MBE Advance Access published online on February 9, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi103
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1 Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
* To whom correspondence should be addressed. We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a pre-specified parametric model of demographic history. We describe a Markov chain Monte Carlo (MCMC) sampling procedure that efficiently samples a variant of the generalized skyline plot given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analysing two real data sets (Hepatitis C virus in Egypt, and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis we detect a severe but previously unrecognised bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.
Accepted January 25, 2005
Research Article
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
A. J. Drummond, E-mail: alexei.drummond{at}zoo.ox.ac.uk
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