Not so isolated: Khoisan tribes have European DNA Ariadne Van Zandbergen/Alamy

Call it humanity’s unexpected U-turn. One of the biggest events in the history of our species is the exodus out of Africa some 65,000 years ago, the start of Homo sapiens‘ long march across the world. Now a study of southern African genes shows that, unexpectedly, another migration took western Eurasian DNA back to the very southern tip of the continent 3000 years ago.

According to conventional thinking, the Khoisan tribes of southern Africa, have lived in near-isolation from the rest of humanity for thousands of years. In fact, the study shows that some of their DNA matches most closely people from modern-day southern Europe, including Spain and Italy.

Because Eurasian people also carry traces of Neanderthal DNA, the finding also shows – for the first time – that genetic material from our extinct cousin may be widespread in African populations.


The Khoisan tribes of southern Africa are hunter-gatherers and pastoralists who speak unique click languages. Their extraordinarily diverse gene pool split from everyone else’s before the African exodus.

Ancient lineages

“These are very special, isolated populations, carrying what are probably the most ancient lineages in human populations today,” says David Reich of Harvard University. “For a lot of our genetic studies we had treated them as groups that had split from all other present-day humans before they had split from each other.”

So he and his colleagues were not expecting to find signs of western Eurasian genes in 32 individuals belonging to a variety of Khoisan tribes. “I think we were shocked,” says Reich.

The unexpected snippets of DNA most resembled sequences from southern Europeans, including Sardinians, Italians and people from the Basque region (see “Back to Africa – but from where?“). Dating methods suggested they made their way into the Khoisan DNA sometime between 900 and 1800 years ago – well before known European contact with southern Africa (see map).

Archaeological and linguistic studies of the region can make sense of the discovery. They suggest that a subset of the Khoisan, known as the Khoe-Kwadi speakers, arrived in southern Africa from east Africa around 2200 years ago. Khoe-Kwadi speakers were – and remain – pastoralists who make their living from herding cows and sheep. The suggestion is that they introduced herding to a region that was otherwise dominated by hunter-gatherers.

Khoe-Kwadi tribes

Reich and his team found that the proportion of Eurasian DNA was highest in Khoe-Kwadi tribes, who have up to 14 per cent of western Eurasian ancestry. What is more, when they looked at the east African tribes from which the Khoe-Kwadi descended, they found a much stronger proportion of Eurasian DNA – up to 50 per cent.

That result confirms a 2012 study by Luca Pagani of the Wellcome Trust Sanger Institute in Hinxton, UK, which found non-African genes in people living in Ethiopia. Both the 2012 study and this week’s new results show that the Eurasian genes made their way into east African genomes around 3000 years ago. About a millennium later, the ancestors of the Khoe-Kwadi headed south, carrying a weaker signal of the Eurasian DNA into southern Africa.

The cultural implications are complex and potentially uncomfortably close to European colonial themes. “I actually am not sure there’s any population that doesn’t have west Eurasian [DNA],” says Reich.

“These populations were always thought to be pristine hunter-gatherers who had not interacted with anyone for millennia,” says Reich’s collaborator, linguist Brigitte Pakendorf of the University of Lyon in France. “Well, no. Just like the rest of the world, Africa had population movements too. There was simply no writing, no Romans or Greeks to document it.”

Twist in tale

There’s one more twist to the tale. In 2010 a research team – including Reich – published the first draft genome of a Neanderthal. Comparisons with living humans revealed traces of Neanderthal DNA in all humans with one notable exception: sub-Saharan peoples like the Yoruba and Khoisan.

That made sense. After early humans migrated out of Africa around 60,000 years ago, they bumped into Neanderthals somewhere in what is now the Middle East. Some got rather cosy with each other. As their descendants spread across the world to Europe, Asia and eventually the Americas, they spread bits of Neanderthal DNA along with their own genes. But because those descendants did not move back into Africa until historical times, most of this continent remained a Neanderthal DNA-free zone.

Or so it seemed at the time. Now it appears that the Back to Africa migration 3000 years ago carried a weak Neanderthal genetic signal deep into the homeland. Indeed one of Reich’s analyses, published last month, found Neanderthal traces in Yoruba DNA (Nature, DOI: 10.1038/nature12886).

In other words, not only is western Eurasian DNA ancestry a global phenomenon, so is having a bit of Neanderthal living on inside you.

Journal reference: PNAS, DOI: 10.1073/pnas.1313787111

Back to Africa – but from where? Reich and his colleagues found that DNA sequences in the Khoisan people most closely resemble some found in people who today live in southern Europe. That, however, does not mean the migration back to Africa started in Italy or Spain. More likely, the migration began in what is now the Middle East. We know that southern Europeans can trace their ancestry to the Middle East. However, in the thousands of years since they – and the ancestors of the Khoisan – left the region, it has experienced several waves of immigration. These waves have had a significant effect on the genes of people living in the Middle East today, and and means southern Europeans are much closer to the original inhabitants of the Levant than modern-day Middle Easterners.