To assess the evidence for widespread local adaptation influencing non-synonymous mutations we considered the distribution of integrated extended haplotype homozygosity (iEHH) statistics9,44 (Fig. 6c). We find no evidence for systematic differences between non-synonymous and synonymous SNPs, suggesting that local adaptation does not explain their higher differentiation. Although hitch-hiking effects will tend to obscure differences between selected and neutral SNPs, these results are consistent with a scenario in which the higher differentiation of non-synonymous SNPs is primarily driven by a reduction in the strength or efficacy of purifying selection in non-African populations.
