STACEY: species delimitation and phylogeny estimation under the multispecies coalescent

This article describes a new package called STACEY for BEAST2 which is capable of both species delimitation and species tree estimation using DNA sequences from multiple loci. The focus in this article is on species delimitation. STACEY is based on the multispecies coalescent model, and builds on earlier software (DISSECT), which uses a ‘birth-death-collapse’ prior to deal with delimitations without the need for reversible-jump Markov chain Monte Carlo moves. Like DISSECT, it requires no a priori assignment of individuals to species or populations, and no guide tree. This paper introduces two innovations. The first is a new model for the populations along the branches of the species tree, and the second is a new MCMC move for exploring the posterior when the multispecies coalescent model is assumed. The main benefit of STACEY over DISSECT is much better convergence. Current practice, using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data. The same simulated data set is used to demonstrate the accuracy and efficiency of STACEY.