@article {333557, title = {A catalogue of early diverged contemporary human genome variation reveals distinct Khoe-San populations}, journal = {Nature Communications}, volume = {17}, year = {2026}, month = {2026/02/10}, abstract = {

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.

}, isbn = {2041-1723}, doi = {https://doi.org/10.1038/s41467-026-69269-4}, url = {https://www.nature.com/articles/s41467-026-69269-4}, author = {Jaratlerdsiri, Weerachai and Soh, Pamela X. Y. and Gong, Tingting and Jiang, Jue and Simayi, Zolani and Petersen, Desiree C. and Holland, Errol and Chan, Eva K. F. and Theron, Kathrine E. and Haacke, Wilfrid H. G. and F{\"o}rtsch, Hagen E. A. and Bornman, M. S. Riana and Thomas, David M. and Mphahlele, Jeffrey and Hayes, Vanessa M.} }