Estimation of 2Nes From Temporal Allele Frequency Data Journal Article

Author(s): Bollback, Jonathan P; York, Thomas L; Nielsen, Rasmus
Article Title: Estimation of 2Nes From Temporal Allele Frequency Data
Abstract: We develop a new method for estimating effective population sizes, Ne, 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-Δ32 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.
Keywords: Population Density; Selection, Genetic; Humans; Models, Genetic; Mutation/genetics; Genetics, Population; Gene Frequency; Levivirus/genetics; Receptors, CCR5/genetics; Substances; Receptors, CCR5
Journal Title: Genetics
Volume: 179
Issue 1
ISSN: 0016-6731
Publisher: Genetics Society of America  
Date Published: 2008-05-01
Start Page: 497
End Page: 502
DOI: 10.1534/genetics.107.085019
Open access: yes (repository)