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Open Access Software

msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation

Michael J Hickerson1*, Eli Stahl2 and Naoki Takebayashi3

Author Affiliations

1 Biology Department, Queens College, CUNY, 65-30 Kissena Blvd, Flushing, NY 11367-1597, USA

2 Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Rd, North Dartmouth, MA 02747, USA

3 Institute of Arctic Biology and Department of Biology and Wildlife, 311 Irving I Bldg, University of Alaska, Fairbanks, AK 99775, USA

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BMC Bioinformatics 2007, 8:268  doi:10.1186/1471-2105-8-268

Published: 26 July 2007

Abstract

Background

Although testing for simultaneous divergence (vicariance) across different population-pairs that span the same barrier to gene flow is of central importance to evolutionary biology, researchers often equate the gene tree and population/species tree thereby ignoring stochastic coalescent variance in their conclusions of temporal incongruence. In contrast to other available phylogeographic software packages, msBayes is the only one that analyses data from multiple species/population pairs under a hierarchical model.

Results

msBayes employs approximate Bayesian computation (ABC) under a hierarchical coalescent model to test for simultaneous divergence (TSD) in multiple co-distributed population-pairs. Simultaneous isolation is tested by estimating three hyper-parameters that characterize the degree of variability in divergence times across co-distributed population pairs while allowing for variation in various within population-pair demographic parameters (sub-parameters) that can affect the coalescent. msBayes is a software package consisting of several C and R programs that are run with a Perl "front-end".

Conclusion

The method reasonably distinguishes simultaneous isolation from temporal incongruence in the divergence of co-distributed population pairs, even with sparse sampling of individuals. Because the estimate step is decoupled from the simulation step, one can rapidly evaluate different ABC acceptance/rejection conditions and the choice of summary statistics. Given the complex and idiosyncratic nature of testing multi-species biogeographic hypotheses, we envision msBayes as a powerful and flexible tool for tackling a wide array of difficult research questions that use population genetic data from multiple co-distributed species. The msBayes pipeline is available for download at http://msbayes.sourceforge.net/ webcite under an open source license (GNU Public License). The msBayes pipeline is comprised of several C and R programs that are run with a Perl "front-end" and runs on Linux, Mac OS-X, and most POSIX systems. Although the current implementation is for a single locus per species-pair, future implementations will allow analysis of multi-loci data per species pair.