Selective sweep
The pattern of genetic variation across the genome of Drosophila is consistent with frequent "selective sweeps" in which new favorable mutations become incorporated into the species so quickly that linked alleles undergo "hitchhiking" and also become fixed. Because of the hitchhiking of linked genes, it is generally difficult to identify the target of any selective sweep. We have identified a putative selective sweep in D. simulans in a region of chromosome 3 containing three closely linked paralogous genes (janusA, janusB and ocnus). In a sample of eight alleles from a worldwide distribution we found that, in a 1.7-kb region containing the janA and janB genes, 30 out of 31 segregating sites contained variants present only once in the sample, and 29 of these unique variants were found in the same allele. A restriction survey of an additional 28 lines of D. simulans revealed strong linkage disequilibrium over the janA-janB region and identified six more alleles matching the rare haplotype. Among the rare alleles, the level of DNA sequence variation was typical for D. simulans autosomal genes and showed no departure from neutrality. In addition, the rare haplotype was more similar to the D. melanogaster sequence, indicating that it was the ancestral form. These results suggest that the derived haplotype has risen to high worldwide frequency relatively recently, most likely as a result of natural selection.