The genetic prehistory of the Khoe and San

This paper focuses on the use of genetic markers, mitochondrial DNA (mtDNA) and Y chromosome DNA polymorphisms, in elucidating the prehistory of Khoe (herders) and San (hunter-gatherers) populations, often lumped together as Khoe-San. More specifically, we examine whether these genetic markers have the power of resolution to distinguish between the San and Khoe. After examining 179 individuals for mtDNA control region sequence variation (nucleotide positions 16024-16400) in five Khoe-San-speaking groups (35 !Kung, 33 Khwe, 45 !Xun, 29 Nama and 37 Damara) we found that the mtDNA haplogroup L0d/k was found at an overall frequency of 70.4 % in the combined sample, ranging in frequency between 60 and 90 % in San groups and found at a frequency of 90 % in the Nama (Khoe). The mtDNA data are strongly suggestive of a common matrilineal ancestry of the San and Khoe, with differences being introduced as a result of varying degrees of gene flow from other groups over time. The patterns of Y chromosome haplogroup variation based on the presence or absence of single nucleotide polymorphisms reveals a high degree of variation among the various Khoe-San groups (total sample 215 individuals). Using Y chromosome data gives a far more diverse picture of the Khoe and San gene pools than that painted by the mtDNA data. Haplogroups A-M23, A-M51, B-M112 and E-M35 could have been present in a common Khoe-San gene pool, with differences arising as a result of varying degrees of admixture from Bantu-speaking groups and sea-borne immigrants, and/or genetic drift. Given the level of mtDNA and Y chromosome haplogroup sharing between Khoe and San populations studied, we conclude that it is not possible to use mtDNA and Y chromosome variation to differentiate between the two groups. While there are archaeological and linguistic differences between these groups, the genetic data presented herein suggests an ancient common origin that predates their cultural and linguistic differences.