The genetic prehistory of southern Africa

Abstract

Southern and eastern African populations that speak non-Bantu languages with click consonants are known to harbour some of the most ancient genetic lineages in humans, but their relationships are poorly understood. Here, we report data from 23 populations analysed at over half a million single-nucleotide polymorphisms, using a genome-wide array designed for studying human history. The southern African Khoisan fall into two genetic groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. We find that all individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began ∼1,200 years ago. In addition, the East African Hadza and Sandawe derive a fraction of their ancestry from admixture with a population related to the Khoisan, supporting the hypothesis of an ancient link between southern and eastern Africa.

The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists

“…Our results suggest instead that admixture started extensively at a later stage, well after the introduction of iron tools and plant cultivation and the subsequent rise of territorial chiefdoms, profoundly transforming the interactions between the two communities 15,42 . This slow, two-phased process of interactions greatly differs from that recently documented in Southern Africa 55 , where it appears to have been more rapid and different in its outcome. Indeed, as soon as agro-pastoralists reached the Kalahari desert B1,200 YBP 3,56,57 , their encounters with local Khoisan hunter-gatherers resulted in immediate genetic exchanges 55 but not in language shifts, as Khoisan groups have retained their own non-Bantu languages with click consonants.…”

“…This slow, two-phased process of interactions greatly differs from that recently documented in Southern Africa 55 , where it appears to have been more rapid and different in its outcome. Indeed, as soon as agro-pastoralists reached the Kalahari desert B1,200 YBP 3,56,57 , their encounters with local Khoisan hunter-gatherers resulted in immediate genetic exchanges 55 but not in language shifts, as Khoisan groups have retained their own non-Bantu languages with click consonants. Conversely, the long period of intimate interactions between RHG and AGR in Central Africa, owing to their socioeconomic and ecological interdependence 42 , was accompanied by complete language shifts in all RHG groups 33 .…”

Extensive Population Structure in San, Khoe, and Mixed Ancestry Populations from Southern Africa Revealed by 44 Short 5-SNP Haplotypes

“…These studies, however, were not representative of all the linguistic families and collectively only included two Juspeaking groups, namely, the Ju/'hoansi and the !Xun and one Khoe-speaking group, namely, the Khwe. Recently two independent studies described genetic results obtained from high-density genome-wide SNP-arrays, for an extensive collection of Khoe and San groups, representing all three main southern Khoisan linguistic divisions (Schlebusch et al, 2012, Pickrell et al, 2012. The current article present genetic results for 181 individuals that overlap with Khoe, San, Coloured and Bantuspeaking individuals from Schlebusch et al, (2012), an additional 102 individuals from these already mentioned population groups and 69 individuals from four other Pre-print version.…”

“…Some of the most divergent haplogroups known among modern humans, for mitochondrial DNA and the Ychromosome, are found commonly and at their highest frequencies in the Khoe-San people (Behar et al, 2008, Chen et al, 2000, Karafet et al, 2008, Knight et al, 2003, Naidoo et al, 2010, Schlebusch et al, 2009, Scozzari et al, 1999, Tishkoff et al, 2007, Underhill et al, 2001, Batini et al, 2011, Schlebusch et al, 2011. Additionally, in autosomal studies, San people group in a distinct cluster from that of Bantuspeakers (Cavalli-Sforza et al, 1994, Tishkoff et al, 2009, Li et al, 2008, Schlebusch et al, 2012, Pickrell et al, 2012.…”

Ancient DNA comes of age

“…The latest research has looked at nuclear autosomal DNA and has begun to provide data on admixture between populations and the impact of natural selection on specific genetic traits. [9][10][11][12] The 'Holy Grail' in ancient DNA work is now to extract this nuclear information from long dead southern African individuals and even possibly to generate a complete genome for a representative individual. I suspect that a publication announcing this feat will not be too far in the future.…”