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<p>Creating a catalogue of early diverged genome variation is critical to determine the true extent of human diversity and associated medical impact. Generating deep whole genome data for 150 Khoe-San (12 groups, 1 unclassified), and 40 regionally comparative Southern Africans (3 groups), we identify ~30 million small-to-large variants - over 1.3 million unknown single nucleotide variants. Representing shared traditionally forager lifestyles and click-speaking languages, we identify San and Damara as separate phylogenetic lineages, contributing two admixture waves to Nama. While San represented modern humans’ deep divergence (~115 thousand years ago), Damara divergence is recent, with both showing high effective population sizes between 45–150 thousand years ago. Developing an assembly-based test we report 1,376 genes under positive selection (<i>dN</i>/<i>dS</i> = 19.46) of which 479 are significantly associated with forager peoples and, therefore, maintained ancestral alleles that differ from derived genetic variation observed in non-African biomedical resources.</p>

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A catalogue of early diverged contemporary human genome variation reveals distinct Khoe-San populations

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月10日

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  • Weerachai Jaratlerdsiri,
  • Pamela X. Y. Soh,
  • Tingting Gong,
  • Jue Jiang,
  • Zolani Simayi,
  • Desiree C. Petersen,
  • Errol Holland,
  • Eva K. F. Chan,
  • Kathrine E. Theron,
  • Wilfrid H. G. Haacke,
  • Hagen E. A. Förtsch,
  • M. S. Riana Bornman,
  • David M. Thomas,
  • Jeffrey Mphahlele,
  • Vanessa M. Hayes

摘要

Creating a catalogue of early diverged genome variation is critical to determine the true extent of human diversity and associated medical impact. Generating deep whole genome data for 150 Khoe-San (12 groups, 1 unclassified), and 40 regionally comparative Southern Africans (3 groups), we identify ~30 million small-to-large variants - over 1.3 million unknown single nucleotide variants. Representing shared traditionally forager lifestyles and click-speaking languages, we identify San and Damara as separate phylogenetic lineages, contributing two admixture waves to Nama. While San represented modern humans’ deep divergence (~115 thousand years ago), Damara divergence is recent, with both showing high effective population sizes between 45–150 thousand years ago. Developing an assembly-based test we report 1,376 genes under positive selection (dN/dS = 19.46) of which 479 are significantly associated with forager peoples and, therefore, maintained ancestral alleles that differ from derived genetic variation observed in non-African biomedical resources.