Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation

Laura B. Scheinfeldt, Sameer Soi, Charla Lambert, Wen Ya Ko, Aoua Coulibaly, Alessia Ranciaro, Simon Thompson, Jibril Hirbo, William Beggs, Muntaser Ibrahim, Thomas Nyambo, Sabah Omar, Dawit Woldemeskel, Gurja Belay, Alain Froment, Junhyong Kim, Sarah A. Tishkoff*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

18 Scopus citations

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 genomewide 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.

Original languageEnglish
Pages (from-to)4166-4175
Number of pages10
JournalProceedings of the National Academy of Sciences of the United States of America
Volume116
Issue number10
DOIs
StatePublished - 2019

Keywords

  • African diversity
  • African hunter-gatherers
  • Human evolution
  • Natural selection
  • Population genetics

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