How a gene from Europe made Khoi-San skin lighter

It usually takes a long time for significant evolutionary changes to occur. However, the Khoi-San received a gene in a remarkable way that lightened their skin colour within only 2,000 years. This is a rare example of rapid and intense evolutionary adaptation in recent human history.

The gene responsible for this, SLC24A5, plays a key role in the light skin of European people. But the Khoi-San were already light in colour when ships from the Dutch East India Company (VOC) arrived here in 1652.

Genes and skin pigmentation

The story of the gene's arrival has been unravelled for the first time by professors Eileen Hoal and Marlo Möller from Stellenbosch University's Department of Molecular Biology and Human Genetics, who were part of an international research team that published its findings in the journal Proceedings of the National Academy of Sciences.

Hoal explains that the gene originated 30,000 years ago in Europe and is now present in everyone of European descent. However, it is one of many genes responsible for skin pigmentation.

After humans migrated out of Africa between 80,000 and 60,000 years ago, they kept moving — and sometimes returned. “The migration was not a one-time event; groups of people were moving back and forth all the time," says Hoal.

At some point, a group or groups had contact with the pastoralists of East Africa and transferred SLC24A5 to them. These were people who kept sheep and goats, no longer hunter-gatherers.

Thus, these people from East Africa were the ones who initially received the gene from individuals who migrated back to Africa thousands of years ago, technically people from contemporary Europe.

Migration

“Many pieces of evidence have been found in Southern Africa of the continued presence of sheep and goats, especially. People from East Africa migrated to Southern Africa with their sheep and goats and, of course, the gene," Hoal explains.

“For some reason, this gene was strongly selected for in the south. Why, we still don't know. Some of the Khoi-San groups also began to keep livestock." It is possible that with the arrival of sheep and goats, the people moved away from the coast and consumed less seafood, which is rich in vitamin D. This could have contributed to positive selection of the gene.

This genetic story could be traced back 2,000 years because it can be observed in the human genome (your complete genetic composition). It's almost like Hansel and Gretel's story with the bread crumbs (that don't disappear): Geneticists can reverse and step back on a genetic trail.

Möller explains that the influence of the gene was significant. They involved 450 individuals in the study and conducted a genome-wide analysis by tracing their ancestry in the Kalahari and Richtersveld regions, among the Nama and Khomani-San, as identified by the people themselves.

The gene is present in 55.5% of the Nama and 32.5% of the Khomani. In the contemporary Khoi-San as a group, it is present in 40%.

Since it is not the only gene determining pigmentation, it means 15% of the Khoi-San's light skin colour can be attributed to this gene. “In genetics, 15% is significant; just a few percent can make a difference," says Hoal.

She explains that the Khoi-San were spread throughout the entire country at the time, not just in the desert. This brought them into contact with other groups.

Click sounds

Around 1,500 years ago, the Bantu-speaking people, as referred to by science, migrated here from the north. They came into contact with the Khoi-San and picked up the click sounds that are part of the Xhosa language.

The third migration to South Africa was that of the colonisers, who also imported slaves from West and East Africa, and Southeast Asia. Significant mixing occurred from this. “Everyone in South Africa is mixed," says Hoal. 

In other work, the team found that having Khoi-San ancestry makes people more susceptible to tuberculosis. Some of the genes that make a person susceptible to the disease are more readily found in individuals with this  ancestry. The research continues.

“What we need to do is to better understand the genetics of populations in Africa because the composition and diversity are not the same as elsewhere. Most of the work is still being done among American and European populations," says Möller.

Many populations experienced a genetic bottleneck that left very few individuals.  This leads to a loss of genetic diversity, but it has not occurred in African populations, explains Hoal.

The lack of ethnic diversity in genetics has serious implications for science and medicine because the data does not include everyone. Involving African-Americans in a study may be relevant to their health and genetic diversity, but it does not represent the diverse population groups in Africa.

Prof Sarah Tishkoff, affiliated with the Department of Biology and Genetics at the University of Pennsylvania, said excluding population groups from studies is scientifically harmful, unfair, and may result in missing important genetic variants relevant to medicine.

In a study published in the journal Cell, she found that individuals included in genome-wide studies are 78% European, 10% Asian, 2% African and 1% Hispanic American, with 1% from other groups. This means these studies rely much too heavily on European genetics.

Genome-wide studies search for small genetic variations that occur more frequently in people with a specific disease, trait or condition compared to those without it. Human genetic variation is explained by differences in the evolutionary history of populations.

Only by understanding everyone and their relationship with diseases can the landscape of human variation be fully understood and represented.

• Sources: PNAS; Cell 

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