Complete Khoisan and Bantu genomes from southern Africa

Stephan C. Schuster, Webb Miller, Aakrosh Ratan, Lynn P. Tomsho, Belinda Giardine, Lindsay R. Kasson, Robert S. Harris, Desiree C. Petersen, Fangqing Zhao, Ji Qi, Can Alkan, Jeffrey M. Kidd, Yazhou Sun, Daniela I. Drautz, Pascal Bouffard, Donna M. Muzny, Jeffrey G. Reid, Lynne V. Nazareth, Qingyu Wang, Richard BurhansCathy Riemer, Nicola E. Wittekindt, Priya Moorjani, Elizabeth A. Tindall, Charles G. Danko, Wee Siang Teo, Anne M. Buboltz, Zhenhai Zhang, Qianyi Ma, Arno Oosthuysen, Abraham W. Steenkamp, Hermann Oostuisen, Philippus Venter, John Gajewski, Yu Zhang, B. Franklin Pugh, Kateryna D. Makova, Anton Nekrutenko, Elaine R. Mardis, Nick Patterson, Tom H. Pringle, Francesca Chiaromonte, James C. Mullikin, Evan E. Eichler, Ross C. Hardison, Richard A. Gibbs, Timothy T. Harkins, Vanessa M. Hayes

Research output: Contribution to journalArticle

262 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)943-947
Number of pages5
JournalNature
Volume463
Issue number7283
DOIs
StatePublished - Feb 18 2010

All Science Journal Classification (ASJC) codes

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    Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B., Kasson, L. R., Harris, R. S., Petersen, D. C., Zhao, F., Qi, J., Alkan, C., Kidd, J. M., Sun, Y., Drautz, D. I., Bouffard, P., Muzny, D. M., Reid, J. G., Nazareth, L. V., Wang, Q., ... Hayes, V. M. (2010). Complete Khoisan and Bantu genomes from southern Africa. Nature, 463(7283), 943-947. https://doi.org/10.1038/nature08795