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, 66 (4), 1362-83

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

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

Y S Chen et al. Am J Hum Genet.

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.

Figures

Figure  1
Figure 1
Map of southern Africa, and geographic locations of Khoisan and non-Khoisan populations surveyed for mtDNA variation.
Figure  2
Figure 2
MP tree showing evolutionary relationships among 107 haplotypes (AF1–AF107) observed in 214 sub-Saharan Africans (Chen et al. ; present study). The tree is 200 steps in length, has consistency and retention indices (CI and RI) of .745 and .893, respectively, and is one of 3,000 MP trees generated by the TBR algorithm. It was rooted from a chimpanzee haplotype defined by sequence analysis (Horai et al. 1995) (see text). The RFLPs that define each of the major branches of the MP tree are indicated by the number of the first nucleotide of the respective recognition sites, according to the CR sequence (Anderson et al. 1981), with the restriction enzymes being indicated by single-letter codes as given in Appendix A. The length of the horizontal branches is proportional to the number of mutations that separate the haplotypes. The three major haplogroups are denoted by the light-gray shading, whereas the subhaplotype clusters, defined in table 2, are indicated by the smaller unshaded boxes. The “AF”-prefixed numbers at the end of each branch denote the individual haplotypes, and the population(s) in which the individual haplotypes were detected are indicated by symbols as defined in the key. All population-specific lineages are encompassed by dark-gray shading and are also denoted by Greek letters as defined in the key. Haplotypes AF1 and AF2, which are aligned with European haplogroup U, are located in L3d and are indicated by a section symbol (§). Haplotype AF24, which is aligned with Asian macrohaplogroup M, is indicated by a double section symbol (§§). The bootstrap values for the major branches of the MP tree were calculated by use of 100 replicates, with resampling by the TBR algorithm. L1a2 cluster AF87–AF90 has a bootstrap value of 92%; subcluster AF88–AF90 has a bootstrap value of 100%. L1a2 cluster AF91–AF92 has a bootstrap value of 95%; but AF93 and AF94 were not resolved at bootstrap values >50%. L1a1 cluster AF97–AF101 has a bootstrap value of 100%; and subclusters AF99–AF101 and AF60–AF61 have bootstrap values of 52% and 60%, respectively; but AF60 and AF61 were not resolved at bootstrap values >50%. L1b1 cluster AF70–AF71/AF77–AF78 has a bootstrap value of 100%, as does subcluster AF71/AF77/AF78. L1b2 cluster AF62–AF69 has a bootstrap value of 100%, as do subclusters AF62–AF63 and AF67–AF69, whereas subcluster AF62–AF64/AF66–AF69 has a bootstrap value of 55%. L2 cluster AF26–AF38/AF40–AF50/AF52–AF53/AF55–AF58/AF105–AF107 has a bootstrap value of 52%. L2a cluster AF26–AF38/AF40–AF42 has a bootstrap value of 58%. L2b cluster AF46–AF47 has a bootstrap value of 100%. L2c cluster AF49–AF50/AF52–AF53/AF55–AF58 has a bootstrap value of 100%, and cluster AF106–AF107 has a bootstrap value of 52%. L3a cluster AF22–AF23 has a bootstrap value of 100%, whereas subclusters AF19–AF21/AF24 and AF80–AF84 were not resolved at bootstrap values >50%. L3b cluster AF8/AF85–AF86 has a bootstrap value of 100%, as does subcluster AF85–AF86, but cluster AF4/AF6/AF9/AF11 was not resolved at a bootstrap value of 50%. L3c cluster AF12/AF14–AF18 has a bootstrap value of 100%, as does subcluster AF14–AF18. L3d cluster AF1–AF3 has a bootstrap value of 97%.
Figure  3
Figure 3
NJ tree constructed on the basis of mean character genetic differences of the RFLP haplotypes. The numbers represent the AF haplotype numbers shown in figure 2. The bootstrap values for various haplotype clusters of the NJ tree were calculated by use of 500 replicates, with resampling. The L1a2 cluster of haplotypes separated from all other African haplotypes, with a bootstrap value of 55%. L1a2 cluster AF87–AF88/AF90–AF93 has a bootstrap value of 54%; subcluster AF91–AF93 has a bootstrap value of 59%; subsubcluster AF91–AF92 has a bootstrap value of 65%; subcluster AF87–AF88/AF90 has a bootstrap value of 99%; and subsubcluster AF88–AF90 has a bootstrap value of 75%. L1b1+L1b2 cluster AF62–AF65/AF67–AF68/AF70–AF72/AF78 has a bootstrap value of 56%. L1b1 cluster AF70–AF72/AF78 has a bootstrap value of 94%; subcluster AF71–AF72/AF78 has a bootstrap value of 67%; and subsubcluster AF71, 72 has a bootstrap value of 60%. L1b2 cluster AF62–AF65/AF67–AF68 has a bootstrap value of 70%; subcluster AF67–AF68 has a bootstrap value of 100%; and subcluster AF62–AF63 has a bootstrap value of 69%. L1a1 cluster AF59–AF61/AF96–AF98/AF100–AF101/AF103 has a bootstrap value of 60%; subcluster AF60–AF61 has a bootstrap value of 90%; subcluster AF97–AF98/AF100–AF101 has a bootstrap value of 96%; subsubcluster AF97–AF98 has a bootstrap value of 72%; and subsubcluster AF100–AF101 has a bootstrap value of 67%. L2c cluster AF49–AF53/AF56/AF58 has a bootstrap value of 83%; subcluster AF49–AF53 has a bootstrap value of 53%; and subcluster AF56–AF58 of 63%. L2b cluster AF45–AF47/AF105 has a bootstrap value of 53%; subcluster AF46–AF47/AF105 has a bootstrap value of 74%; and subcluster AF46–AF47 has a bootstrap value of 76%. L2 cluster AF43–AF44 has a bootstrap value of 87%. L2a subcluster AF38–AF41 has a bootstrap value of 84%; subsubcluster AF38–AF39 has a bootstrap value of 66%; and subsubcluster AF40–AF41 has a bootstrap value of 70%. L2a subcluster AF36–AF37 has a bootstrap value of 69%; subcluster AF29–AF30 has a bootstrap value of 84%, whereas subclusters AF26–AF28 and AF33–AF35 were not resolved at bootstrap values >50%. L3d subcluster AF1–AF2 has a bootstrap value of 69%, whereas AF3 was not resolved at a bootstrap value >50%. L3c subcluster AF14–AF16 has a bootstrap value of 51%, although AF12 and AF13 were not resolved at a value of 50%. L3b cluster AF8/AF85–AF86 has a bootstrap value of 88%; and subcluster AF85–AF86 has a bootstrap value of 96%; however, clusters AF4–AF7 and AF9–AF11 were not resolved at a value of 50%. L3 cluster AF24–AF25 and L3a cluster AF80–AF83 were not resolved at a value of 50%.
Figure  4
Figure 4
NJ tree of ML genetic distances for major African populations (table 5).
Figure  5
Figure 5
NJ tree based on HVS-I and HVS-II sequences from Vasikela Kung and Khwe (present study) and Botswana Kung (Vigilant et al. 1989). The CR sequence numbers are positioned at the end of each branch; VK = Vasikela Kung sequence, KW = Khwe sequence, and BK = Botswana Kung sequences; and the associated HR haplotypes are in parentheses. LR types are indicated in boldface italic, and the square brackets indicate all CR sequences associated with them. The major haplogroups and subhaplogroups to which these mtDNAs belong are shown within the boxes. Bootstrap values for each major branch of the tree are shown at their corresponding positions. This tree was rooted from a chimpanzee CR sequence (Horai et al. 1995).

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