mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations

Abstract

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 resulting data were combined with published RFLP haplotype and CR sequence data from sub-Saharan African populations and then were subjected to phylogenetic analysis to deduce the evolutionary relationships among them. More than 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 position 3592), which is prevalent in sub-Saharan African populations. Additional sets of RFLPs subdivided macrohaplogroup L* into two extended haplogroups-L1 and L2-both of which appeared in the Kung and Khwe. Besides revealing the significant substructure of macrohaplogroup L* in African populations, these data showed that the Biaka Pygmies have one of the most ancient RFLP sublineages observed in African mtDNA and, thus, that they could represent one of the oldest human populations. In addition, the Kung exhibited a set of related haplotypes that were positioned closest to the root of the human mtDNA phylogeny, suggesting that they, too, represent one of the most ancient African populations. Comparison of Kung and Khwe CR sequences with those from other African populations confirmed the genetic association of the Kung with other Khoisan-speaking peoples, whereas the Khwe were more closely linked to non-Khoisan-speaking (Bantu) populations. Finally, the overall sequence divergence of 214 African RFLP haplotypes defined in both this and an earlier study was 0.364%, giving an estimated age, for all African mtDNAs, of 125,500-165,500 years before the present, a date that is concordant with all previous estimates derived from mtDNA and other genetic data, for the time of origin of modern humans in Africa.

Prehistoric and historic traces in the mtDNA of Mozambique: insights into the Bantu expansions and the slave trade

“…A schematic phylogeny of African haplogroups used in our classification of sequences from Mozambique. We have drawn on information from Watson et al (1997), Chen et al (2000) (although our naming scheme is different from theirs), Alves-Silva et al (2000), , Ingman et al (2000), Bandelt et al (in press) and also on some unpublished information. Triangles represent wellcharacterized clades in the mtDNA phylogeny.…”

“…Several studies of restriction-fragment length polymorphisms (RFLPs) (Cann et al 1987 ;Chen et al 1995), of control region sequences (Vigilant et al 1991 ;Soodyall, 1993 ;Krings et al 1999) or a combination of both (Graven et al 1995 ;Watson et al 1997 ;Chen et al 2000), have involved African populations. However, the sampling is still surprisingly patchy, and quite poor in the southeast.…”

Composition of the Kirsten Skeletal Collection at Stellenbosch University

“…The Western Cape Province of South Africa has a rich genetic history, arising from many parts of the world including the local ancient Khoisan population [8][9][10][11] , the greater Bantu groups from the Niger-Congo phylum 12,[14][15][16] , European settlers 17,18 and slaves from the East 18,19 . Marriages amongst the different population groups were once common 17,20 , and produced a heterogeneous new and genetically unique population in the Western Cape, until apartheid was introduced and resulted in a drastic decrease in cross-population gene flow 6,20,25 .…”

“…For centuries, the southwestern corner of Africa was home to the oldest known lineage of modern humans 8,9 -descendants of the original Khoikhoi (pastoralists) and the San (hunter-gatherers) populations 10 . These two historical groups are collectively referred to as the Khoisan or the Khoe-San, and speak a distinctive click language.…”

Comparing Timeline Rhythms in Pygmy and Bushmen Music

“…Drawing on the 'Out-of-Africa' model (Cavalli-Sforza et al, 1994;Chen et al, 2000;Oppenheimer, 2012), as well as studies in archaeology, ethnomusicology, anthropology, linguistics, and his work with Alan Lomax on the Cantometric project, Victor Grauer (2011) argues that eastern Pygmy, western Pygmy, and Bushmen cultural practices are derived from a "Hypothetical Baseline Culture," which represents the core values of a common ancestral group (p. 3) [10]. The location of this ancestral group is "unknown" but is possibly the "tropical forest or East African savannah" (p. 57).…”