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

Schlebusch, Carina M.; Soodyall, Himlya

doi:10.3378/027.084.0603

Cited by 14 publications

(8 citation statements)

References 59 publications

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“…Excluding H22, the oldest lineages H19–H21 and H17 belong to Khoe-San from South-Africa and Namibia, consistent with Khoe-San representing the oldest of all extant populations [68]-[73]. Our results are in line with earlier evidence from uniparentally transmitted markers [24], [74]–[77] and from microsatellite data [20].…”

Section: Discussionsupporting

confidence: 90%

X-Linked MTMR8 Diversity and Evolutionary History of Sub-Saharan Populations

et al. 2013

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The genetic diversity within an 11 kb segment of the MTMR8 gene in a sample of 111 sub-Saharan and 49 non-African X chromosomes was investigated to assess the early evolutionary history of sub-Saharan Africans and the out-of-Africa expansion. The analyses revealed a complex genetic structure of the Africans that contributed to the emergence of modern humans. We observed partitioning of two thirds of old lineages among southern, west/central and east African populations indicating ancient population stratification predating the out of Africa migration. Age estimates of these lineages, older than coalescence times of uniparentally inherited markers, raise the question whether contemporary humans originated from a single population or as an amalgamation of different populations separated by years of independent evolution, thus suggesting a greater antiquity of our species than generally assumed. While the oldest sub-Saharan lineages, ∼500 thousand years, are found among Khoe-San from southern-Africa, a distinct haplotype found among Biaka is likely due to admixture from an even older population. An East African population that gave rise to non-Africans underwent a selective sweep affecting the subcentromeric region where MTMR8 is located. This and similar sweeps in four other regions of the X chromosome, documented in the literature, effectively reduced genetic diversity of non-African chromosomes and therefore may have exacerbated the effect of the demographic bottleneck usually ascribed to the out of Africa migration. Our data is suggestive, however, that a bottleneck, occurred in Africa before range expansion.

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Section: Discussionsupporting

confidence: 90%

X-Linked MTMR8 Diversity and Evolutionary History of Sub-Saharan Populations

et al. 2013

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“…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).…”

Section: Resultscontrasting

confidence: 75%

“…New genetic data indicate that there is deep population divergence even among KhoeSan groups (Pickrell et al 2012;Schlebusch et al , 2013Schlebusch and Soodyall 2012;Barbieri et al 2013), with populations living in the northern Kalahari estimated to have split from southern groups 30,000-35,000 years ago (Pickrell et al 2012;Schlebusch and Soodyall 2012). Pickrell et al (2012) estimate a time of divergence between the northwestern Kalahari and southeastern Kalahari population dating back to 30,000 years ago; "northwestern" refers to Juu-speaking groups like the !Xun and Ju|'hoansi, while "southeastern" refers to Taa speakers.…”

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confidence: 99%

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

et al. 2016

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Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until 2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genomewide polymorphism data and whole mitochondrial genomes for .100 South Africans from the 6 ¼Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking 6 ¼Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, 14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.

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“…The most dominant contribution to the Afrikaner population came from European immigrants ( [9,30,31] and Additional file 1: Supplementary Text), whereas the Coloured population has more diverse ancestries [34][35][36][37][38][39][40][41][42][43]. The colonization of southern Africa started in 1652 when the Dutch East India Company (DEIC) established a refreshment station at the Cape of Good Hope (Cape Town today).…”

Section: Introductionmentioning

confidence: 99%

Patterns of African and Asian admixture in the Afrikaner population of South Africa

et al. 2020

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Background: The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured populations of South Africa. Differences in ancestry, social class, culture, sex ratio and geographic structure led to distinct and characteristic admixture patterns in the Afrikaner and Coloured populations. The Afrikaner population has a predominant European composition, whereas the Coloured population has more diverse ancestries. Genealogical records previously estimated the contribution of non-Europeans into the Afrikaners to be between 5.5 and 7.2%. Results: To investigate the genetic ancestry of the Afrikaner population today (11-13 generations after initial colonization), we genotyped approximately five million genome-wide markers in 77 Afrikaner individuals and compared their genotypes to populations across the world to determine parental source populations and admixture proportions. We found that the majority of Afrikaner ancestry (average 95.3%) came from European populations (specifically northwestern European populations), but that almost all Afrikaners had admixture from non-Europeans. The non-European admixture originated mostly from people who were brought to South Africa as slaves and, to a lesser extent, from local Khoe-San groups. Furthermore, despite a potentially small founding population, there is no sign of a recent bottleneck in the Afrikaner compared to other European populations. Admixture amongst diverse groups from Europe and elsewhere during early colonial times might have counterbalanced the effects of a small founding population. Conclusions: While Afrikaners have an ancestry predominantly from northwestern Europe, non-European admixture signals are ubiquitous in the Afrikaner population. Interesting patterns and similarities could be observed between genealogical predictions and our genetic inferences. Afrikaners today have comparable inbreeding levels to currentday European populations.

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

Cited by 14 publications

References 59 publications

X-Linked MTMR8 Diversity and Evolutionary History of Sub-Saharan Populations

X-Linked MTMR8 Diversity and Evolutionary History of Sub-Saharan Populations

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

Patterns of African and Asian admixture in the Afrikaner population of South Africa

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