Open Access Preprint
The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. Genetic studies (mitochondrial DNA and Y-chromosome) conducted on San and Khoe groups revealed that they harbour some the most divergent lineages found in living peoples throughout the world. Recently, high-density autosomal SNP-array studies confirmed the early divergence of Khoe-San population groups from all other human populations. The present study made use of 220 autosomal SNP markers, in the format of both haplotypes and genotypes, to examine the population structure of various San and Khoe groups and their relatedness to other neighbouring groups. While analyses based on the genotypic SNP data only supported the division of the included populations into three main groups, Khoe-San, Bantu-spe kers and non- African populations, haplotype analyses revealed finer structure within Khoe-San populations. Through using only 44 short SNP haplotypes (compiled from a total of 220 SNPs), most of the Khoe-San groups could be resolved as separate groups by applying STRUCTURE analyses. Therefore, by carefully selecting a few SNPs and combining them into haplotypes, we were able to achieve the same level of population distinction as achieved previously in high-density SNP studies on the same population groups. Using haplotypes proved to be a very efficient and cost-effective way to study population structure.
Schlebusch, Carina M. and Soodyall, Himla, "Extensive Population Structure in San, Khoe and Mixed Ancestry Populations from Southern Africa Revealed by 44 Short 5-SNP Haplotypes" (2012). Human Biology Open Access Pre-Prints. Paper 26.