Ancient west Eurasian ancestry in southern and eastern Africa

Abstract

(both pastoralists and agriculturalists), and a culturally diverse set of populations occupy the region today. Because written history was unavailable until recently in southern Africa, inferences about the migration patterns leading to the present distribution of populations have largely been informed by archaeology and linguistics. Genetic data are an additional source of information about population history, but extracting this information remains challenging. Studies of diversity in southern Africa have highlighted the influence of precolonial population admixture on the genetic structure of populations in the region (2–4) but have come to different conclusions about the historical scenarios that led to this admixture. In particular, although there is agreement that the arrival of Bantu-speaking agriculturalist populations had a major demographic impact in many populations, the importance of population movements from other parts of Africa or the world is unclear. Schlebusch et al. (2) argued for eastern African ancestry specifically in the Nama, a pastoralist population, and Pickrell et al. (3) raised this possibility not just for the Nama but for several Khoe-speaking populations. Identifying the sources of non-Khoisan ancestry in southern Africa could shed light on the historical processes that led to the extensive linguistic and cultural diversity of the region. Here, we develop techniques based on the extent of linkage disequilibrium to thoroughly examine the signal of admixture in the southern African Khoisan (defined here as indigenous populations speaking non-Bantu languages with click consonants, without implying cultural, linguistic, or genetic homogeneity of Khoisan 2632–2637 | PNAS | February 18, 2014 | vol. 111 | no. 7