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Adv."],"published-print":{"date-parts":[[2026,9,4]]},"abstract":"<jats:p>San populations from Botswana and Namibia retain exceptional linguistic, cultural, and genetic diversity, but few Khoisan-speaking groups remain south of the Kalahari Desert. However, historically, far southern Africa was home to many San and Khoekhoe groups. Popular opinion often implies that such populations do not contribute to the ancestry of contemporary South Africans. Here, we characterize the genetic ancestry of self-identified South African Coloured groups and reconstruct precolonial and colonial population structures from 620 newly sampled individuals. These groups retain the majority of Khoe-San genetic ancestry (&gt;48%), suggesting the persistence of Khoe-San ancestry to the present day. By isolating the Khoe-San ancestry component, we show that it is intermediate between the \u2260Khomani San and Nama and distinct from Kalahari Khoe-San populations. We also find that signatures of the Indian Ocean slave trade can be traced to Indonesian islands such as Sulawesi, Java, and Flores, while the South Asian ancestry is regionally nonspecific.<\/jats:p>","DOI":"10.1126\/sciadv.adz7115","type":"journal-article","created":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T17:59:26Z","timestamp":1788371966000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":1,"title":["Recovering the precolonial population structure of Khoe-San descendant populations"],"prefix":"10.1126","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8143-9135","authenticated-orcid":true,"given":"Stacy L.","family":"Edington","sequence":"first","affiliation":[{"name":"Department of Biology, Baylor University, Waco, TX, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-2057-889X","authenticated-orcid":true,"given":"Dana 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USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin W.","family":"Myrick","sequence":"additional","affiliation":[{"name":"Department of Anthropology, University of California Davis, Davis, CA, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8370-7703","authenticated-orcid":true,"given":"Paul J.","family":"Norman","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2358-0135","authenticated-orcid":true,"given":"Caitlin","family":"Uren","sequence":"additional","affiliation":[{"name":"South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa."},{"name":"Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa."},{"name":"National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch University, Stellenbosch, South Africa."},{"name":"Genomics for Health in Africa (GHA), Africa-Europe Cluster of Research Excellence (CoRE), University of Ghana, Legon, Ghana."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0805-6741","authenticated-orcid":true,"given":"Marlo","family":"M\u00f6ller","sequence":"additional","affiliation":[{"name":"South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa."},{"name":"Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa."},{"name":"National Institute for Theoretical and Computational Sciences 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Bustamante D. M. Montserrat A. G. Ioannidis High resolution ancestry deconvolution for next generation genomic data. bioRxiv 460980 [Preprint] (2021); www.biorxiv.org\/content\/10.1101\/2021.09.19.460980v1.","DOI":"10.1101\/2021.09.19.460980"},{"key":"e_1_3_2_35_2","unstructured":"B. Heine D. Nurse K. Williamson R. Blench L. M. Bender R. J. Hayward T. G\u00fcldemann R. Vossen G. N. Clements G. J. Dimmendaal J. R. Watters D. Creissels P. Newman C. Ehret H. Ekkehard Wolff African Languages (Cambridge Univ. Press 2000)."},{"key":"e_1_3_2_36_2","unstructured":"R. Blench Archaeology Language and the African Past (AltaMira Press 2006)."},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genom-083117-021759"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.116.189209"},{"key":"e_1_3_2_39_2","doi-asserted-by":"crossref","unstructured":"R. B. 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