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msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation
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...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949838/ https://www.ncbi.nlm.nih.gov/pubmed/17655753 http://dx.doi.org/10.1186/1471-2105-8-268 |
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author | Hickerson, Michael J Stahl, Eli Takebayashi, Naoki |
author_facet | Hickerson, Michael J Stahl, Eli Takebayashi, Naoki |
author_sort | Hickerson, Michael J |
collection | PubMed |
description | 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 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. |
format | Text |
id | pubmed-1949838 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-19498382007-08-17 msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation Hickerson, Michael J Stahl, Eli Takebayashi, Naoki BMC Bioinformatics Software 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 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. BioMed Central 2007-07-26 /pmc/articles/PMC1949838/ /pubmed/17655753 http://dx.doi.org/10.1186/1471-2105-8-268 Text en Copyright © 2007 Hickerson et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Hickerson, Michael J Stahl, Eli Takebayashi, Naoki msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation |
title | msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation |
title_full | msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation |
title_fullStr | msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation |
title_full_unstemmed | msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation |
title_short | msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation |
title_sort | msbayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate bayesian computation |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1949838/ https://www.ncbi.nlm.nih.gov/pubmed/17655753 http://dx.doi.org/10.1186/1471-2105-8-268 |
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