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The Indian Ocean slave trade and colonial expansion resulted in strong sex-biased admixture in South Africa.

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Title: The Indian Ocean slave trade and colonial expansion resulted in strong sex-biased admixture in South Africa.
Authors: Reynolds AW; Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA; Department of Anthropology, University of California, Davis, Davis, CA 95694, USA., Schurz H; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; 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, 8000, South Africa., Meeks G; Program in Integrative Genetics and Genomics, University of California, Davis, Davis, CA 95694, USA., Gravel S; Department of Human Genetics, McGill University, Montreal, QC, Canada., Myrick JW; UC Davis Genome Center, University of California, Davis, Davis, CA 95694, USA., Edington S; Department of Biology, Baylor University, Waco, TX 76706, USA., Mendez FL; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Werely CJ; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; 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, 8000, South Africa., van Helden PD; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; 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, 8000, South Africa., Hoal EG; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; 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, 8000, South Africa., Poznik GD; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Kim M; Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA., Uren C; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; 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, 8000, South Africa; Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa., Underhill PA; Department of Genetics, Stanford University, Stanford, CA 94305, USA., Möller M; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research; 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, 8000, South Africa; Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa., Henn BM; Department of Anthropology, University of California, Davis, Davis, CA 95694, USA; UC Davis Genome Center, University of California, Davis, Davis, CA 95694, USA. Electronic address: bmhenn@ucdavis.edu.
Source: American journal of human genetics [Am J Hum Genet] 2025 Oct 02; Vol. 112 (10), pp. 2520-2537. Date of Electronic Publication: 2025 Sep 23.
Publication Type: Journal Article; Research Support, N.I.H., Extramural
Language: English
Journal Info: Publisher: Cell Press Country of Publication: United States NLM ID: 0370475 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1537-6605 (Electronic) Linking ISSN: 00029297 NLM ISO Abbreviation: Am J Hum Genet Subsets: MEDLINE
Imprint Name(s): Publication: 2008- : [Cambridge, MA] : Cell Press
Original Publication: Baltimore, American Society of Human Genetics.
MeSH Terms: Black People*/genetics , White People*/genetics , African People*/genetics , Colonialism* , Enslavement* , Human Migration*, Chromosomes, Human, Y/genetics ; South Africa/ethnology ; Female ; Humans ; Male ; Enslaved Persons ; Gene Flow ; Genetics, Population ; Indian Ocean
Abstract: The colonial-period arrival of Europeans in southern Africa is associated with strong sex-biased migration by which male settlers displaced Indigenous Khoekhoe and San men. Concurrently, the importation of enslaved individuals from South Asia, Indonesia, and eastern Africa likely contributed to female-biased migration. Using genetic data from over 1,400 individuals, we examine the spatial and temporal spread of sex-biased migration from the Cape to the northern edges of the historic colonial frontier. In all regions, admixture patterns were sex biased, with evidence of a greater male contribution of European ancestry and greater female contribution of Khoe-San ancestry. While admixture among Khoe-San, European, equatorial African, and Asian groups has likely been continuous from the founding of Cape Town to the present day, we find that Khoe-San groups further north experienced a single pulse of European admixture 6-8 generations ago. European admixture was followed by additional Khoe-San gene flow, potentially reflecting an aggregation of Indigenous groups due to disruption by colonial interlopers. Male migration into the northern frontier territories was not a homogenous group of expanding Afrikaners and slaves. The Nama exhibit distinct founder effects and derive 15% of their Y chromosome haplogroups from Asian lineages, a pattern absent in the ≠Khomani San. Khoe-San ancestry from the paternal line is greatly diminished in populations from Cape Town, the Cederberg Mountains, and Upington but remains more frequent in self-identified Indigenous ethnic groups. Strikingly, we estimate that Khoe-San Y chromosomes were experiencing unprecedented population growth at the time of European arrival. Our findings shed light on the patterns of admixture and population history of South Africa as the colonial frontier expanded.
(Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved.)
Competing Interests: Declaration of interests The authors declare no competing interests.
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Grant Information: R35 GM133531 United States GM NIGMS NIH HHS
Contributed Indexing: Keywords: Khoe-San; South Africa; Y chromosome; admixture; ancestry; colonialism; population genetics; sex bias
Entry Date(s): Date Created: 20250924 Date Completed: 20251003 Latest Revision: 20260603
Update Code: 20260603
PubMed Central ID: PMC12696499
DOI: 10.1016/j.ajhg.2025.08.012
PMID: 40992378
Database: MEDLINE
Description
ISSN:1537-6605
DOI:10.1016/j.ajhg.2025.08.012