The fraction of neutral mutations and adaptive divergence estimated from diversity and divergence in D. melanogaster.

Average pairwise diversity (π) and divergence (K) per site are from [26]. An estimate of the fraction of neutral mutations, f, was obtained from equation 3, assuming that the expected neutral diversity, π0, is equal to the average π at synonymous sites. An estimate of the fraction of adaptive divergence, α, was obtained from equation 4 and averages of π and K across loci.