Abstract
BackgroundAlthough 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.ResultsmsBayes 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".ConclusionThe 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 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.
Highlights
Testing for simultaneous divergence 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
Testing for simultaneous divergence across different population-pairs that span the same historical barrier to gene flow is of central importance to evolutionary biology, biogeography and community ecology [1,2,3,4]
Estimating a population divergence time with an appropriate statistical model [5] can be accomplished in a variety of ways [6,7,8], yet analyzing comparative phylogeographic data with multiple co-occurring species pairs that vary with respect to demographic parameters and pairwise coalescent times is less straightforward
Summary
The msBayes software pipeline will increasingly become an important tool as the field of comparative phylogeography progresses to become a more rigorous and statistical enterprise [5]. Given the complex and idiosyncratic nature of testing multi-species biogeographic hypotheses, we envision msBayes as a powerful and flexible tool that is open for modification when faced with difficult research questions. Due to its flexible and modular design, msBayes will be a well-suited tool for the heterogeneous data sets that are emerging and being combined to test complex historical hypotheses. MJH developed the idea for using ABC within a hierarchical model to analyze multiple population pairs simultaneously. MJH and NT developed C, R, and Perl routines and modified pre-existing R and C routines to comprise an ABC algorithm that makes use of a Hierarchical model. NT extensively developed the C and Perl routines that comprise the user version of msBayes available. NT and MJH maintains the msBayes website and NT developed the installation configurations and precompiled binaries. All authors read and approved the final version of the manuscript
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