Copyright © 2000 The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics, Volume 66, Issue 4, 1362-1383, 1 April 2000
doi:10.1086/302848
mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations
Yu-Sheng Chen1, *, Antonel Olckers4, Theodore G. Schurr1, 2, †, Andreas M. Kogelnik1, 3, Kirsi Huoponen1, ‡ and Douglas C. Wallace1, 2, 
, 
1 Center for Molecular Medicine, Emory University, Atlanta
2 Department of Anthropology, Emory University, Atlanta
3 Program in Biomedical Engineering, College of Computing, Georgia Institute of Technology, Atlanta
4 Department of Human Genetics, University of Pretoria, Pretoria
Address for correspondence and reprints: Dr. Douglas C. Wallace, Director, Center for Molecular Medicine, Emory University School of Medicine, 1462 Clifton Road, N.E., Atlanta, GA 30322* Present affiliation: Department of Psychiatry, University of Chicago Medical School, Chicago.
† Present affiliation: Southwest Foundation for Biomedical Research, Department of Genetics, San Antonio.
‡ Present affiliation: Laboratory of Genetics, Department of Biology, University of Turku, Turku, Finland.
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.
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