Hunter-gatherer genomic diversity suggests a southern African origin for modern humans
Brenna M. Henn a,1, Christopher R. Gignoux b, Matthew Jobin c,d, Julie M. Granka e, J. M. Macpherson f, Jeffrey M. Kidd a, Laura Rodríguez-Botigué g, Sohini Ramachandran h, Lawrence Hon f, Abra Brisbin i, Alice A. Lin j, Peter A. Underhill j, David Comas g, Kenneth K. Kidd k, Paul J. Norman l, Peter Parham l, Carlos D. Bustamante a, Joanna L. Mountain f, and Marcus W. Feldman e
-Author Affiliations
aDepartment of Genetics, Stanford University, Stanford, CA 94305;
bUniversity of California, San Francisco, CA 94158;
cDepartment of Anthropology, Santa Clara University, Santa Clara, CA 95050;
dDepartment of Anthropology, Stanford University, Stanford, CA 94305;
eDepartment of Biological Sciences, Stanford University, Stanford CA 94305;
f23andMe, Inc., Mountain View, CA 94043;
gInstitute of Evolutionary Biology, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
hDepartment of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912;
iDepartment of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14850;
jDepartment of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305;
kDepartment of Genetics, Yale University School of Medicine, New Haven, CT 06520; and
lDepartment of Structural Biology, Stanford University, Stanford, CA 94305
Edited by Mary-Claire King, University of Washington, Seattle, WA, and approved February 3, 2011 (received for review November 29, 2010)
1To whom correspondence should be addressed.
E-mail: bmhenn@stanford.edu.
Abstract
Africa is inferred to be the continent of origin for all modern human populations, but the details of human prehistory and evolution in Africa remain largely obscure owing to the complex histories of hundreds of distinct populations. We present data for more than 580,000 SNPs for several hunter-gatherer populations: the Hadza and Sandawe of Tanzania, and the ≠Khomani Bushmen of South Africa, including speakers of the nearly extinct N|u language. We find that African hunter-gatherer populations today remain highly differentiated, encompassing major components of variation that are not found in other African populations. Hunter-gatherer populations also tend to have the lowest levels of genome-wide linkage disequilibrium among 27 African populations. We analyzed geographic patterns of linkage disequilibrium and population differentiation, as measured by FST, in Africa. The observed patterns are consistent with an origin of modern humans in southern Africa rather than eastern Africa, as is generally assumed. Additionally, genetic variation in African hunter-gatherer populations has been significantly affected by interaction with farmers and herders over the past 5,000 y, through both severe population bottlenecks and sex-biased migration. However, African hunter-gatherer populations continue to maintain the highest levels of genetic diversity in the world.
human evolution, population genetics, Khoisan
Footnotes
Author contributions: B.M.H., P.A.U., C.D.B., and M.W.F. designed research; B.M.H., C.R.G., S.R., and A.A.L. performed research; M.J., L.H., A.B., D.C., K.K.K., P.P., and J.L.M. contributed new reagents/analytic tools; B.M.H., C.R.G., M.J., J.M.G., J.M.M., J.M.K., L.R.-B., and P.J.N. analyzed data; and B.M.H., C.R.G., P.J.N., C.D.B., J.L.M., and M.W.F. wrote the paper.
This Feature Article is part of a series identified by the Editorial Board as reporting findings of exceptional significance.
Conflict of interest statement: The authors from 23andMe, Inc. (C.R.G., J.M.M., L.H., and J.L.M.) declare competing financial interests as employees at and stock holders of 23andMe, Inc. SNP arrays designed by 23andMe were used to generate a unique dataset reported in this article. To our knowledge, affiliation with 23andMe, Inc. did not bias the results or discussion of results reported in this article.
This article is a PNAS Direct Submission.
Data deposition: Genotype data will be hosted on a Stanford University website:
This article contains supporting information online at
Freely available online through the PNAS open access option.
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