Rapid evolution of a skin-lightening allele in southern African KhoeSan

Abstract

Amhara or another group who themselves are substantially admixed with Near Eastern people has been proposed (13, 14). The second major migration brought Bantu-speaking populations practicing agriculture into southern Africa from central/western Africa, where they are now the demographic majority. Bantuspeaking populations have dark skin pigmentation derived from their equatorial origin (15). The dating of Bantu expansion into southern Africa varies between 1,500 y and 500 y ago, depending on the precise location within southern Africa. Finally, the Dutch East India Company established a refreshment station at present-day Cape Town in 1652; subsequently, Dutch and other European colonists expanded northward from the Cape into the Karoo and southern Kalahari, particularly after 1740 (16). Significance Skin pigmentation reflects strong local adaptation to latitude after humans migrated around the globe. In the Northern Hemisphere, the gene SLC24A5 plays a key role in the genetic basis of light skin pigmentation, where a nonsynonymous mutation in the gene has swept to fixation in contemporary Europeans. Although considered European-specific, we find this mutation at an unexpectedly high frequency in light-skinned KhoeSan from South Africa, far exceeding the European gene flow during colonial migration. Using haplotype analysis and comprehensive demographic modeling including positive selection, we show that this is an example of surprisingly strong adaptation of a recently introduced allele, via back-to-Africa migration, which occurred less than 2,000 y ago.