Genome-Wide Analysis of Long-Term Evolutionary Domestication in Drosophila melanogaster

Consistent directional selection applied to populations across multiple generations is expected to produce genome-wide reduction in sequence polymorphism. Our goal was to test this hypothesis using five replicate populations of Drosophila melanogaster that have been subjected to over 900 generations of laboratory domestication. To this end, we sampled and sequenced pools of individuals from each of these populations. The resulting sequence data were then aligned to a reference genome, SNPs were identified, and their frequencies were estimated for each population. Measures of sequence polymorphism were then made across the genome, with sequence data from generation zero of another another D. melanogaster domestication experiment serving as a baseline. Several major dips in heterozygosity were found throughout the genome, many of which were consistent across all five replicates. These localized losses of heterozygosity are consistent with patterns associated with adaptation via selective sweeps. However, we found no regions where heterozygosity was completed depleted in the manner indicative of hard sweeps, thereby suggesting laboratory adaptation may have proceeded through soft sweeps stemming from selection on standing genetic variation. Lastly, despite these depressions, we found that the populations were generally not genetically depauperate.  A surprising fact given the moderate Ne estimates (~1000) for these populations.  If the only evolutionary processes acting on these  populations were selective sweeps, background selection, and genetic drift, then it seems odd that such extensive genetic variation would be maintained. We believe that this suggests that some type(s) of balancing selection is at work sustaining genetic diversity in these populations.