Complete Khoisan and Bantu genomes from southern Africa.

TitleComplete Khoisan and Bantu genomes from southern Africa.
Publication TypeJournal Article
Year of Publication2010
AuthorsSchuster, SC, Miller, W, Ratan, A, Tomsho, LP, Giardine, B, Kasson, LR, Harris, RS, Petersen, DC, Zhao, F, Qi, J, Alkan, C, Kidd, JM, Sun, Y, Drautz, DI, Bouffard, P, Muzny, DM, Reid, JG, Nazareth, LV, Wang, Q, Burhans, R, Riemer, C, Wittekindt, NE, Moorjani, P, Tindall, EA, Danko, CG, Teo, WSiang, Buboltz, AM, Zhang, Z, Ma, Q, Oosthuysen, A, Steenkamp, AW, Oostuisen, H, Venter, P, Gajewski, J, Zhang, Y, B Pugh, F, Makova, KD, Nekrutenko, A, Mardis, ER, Patterson, N, Pringle, TH, Chiaromonte, F, Mullikin, JC, Eichler, EE, Hardison, RC, Gibbs, RA, Harkins, TT, Hayes, VM
JournalNature
Volume463
Issue7283
Pagination943-7
Date Published2010 Feb 18
ISSN1476-4687
KeywordsAfrican Continental Ancestry Group, Asian Continental Ancestry Group, Ethnic Groups, European Continental Ancestry Group, Exons, Genetics, Medical, Genome, Human, Humans, Phylogeny, Polymorphism, Single Nucleotide, South Africa
Abstract

The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now, fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.

DOI10.1038/nature08795
Alternate JournalNature
PubMed ID20164927
PubMed Central IDPMC3890430
Grant ListR01GM087472 / GM / NIGMS NIH HHS / United States
R01 HG004909 / HG / NHGRI NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
/ / Intramural NIH HHS / United States
R01 GM087472 / GM / NIGMS NIH HHS / United States
R01 HG004160 / HG / NHGRI NIH HHS / United States