mtDNA variation in the South African Kung and Khwe - and their genetic relationships to other African populations

The mtDNA variation of 74 Khoisan-speaking individuals (Kung and Khwe) from Schmidtsdrift, in the Northern Cape Province of South Africa, was examined by high-resolution RFLP analysis and control region (CR) sequencing. The r esulting data were combined with published RFLP haplotype and CR sequence d ata from sub-Saharan African populations and then were subjected to phyloge netic analysis to deduce the evolutionary relationships among them. More th an 77% of the Kung and Khwe mtDNA samples were found to belong to the major mtDNA lineage, macrohaplogroup L* (defined by a HpaI site at nucleotide po sition 3592), which is prevalent in sub-Saharan African populations. Additi onal sets of RFLPs subdivided macrohaplogroup L* into two extended haplogro ups-L1 and L2-both of which appeared in the Kung and Khwe. Besides revealin g the significant substructure of macrohaplogroup L* in African populations , these data showed that the Biaka Pygmies have one of the most ancient RFL P sublineages observed in African mtDNA and, thus, that they could represen t one of the oldest human populations. In addition, the Kung exhibited a se t of related haplotypes that were positioned closest to the root of the hum an mtDNA phylogeny, suggesting that they, too, represent one of the most an cient African populations. Comparison of Kung and Khwe CR sequences with th ose from other African populations confirmed the genetic association of the Kung with other Khoisan-speaking peoples, whereas the Khwe were more close ly linked to non-Khoisan-speaking (Bantu) populations. Finally, the overall sequence divergence of 214 African RFLP haplotypes defined in both this an d an earlier study was 0.364%, giving an estimated age, for all African mtD NAs, of 125,500-165,500 years before the present, a dare that is concordant with all previous estimates derived from mtDNA and other genetic data, for the time of origin of modern humans in Africa.