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doi:10.1534/genetics.105.048447
A more recent version of this article appeared on March 1, 2006.
REGULAR RESEARCH PAPERS |
Allele frequency distribution under recurrent selective sweeps
Yuseob Kim 1*
1 University of Rochester
* To whom correspondence should be addressed. E-mail: ykim{at}mail.rochester.edu.
Submitted on July 18, 2005
Revised on October 1, 2005
Accepted on 29 November 2005
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 multi-locus polymorphism data, genome-wide parameters of directional selection can be estimated.
Key Words: diffusion approximation, frequency spectrum, hitchhiking, positive seletion, selective sweeps
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