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MBE Advance Access published online on February 22, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msj111
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted February 7, 2006

Research Article

Coalescent-Based Estimation of Population Parameters When the Number of Demes Changes over Time

Greg Ewing 1 and Allen Rodrigo 1 *

1 The Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand; The Bioinformatics Institute, University of Auckland, Private Bag 92019, Auckland, New Zealand

* To whom correspondence should be addressed.
Allen Rodrigo, E-mail: a.rodrigo{at}auckland.ac.nz


  Abstract

We expand a coalescent-based method that uses serially sampled genetic data from a subdivided population to incorporate changes to the number of demes and patterns of colonization. Often, when estimating population parameters or other parameters of interest from genetic data, the demographic structure and parameters are not constant over evolutionary time. In this paper we develop a Bayesian MCMC method that allows for step changes in mutation, migration, and population sizes, as well as changing numbers of demes, where the times of these changes are also estimated. We show that in parameter ranges of interest, reliable estimates can often be obtained, including the historical times of parameter changes. However posterior densities of migration rates can be quite diffuse and estimators somewhat biased, as reported by other authors.

Keywords: Coalescent; Migration; Markov Chain Monte Carlo; Bayesian Inference; Serial Samples; Measurably Evolving Populations.
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