Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation
Contributed by Sarah A. Tishkoff, January 5, 2019 (sent for review October 15, 2018; reviewed by Rob J. Kulathinal and Mark D. Shriver)
Significance
African populations have been underrepresented in human genomics research yet are important for understanding modern human origins and the genetic basis of adaptive traits. Here we analyze a genome-wide dataset in 840 ethnically and geographically diverse Africans. We find that geographically distant hunter-gatherer populations from East Africa share unique common ancestry and we see strong signatures of local adaptation near genes that play a role in immune response, as well as lipid and glucose metabolism.
Abstract
Anatomically modern humans arose in Africa ∼300,000 years ago, but the demographic and adaptive histories of African populations are not well-characterized. Here, we have generated a genome-wide dataset from 840 Africans, residing in western, eastern, southern, and northern Africa, belonging to 50 ethnicities, and speaking languages belonging to four language families. In addition to agriculturalists and pastoralists, our study includes 16 populations that practice, or until recently have practiced, a hunting-gathering (HG) lifestyle. We observe that genetic structure in Africa is broadly correlated not only with geography, but to a lesser extent, with linguistic affiliation and subsistence strategy. Four East African HG (EHG) populations that are geographically distant from each other show evidence of common ancestry: the Hadza and Sandawe in Tanzania, who speak languages with clicks classified as Khoisan; the Dahalo in Kenya, whose language has remnant clicks; and the Sabue in Ethiopia, who speak an unclassified language. Additionally, we observed common ancestry between central African rainforest HGs and southern African San, the latter of whom speak languages with clicks classified as Khoisan. With the exception of the EHG, central African rainforest HGs, and San, other HG groups in Africa appear genetically similar to neighboring agriculturalist or pastoralist populations. We additionally demonstrate that infectious disease, immune response, and diet have played important roles in the adaptive landscape of African history. However, while the broad biological processes involved in recent human adaptation in Africa are often consistent across populations, the specific loci affected by selective pressures more often vary across populations.
Data Availability
Data deposition: Genotype data from this study have been deposited in the NIH dbGAP repository, https://www.ncbi.nlm.nih.gov/gap (accession no. phs001780.v1.p1).
Acknowledgments
We thank Joseph Lachance for helpful comments and discussion; and the African volunteers for samples. Genotyping services were provided by Hakon Hakonarsson of the Center for Applied Genomics at the Children’s Hospital of Philadelphia. This research was funded by National Science Foundation Grants BCS-0196183 and BCS-0827436 and National Institutes of Health Grants 8DP1ES022577, 5-R01-GM076637, 1R01DK104339, and 1R01GM113657 (to S.A.T.).
Supporting Information
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Cover image: Pictured is a coral colony (Acropora hyacinthus) with polyps extended for feeding. Russell J. Schmitt et al. conducted field experiments on the reefs of Moorea, French Polynesia, and demonstrated that reef communities can become trapped in a seaweed-dominated state under the same environmental conditions that corals need to thrive. The findings suggest that intense herbivory is needed to remove excess seaweed, and that reef management should include measures to strengthen coral community resilience and prevent shifts toward seaweed. See the article by Schmitt et al. on pages 4372–4381. Image courtesy of Russell J. Schmitt.
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© 2019. Published under the PNAS license.
Data Availability
Data deposition: Genotype data from this study have been deposited in the NIH dbGAP repository, https://www.ncbi.nlm.nih.gov/gap (accession no. phs001780.v1.p1).
Submission history
Published online: February 19, 2019
Published in issue: March 5, 2019
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Acknowledgments
We thank Joseph Lachance for helpful comments and discussion; and the African volunteers for samples. Genotyping services were provided by Hakon Hakonarsson of the Center for Applied Genomics at the Children’s Hospital of Philadelphia. This research was funded by National Science Foundation Grants BCS-0196183 and BCS-0827436 and National Institutes of Health Grants 8DP1ES022577, 5-R01-GM076637, 1R01DK104339, and 1R01GM113657 (to S.A.T.).
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The authors declare no conflict of interest.
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