Genetics, Vol. 179, 497-502, May 2008, Copyright © 2008
doi:10.1534/genetics.107.085019

Estimation of 2N_es From Temporal Allele Frequency Data

Jonathan P. Bollback^*,1, Thomas L. York and Rasmus Nielsen^*

^* Department of Biology and Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark and Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853

¹ Corresponding author: School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, King's Bldgs., W. Mains Rd., Edinburgh EH9 3JT United Kingdom.
E-mail: j.p.bollback{at}ed.ac.uk

We develop a new method for estimating effective population sizes, N_e, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is 0.43.

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