Soft selective sweeps are the primary mode of recent adaptation in Drosophila melanogaster
Nandita R. Garud, Philipp W. Messer, Erkan O. Buzbas, Dmitri A. Petrov
(Submitted on 5 Mar 2013)
Adaptation is often thought to leave the signature of a hard selective sweep, in which a single haplotype bearing the beneficial allele reaches high population frequency. However, an alternative and often-overlooked scenario is that of a soft selective sweep, in which multiple adaptive haplotypes sweep through the population simultaneously. Soft selective sweeps are likely either when adaptation proceeds from standing genetic variation or in large populations where adaptation is not mutation-limited. Current statistical methods are not well designed to test for soft sweeps, and thus are likely to miss these possibly numerous adaptive events because they look for characteristic reductions in heterozygosity. Here, we developed a statistical test based on a haplotype statistic, H12, capable of detecting both hard and soft sweeps with similar power. We used H12 to identify multiple genomic regions that have undergone recent and strong adaptation using a population sample of fully sequenced Drosophila melanogaster strains (DGRP). We then developed a second statistical test based on a statistic H2/H1 | H12, to test whether a given selective sweep detected by H12 is hard or soft. Surprisingly, when applying the test based on H2/H1 | H12 to the top 50 most extreme H12 candidates in the DGRP data, we reject the hard sweep hypothesis in every case. In contrast, all 50 cases show strong support (Bayes Factor >10) for a soft sweep model. Our results suggest that recent adaptation in North American populations of D. melanogaster has led primarily to soft sweeps either because it utilized standing genetic variation or because the short-term effective population size in D. melanogaster is on the order of billions or larger.