close
Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 Dec 4:5:5692.
doi: 10.1038/ncomms6692.

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

Hie Lim Kim  1 , Aakrosh Ratan  2 , George H Perry  3 , Alvaro Montenegro  4 , Webb Miller  5 , Stephan C Schuster  1
Affiliations

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

Hie Lim Kim et al. Nat Commun. .

Abstract

The Khoisan people from Southern Africa maintained ancient lifestyles as hunter-gatherers or pastoralists up to modern times, though little else is known about their early history. Here we infer early demographic histories of modern humans using whole-genome sequences of five Khoisan individuals and one Bantu speaker. Comparison with a 420 K SNP data set from worldwide individuals demonstrates that two of the Khoisan genomes from the Ju/'hoansi population contain exclusive Khoisan ancestry. Coalescent analysis shows that the Khoisan and their ancestors have been the largest populations since their split with the non-Khoisan population ~100-150 kyr ago. In contrast, the ancestors of the non-Khoisan groups, including Bantu-speakers and non-Africans, experienced population declines after the split and lost more than half of their genetic diversity. Paleoclimate records indicate that the precipitation in southern Africa increased ~80-100 kyr ago while west-central Africa became drier. We hypothesize that these climate differences might be related to the divergent-ancient histories among human populations.

PubMed Disclaimer

Figures

Figure 1
Figure 1. Genetic relationships of six southern African individuals and worldwide populations.
(a) Population structure in human populations was inferred by ADMIXTURE using 417,593 SNPs from 490 individuals. (b) The ADMIXTURE plot for the 14 complete-genome data sets is shown separately. (c) Genetic relationships of our six southern African individuals and various African populations were estimated by the PCA analysis on the basis of the 417,593 SNPs from southern African and Yoruba populations. NB1 and NB8 are closely clustered with the Ju/’hoansi group, which was sampled from the northern Kalahari region in Namibia. The Ju/’hoansi samples are furthest from the Yoruba populations. MD8, from the northwestern Kalahari region, clusters with the !Xun, which belong to the same language group. KB1 and KB2, from the Tuu-speakers of the southern Kalahari, are close to the !Xun and /Gui and //Gana who lived in the central Kalahari region, but are not clearly related to them. Hence, we do not have any population data that is closely related to these two samples. ABT, a southern African Bantu, clusters with the southeastern Bantu samples.
Figure 2
Figure 2. The local ancestry estimation for individual genomes.
Along the genome, local ancestries are inferred by PCAdmix for NB8 (a), ABT (b) and NA18507 (c) and are illustrated on the genome map. Blue, red, yellow colors indicate the Khoisan (combined northern and southern Khoisan), western African and European ancestries, respectively. Light purple color represents undetermined ancestry that is not significant enough to estimate the ancestry. The western African haplotypes shown in the NB8 genome are not detected by the other two different methods (Supplementary Fig. 6 and Supplementary Table 2).
Figure 3
Figure 3. The changes in the effective population size on the basis of the 14 individual genomes.
(a) The average Ne of each of four populations (see Methods). The pink shadow indicates the period where the changes in Ne varied most among the four populations. (b) Ne changes of five Khoisan genomes, (c) Ne changes of three Yoruba and one Bantu genome, (d) Ne changes of two European genomes, and (e) Ne changes of three Asian genomes. Four genomes sequenced to a relatively low coverage were corrected using the FNR option provided by the PSMC package. Estimates both with and without corrections are shown.
Figure 4
Figure 4. The climate changes in the African continent.
Modes of African rainfall variability characterized by opposite changes in precipitation along the north–south axis. With the exception of the light green area over southwestern Africa, colors and patterns refer to modelled results. Symbols refer to proxy records. Local conditions during particular periods are given by dates in front of some legend entries. Stadials have millennial time scale and were recorded several times around ~100 kyr ago. The names of our six southern African and Yoruba (YRI) individuals refer to their sampling location. References for this figure are indicated in Supplementary Table 3. The original map was retrieved from d-maps.com and edited by authors.
See this image and copyright information in PMC

References

    1. de Filippo C., Bostoen K., Stoneking M. & Pakendorf B. Bringing together linguistic and genetic evidence to test the Bantu expansion. Proc. Biol. Sci 279, 3256–3263 (2012). - PMC - PubMed
    1. Biesele, M. and Royal-/o/oo, K. in The Cambridge Encyclopedia of Hunters and Gatherers (eds Lee, R. B. & Daly, R.) 205–209 Cambridge Univ. Press (1999).
    1. Tishkoff S. A. et al. The genetic structure and history of Africans and African Americans. Science 324, 1035–1044 (2009). - PMC - PubMed
    1. Henn B. M. et al. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc. Natl Acad. Sci. USA 108, 5154–5162 (2011). - PMC - PubMed
    1. Schlebusch C. M. et al. Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338, 374–379 (2012). - PMC - PubMed

Publication types

Associated data

LinkOut - more resources