The genetic basis of evolutionary change in Drosophila melanogaster with accelerated development

Relatively little is known about the molecular population genetics of adaptation across the entire genome of sexual species. Here we present whole-genome resequencing data from Drosophila melanogaster populations that have undergone 600 generations of laboratory selection for accelerated development. Based on 688,520 intermediate frequency high quality single nucleotide polymorphisms (SNPs), we identify several dozen genomic regions that show strong allele-frequency differentiation in response to selection. Observed patterns of heterozygosity are inconsistent with selection response being due to newly arising unconditionally advantageous mutations unless per locus selection coefficients are generally less than 0.1 – 1%. If per locus selection coefficients are generally larger than 1%, then “soft sweeps” starting from standing variation more parsimoniously explain the data. We show that differentiated nonsynonymous SNPs implicate genes affecting imaginal disc development, morphogenesis, and metamorphosis in the response to selection. Our results demonstrate that whole-genome resequencing of experimentally-evolved sexually reproducing populations can provide a powerful tool for probing the genomics of development.