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Genetics, Vol. 168, 2407-2420, December 2004, Copyright © 2004
doi:10.1534/genetics.104.030411

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Using Temporally Spaced Sequences to Simultaneously Estimate Migration Rates, Mutation Rate and Population Sizes in Measurably Evolving Populations

Greg Ewing*,{dagger}, Geoff Nicholls*,{ddagger} and Allen Rodrigo*,{dagger},1

* Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand 1020
{dagger} Bioinformatics Institute, University of Auckland, Auckland, New Zealand 1020
{ddagger} Department of Mathematics, University of Auckland, Auckland, New Zealand 1020

1 Corresponding author: School of Biological Sciences, Computational and Evolutionary Biology Lab, University of Auckland, Private Bag 92019, Auckland, New Zealand 1020.
E-mail: a.rodrigo{at}auckland.ac.nz

We present a Bayesian statistical inference approach for simultaneously estimating mutation rate, population sizes, and migration rates in an island-structured population, using temporal and spatial sequence data. Markov chain Monte Carlo is used to collect samples from the posterior probability distribution. We demonstrate that this chain implementation successfully reaches equilibrium and recovers truth for simulated data. A real HIV DNA sequence data set with two demes, semen and blood, is used as an example to demonstrate the method by fitting asymmetric migration rates and different population sizes. This data set exhibits a bimodal joint posterior distribution, with modes favoring different preferred migration directions. This full data set was subsequently split temporally for further analysis. Qualitative behavior of one subset was similar to the bimodal distribution observed with the full data set. The temporally split data showed significant differences in the posterior distributions and estimates of parameter values over time.




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 Mol Biol EvolHome page
G. Ewing and A. Rodrigo
Coalescent-Based Estimation of Population Parameters When the Number of Demes Changes Over Time
Mol. Biol. Evol., May 1, 2006; 23(5): 988 - 996.
[Abstract] [Full Text] [PDF]


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