title: Complete Khoisan and Bantu genomes from southern 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.
authors.affiliation: Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Lab, University Park, Pennsylvania 16802, USA. scs@bx.psu.edu
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
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authors.lastname: Giardine
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authors.forename: Yazhou
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authors.lastname: Sun
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authors.lastname: Nazareth
authors.forename: Qingyu
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authors.lastname: Wang
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authors.lastname: Wittekindt
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authors.lastname: Moorjani
authors.forename: Elizabeth A
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authors.lastname: Tindall
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authors.lastname: Danko
authors.forename: Wee Siang
authors.initials: WS
authors.lastname: Teo
authors.forename: Anne M
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authors.lastname: Buboltz
authors.forename: Zhenhai
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authors.lastname: Zhang
authors.forename: Qianyi
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authors.lastname: Ma
authors.forename: Arno
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authors.lastname: Oosthuysen
authors.forename: Abraham W
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authors.lastname: Steenkamp
authors.forename: Hermann
authors.initials: H
authors.lastname: Oostuisen
authors.forename: Philippus
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authors.lastname: Venter
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authors.lastname: Gajewski
authors.forename: Yu
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authors.lastname: Zhang
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authors.lastname: Pugh
authors.forename: Kateryna D
authors.initials: KD
authors.lastname: Makova
authors.forename: Anton
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authors.lastname: Nekrutenko
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Nick
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authors.lastname: Patterson
authors.forename: Tom H
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authors.lastname: Pringle
authors.forename: Francesca
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authors.lastname: Chiaromonte
authors.forename: James C
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authors.lastname: Mullikin
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authors.lastname: Eichler
authors.forename: Ross C
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authors.lastname: Hardison
authors.forename: Richard A
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authors.lastname: Gibbs
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authors.lastname: Harkins
authors.forename: Vanessa M
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mesh_terms: D044466:Asian People / Q000235:genetics; D044383:Black People / Q000235:genetics*; D005006:Ethnicity / Q000235:genetics*; D005091:Exons / Q000235:genetics; D005826:Genetics, Medical; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D013019:South Africa / Q000208:ethnology; D044465:White People / Q000235:genetics