Complete Khoisan and Bantu genomes from southern Africa

Stephan C. Schuster, Webb Miller, Aakrosh Ratan, Lynn P. Tomsho, Belinda Giardine, Lindsay R. Kasson, Robert Scott 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, Benjamin Franklin Pugh, Kateryna Dmytrivna Makova, Anton Nekrutenko, Elaine R. Mardis, Nick Patterson, Tom H. Pringle, Francesca Chiaromonte, James C. Mullikin, Evan E. Eichler, Ross Cameron Hardison, Richard A. Gibbs, Timothy T. Harkins, Vanessa M. Hayes

Research output: Contribution to journalArticle

255 Citations (Scopus)

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

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Southern Africa
Genome
Botswana
Medical History Taking
Exome
Genetic Structures
Human Genome
Open Reading Frames
Biomedical Research
Life Style
Nucleotides
Databases
Amino Acids
DNA
Population

All Science Journal Classification (ASJC) codes

  • General

Cite this

Schuster, S. C., Miller, W., Ratan, A., Tomsho, L. P., Giardine, B., Kasson, L. R., ... Hayes, V. M. (2010). Complete Khoisan and Bantu genomes from southern Africa. Nature, 463(7283), 943-947. https://doi.org/10.1038/nature08795
Schuster, Stephan C. ; Miller, Webb ; Ratan, Aakrosh ; Tomsho, Lynn P. ; Giardine, Belinda ; Kasson, Lindsay R. ; Harris, Robert Scott ; Petersen, Desiree C. ; Zhao, Fangqing ; Qi, Ji ; Alkan, Can ; Kidd, Jeffrey M. ; Sun, Yazhou ; Drautz, Daniela I. ; Bouffard, Pascal ; Muzny, Donna M. ; Reid, Jeffrey G. ; Nazareth, Lynne V. ; Wang, Qingyu ; Burhans, Richard ; Riemer, Cathy ; Wittekindt, Nicola E. ; Moorjani, Priya ; Tindall, Elizabeth A. ; Danko, Charles G. ; Teo, Wee Siang ; Buboltz, Anne M. ; Zhang, Zhenhai ; Ma, Qianyi ; Oosthuysen, Arno ; Steenkamp, Abraham W. ; Oostuisen, Hermann ; Venter, Philippus ; Gajewski, John ; Zhang, Yu ; Pugh, Benjamin Franklin ; Makova, Kateryna Dmytrivna ; Nekrutenko, Anton ; Mardis, Elaine R. ; Patterson, Nick ; Pringle, Tom H. ; Chiaromonte, Francesca ; Mullikin, James C. ; Eichler, Evan E. ; Hardison, Ross Cameron ; Gibbs, Richard A. ; Harkins, Timothy T. ; Hayes, Vanessa M. / Complete Khoisan and Bantu genomes from southern Africa. In: Nature. 2010 ; Vol. 463, No. 7283. pp. 943-947.
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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.",
author = "Schuster, {Stephan C.} and Webb Miller and Aakrosh Ratan and Tomsho, {Lynn P.} and Belinda Giardine and Kasson, {Lindsay R.} and Harris, {Robert Scott} and Petersen, {Desiree C.} and Fangqing Zhao and Ji Qi and Can Alkan and Kidd, {Jeffrey M.} and Yazhou Sun and Drautz, {Daniela I.} and Pascal Bouffard and Muzny, {Donna M.} and Reid, {Jeffrey G.} and Nazareth, {Lynne V.} and Qingyu Wang and Richard Burhans and Cathy Riemer and Wittekindt, {Nicola E.} and Priya Moorjani and Tindall, {Elizabeth A.} and Danko, {Charles G.} and Teo, {Wee Siang} and Buboltz, {Anne M.} and Zhenhai Zhang and Qianyi Ma and Arno Oosthuysen and Steenkamp, {Abraham W.} and Hermann Oostuisen and Philippus Venter and John Gajewski and Yu Zhang and Pugh, {Benjamin Franklin} and Makova, {Kateryna Dmytrivna} and Anton Nekrutenko and Mardis, {Elaine R.} and Nick Patterson and Pringle, {Tom H.} and Francesca Chiaromonte and Mullikin, {James C.} and Eichler, {Evan E.} and Hardison, {Ross Cameron} and Gibbs, {Richard A.} and Harkins, {Timothy T.} and Hayes, {Vanessa M.}",
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Schuster, 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, WS, Buboltz, AM, Zhang, Z, Ma, Q, Oosthuysen, A, Steenkamp, AW, Oostuisen, H, Venter, P, Gajewski, J, Zhang, Y, Pugh, BF, Makova, KD, Nekrutenko, A, Mardis, ER, Patterson, N, Pringle, TH, Chiaromonte, F, Mullikin, JC, Eichler, EE, Hardison, RC, Gibbs, RA, Harkins, TT & Hayes, VM 2010, 'Complete Khoisan and Bantu genomes from southern Africa', Nature, vol. 463, no. 7283, pp. 943-947. https://doi.org/10.1038/nature08795

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

In: Nature, Vol. 463, No. 7283, 18.02.2010, p. 943-947.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Complete Khoisan and Bantu genomes from southern Africa

AU - Schuster, Stephan C.

AU - Miller, Webb

AU - Ratan, Aakrosh

AU - Tomsho, Lynn P.

AU - Giardine, Belinda

AU - Kasson, Lindsay R.

AU - Harris, Robert Scott

AU - Petersen, Desiree C.

AU - Zhao, Fangqing

AU - Qi, Ji

AU - Alkan, Can

AU - Kidd, Jeffrey M.

AU - Sun, Yazhou

AU - Drautz, Daniela I.

AU - Bouffard, Pascal

AU - Muzny, Donna M.

AU - Reid, Jeffrey G.

AU - Nazareth, Lynne V.

AU - Wang, Qingyu

AU - Burhans, Richard

AU - Riemer, Cathy

AU - Wittekindt, Nicola E.

AU - Moorjani, Priya

AU - Tindall, Elizabeth A.

AU - Danko, Charles G.

AU - Teo, Wee Siang

AU - Buboltz, Anne M.

AU - Zhang, Zhenhai

AU - Ma, Qianyi

AU - Oosthuysen, Arno

AU - Steenkamp, Abraham W.

AU - Oostuisen, Hermann

AU - Venter, Philippus

AU - Gajewski, John

AU - Zhang, Yu

AU - Pugh, Benjamin Franklin

AU - Makova, Kateryna Dmytrivna

AU - Nekrutenko, Anton

AU - Mardis, Elaine R.

AU - Patterson, Nick

AU - Pringle, Tom H.

AU - Chiaromonte, Francesca

AU - Mullikin, James C.

AU - Eichler, Evan E.

AU - Hardison, Ross Cameron

AU - Gibbs, Richard A.

AU - Harkins, Timothy T.

AU - Hayes, Vanessa M.

PY - 2010/2/18

Y1 - 2010/2/18

N2 - 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.

AB - 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.

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Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR et al. Complete Khoisan and Bantu genomes from southern Africa. Nature. 2010 Feb 18;463(7283):943-947. https://doi.org/10.1038/nature08795