Contemporary Methods and Evidence for Species Delimitation

Ichthyology & Herpetology, Год журнала: 2021, Номер 109(3)

Опубликована: Сен. 29, 2021

Over the last two decades, mitochondrial DNA (mtDNA) sequence data, as well analyses of nuclear based on multispecies coalescent model, have increasingly been used to delimit species, sometimes limited sampling and without other supporting evidence. We argued elsewhere that uncritical use these approaches has resulted in unnecessary unwarranted taxonomic changes real long-lasting consequences for science society. Unfortunately, arguments misrepresented by Burbrink Ruane's Point View “contemporary” species delimitation this issue. Here, we discuss role models research, again argue careful consideration model assumptions (and their potential violation) is necessary when inferring population history delimiting species. echo recent calls targeted, thorough geographic across contact zones into parapatric ranges test reproductive isolation draw inferences about evolutionary independence (or lack thereof) populations exchange genes. Finally, despite our very different views how best identify make changes, end highlighting areas where agree with offer suggestions future research.

Язык: Английский

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The Importance of Contact Zones for Distinguishing Interspecific from Intraspecific Geographic Variation

Systematic Biology, Год журнала: 2022, Номер 72(2), С. 357 - 371

Опубликована: Авг. 22, 2022

Abstract With limited sampling, geographic variation within a single species can be difficult to distinguish from interspecific variation, confounding our ability draw accurate boundaries. We argue that thorough sampling and analysis of contact zones between putative taxa determine if assortative mating or selection against hybrids exists (supporting the presence two distinct species), alternatively is random among genotypes admixture adjacent populations gradual continuous species). Here, we test alternative hypotheses for pairs named at American milksnake (Lampropeltis triangulum) complex. A prior morphological found areas intergradation taxa, concluded represented geographical races polytypic species. In contrast, subsequent gene sequence data, but with near zones, hypothesized boundaries zones. At zone proposed L. triangulum Lampropeltis gentilis, examined $\sim$700 km-wide transect across states Kansas Missouri, reduced-representation genomic-level sequencing, opposing taxonomic hypotheses. Our analyses included examinations population structure, fixed differences, cline-fitting, an index analysis. These all supported cline broad intergrade forms triangulum, thus providing strong support in this region (and no recognition gentilis as second elapsoides (but variously treated subspecies by different researchers) Kentucky Tennessee, re-evaluated data. case, indicated sympatry reproductive isolation strongly conclude detailed studies based on either genetic are essential distinguishing intraspecific case widely continuously distributed taxa. [Contact zones; speciation; concepts; delimitation; taxonomy.]

Язык: Английский

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Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude

Cladistics, Год журнала: 2022, Номер 39(2), С. 129 - 143

Опубликована: Дек. 28, 2022

DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA-based assessments of diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount evidence indicate that markers alone can lead to misleading estimates due mito-nuclear discordance. Therefore, reports putative based solely should be verified by other methods, especially in cases where COI sequences are identical for different morphospecies or divergence within same is high. Freshwater amphipods particularly interesting this context because numerous have been reported. Here, we investigated status molecular operational taxonomic units (MOTUs) found Echinogammarus sicilianus. We used an integrative approach combining barcoding with mate selection observations, detailed morphometrics and genome-wide double digest restriction site-associated sequencing (ddRAD-seq). Within relatively small sampling area, detected twelve MOTUs (divergence = 1.8-20.3%), co-occurring syntopy at two-thirds sites. pair formation was random there extensive nuclear gene flow among ten river stretch. The four most common were also indistinguishable respect functional morphology. best fits hypothesis single, yet genetically diverse, main system. only two sampled outside focal area distinct level may represent species. Our study reveals COI-based delimitation significantly overestimate diversity, highlighting importance taxonomy validation, hyperdiverse complexes syntopically occurring MOTUs.

Язык: Английский

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Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)

Systematic Biology, Год журнала: 2022, Номер 72(1), С. 179 - 197

Опубликована: Сен. 28, 2022

Abstract Significant advances have been made in species delimitation and numerous methods can test precisely defined models of speciation, though the synthesis phylogeography taxonomy is still sometimes incomplete. Emerging consensus treats distinct genealogical clusters genome-scale data as strong initial evidence speciation most cases, a hypothesis that must therefore be falsified under an explicit evolutionary model. We now hypotheses linking trait differentiation to specific mechanisms divergence with increasingly large sets. Integrative can, therefore, reflect understanding how each axis variation relates underlying processes, nomenclature for lineages. illustrate this approach here Seal Salamanders (Desmognathus monticola) introduce new unsupervised machine-learning delimitation. Plethodontid salamanders are renowned their morphological conservatism despite extensive phylogeographic divergence. discover 2 geographic genetic clusters, which demographic spatial ecology gene flow provide robust support ecogeographic limited phenotypic These integrated (e.g., spatially localized reduced migration) reflected emergent properties expected reinforcement ethological isolation selection against hybrids). Their prima facie species-level distinctiveness, supported by along axes such behavior, geography, climate suggest ecological basis subsequent through prezygotic isolation. As sets grow more comprehensive, species-delimitation tested, rejected, or corroborated hypotheses, providing reciprocal illumination processes integrative taxonomies. [Desmognathus; taxonomy; machine learning; delimitation.]

Язык: Английский

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Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

Molecular Ecology, Год журнала: 2023, Номер 32(17), С. 4844 - 4862

Опубликована: Июль 29, 2023

Abstract Many organisms possess multiple discrete genomes (i.e. nuclear and organellar), which are inherited separately may have unique even conflicting evolutionary histories. Phylogenetic reconstructions from these can yield different patterns of relatedness, a phenomenon known as cytonuclear discordance. In many animals, mitonuclear discordance discordant histories between the mitochondrial genomes) has been widely documented, but its causes often considered idiosyncratic inscrutable. We show that case in Todiramphus kingfishers be explained by extensive genome‐wide incomplete lineage sorting (ILS), likely result explosive diversification history this genus. For kingfishers, quartet frequencies reveal genome is dominated topologies, with none internal branches our consensus tree recovered >50% gene trees. Meanwhile, lack inter‐species shared ancestry, non‐significant pairwise tests for flow, little evidence meaningful migration edges species, leads to conclusion flow cannot explain we observe. This combined discordance, hallmark ILS, us conclude observe results specifically deep coalescence genome. Based on study, hypothesize similar demographic other ‘great speciator’ taxa across Indo‐Pacific predispose groups high levels ILS likelihoods

Язык: Английский

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Species boundaries to the limit: Integrating species delimitation methods is critical to avoid taxonomic inflation in the case of the Hajar banded ground gecko (Trachydactylus hajarensis)

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 186, С. 107834 - 107834

Опубликована: Май 30, 2023

Язык: Английский

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COI-Barcoding and Species Delimitation Assessment of Toad-Headed Agamas of the Genus Phrynocephalus (Agamidae, Squamata) Reveal Unrecognized Diversity in Central Eurasia

Diversity, Год журнала: 2023, Номер 15(2), С. 149 - 149

Опубликована: Янв. 21, 2023

We provide a diversity assessment of the agamid genus Phrynocephalus Kaup, 1825. analyze COI mtDNA barcodes from 385 individuals sampled all over range. apply ABGD, ASAP, bGMYC, mlPTP and hsPTP species delimitation algorithms to gene fragment variation assess in Phrynocephalus. Nine groups are revealed agreement with earlier studies on phylogenetic relationships genus. demonstrate that present taxonomy likely underestimates actual Alternative confusingly wide range possible number species—from 54 103 MOTUs (molecular operational taxonomic units). The ASAP scheme recognizing 63 most closely fits currently recognized framework also report 13 previously unknown lineages as unverified candidate species. ABGD reflect Phrynocephalus, while largely overestimate it. argue these lizards based exclusively markers is insufficient, call for further integrative joining data morphology, nuDNA fully stabilize lizards.

Язык: Английский

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How not to describe a species: lessons from a tangle of anacondas (Boidae: Eunectes Wagler, 1830)

Zoological Journal of the Linnean Society, Год журнала: 2024, Номер 201(4)

Опубликована: Авг. 1, 2024

Abstract A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with description a new species green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies evidence used and errors in nomenclature. We here use case this problematic publication to: (i) highlight common issues affecting delimitations, especially an over-reliance on mitochondrial DNA data, reiterate best practices; (ii) reanalyse data available for establish true current state knowledge lines further research; (iii) analyse nomenclatural history status genus. While our analysis reveals significant morphological variation both yellow anacondas, denser sampling informative nuclear markers are required meaningful delimitation Eunectes. Tracing name-bearing types establishes Trinidad as type locality Boa murina Linnaeus, 1758 allows identification extant lectotype species. Finally, we emphasize responsibility journals authors ensure that published taxonomic work meets burden substantiate descriptions named compliance rules zoological

Язык: Английский

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An integrative taxonomic revision of slug-eating snakes (Squamata: Pareidae: Pareineae) reveals unprecedented diversity in Indochina

PeerJ, Год журнала: 2022, Номер 10, С. e12713 - e12713

Опубликована: Янв. 10, 2022

Slug-eating snakes of the subfamily Pareinae are an insufficiently studied group specialized in feeding on terrestrial mollusks. Currently encompass three genera with 34 species distributed across Oriental biogeographic region. Despite recent significant progress understanding diversity, remains taxonomically challenging. Here we present updated phylogeny a comprehensive taxon sampling including 30 currently recognized and several previously unknown candidate lineages. Phylogenetic analyses mtDNA nuDNA data supported monophyly Asthenodipsas , Aplopeltura Pareas . Within both our recovered deep differentiation each genus being represented by two morphologically diagnosable clades, which treat as subgenera. We further apply integrative taxonomic approach, molecular morphological data, along examination available type materials, to address longstanding questions subgenus reveal high level hidden diversity these Indochina. restrict distribution P. carinatus southern Southeast Asia, recognize subspecies within it, one new proposed for populations from Thailand Myanmar. revalidate berdmorei synonymize menglaensis this taxon, erected Laos Vietnam. Furthermore, describe Vietnam: belonging Vietnam, member nuchalis central provide temporalis report range extension Our phylogeny, clock ancestral area analyses, complex diversification pattern involving degree sympatry widespread endemic species. support “upstream” colonization hypothesis and, thus, appears have originated Sundaland during middle Eocene then colonized mainland Asia early Oligocene. Eastern Indochina appear played key roles centers diversification. results that vicariance dispersal responsible current patterns Pareinae, tectonic movements, orogeny paleoclimatic shifts probable drivers study brings total number Pareidae 41 highlights importance revisions not only better biodiversity its evolution, but also elaboration adequate conservation actions.

Язык: Английский

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The opposed forces of differentiation and admixture across glacial cycles in the butterfly Aglais urticae

Molecular Ecology, Год журнала: 2024, Номер 33(7)

Опубликована: Фев. 29, 2024

Abstract Glacial cycles lead to periodic population interbreeding and isolation in warm‐adapted species, which impact genetic structure evolution. However, the effects of these processes on highly mobile more cold‐tolerant species are not well understood. This study aims shed light phylogeographic history Aglais urticae , a butterfly with considerable dispersal ability, wide Palearctic distribution reaching Arctic. Through analysis genomic data, four main lineages identified: European, Sierra Nevada, Sicily/Calabria/Peloponnese, Eastern. The results indicate that Sardo‐Corsican endemic taxon ichnusa is distinct species. split between relict southern Europe European lineage estimated have happened 400–450 thousand years ago, admixture observed during Quaternary glacial cycles, still ongoing, albeit much smaller extent. These suggest may be better treated as subspecific parapatric taxa. Ecological niche modelling supported existence both Mediterranean extra‐Mediterranean refugia periods, one located Atlantic coast. Nevertheless, gene flow populations was possible, indicating differentiation acted continuously across this butterfly, generally balancing each other but producing differentiated peninsulas. We conclude dynamics shaping cold‐adapted ice ages different than those classically accepted for

Язык: Английский

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