A genomic analysis of over 600 people from across South Africa reveals the enduring legacy of Indigenous ancestry in the country’s modern population, a history often obscured by its colonial past.
In a study appearing in Science Advances, researchers analyzed genetic samples from individuals who self-identified as South African Colored, a term denoting mixed ancestry. The researchers found that modern populations of this group in the Western and Northern Cape provinces retain majority Khoe-San genetic ancestry, exceeding 48%.
“This is the first study to sample across a wide geographic area in this part of southern Africa,” said study co-author Austin Reynolds, a former UC Davis postdoctoral scholar who is now an assistant professor of microbiology, immunology and genetics at UNT Health Fort Worth. “Several studies have been done before closer to Cape Town, which was historically the colonial center, and studies have been done further north in Khoe-San communities as well, but we’re filling in that geographic gap.”
How did the colonial slave trade shape South African ancestry?
The Khoe-San have lived in southern Africa for thousands of years.
“The Khoe-San are the Indigenous peoples of southern Africa and they are two distinct cultural groups that share a language family and some genetic ancestry,” said Reynolds, who worked in the lab of Brenna Henn, an associate professor of anthropology at UC Davis and another co-author of the study. “The San were historically foragers and the Khoe were historically pastoralists in the region.”
The arrival of the Dutch East India Company in 1652 initiated a colonial period in the region that lasted hundreds of years. This era, shaped by the slave trade, introduced not only European ancestry into southern African populations but also ancestry from western and eastern Africa, South Asia, Malaysia, Madagascar and Indonesia — regions also shaped by the slave trade.
Due to systematic displacement that occurred during this period, few modern South Africans self-identify as a member of the Khoe-San group. The new research, however, shows that the Khoe-San genetic legacy persists to this day.
What does genetics reveal about Khoe-San ancestry?
The 620 newly collected genetic samples span four southern African regions, including the Cederberg, Karoo, Middle Orange River and around the city of Upington.
“We can track through ancestry patterns how this colonial frontier spread in space and time,” Reynolds said. “We can see that reflected in the proportion of Khoe-San ancestry in our study communities.”
Additionally, the researchers pinpointed through their analyses the likely source of East Asian ancestry identified in genetic samples of individuals self-identifying as South African Colored. The genomic analyses revealed Indonesia as the likely source population. The finding aligns with the historical record, which identified one-fourth of all enslaved individuals at the Cape Colony as of Malay and Indonesian descent.
“The East Asian components of the ancestry look really similar to contemporary Indonesian islanders today, which fits really well with the historical record” Reynolds said. “We know the Dutch had slave ports on certain islands of Indonesia, like Java. The history is well-recorded, but up until this point we haven’t been able to look at it from a genetic perspective.”
How can genomics help reconstruct South Africa’s history?
Reynolds said the research dovetails with a larger movement to preserve and revitalize connections to Khoe-San ancestry in South Africa.
“This work is part of a broader recognition of this history for these communities,” he said. “There are lots of people working on this, including us, who are trying to get more fine-grained ancestries and reconstructing more recent historic patterns of genetic movement.”
Reynolds and his colleagues hope to dig deeper into this history. They want to collect genetic samples countries north of South Africa, such as Botswana and Namibia, to track pre-colonial genetic patterns.
“We want to work with our colleagues who do ancient DNA research to get at not just contemporary patterns but also the prehistoric patterns,” Reynolds said. “I think there are some exciting ways we can go.”
This research was supported by the National Institutes of Health and the National Science Foundation.
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