Analysis of the small set of variants with large frequency differences between closely related populations can identify targets of recent, localized adaptation. We used the FST-based population branch statistic (PBS)16 to identify genes with strong differentiation between pairs of populations in the same continental group (Fig. 3b). This approach reveals a number of previously identified selection signals (such as SLC24A5 associated with skin pigmentation17, HERC2 associated with eye colour18, LCT associated with lactose tolerance, and the FADS cluster that may be associated with dietary fat sources19). Several potentially novel selection signals are also highlighted (such as TRBV9, which appears particularly differentiated in South Asia, PRICKLE4, differentiated in African and South Asian populations, and a number of genes in the immunoglobulin cluster, differentiated in East Asian populations; Extended Data Fig. 8), although at least some of these signals may result from somatic rearrangements (for example, via V(D)J recombination) and differences in cell type composition among the sequenced samples. Nonetheless, the relatively small number of genes showing strong differentiation between closely related populations highlights the rarity of strong selective sweeps in recent human evolution20.
