Species Delimitation using Genome-Wide SNP Data

Abstract

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 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. 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. [Bayes factor; model testing; phylogeography; RADseq; simulation; speciation.].

Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization

“…In addition to the SNAPP runs described above, we performed a species delimitation analysis as implemented in BFD* (Leaché et al, 2014) to further test for phylogenetic differentiation among genetic clusters. Because BFD* relies on SNAPP, this analysis was subject to similar computational demands as those described above.…”

“…Highthroughput sequencing technologies, novel cost-effective methods for constructing reduced representation libraries (that is, restriction siteassociated DNA sequencing (RADseq); and the development of statistical approaches that allow historical demographic analyses of these data (that is, Gutenkunst et al, 2009;Excoffier et al, 2013;Leaché et al, 2014) are important factors contributing to this transformation. These novel genomic-scale data sets can reveal cryptic genetic diversity within recognized taxa, estimate demographic parameters characterizing populations and identify important recent and historical events that have shaped existing genetic diversity, such as hybridization between lineages (Luikart et al, 2003;Ellegren, 2013).…”

Concordant genetic structure in two species of woodpecker distributed across the primary West African biogeographic barriers

“…The Sanaga River is, for example, a biogeographic barrier to gene flow between Chimpanzee populations distributed on either side of it, although occasional hybridization occurs (Gonder et al 2011). A phylogeographic study based on genome-wide single nucleotide polymorphims of Hemidactylus geckos also suggested a role for the Sanaga River acting as a barrier to gene flow (Leaché et al 2014). Other studies revealed no impact of the Sanaga River on the broad scale phylogeographic structure of terrestrial vertebrates, with individuals sampled on both side of the river being part of the same terminal clade (Nicolas et al 2008(Nicolas et al , 2010.…”

“…Nesi et al 2013, Leaché et al 2014. For example, no haplotypes were shared between morphologically similar populations sampled across the Dahomey gap for two songbird species, Stiphrornis erythrothorax (Beresford and Cracraft 1999;Schmidt et al 2008) and Hylia prasina (Marks 2010).…”

Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs

“…In addition, there are a number of approaches to species delimitation that incorporate model selection. These include methods that identify the optimal species delimitation using likelihood ratio tests (70), reversible-jump Markov chain Monte Carlo (71,72), information theory (73), ABC (74), and marginalized likelihoods (75). Methods for analyzing comparative phylogeographic data are also under active development, including the use of hierarchical Bayesian models to test simultaneous divergence (76,77) or simultaneous population expansion (78,79).…”