Complete Khoisan and Bantu genomes from southern Africa.
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.
Schuster
Stephan C
SC
Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Lab, University Park, Pennsylvania 16802, USA. scs@bx.psu.edu
Miller
Webb
W
Ratan
Aakrosh
A
Tomsho
Lynn P
LP
Giardine
Belinda
B
Kasson
Lindsay R
LR
Harris
Robert S
RS
Petersen
Desiree C
DC
Zhao
Fangqing
F
Qi
Ji
J
Alkan
Can
C
Kidd
Jeffrey M
JM
Sun
Yazhou
Y
Drautz
Daniela I
DI
Bouffard
Pascal
P
Muzny
Donna M
DM
Reid
Jeffrey G
JG
Nazareth
Lynne V
LV
Wang
Qingyu
Q
Burhans
Richard
R
Riemer
Cathy
C
Wittekindt
Nicola E
NE
Moorjani
Priya
P
Tindall
Elizabeth A
EA
Danko
Charles G
CG
Teo
Wee Siang
WS
Buboltz
Anne M
AM
Zhang
Zhenhai
Z
Ma
Qianyi
Q
Oosthuysen
Arno
A
Steenkamp
Abraham W
AW
Oostuisen
Hermann
H
Venter
Philippus
P
Gajewski
John
J
Zhang
Yu
Y
Pugh
B Franklin
BF
Makova
Kateryna D
KD
Nekrutenko
Anton
A
Mardis
Elaine R
ER
Patterson
Nick
N
Pringle
Tom H
TH
Chiaromonte
Francesca
F
Mullikin
James C
JC
Eichler
Evan E
EE
Hardison
Ross C
RC
Gibbs
Richard A
RA
Harkins
Timothy T
TT
Hayes
Vanessa M
VM
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