Unraveling the complex maternal history of Southern African Khoisan populations

Abstract

The Khoisan populations of southern Africa are known to harbor some of the deepest-rooting lineages of human mtDNA; however, their relationships are as yet poorly understood. Here, we report the results of analyses of complete mtDNA genome sequences from nearly 700 individuals representing 26 populations of southern Africa who speak diverse Khoisan and Bantu languages. Our data reveal a multilayered history of the indigenous populations of southern Africa, who are likely to be the result of admixture of different genetic substrates, such as resident forager populations and pre-Bantu pastoralists from East Africa. We find high levels of genetic differentiation of the Khoisan populations, which can be explained by the effect of drift together with a partial uxorilocal/multilocal residence pattern. Furthermore, there is evidence of extensive contact, not only between geographically proximate groups, but also across wider areas. The results of this contact, which may have played a role in the diffusion of common cultural and linguistic features, are especially evident in the Khoisan populations of the central Kalahari.

Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries

“…The distribution of the five ancestries corresponds to: a northern Kalahari ancestry, central Kalahari ancestry, circum-Kalahari ancestry, a northwestern Namibian savannah ancestry, and ancestry from eastern Bantu speakers (Figure 2). This geographic patterning does not neatly correspond to linguistic or subsistence categories, in contrast to previous discussions (Pickrell et al 2012;Barbieri et al 2014).…”

“…Visualization of these ancestries according to geographic sampling location specifically demonstrates fine-scale structure in and around the Kalahari Desert ( Figure 2). While prior studies have argued for a northern vs. southern divergence of KhoeSan populations (Pickrell et al 2012;Schlebusch and Soodyall 2012;Barbieri et al 2013Barbieri et al , 2014, the structure inferred from our data set indicates a more geographically complex pattern of divergence and gene flow. Even recent migration events into southern Africa remain structured, consistent with ecological boundaries to gene flow (see below).…”

Prehistoric Bantu-Khoisan language contact

“…In southern Africa, most Khoisan-speaking populations are characterized by high frequencies of specific mtDNA and Y-chromosome haplogroups, which are otherwise found only in populations that are very likely to have been in intimate contact with Khoisan-speaking groups (Wood et al, 2005;Behar et al, 2008;Soodyall et al, 2008;Barbieri et al, 2013b;Barbieri et al, 2014a;Barbieri et al, 2014b). The mtDNA haplogroups that are characteristic of Khoisanspeaking populations are labelled L0d and L0k, the Y-chromosomal ones are A2, A3b1, and B2b.…”

“…2, Table 2 bottom). For example, the Kgalagadi have the highest frequency of haplogroup L0d recorded to date in any Bantu-speaking population (53%; Barbieri et al, 2014a) as well as carrying 15% autochthonous paternal lineages (Bajić et al, in preparation), but clicks in this language are extremely marginal, occurring in only one or two words depending on the variety17 (van der Merwe and Schapera, 1943;Dickens, 1986). Similarly, the frequency of Khoisan mtDNA lineages in the Tswana and Kalanga (30% and 35%, respectively) is comparable to that found in the groups we here call seb, and the frequency of haplogroups L0d and L0k in the Shanjo is on a par with that in the Mbukushu-and yet the Tswana, Kalanga and Shanjo do not speak languages with click consonants.…”

Ancient DNA comes of age, but still has some teenage problems

“…8 This hive of African DNA analysis does not even include a wider range of research on the genetic lineages of living African peoples in search of the elusive point of divergence of our ancestors from the Neanderthals and other archaic populations and the subsequent divergence of populations in Africa. [9][10][11][12][13][14] But there are problems. This rush to extract the secrets of ancient DNA in Africa has presented the curators of the collections of archaeological skeletons with ethical issues because the research requires the destruction of human bone.…”