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A genomic analysis of over 1,200 people from across South Africa reveals how colonial-era European, Indigenous Khoe-San peoples, and enslaved people contributed to the modern-day gene pool in South Africa.

Publishing in The American Journal of Human Genetics, found that genes inherited from both colonial Europeans and enslaved people are most common in Cape Town and become less frequent with distance from the colony's epicenter.

The results also show that European ancestors were more likely to be male, whereas Indigenous Khoe-San ancestors were more likely to be female.

"These genetic data show the direct impact of European colonialism on population structure in southern Africa," says first author Austin Reynolds, human geneticist at UNT Health Fort Worth.

"The patterns we found are more similar to what we see in Mexico and South America, where Indigenous communities were variously incorporated into the colonial way of life, compared to the US, where there was less incorporation of Indigenous communities."

In 1652, the Dutch East India Company (VOC) opened a small trading station in what is now Cape Town, and European colonizers continued to settle in the area for the next 250 years.

Between 1652 and 1808, the VOC enslaved around 63,000 people from equatorial Africa, South and South-East Asia, and Madagascar and brought them to the region.

The VOC also hired laborers from the local Indigenous Khoe-San communities. Sexual interactions between these groups—which were sometimes violent, the authors note—resulted in communities of people with multiple ancestries.

"We have historical records of the names of men and women that were brought into Cape Town, but we don't always know who survived, or who was allowed to actually reproduce, which is why the genetics is so powerful here," says senior author Brenna Henn, anthropologist at the University of California, Davis.

To understand how European colonizers, Indigenous peoples, and enslaved people contributed to the genomes of modern-day South Africans, the researchers analyzed genomes from over 1,200 contemporary individuals from different regions in South Africa, spanning from southern Cape Town to Nama and ≠Khomani San Indigenous communities living in northern and north-eastern South Africa.

Over 90% of the study's participants identify as "Colored," an Apartheid-era institutionalized racial category.

"We tried to capture the temporal and geographic component of the colonial period by sampling all the way from the tip of the Cape to the very border with Botswana and Namibia," says Henn.

By comparing these genomes to those in publicly available datasets, the researchers were able to estimate how much of each person's ancestry is derived from the various lineages. They also investigated whether male and female individuals of different lineages were more or less likely to leave descendants by comparing genes on each person's X and Y chromosomes to their non-sex chromosomes.

Across geographic regions, there was a male sex bias for European ancestry, meaning that European genetic sequences were predominately inherited from male ancestors.

In contrast, there was a female bias for Khoe-San ancestry, indicating that ancestors from these lineages were more often female. Enslaved people from equatorial Africa and South and South-East Asia also contributed to the gene pool, but there was not a sex bias for these lineages.

European and Asian genes were less frequent further from Cape Town, and the researchers estimated that these genes arrived earliest in Cape Town and latest in the communities that are most distant from the Cape.

"This matches with the historical record, where Cape Town was the colonial center, and people moved out slowly over the past few hundred years and set up homes or incorporated themselves into communities one way or another," says Reynolds.

For the Nama and ≠Khomani San, the researchers estimated that there was a single influx of European ancestry into each population around seven to eight generations or 210–240 years ago.

Genes from enslaved people were also present in these Indigenous communities. Notably, the researchers found that 15% of all Y chromosomes in the Nama bear genetic segments from Asian lineages, but these same sequences were not present in the ≠Khomani San.

"These men were brought into Cape Town, and they managed to either be freed or escape all the way north—it's a 12-hour drive from the Cape to those communities now, so it's a pretty long distance," says Henn. "And then they actually managed to become incorporated into those communities, and today their male descendants speak Nama and practice Nama culture."

In the future, the researchers plan to do a more fine-scale genomic analysis of where exactly in Asia and equatorial Africa, the enslaved people originated.

"I'm also very interested in tracing some of these Y chromosome lineages that were disproportionately successful in one area versus another area, for example, to see whether they are linked to particular surnames," says Henn.