Some common variants show strong differentiation between populations within ancestry-based groups (Table S12), many of which are likely to have been driven by local adaptation either directly or through hitch-hiking. For example, the strongest differentiation between AFR populations is in NRSF transcription-factor peak (PANC1-cell-line)13 upstream of ST8SIA1 (difference in derived allele frequency LWK-YRI of 0.475 at rs7960970), whose product is involved in ganglioside generation14. Overall, we find a range of 17-343 SNPs (fewest = CEU-GBR, most = FIN-TSI) showing a difference in frequency of at least 0.25 between pairs of populations within an ancestry-group.
