Who was the Nama people’s mystery man from the East?

About 200 years ago a mystery man from South Asia trekked beyond the reach of the Cape colony and settled among the Nama. Perhaps he was a slave or an outlaw; what is certain is that he went on to sire many children.

The man’s name is long forgotten, but he left his genetic fingerprint among the Nama who still live in the Northern Cape. A new genetic study found 15% of the Y chromosomes in a particular part of the population come from him.

The mystery man was a surprise in the study, which examined the Y chromosome of 1,200 participants from across the Western and Northern Cape. This chromosome is passed from fathers to their sons.

The study produces a snapshot of who was living in colonial-era South Africa and how these ancestors have shaped the modern-day gene pool of the nation.

The study found that between the 1600s and early 1800s the community was made up of Europeans, indigenous Khoe-Sān peoples and enslaved people from other corners of the world. Their genetic signatures were sequenced from saliva samples of the study participants.

Those who gave samples came from areas that include Cape Town and stretch as far as places where Nama and ǂKhomani San indigenous communities live in the Northern Cape. More than 90% of the participants identified as coloured.

The research reveals that the male European ancestors usually had Khoe-Sān women as partners.

“European females didn’t usually come to South Africa at the time the mystery man arrived, and Khoe-Sān females were available,” says Marlo Möller, an associate professor in the division of molecular biology & human genetics at Stellenbosch University. “Interestingly, later on, females such as orphans were imported from the Netherlands.”

The sexual interactions between Europeans and Khoe-Sān women were sometimes violent, with Europeans holding the power.

It is estimated that between 1652 and 1808 the Dutch East India Co enslaved about 63,000 people. They came from South and Southeast Asia, Madagascar and equatorial Africa.

“We have historical records of the names of men and women who were brought to Cape Town, but we don’t always know who survived or who were allowed to reproduce, which is why the study of genetics is so powerful here,” says Brenna Henn, an associate professor of anthropology at the University of California, Davis. She is a senior author of the research paper on the study that appeared in The American Journal of Human Genetics.

In Cape Town someone who self-identifies as coloured retains maybe about a 30% Khoe-Sān ancestry

—   Brenna Henn

What the geneticists also discovered was that European and Asian genes become less frequent the further away from Cape Town the samples are taken.

Many people who live in the Mother City still hold on to their Khoe-Sān heritage. “In Cape Town someone who self-identifies as coloured retains maybe about a 30% Khoe-Sān ancestry,” says Henn.

Asian genes are less prevalent in communities further away. The anomaly lies with the Nama and the South Asian mystery man, about whom little is known besides his genetic signature.

Henn and Möller can only guess who he was and why he singlehandedly had such an impact on Nama genetics.

“He was probably a slave, and we know that slaves eventually moved further north to farms and that some escaped and established their own communities,” says Henn.

“He must have had special attributes. Maybe he spoke Afrikaans and was able to negotiate between the local farmers and the indigenous community. Maybe he had local knowledge of farming techniques or supplies they didn’t have, such as guns, and that made him a more attractive partner.”

It is possible that one day the mystery man might be named. Henn says: “What you can do is to take all the lineages that are unique, map the surnames in the area and look for a common surname among those lineages.”

Beyond the value the study has for science, Möller and Henn found that people were eager to learn more about their heritage.

“People really want to know; they have a desire to recover their history, but they don’t have a mechanism to do so, because there are very few written records,” says Henn.

The plan is to undertake an even more fine-scale genomic analysis to answer questions about the colonial past. The researchers want to trace the routes that brought enslaved people to South Africa by identifying where in Asia and Africa they came from.

Henn wants to understand more about what happened to the last of the Khoi, who disappeared within living memory. “With some of the participants there are stories about Khoi people who spoke the language and lived in traditional matjieshuise. But they are not around any more. [Their descendants] didn’t go anywhere; they have just transitioned to Western-style housing.”