspecies, thus avoiding taxonomic oversplitting inflation. At same time, comprehensive DNA barcoding metabarcoding efforts uncovering an enormous proportion undiscovered biotic diversity, we encourage development bioinformatic pipelines combine discovery with diagnosis scientific naming, approach a inventory globe without abandoning established Linnaean system.

Language: Английский

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iTaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

Megataxa, Journal Year: 2021, Volume and Issue: 6(2)

Published: July 23, 2021

While powerful and user-friendly software suites exist for phylogenetics, an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting diagnosing species, is still its infancy. Here we present a project to develop bioinformatic toolkit taxonomy, based on open-source Python code, including tools focusing delimitation diagnosis centered around specimen identifiers. At core iTaxoTools user-friendliness, with numerous autocorrect options data files intuitive graphical user interfaces. Assembled standalone executables all or suite launcher window will be distributed Windows, Linux, Mac OS systems, future also implemented web server. The initial version (iTaxoTools 0.1) this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains interface (GUI) versions six programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) simple threshold-clustering tool. There are new implementations existing algorithms, compute pairwise DNA distances, ultrametric time trees non-parametric rate smoothing, species-diagnostic nucleotide positions, standard morphometric analyses. Other utilities convert among different formats molecular sequences, geographical coordinates, units; merge, split prune sequence files, tables partition files; perform statistical tests. As perspective, envisage become part pipeline next-generation taxonomy that accelerates inventory life while maintaining high-quality hypotheses. open source code binaries available from Github (https://github.com/iTaxoTools) further information website (http://itaxotools.org).

Language: Английский

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Unnecessary splitting of genus-level clades reduces taxonomic stability in amphibians

Vertebrate Zoology, Journal Year: 2024, Volume and Issue: 74, P. 249 - 277

Published: March 26, 2024

Abstract Although the differentiation of clades at species level is usually based on a justifiable and testable conceptual framework, demarcation supraspecific boundaries less objective often subject to differences opinion. The increased availability large-scale phylogenies has in part promulgated practice what we consider excessively splitting “genus” level. Many these new genus-level splits are predicated untenable supporting evidence (e.g., weakly supported purportedly “diagnostic” but actually variable, non-exclusive, or otherwise problematic opposing character state differences) without careful consideration effects downstream applications. As case studies, critically evaluate several recent examples established monophyletic genera four amphibian families that resulted creation/elevation 20 names (Dicroglossidae: Phrynoglossus , Oreobatrachus Frethia split from Occidozyga ; Microhylidae: Nanohyla Microhyla Ranidae: Abavorana Amnirana Chalcorana Humerana Hydrophylax Indosylvirana Papurana Pulchrana Sylvirana Hylarana Rhacophoridae: Tamixalus Vampyrius Leptomantis Zhangixalus Rhacophorus Rohanixalus Feihyla Orixalus Gracixalus Taruga Polypedates ), also address taxonomic status monotypic genus Pterorana relative . We reassess original claims diagnosability justifications for argue many cases, generic not only unnecessary destabilizes taxonomy, leading host issues affect categories user community (stakeholders such as taxonomists, conservationists, evolutionary biologists, biogeographers, museum curators, educators, lay public). an alternative, advocate use subgenus rank some which can be implemented establish informative partitions future research compromising information content, while avoiding gratuitous (and transient) binomial (genus-species couplet) rearrangements. encourage taxonomists actual needs interests larger non-taxonomic end-user who fund majority research, require system remains reasonably stable relatively intuitive, need inaccessible laboratory equipment advanced technical scientific knowledge identify

Language: Английский

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Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic

Zoological Journal of the Linnean Society, Journal Year: 2021, Volume and Issue: 195(3), P. 695 - 760

Published: Sept. 8, 2021

Abstract Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit map described undescribed lineages of anuran amphibians in Eastern Palaearctic (EP) region its broad sense. Through a literature review, evaluated status considering reproductive isolation genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native 46 genera ten families were retrieved, plus eight additional introduced other realms. Independent hotspots richness concentrated southern Tibet (Medog County), circum-Sichuan Basin region, Taiwan, Korean Peninsula main Japanese islands. Phylogeographic breaks responsible for recent situ speciation events shared around Sichuan Mountains, across Honshu between Ryukyu Island groups, but not shallow water bodies like Yellow Sea Taiwan Strait. Anuran compositions suggested restrict zoogeographical limits EP East Asia. rapidly evolving field, our study provides checkpoint appreciate patterns diversity under single, spatially explicit, framework that integrates phylogeographic data taxonomic research.

Language: Английский

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Standardized nuclear markers improve and homogenize species delimitation in Metazoa

Methods in Ecology and Evolution, Journal Year: 2022, Volume and Issue: 14(2), P. 543 - 555

Published: Dec. 11, 2022

Abstract Species are the fundamental units of life and evolution. Their recognition is essential for science society. Molecular methods have been increasingly used identification animal species, despite several challenges. Here, we explore with genomic data from nine lineages a set nuclear markers, namely metazoan‐level universal single‐copy orthologs (metazoan USCOs), their use in species delimitation. Our sets include arthropods vertebrates. We various assembly strategies coalescent‐based inference as well population admixture analyses phenetic methods. demonstrate that metazoan USCOs distinguish closely related morphospecies consistently outperform classical mitochondrial DNA barcoding discriminating different taxa, judged by comparison delimitations. overcome general shortcomings barcodes, due to standardization across Metazoa, also those other approaches. They accurately assign samples not only lower but higher taxonomic levels. Metazoan provide powerful unifying framework DNA‐based delimitation taxonomy animals employment could result more efficient research resources.

Language: Английский

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Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability

Studies in Mycology, Journal Year: 2022, Volume and Issue: 102(1), P. 53 - 93

Published: June 30, 2022

Language: Английский

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Reducing the number of accepted species inAspergillusseriesNigri

Studies in Mycology, Journal Year: 2022, Volume and Issue: 102(1), P. 95 - 132

Published: June 30, 2022

Language: Английский

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