A landmark DNA study led by an international team including researchers from Stellenbosch University has confirmed what many in Cape Town’s Coloured communities have long maintained: Khoe-San ancestry runs deep in their bloodlines, surviving centuries of colonisation, displacement and forced migration.
The study, published in the journal Science Advances on 2 September 2026, analysed the largest set of South African Coloured (SAC) genetic samples ever assembled from outside of Cape Town — 997 individuals drawn from communities across the Cederberg, the Great Karoo, the Richtersveld, the Middle Orange River and the southern Kalahari near Upington.
The findings are unambiguous. The paper reports that these communities ‘retain majority Khoe-San genetic ancestry (>48%), suggesting the persistence of Khoe-San ancestry to the present day’.
A gradient from the Cape to the Kalahari
The research reveals a striking geographic pattern. Khoe-San ancestry is lowest — roughly 40% — in communities closest to Cape Town, where centuries of European settlement and the forced importation of enslaved people left a deeper genetic imprint. It rises steadily as one moves inland and northward, reaching approximately 80% among communities in the southern Kalahari.
This gradient, the authors argue, reflects the Cape Colony’s role as the earliest and most intense centre of European and enslaved-person gene flow. Communities farther from the colonial epicentre retained more of their indigenous Khoe-San heritage.
For readers in TygerBurger‘s coverage areas — Bonteheuwel, Elsies River, Ravensmead, Belhar and the wider northern suburbs — the study’s geographic comparison suggests that communities nearer to Cape Town carry roughly 40% Khoe-San ancestry, with higher proportions of European and Asian ancestry introduced through colonial settlement and the Indian Ocean slave trade. The further one travels from the Cape, the more pronounced the indigenous component becomes.
Not a single story, but many threads
The study is careful to emphasise that these communities are not genetically ‘pure’ Khoe-San populations. Rather, they are admixed populations in which Khoe-San ancestry remains substantial but sits alongside contributions from at least five other ancestral sources.
The researchers assembled a comprehensive reference panel of 1 165 individuals representing six broad genetic ancestries: Niger-Congo, Khoe-San, European, South Asian, Southeast Asian (Indonesian) and East Asian — with more than 120 samples representing each ancestry.
“We include populations to capture western and eastern African Bantu expansion streams, five East African populations, 130 Indonesian genomes, and more than 500 individuals representing four Khoe and San populations to capture both northern and southern Kalahari genetic signals,” the authors write.
The final merged dataset comprised 806 460 autosomal markers, analysed using Illumina’s H3Africa array, which screened more than 2.2 million single-nucleotide polymorphisms (SNPs) in the 620 newly collected samples.
Tracing the Indian Ocean Slave Trade
One of the study’s most significant findings relates to the genetic legacy of the Indian Ocean slave trade. The researchers were able to trace specific ancestry signals to Indonesian islands including Sulawesi, Java and Flores — a direct genetic fingerprint of the enslaved people brought to the Cape from the Dutch East Indies.
“Signatures of the Indian Ocean slave trade can be traced to Indonesian islands such as Sulawesi, Java, and Flores,” the paper states, “while the South Asian ancestry is regionally non-specific.”
In other words, while the Indonesian contribution can be pinned to specific islands, the South Asian signal — linked to enslaved people brought from the Indian subcontinent — is more diffuse and could not be attributed to a single region.
A distinctive Khoe-San signature
Crucially, the study did not simply treat “Khoe-San” as a single, homogeneous category. By isolating the Khoe-San ancestry component from the admixed genomes, the researchers showed that it is “intermediate between the ≠Khomani San and Nama, and distinct from Kalahari Khoe-San populations”.
This means the Khoe-San ancestry preserved in these communities is most closely related to southern Kalahari populations — the ≠Khomani San and the Nama — rather than to the central and northern Kalahari groups such as the !Xoo and Ju|’hoansi of Botswana. The Kalahari Desert, the authors note, appears to have acted as a barrier to gene flow, separating the southern populations from their central and northern counterparts.
Within that southern signal, the study found further fine-scale differences. In multidimensional-scaling analyses, the Karoo and Orange River population centroids clustered closer to the ≠Khomani San than to the Nama, indicating that the reconstructed ancestry does not correspond to a single, uniform population but reflects a mosaic of related but distinct indigenous groups.
Correcting a historical misconception
The paper opens by addressing a persistent narrative head-on. “Popular opinion often implies that such populations do not contribute to the ancestry of contemporary South Africans,” the authors write, referring to the San and Khoekhoe groups who once populated far southern Africa.
The study’s central contribution is to demonstrate the opposite — that Khoe-San ancestry did not disappear through colonial-era displacement, admixture or social classification, but persists as a living, measurable component of present-day South African communities.
The authors are cautious in their language. The data “suggest[s] the persistence of Khoe-San ancestry to the present day”, rather than claiming that modern communities map unchanged onto a single precolonial group. The study reports population-level estimates, not individual ancestry tests or a citywide census.
Local research, global collaboration
The study carries particular significance for the Western Cape. Two of the paper’s authors — Dr Caitlin Uren and Professor Marlo Möller — are based at the South African Medical Research Council Centre for Tuberculosis Research within the Division of Molecular Biology and Human Genetics at Stellenbosch University’s Faculty of Medicine and Health Sciences.
The research was led by Stacy L. Edington of Baylor University and Austin W. Reynolds of the University of North Texas Health Science Center, with senior authorship shared with Brenna M. Henn of the University of California, Davis. The full author list also includes Dana R. Al-Hindi, Neus Font-Porterias, Alexandra Surowiec, William J. Palmer, Justin W. Myrick and Paul J. Norman.
The work was supported by grants from the US National Institutes of Health and the National Science Foundation.
What it means for Cape communities
For the communities of Cape Town’s northern suburbs and the wider Western Cape, the study offers scientific confirmation of a heritage that many have spoken of for generations. The Khoe-San peoples — the original inhabitants of southern Africa — did not vanish. Their ancestry survives in the DNA of their descendants, woven together with the threads of every migration, settlement and forced journey that shaped the Cape’s complex past.
The full paper, “Recovering the precolonial population structure of Khoe-San descendant populations”, is published in Science Advances, Volume 12, Issue 36 (DOI: 10.1126/sciadv.adz7115).
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