Genetic substructure and complex demographic history of South African Bantu speakers.

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.

Sex, disease and stigma in South Africa: historical perspectives.

This paper attempts to analyse historically why stigma and denial around HIV/AIDS is so powerful in South Africa, so powerful that ailing family members can be shunned and evicted. For many observers, the answer lies simply in its being a venereal disease, in its connotation with promiscuity and unregulated sexuality. We argue that this is not an adequate explanation. Pre-colonial African societies were relatively open about sexuality. Though pre-marital and adulterous pregnancy certainly caused social disruption, extra-marital sex per se was not stigmatised. Even the sexual shame introduced (unevenly) by Christianity and its hybridised forms is inadequate in explaining the degree of stigma associated with HIV/AIDS. We extend the discussion by exploring the stigma associated with various forms of pollution and the inevitability of death. The peculiarly interwoven mixture of sexual transgression, pollution and delayed death, we argue, makes HIV/AIDS an extraordinarily powerful generator of stigma.