Species delimitation and phylogeny estimation under the multispecies coalescent

This article describes a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using DNA sequences from multiple loci. The focus here is on species delimitation with no a priori assignment of individuals to species, and no guide tree. The method uses a new model for the population sizes along the branches of the species tree, and three new operators for sampling from the posterior using the Markov chain Monte Carlo (MCMC) algorithm. The correctness of the moves is demonstrated both by proofs and by tests of the implementation. Current practice, using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data [10]. The same simulated data set is used to demonstrate the accuracy and efficiency of the present method. The method is implemented in a package called STACEY for BEAST2.