Estimation of 2Nes from temporal allele frequency data.

Bollback JP, York T & Nielsen R

(2008) Genetics 179, 497?502.

We develop a new method for estimating effective population sizes, Ne , and selection coef?cients, 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 coef?cients acting on the CCR5- ?32 mutation based on published samples of contemporary and ancient human DNA. We show that the data is 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 coef?cient acting on a mutation segregating in an experimental phage population. We show that the selection coef?cient acting on this mutation is approximately 0.43.

Andrew Rambaut, 2007