Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 37, Issue 10, Pages 2944-2954Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msaa140
Keywords
Khoe-San; southern Africa; population structure
Funding
- Swedish Research Council for Infrastructures and Science for Life Laboratory, Sweden
- Knut and Alice Wallenberg Foundation
- Working Group of Indigenous Minorities in Southern Africa (WIMSA)
- South African San Council
- University of Witwatersrand (South Africa) Human Research Ethics Committee [M180654]
- Swedish Ethical Review Authority [Dnr 2019-05174]
- Swedish Research Council [621-2014-5211, 642-2013-8019]
- Lars Hierta Foundation
- NilssonEhle Endowments
- European Research Council (ERC) [759933]
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The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.
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