Abstract
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.
Highlights
South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa
The distribution of the SEB groups on the Principal Component (PC) plot largely mirrors the linguistic majority areas (LMAs) of these groups on the South African map (Fig. 1a, b) suggesting a correlation between genetic variation and geography
These recent admixtures could result in incomplete boundaries observed between the SEB groups in the PC plot
Summary
South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Three sets of migration events have dramatically reshaped the genetic landscape of this geographic region in the last two millennia The first of these was a relatively small scale migration of East African pastoralists, who introduced pastoralism to Southern Africa ~2 kya[4,5,6,7]. The third major movement into Southern Africa was during the colonial era in the last four centuries when European colonists settled the area During this period slave trade introduced additional intercontinental gene flow giving rise to complex genomic admixture patterns in current-day Southern African populations[20,21,22,23]. The eight SEB groups have very specific geographic distributions of linguistic majority areas (LMAs) within the country, for our study they were sampled at three sites; Soweto (SWT) in Gauteng, Agincourt (AGT) in Mpumalanga, and Dikgale (DKG) in Limpopo province (Table 1 and Fig. 1a)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
