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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Multispecies coalescent delimits structure, not species

Proceedings of the National Academy of Sciences, Journal Year: 2017, Volume and Issue: 114(7), P. 1607 - 1612

Published: Jan. 30, 2017

Significance Despite its widespread application to the species delimitation problem, our study demonstrates that what multispecies coalescent actually delimits is structure. The current implementations of under do not provide any way for distinguishing between structure due population-level processes and boundaries. overinflation misidentification general genetic boundaries has profound implications understanding generation dynamics biodiversity, because ecological or evolutionary studies rely on as their fundamental units will be impacted, well very existence this conservation planning undermined isolated populations incorrectly being treated distinct species.

Language: Английский

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The BPP program for species tree estimation and species delimitation

Current Zoology, Journal Year: 2015, Volume and Issue: 61(5), P. 854 - 865

Published: Oct. 1, 2015

Abstract This paper provides an overview and a tutorial of the BPP program, which is Bayesian MCMC program for analyzing multi-locus genomic sequence data under multispecies coalescent model. An example dataset five nuclear loci from East Asian brown frogs used to illustrate four different analyses, including estimation species divergence times population size parameters model on fixed phylogeny (A00), tree when assignment delimitation are (A01), using guide (A10), joint species-tree or unguided (A11). For analysis (A11), two new priors introduced, assign uniform probabilities numbers delimited species, may be useful assignment, delimitation, all inferred in one analysis. The ends with discussion assumptions, strengths weaknesses

Language: Английский

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Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex

Fungal Genetics and Biology, Journal Year: 2015, Volume and Issue: 78, P. 16 - 48

Published: Feb. 23, 2015

Phylogenetic analysis of 11 genetic loci and results from many genotyping studies revealed significant diversity with the pathogenic Cryptococcus gattii/Cryptococcus neoformans species complex. Genealogical concordance, coalescence-based, tree approaches supported presence distinct concordant lineages within Consequently, we propose to recognize current C. var. grubii as separate species, five gattii. The type strain CBS132 represents a serotype AD hybrid is replaced. newly delimited differ in aspects pathogenicity, prevalence for patient groups, well biochemical physiological aspects, such susceptibility antifungals. MALDI-TOF mass spectrometry readily distinguishes recognized species.

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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Species Delimitation using Genome-Wide SNP Data

Systematic Biology, Journal Year: 2014, Volume and Issue: 63(4), P. 534 - 542

Published: March 12, 2014

The multispecies coalescent has provided important progress for evolutionary inferences, including increasing the statistical rigor and objectivity of comparisons among competing species delimitation models. However, Bayesian methods typically require brute force integration over gene trees via Markov chain Monte Carlo (MCMC), which introduces a large computation burden precludes their application to genomic-scale data. Here we combine recently introduced dynamic programming algorithm estimating that bypasses MCMC with sophisticated marginal likelihoods, needed model selection, provide rigorous computationally tractable technique genome-wide delimitation. We critical yet simple correction brings likelihoods different trees, more importantly corresponding same common denominator, enables direct accurate models using Bayes factors. test this approach, call factor (*with genomic data; BFD*), scenarios computer simulations. Varying numbers loci number samples suggest approach can distinguish true even few limited per species. Misspecification prior population size θ little impact on support model. apply West African forest geckos (Hemidactylus fasciatus complex) SNP This new method builds growing trend objective explicit assumptions are easily tested. [Bayes factor; testing; phylogeography; RADseq; simulation; speciation.].

Language: Английский

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Genetic Diversity and Conservation Units: Dealing With the Species-Population Continuum in the Age of Genomics

Frontiers in Ecology and Evolution, Journal Year: 2018, Volume and Issue: 6

Published: Oct. 23, 2018

Current approaches to biodiversity conservation are largely based on geographic areas, ecosystems, ecological communities and species, with less attention ongenetic diversity the evolutionary continuum from populations species. Conservation management generally rests discrete categories, such as identified and, for threated taxa, intraspecific units. Species, in particular, provide a common measure of yet both theory nature, speciation is typically protracted process progressing connected unambiguous species variable rates phenotypic, genetic divergence. Thus, most recognised not genetically uniform sometimes highly structured into historically isolated worthy consideration units that represent unique conservation. Genome screens offer unprecedented resolution structure across taxonomic boundaries complexes, have potential oversplit if interpreted conservatively. This highlights blurred line between can confound simple dichotomies 'species' versus 'not species'. At same time, like plants, there increasing evidence than even distantly related animal hybridize exchange genes. A review legislation reveals legal definitions quite flexible accommodate range infra-specific taxa divergent populations, well taxonomically For example, legislative definition around world include: subspecies, varieties, geographically and/or distinct populations. In principle, this flexibility allows protection maintenance processes at broad levels. However, biologists often fail adequately justify then translate their defined categories suited assessment under local legislation. We recommend (i). genomic data should be conservatively when formally naming (ii). concomitantly, stronger impetus more approach identifying clearly justified units, (iii). guidelines developed recognising labelling align best scientific practice, (iv). nuanced view emerging analyses communicated effectively by scientists decision makers.

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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DNA-based species delimitation in algae

European Journal of Phycology, Journal Year: 2014, Volume and Issue: 49(2), P. 179 - 196

Published: April 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.

Language: Английский

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Inordinate Fondness Multiplied and Redistributed: the Number of Species on Earth and the New Pie of Life

The Quarterly Review of Biology, Journal Year: 2017, Volume and Issue: 92(3), P. 229 - 265

Published: Aug. 24, 2017

The number of species on Earth is one the most fundamental numbers in science, but that remains highly uncertain. Clearly, more exist than present formally described (approximately 1.5 million), projected differ dramatically among studies. Recent estimates range from about 2 million to approximately 1 trillion, project around 11 or fewer. Numerous studies have focused insects as a major component overall richness, and many excluded other groups, especially non-eukaryotes. Here, we re-estimate global biodiversity. We also estimate relative richness clades living organisms, summarized “Pie Life.” Unlike previous estimates, incorporate morphologically cryptic arthropod molecular-based delimitation. include numerous groups organisms not been simultaneously included those often associated with particular insect host (including mites, nematodes, apicomplexan protists, microsporidian fungi, bacteria). Our suggest there are likely be at least 6 billion Earth. Furthermore, contrast new Pie Life dominated by bacteria 70–90% species) only hyperdiverse groups.

Language: Английский

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