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Originally published as Genetics Published Articles Ahead of Print on December 15, 2005.
Genetics, Vol. 172, 1967-1978, March 2006, Copyright © 2006
doi:10.1534/genetics.105.048447
Allele Frequency Distribution Under Recurrent Selective Sweeps
Yuseob Kim1
Department of Biology, University of Rochester, Rochester, New York 14620
1 Address for correspondence: Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301.
E-mail: yuseob.kim{at}asu.edu
The allele frequency of a neutral variant in a population is pushed either upward or downward by directional selection on a linked beneficial mutation ("selective sweeps"). DNA sequences sampled after the fixation of the beneficial allele thus contain an excess of rare neutral alleles. This study investigates the allele frequency distribution under selective sweep models using analytic approximation and simulation. First, given a single selective sweep at a fixed time, I derive an expression for the sampling probabilities of neutral mutants. This solution can be used to estimate the time of the fixation of a beneficial allele from sequence data. Next, I obtain an approximation to mean allele frequencies under recurrent selective sweeps. Under recurrent sweeps, the frequency spectrum is skewed toward rare alleles. However, the excess of high-frequency derived alleles, previously shown to be a signature of single selective sweeps, disappears with recurrent sweeps. It is shown that, using this approximation and multilocus polymorphism data, genomewide parameters of directional selection can be estimated.
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