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Edited by Lynn B. Jorde, University of Utah, Salt Lake City, UT, and accepted by the Editorial Board January 2, 2014 (received for review July 30, 2013)
Significance
The hunter–gatherer and pastoralist populations of southern Africa are among the culturally, linguistically, and genetically most diverse human populations. However, little is known about their history. We show that all of these populations have some ancestry most closely related to Europeans and Middle Easterners and use this to reconstruct the history of population movements between Eurasia, eastern Africa, and southern Africa.
Abstract
The history of southern Africa involved interactions between indigenous hunter–gatherers and a range of populations that moved into the region. Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter–gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger–Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to ∼900–1,800 y ago and show that it had the largest demographic impact in Khoisan populations that speak Khoe–Kwadi languages. A similar signal of west Eurasian ancestry is present throughout eastern Africa. In particular, we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to ∼2,700–3,300 y ago. We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa and show that this population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa.
Footnotes
- ↵1To whom correspondence may be addressed. E-mail: jkpickrell{at}nygenome.org, brigitte.pakendorf{at}cnrs.fr, or reich{at}genetics.med.harvard.edu.
2Present address: New York Genome Center, New York, NY 10013.
Author contributions: J.K.P., M.S., B.P., and D.R. designed research; J.K.P., N.P., P.-R.L., M.L., and B.B. contributed new reagents/analytic tools; J.K.P. analyzed data; and J.K.P., M.S., B.P., and D.R. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission. L.B.J. is a guest editor invited by the Editorial Board.
↵*Myers S, et al., LD patterns in dense variation data reveal information about the history of human populations worldwide. Presented at the 61st Annual Meeting of the American Society of Human Genetics, October 11–15, 2011, Montreal, QC, Canada.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1313787111/-/DCSupplemental.
Freely available online through the PNAS open access option.
Eurasian ancestry in Africa
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