Venda and Tsonga tend to be seen as independent linguistic entities 24, 25, 26, 27. Within these nine languages two large subclusters are traditionally distinguished: Nguni (including Zulu, Xhosa, Swazi, and Ndebele) and Sotho-Tswana (including Sotho, Tswana, and Pedi). South Africa has 11 official languages of which nine are Bantu languages belonging to this family’s South-Eastern branch. 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 third major movement into Southern Africa was during the colonial era in the last four centuries when European colonists settled the area. These archaeologically distinct groups gradually spread across present-day South Africa, interacting to various degrees with the Khoe-San groups, eventually giving rise to South Africa’s diverse BS communities. The earliest communities spread along the East coast to reach the KwaZulu-Natal South coast by the mid-fifth century AD while the final major episode of settlement is estimated to be around AD 1350 18, 19. The archaeological record suggests that ancestors of the current-day BS populations undertook different waves of migration instead of a single large-scale movement 15, 16, 17. The introduction of pastoralism in the region was closely followed by the arrival of the second set of migrants i.e., the Bantu-speaking (BS) agro-pastoralists. While Khoe-San groups are distributed over a large geographic area today (spanning the Northern Cape Province of South Africa, large parts of Namibia, Botswana, and Southern Angola), these groups are scattered, small, and marginalised 13, 14. Today, Southern African Khoe and San populations collectively refer to hunter-gatherer (San) and herder (Khoekhoe) communities. This population was subsequently assimilated by local Southern African San hunter-gatherer groups, forming a new population that was ancestral to the Khoekhoe herder populations 8, 9, 10, 11, 12. 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. Three sets of migration events have dramatically reshaped the genetic landscape of this geographic region in the last two millennia. The sarchaeological record and rock art evidence trace the presence of San-like hunter-gatherer culture in Southern Africa to at least 20–40 thousand years ago (kya) 1, 2, 3. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa. The comparisons with five Iron Age farmer genomes further support genetic continuity over ~400 years in certain regions of the country. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. 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). Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Nature Communications volume 12, Article number: 2080 ( 2021) Genetic substructure and complex demographic history of South African Bantu speakers
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