  Rapid adaptation has been observed in numerous organisms in response to
selective pressures, such as the application of pesticides and the presence of
pathogens. When rapid adaptation is driven by rare alleles from the standing
genetic variation or by a high population rate of de novo adaptive mutation,
positive selection should commonly generate soft rather that hard selective
sweeps. In a soft sweep, multiple adaptive haplotypes sweep through the
population simultaneously, in contrast to hard sweeps in which only a single
adaptive haplotype rises to high frequency. Current statistical methods were
not designed to detect soft sweeps, and are therefore likely to miss these
possibly numerous adaptive events. Here, we develop a statistical test (H12)
based on haplotype homozygosity that is capable of detecting both hard and soft
sweeps with similar power. We use H12 to identify multiple genomic regions that
have undergone recent and strong adaptation in a population sample of fully
sequenced Drosophila melanogaster strains from the Drosophila Genetic Reference
Panel (DGRP). Visual inspection of the top 50 peaks revealed that multiple
haplotypes are at high frequency, consistent with signatures of soft sweep. We
developed a second statistic (H2/H1) that is sensitive to signatures common to
soft sweeps but not hard sweeps, in order to determine whether sweeps detected
by H12 can be more easily generated by hard versus soft sweeps. Surprisingly,
we find that the H12 and H2/H1 values for all top 50 peaks are more easily
generated by soft sweeps than hard sweeps under several evolutionary scenarios.
