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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Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo

Bioinformatics, Journal Year: 2017, Volume and Issue: 33(11), P. 1630 - 1638

Published: Jan. 20, 2017

In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast discovery biodiversity estimates. Among those, distance-based the most common choice scale well with large datasets; however, sensitive to similarity threshold parameters ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is phylogeny-aware that does not rely on such thresholds. Yet, two weaknesses PTP impact its accuracy practicality when applied it account divergent intraspecific variation slow number sequences.We introduce multi-rate (mPTP), an improved alleviates theoretical technical shortcomings PTP. It incorporates different levels genetic diversity deriving from differences either history or sampling each species. Results empirical data suggest mPTP superior popular it, consistently yields more accurate delimitations respect taxonomy (i.e., identifies taxonomic species, infers numbers closer taxonomy). Moreover, require any input. novel dynamic programming algorithm attains speedup at least five orders magnitude compared PTP, allowing delimit (meta-) barcoding data. addition, Markov Chain Monte Carlo provides comprehensive evaluation inferred just few seconds millions steps, independently tree size.mPTP implemented C available download http://github.com/Pas-Kapli/mptp under GNU Affero 3 license. A web-service http://mptp.h-its.org .: [email protected] [email protected] [email protected] Bioinformatics online.

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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How reticulated are species?

BioEssays, Journal Year: 2015, Volume and Issue: 38(2), P. 140 - 149

Published: Dec. 28, 2015

Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well microbes plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but multicellular eukaryotes hybridization introgression among probably more important. Because species, including ancestors ancient major lineages, seem to evolve rapidly adaptive radiations, some sexual compatibility may exist them. Introgression reticulation can thereby affect all parts tree life, not just recent at tips. Our understanding evolution, speciation, phylogenetics, comparative biology must adapt these mostly findings. has important practical implications well, least for management genetically modified organisms pest disease control.

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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StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

Molecular Biology and Evolution, Journal Year: 2017, Volume and Issue: 34(8), P. 2101 - 2114

Published: April 13, 2017

Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many with is intractably slow. An alternative to use heuristic which compromise accuracy or completeness in return speed. A common concatenation, assumes the evolutionary history each gene tree identical tree. This an inconsistent estimator topology, worse divergence times, and induces spurious substitution rate variation when incomplete lineage sorting present. Another class heuristics directly motivated by MSC avoids pitfalls concatenation cannot used times. To enable fuller available data more accurate inference topologies, rates, we have developed new version called StarBEAST2. improve convergence rates add analytical integration population sizes, novel MCMC operators other optimizations. Computational performance improved 13.5× 13.8× respectively analyzing two empirical sets, average 33.1× across 30 simulated sets. estimates per-species introduce relaxed clocks, show StarBEAST2 powerful robust than concatenation. through BEAUTi package manager BEAST 2.4 above.

Language: Английский

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Phylogenetic tree building in the genomic age

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 21(7), P. 428 - 444

Published: May 18, 2020

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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