ABSTRACT
Selective sweeps are thought to play a significant role in shaping patterns of variability across genomes; accurate predictions of their effects are, therefore, important for understanding these patterns. A commonly used model of selective sweeps assumes that coalescent events that occur during a sweep can be neglected, leading to simple expressions for the effects of sweeps on pairwise nucleotide site diversities and site frequency spectra. It is shown here that there is a significant probability that a pair of alleles sampled at the end of a sweep coalesce during the sweep. In the case of a favorable mutation with intermediate dominance, this probability is approximately equal to 0.135 in the absence of recombination. Expressions are derived for the expected reductions in pairwise neutral diversities caused by both single and recurrent sweeps in the presence of within-sweep coalescence, although the effects of multiple recombination events during a sweep are only treated heuristically. The accuracies of the resulting expressions were checked against the results of simulations. For high ratios of the recombination rate to the selection coefficient, the approximation that neglects within-sweep coalescence can be inaccurate by several orders of magnitude. The selection model used here can be applied to favorable mutations with arbitrary dominance coefficients, to sex-linked loci with sex-specific selection coefficients, and to inbreeding populations. Using the results from this model, the expected differences in levels of variability on X chromosomes and autosomes under selection at linked sites are discussed, and compared with data on a population of Drosophila melanogaster.
