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Species delimitation and phylogeny estimation under the multispecies coalescent

Graham Jones
doi: https://doi.org/10.1101/010199
Graham Jones
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Abstract

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted March 22, 2015.
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Species delimitation and phylogeny estimation under the multispecies coalescent
Graham Jones
bioRxiv 010199; doi: https://doi.org/10.1101/010199
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Species delimitation and phylogeny estimation under the multispecies coalescent
Graham Jones
bioRxiv 010199; doi: https://doi.org/10.1101/010199

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