ASAP: assemble species by automatic partitioning

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(2), P. 609 - 620

Published: Oct. 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.

Language: Английский

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Bayesian Evolutionary Analysis with BEAST

Published: Aug. 6, 2015

What are the models used in phylogenetic analysis and what exactly is involved Bayesian evolutionary using Markov chain Monte Carlo (MCMC) methods? How can you choose apply these models, which parameterisations priors make sense, how diagnose MCMC when things go wrong? These just a few of questions answered this comprehensive overview approaches to phylogenetics. This practical guide: • Addresses theoretical aspects field Advises on prepare perform Helps with interpreting analyses visualisation phylogenies Describes software architecture developing BEAST 2.2 extensions allow be extended further. With an accompanying website providing example files tutorials (http://beast2.org/), one-stop reference applying latest 2 will provide essential guidance for all users – from those tools, computational biologists statisticians.

Language: Английский

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Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci

Molecular Biology and Evolution, Journal Year: 2014, Volume and Issue: 31(12), P. 3125 - 3135

Published: Oct. 1, 2014

A method was developed for simultaneous Bayesian inference of species delimitation and phylogeny using the multispecies coalescent model. The eliminates need a user-specified guide tree in incorporates phylogenetic uncertainty framework. nearest-neighbor interchange algorithm adapted to propose changes tree, with gene trees multiple loci altered proposal avoid conflicts newly proposed tree. We also modify our previous scheme specifying priors models construct joint phylogeny. As earlier method, modified integrates over trees, taking account topology branch lengths given sequence data. conducted simulation study examine statistical properties six populations (two sequences each) true number three species, values divergence times ancestral population sizes that are realistic recently diverged species. results suggest tends be conservative high posterior probabilities being confident indicator status. Simulation indicate power delimit increases an increase increased loci. Reanalyses two data sets cavefish coast horned lizards considerable even though informative about delimitation. discuss impact prior on size parameters (θ)

Language: Английский

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

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(3), P. 613 - 635

Published: Jan. 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.

Language: Английский

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Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios

Systematic Biology, Journal Year: 2018, Volume and Issue: 67(5), P. 830 - 846

Published: Feb. 15, 2018

Species are fundamental units in biological research and can be defined on the basis of various operational criteria. There has been growing use molecular approaches for species delimitation. Among most widely used methods, generalized mixed Yule-coalescent (GMYC) Poisson tree processes (PTP) were designed analysis single-locus data but often applied to concatenations multilocus data. In contrast, Bayesian multispecies coalescent approach software Phylogenetics Phylogeography (BPP) explicitly models evolution this study, we compare performance GMYC, PTP, BPP using synthetic generated by simulation under speciation scenarios. We show that absence gene flow, main factor influencing these methods is ratio population size divergence time, while number loci sample per have smaller effects. Given appropriate priors correct guide trees, shows lower rates overestimation underestimation, generally robust potential confounding factors except high levels flow. The single-threshold GMYC best strategy identified PTP perform well scenarios involving more than a single putative when flow absent, outperforms fewer involved. Both sensitive effects factors. Case studies bears bees further validate some findings from our reveal importance an informed starting point Our results highlight key affecting delimitation, with benefits within integrative taxonomic framework.

Language: Английский

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From Integrative Taxonomy to Species Description: One Step Beyond

Systematic Biology, Journal Year: 2014, Volume and Issue: 64(1), P. 152 - 160

Published: Oct. 29, 2014

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

Language: Английский

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Guidelines for DNA taxonomy, with a focus on the meiofauna

Marine Biodiversity, Journal Year: 2015, Volume and Issue: 45(3), P. 433 - 451

Published: Feb. 27, 2015

Language: Английский

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

Molecular Ecology, Journal Year: 2014, Volume and Issue: 24(3), P. 525 - 544

Published: Dec. 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.

Language: Английский

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DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent

Bioinformatics, Journal Year: 2014, Volume and Issue: 31(7), P. 991 - 998

Published: Nov. 12, 2014

The multispecies coalescent model provides a formal framework for the assignment of individual organisms to species, where species are modeled as branches sp tree. None available approaches so far have simultaneously co-estimated all relevant parameters in model, without restricting parameter space by requiring guide tree and/or prior individuals clusters or species.We present DISSECT, which explores full possible clusterings and topologies Bayesian framework. It uses an approximation avoid need reversible-jump Markov Chain Monte Carlo, form that is modification birth-death incorporates spike near zero density node heights. has two extra parameters: one controls degree second distribution on numbers species. implemented part BEAST requires only few changes from standard *BEAST analysis. method evaluated simulated data demonstrated empirical dataset. shown be insensitive approximation, but quite sensitive parameter, suggesting large sequences needed draw firm conclusions.http://tree.bio.ed.ac.uk/software/beast/, http://www.indriid.com/dissectinbeast.html.Supplementary at Bioinformatics online.

Language: Английский

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Bayesian species delimitation combining multiple genes and traits in a unified framework

Evolution, Journal Year: 2014, Volume and Issue: 69(2), P. 492 - 507

Published: Dec. 15, 2014

Delimitation of species based exclusively on genetic data has been advocated despite a critical knowledge gap: how might such approaches fail because they rely alone, and would their accuracy be improved by using multiple types. We provide here the requisite framework for addressing these key questions. Because both phenotypic molecular can analyzed in common Bayesian with our program iBPP, we compare delimited taxa alone versus when integrated data. also evaluate integration improve delimitation divergence occurs gene flow and/or is selectively driven. These two realities speciation process are ignored currently available approaches. Our model accommodates characters that exhibit different degrees divergence, allowing neutral traits under selection. found greater estimated boundaries data, strong beneficial influence from selection involves flow. results highlight benefits types, but draws into question rationale

Language: Английский

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