FIG. 4.—

PTCs are more derived than nonsynonymous polymorphisms. We classified each PTC and SCL allele as recently derived in the Raleigh, NC, population (red) or the Malawi population (blue); shared by the two Drosophila melanogaster populations (violet); or shared with Drosophila simulans (green). The number of alleles sampled is shown for each branch (branch lengths are not to scale). The outgroup alleles (D. yakuba and D. erecta) allowed us to determine whether the current D. melanogaster major or minor allele was likely ancestral (side panel minor/major). Almost half of the alleles could not be categorized due to a lack of sequencing/alignment data from one or more species (“Missing data”) or because it was unclear whether the minor or major allele was ancestral (“Ambiguous history”). Pie charts show the proportion of alleles in each described age category for PTCs, SCLs, nonsynonymous SNPs, and synonymous SNPs.