ASAP: assemble species by automatic partitioning

Molecular Ecology Resources, Год журнала: 2020, Номер 21(2), С. 609 - 620

Опубликована: Окт. 15, 2020

Abstract Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough split sets as large 10 4 sequences into putative in several minutes. Although grounded evolutionary theory, the implementation of hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding computational burden phylogenetic reconstruction. Importantly, proposes ranked scoring system no biological prior insight intraspecific diversity. stand‐alone program can be used either through graphical web‐interface or downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP GMYC) on real COI representing various degrees challenge (from small easy cases complicated also Monte‐Carlo simulations multispecies coalescent framework assess strengths weaknesses other programs. Through these analyses, demonstrate has potential become major tool taxonomists it rapidly full exploratory interface relevant hypothesis first step integrative taxonomy process.

Язык: Английский

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Cryptic species as a window into the paradigm shift of the species concept

Molecular Ecology, Год журнала: 2018, Номер 27(3), С. 613 - 635

Опубликована: Янв. 15, 2018

The species concept is the cornerstone of biodiversity science, and any paradigm shift in delimitation affects many research fields. Many biologists now are embracing a new "species" as separately evolving populations using different criteria. Individual criteria can emerge during periods speciation; some may never evolve. As such, relates to this inherent heterogeneity speciation process category-which fundamentally overlooked research. Cryptic fall within shift: they continuously being reported from diverse animal phyla but poorly considered current tests ecological evolutionary theory. aim review integrate cryptic science. In first section, we address that absence morphological diversification an phenomenon, "process" counterpart long-studied mechanisms diversification. next section regarding taxonomy, show molecular heavily biased towards distance-based methods. We also stress importance formally naming for better integration into fields use units analysis. Finally, incorporating leads novel insights patterns processes, including large-scale assessments, geographic variation distribution coexistence. It time multicriteria approaches aiming understand across space taxa, thus allowing conservation while accommodating uncertainty.

Язык: Английский

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DNA-based species delimitation in algae

European Journal of Phycology, Год журнала: 2014, Номер 49(2), С. 179 - 196

Опубликована: Апрель 3, 2014

Given the problems of species delimitation in algae using morphology or sexual compatibility, molecular data are becoming standard for delimiting and testing their traditional boundaries. The idea that separately evolving metapopulation lineages, along with theoretical progress phylogenetic population genetic analyses, has led to development new methods delimitation. We review these recent developments DNA-based methods, discuss how they have changed continue change our understanding algal Although single-locus approaches proven effective a first rapid large-scale assessment diversity, based on single gene trees falls short due tree–species tree incongruence, caused by confounding processes like incomplete lineage sorting, trans-species polymorphism, hybridization introgression. Data from unlinked loci multi-species coalescent which combine principles phylogenetics genetics, may now be able account complicating factors. Several also provide statistical support regarding boundaries, is important because speciation process therefore uncertainty about precise boundaries inevitable recently diverged lineages.

Язык: Английский

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From Integrative Taxonomy to Species Description: One Step Beyond

Systematic Biology, Год журнала: 2014, Номер 64(1), С. 152 - 160

Опубликована: Окт. 29, 2014

published or not.The documents may come from teaching and research institutions in France abroad, public private centers.L'archive ouverte pluridisciplinaire

Язык: Английский

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Species are hypotheses: avoid connectivity assessments based on pillars of sand

Molecular Ecology, Год журнала: 2014, Номер 24(3), С. 525 - 544

Опубликована: Дек. 20, 2014

Connectivity among populations determines the dynamics and evolution of populations, its assessment is essential in ecology general conservation biology particular. The robust basis any ecological study accurate delimitation evolutionary units, such as metapopulations species. Yet a disconnect still persists between work taxonomists describing species working hypotheses use by molecular ecologists interested patterns gene flow. This problem particularly acute marine environment where inventory biodiversity relatively delayed, while for past two decades, studies have shown high prevalence cryptic In this study, we illustrate, based on case studies, how failure to recognize boundaries evolutionary-relevant unit leads heavily biased estimates connectivity. We review conceptual framework within which can be formalized falsifiable show connectivity feed integrative taxonomic vice versa. Finally, suggest strategies spatial, temporal phylogenetic sampling reduce probability inadequately delimiting units when engaging studies.

Язык: Английский

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Sky island diversification meets the multispecies coalescent – divergence in the spruce‐fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia

Molecular Ecology, Год журнала: 2015, Номер 24(13), С. 3467 - 3484

Опубликована: Май 25, 2015

Abstract Microhexura montivaga is a miniature tarantula‐like spider endemic to the highest peaks of southern Appalachian mountains and known only from six allopatric, highly disjunct montane populations. Because severe declines in spruce‐fir forest late 20th century, M. was formally listed as US federally endangered species 1995. Using DNA sequence data one mitochondrial seven nuclear genes, patterns multigenic genetic divergence were assessed for Independent discovery analyses reveal obvious fragmentation both within among populations, with five primary lineages recovered. Multispecies coalescent validation [guide tree unguided Bayesian Phylogenetics Phylogeography ( BPP ), Bayes factor delimitation BFD )] using nuclear‐only congruently recover or distinct lineages; combined plus favour eight lineages. In stark contrast this clear fragmentation, survey secondary sexual features available males indicates morphological conservatism across While it certainly possible that morphologically cryptic speciation has occurred taxon, system may alternatively represent case where extreme population structuring (but not speciation) leads an oversplitting lineage diversity by multispecies methods. Our results have conservation implications taxon illustrate methodological issue expected become more common genomic‐scale sets are gathered taxa found naturally fragmented habitats.

Язык: Английский

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Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics

Fungal Diversity, Год журнала: 2021, Номер 109(1), С. 99 - 154

Опубликована: Июль 1, 2021

Abstract Lichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria photobionts), specific elements of the bacterial microbiome associated with lichen thallus. The question what is a species, both concerning as whole its main fungal component, primary mycobiont, has faced many challenges throughout history reached new dimensions advent molecular phylogenetics phylogenomics. In this paper, we briefly revise definition lichens scientific vernacular naming conventions, concluding that scientific, Latinized name usually invariably refers to whereas encompasses entire lichen. Although same mycobiont may produce different phenotypes when associating photobionts or growing in axenic culture, discrete variation does not warrant application names, but must follow principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such morphologies, chloromorph cyanomorph formed by either green cyanobacteria. taxonomic recognition species lichen-forming other conceptual nomenclatural approaches principles. We identify number current provide recommendations address these. Species delimitation tailored particular concepts instead derived empirical evidence, applying several following principles call LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) (morphological reproductive (R) compatibility isolation (biological component). hypotheses can established based on L P, then using P (plus R) corroborate them. reliability depends only nature characters also context: closer relationship similarity between higher specimens analyzed reliable delimitations. Alpha taxonomy evidence an evolutionary framework offer alternative practical solutions, long these scientifically defendable. Taxa delimited phylogenetically readily identifiable field, genuinely cryptic, rejected due inaccessibility proper tools. they provisionally treated undifferentiated complexes purposes do require precise determinations. infraspecific (gamma) restricted cases where there biological rationale, i.e . , lineages complex show limited phylogenetic no isolation. Gamma denote phenotypical ecotypes warranting distinction at level. pair concept fungi, which recognizes sexually asexually reproducing morphs underlying species. conclude most hold, actual situation necessarily correlated strategy. data available single multi-marker resolution, recommend maintaining pairs until phylogenomic available. This recommendation example Usnea aurantiacoatra U. antarctica resolved approaches, microsatellites RADseq. Overall, consider advanced dramatically over past three decades, solid framework, still missing taxa. Therefore, while focusing examples will increasingly employed resolve difficult complexes, broad screening barcoding markers aid placing taxa possible into matrix. protocol how assess formally treat novelties. While paper focuses aspects discussed herein apply generally taxonomy. combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: cyanea f. Lücking) proposed.

Язык: Английский

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Hybridization patterns in two contact zones of grass snakes reveal a new Central European snake species

Scientific Reports, Год журнала: 2017, Номер 7(1)

Опубликована: Авг. 1, 2017

Recent studies found major conflicts between traditional taxonomy and genetic differentiation of grass snakes identified previously unknown secondary contact zones. Until now, little is known about gene flow across these Using two mitochondrial markers 13 microsatellite loci, we examined One, largely corresponding to the Rhine region, involves western subspecies Natrix natrix helvetica eastern N. n. natrix, whereas in other, more easterly, zone lineages meet that are currently with persa. This second runs Central Europe southern Balkans. Our analyses reveal narrow, parapatrically distributed limited, unidirectional nuclear flow. In contrast, very wide, massive admixture broadly overlapping lineages. combination additional lines evidence (morphology, phylogeny, divergence times), conclude differences reflect different stages speciation process should be regarded as a distinct species. We suggest nomenclatural framework for presently recognized snake taxa highlight need reconciling genetics taxonomy.

Язык: Английский

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High‐stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas

Molecular Ecology, Год журнала: 2014, Номер 24(2), С. 346 - 361

Опубликована: Дек. 10, 2014

A remarkable radiation of completely eyeless, cave-obligate spider species (Cicurina) has been described from limestone caves Texas. This includes over 50 species, with a large number hypothesized single-cave endemics, and four listed as US Federally Endangered. Because this conservation importance, delimitation in the group is 'high-stakes'- it imperative that hypotheses are data rich, objective, robust. study focuses on complex cave-dwelling Cicurina distributed northwestern edge Austin, Several existing weak, based morphological comparisons small samples adult female specimens; one description (for C. wartoni) single specimen. Species limits were newly assessed using morphological, mitochondrial nuclear DNA sequence evidence, analysed variety approaches. All support clear lineage separation between buwata versus travisae (including travisae, wartoni reddelli). Observed congruence across multiple analyses indicate represents formal synonymy presented here important implications. The integrative framework utilized serves potential model for other Texas cave Cicurina, including Endangered species. More generally, illustrates how why taxon-focused efforts must prioritize modern research (if taxonomy weak), before devoting precious downstream resources to efforts. also highlights issue taxonomic type II error diversity biologists increasingly face moves into genomics era.

Язык: Английский

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The Dynamic Discipline of Species Delimitation: Progress Toward Effectively Recognizing Species Boundaries in Natural Populations

Springer eBooks, Год журнала: 2015, Номер unknown, С. 11 - 44

Опубликована: Янв. 1, 2015

Язык: Английский

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