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Sengupta D, Choudhury A, Fortes-Lima C, Aron S, Whitelaw G, Bostoen K, Gunnink H, Chousou-Polydouri N, Delius P, Tollman S, Gómez-Olivé FX, Norris S, Mashinya F, Alberts M, AWI-Gen Study , H3Africa Consortium , Hazelhurst S, Schlebusch CM, Ramsay M
Nat Commun 12 (1) 2080 [2021-04-07; online 2021-04-07]
South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.
PubMed 33828095
DOI 10.1038/s41467-021-22207-y
Crossref 10.1038/s41467-021-22207-y
pmc: PMC8027885
pii: 10.1038/s41467-021-22207-y