Year: 2011
Type: dissertation
Study design: Observational Study
Abstract: The San and Khoe people currently represent remnant groups of a much larger and widely \ndistributed population of hunter gatherers and cattle herders, respectively, who had \nexclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the \npast 1,200 years and sea-borne immigrants within the last 350 years. This project made \nuse of mitochondrial DNA (mtDNA), Y-chromosome DNA and autosomal DNA markers to \nexamine the population structure of various San and Khoe groups and to reconstruct their \nprehistory. The groups included in the study consists of six different Khoe-San groups \n(‡Khomani, Nama, Khwe, !Xun, /Gui + //Gana + Kgalagari and Ju\\’hoansi), four different \nColoured groups and five other population groups that were included in the comparative \nanalysis. \nFor the mtDNA study a minisequencing technique was successfully developed which \nallowed the assignment of mtDNA lineages into the 10 global mtDNA macro-haplogroups. \nHaplogroups were further resolved using control region sequence data obtained from both \nhypervariable regions (HVR I and HVR II). Using this approach 538 individuals (both males \nand females) were screened and their mtDNA types were resolved into 18 haplogroups \nencompassing 245 unique haplotypes. In addition, 353 males were examined for Ychromosome \nDNA variation using 46 bi-allelic Y-chromosome markers and 12 Y-STR \nmarkers. The Y-chromosomes in the sample were assigned into 29 haplogroups (using biallelic \nvariation) following the nomenclature initially recommended by the Y-chromosome \nConsortium and resolved into 268 unique haplotypes (Y-STR variation). To assess the \nlevel of autosomal variation, 220 genome wide autosomal SNPs were typed in 352 \nindividuals. These SNPs were combined in different datasets and analysed using two \ndifferent approaches allowing for genotype and haplotype analyses. Data from these three \nmarker systems were analysed using different analytical methods (distance based \nphylogenetic analysis, network analysis, dating of lineages, principal components analysis, \nphylogeographic analysis, AMOVA analysis, population structure analysis, and population \ngenetic summary statistics) to asses the ancestral associations and the genetic affinities of \nthe various San, Khoe and Coloured populations. \nThe most striking observation from this study was the high frequencies of the oldest \nmtDNA haplogroups (L0d and L0k) and Y-chromosome haplogroups (haplogroups A and \nB) found in Khoe-San and Coloured groups. The sub-haplogroups were, however, \ndifferentially distributed in the different Khoe-San and Coloured groups which suggested \ndifferent demographic histories. \nThe current distribution of Khoe-San groups comprises a wide geographic region extending \nfrom southern Angola in the north to the Cape Province (South Africa) in the south. \nLinguistically Khoe-San groups are also divided into northern Khoisan-speaking groups (Ju \ndivision) and southern Khoisan-speaking groups (Tuu division) with an additional linguistic \ngroup (Khoe) associated with some Khoe-speaking San groups in Botswana and the Khoe \nherders of South Africa and Namibia (such as the Nama). For all three genetic marker \nsystems, northern groups (Ju speaking - !Xun, Ju\\’hoansi and Khoe-speaking San - /Gui + \n//Gana) grouped into one cluster and southern groups (historically Tuu speaking - \n‡Khomani and Coloured groups) grouped into a second cluster with the Khoe group \n(Nama) clustering with the southern Khoe-San and Coloured groups. \nThe Khwe genetic profile was very different from the other Khoe-San groups. Although high \nproportions of Bantu-speaking admixture were identified in the Khwe group, they also \ncontained a unique distribution of other mtDNA and Y-chromosome lineages. A previously \npublished theory suggested that, based on the presence of a specific E-M35 Ychromosome \nhaplotype, the Khwe might be descendants of an east African pastoralist \ngroup that introduced the pastoralist culture to a region located in the present day northern \nBotswana. This pattern also mirrors what archaeologists have found with respect to the \nintroduction of pastoralism to southern Africa. The theory was further supported and \nelaborated on in the present thesis. Considering the frequency and distribution of E-M35, \nthe highest frequency (46%) was found in the Khwe with a present-day distribution in \nnorthern Botswana and southern Angola while a decrease in frequency is observed \ntowards the south with low frequencies (<10%) in the Karoo Coloured groups. Conversely, \nnone of the mtDNA (female) L0k and L0d lineages observed in the Khwe group were \nobserved in the southern Khoe-San and Coloured groups. From these observations a \ntheory was proposed that after introduction into the region of northern Botswana, the \nsouthwards spread of pastoralism was not a clear-cut demic or cultural diffusion. Rather \nsome male individuals integrated with the southern tribes and took with them the pastoralist \npractice and likely also their Khoe-language. \nAltogether this thesis presented new insights into the multifaceted demographic history that \nshaped the existing genetic landscape of the Khoe-San and Coloured populations of \nsouthern Africa.
Author: Carina M. Schlebusch
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2238147730