Abstract
BackgroundThe current San and Khoe populations are remnant groups of a much larger and widely dispersed population of hunter-gatherers and pastoralists, who had exclusive occupation of southern Africa before the influx of Bantu-speakers from 2 ka (ka = kilo annum [thousand years] old/ago) and sea-borne immigrants within the last 350 years. Here we use mitochondrial DNA (mtDNA) to examine the population structure of various San and Khoe groups, including seven different Khoe-San groups (Ju/’hoansi, !Xun, /Gui+//Gana, Khwe, ≠Khomani, Nama and Karretjie People), three different Coloured groups and seven other comparative groups. MtDNA hyper variable segments I and II (HVS I and HVS II) together with selected mtDNA coding region SNPs were used to assign 538 individuals to 18 haplogroups encompassing 245 unique haplotypes. Data were further analyzed to assess haplogroup histories and the genetic affinities of the various San, Khoe and Coloured populations. Where possible, we tentatively contextualize the genetic trends through time against key trends known from the archaeological record.ResultsThe most striking observation from this study was the high frequencies of the oldest mtDNA haplogroups (L0d and L0k) that can be traced back in time to ~100 ka, found at high frequencies in Khoe-San and sampled Coloured groups. Furthermore, the L0d/k sub-haplogroups were differentially distributed in the different Khoe-San and Coloured groups and had different signals of expansion, which suggested different associated demographic histories. When populations were compared to each other, San groups from the northern parts of southern Africa (Ju speaking: !Xun, Ju/’hoansi and Khoe-speaking: /Gui+//Gana) grouped together and southern groups (historically Tuu speaking: ≠Khomani and Karretjie People and some Coloured groups) grouped together. The Khoe group (Nama) clustered with the southern Khoe-San and Coloured groups. The Khwe mtDNA profile was very different from other Khoe-San groups with high proportions of Bantu-speaking admixture but also unique distributions of other mtDNA lineages.ConclusionsOn the whole, the research reported here presented new insights into the multifaceted demographic history that shaped the existing genetic landscape of the Khoe-San and Coloured populations of southern Africa.
Highlights
The current San and Khoe populations are remnant groups of a much larger and widely dispersed population of hunter-gatherers and pastoralists, who had exclusive occupation of southern Africa before the influx of Bantu-speakers from 2 ka and sea-borne immigrants within the last 350 years
By examining the mitochondrial DNA (mtDNA) variation in several San and Khoe groups from different regions in southern Africa as well as three selected Coloured groups from South Africa, we provide insight into how females have contributed to the genetic affinities of the Khoe-San and some Coloured groups, as well as an opportunity to further examine the evolutionary history of mtDNA haplogroups L0d and L0k
The 538 samples used in mtDNA analysis (Table 1, Additional file 2: Figure S1) were first classified into macro-haplogroups using a minisequencing method, and finer scale classification was achieved by analyzing HVS-I and II sequences
Summary
The term “Khoe-San” represents groups with two distinct lifeways, the Khoi (old Nama word) or Khoe (modern Nama word), who were traditionally the pastoralist groups and the San, which included the hunter-gatherer groups [1,2] This grouping was made according to the conventional division that existed between hunter-gatherers and pastoralists at the time of colonization. The current distribution of Khoe-San groups comprises a wide geographic region from southern Angola in the north to the Western Cape Province (South Africa) in the south. They live among, and to some extent are admixed with, the various surrounding Bantu-speaking populations [3,5,6]. Khoe-San groups are divided into northern Khoisan-speaking groups (Ju division) and southern Khoisan-speaking groups (Tuu division) with an additional linguistic group (Khoe-Kwadi) associated with some Khoe-speaking San groups in Botswana and the Khoe herders of South Africa and Namibia (such as the Nama) [7,8]
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