Species Delimitation using Genome-Wide SNP Data

By Adam D. Leaché, M. Fujita, Vladimir N. Minin, Remco R. Bouckaert. bioRxiv, 2013

465 citations recorded by the source corpus.

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

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/87966fc5b205cd33a1f018d58734ab16a855fda1

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Citations in the corpus

The Utility of Single Nucleotide Polymorphism (SNP) Data in Phylogenetics (2017, methodology): “…with SNPs. Creative new solutions for SNP phylogenetics that bypass gene trees have been developed (Bryant et al. 2012, De Maio et al. 2015a), and these methods can be adapted for new applications, such as species delimitation, to further increase the utility of SNPs (Leaché et al. 2014).”
Unguided Species Delimitation Using DNA Sequence Data from Multiple Loci (2014, methodology): “This uncertainty is an important source of inaccuracy for both species delimitation and species tree inference (Leach e and Rannala 2011; Camargo et al. 2012).”
ASAP: assemble species by automatic partitioning (2020, methodology): “In this category, the most popular methods are SpedeSTEM (Ence & Carstens, 2011), BPP (Yang & Rannala, 2014) and BFD (Leaché et al., 2014), reviewed (with other methods) in several articles (Camargo & Sites, 2013; Carstens et al., 2013; Fujita et al., 2012; Leavitt et al., 2015; Rannala, 2015).”
The art and science of species delimitation (2015, unknown): “rent implementation of (Leaché et al., 2014) relies on an MCMC path sampling framework to estimate marginal likelihoods which can be computationally intensive.”