The Khoe-San in Southern Africa split off early from other Africans, but carry DNA from East African herders.

Roger de la Harpe/Newscom

Updated: First big efforts to sequence ancient African DNA reveal how early humans swept across the continent

*Update, 21 September, 12 p.m.: In the first ever large-scale study of ancient African genomes, researchers have found clues to how early farmers and hunter-gatherers swept across the continent thousands of years ago, they report today in Cell. Science covered this study—and a related one on African migration—in early July, when the results were presented at the annual meeting of the Society for Molecular Biology & Evolution in Austin.

Here is our original story, posted on 6 July:

AUSTIN—The study of ancient human DNA has not been an equal opportunity endeavor. Early Europeans and Asians have had portions of their genomes sequenced by the hundreds over the past decade, rewriting Eurasian history in the process. But because genetic material decays rapidly in warm, moist climates, scientists had sequenced the DNA of just one ancient African. Until now.                                                                      

This week, at the annual meeting of the Society for Molecular Biology & Evolution here, scientists announced that they had partially sequenced 15 ancient African genomes, with representatives from all over sub-Saharan Africa. And another group—whose work is still unpublished—has sequenced seven more ancient humans from South Africa. “[Finding] ancient genomes from Africa is pretty amazing,” says Anna-Sapfo Malaspinas, a population geneticist at the University of Bern, who was not involved in either project.

Africa has long been called the “cradle of humanity,” from which our earliest human ancestors spread across the rest of the world some 50,000 years ago. Africa is also where people—ancient and modern—are most genetically diverse. But how such groups, from the Hadza of East Africa to the Khoe-San of Southern Africa, came to be is a mystery. That’s in part because some 2000 years ago, early adopters of agriculture known as the Bantu spread across the continent, erasing the genetic footprint of other Africans. The one ancient African genome that has been sequenced—an Ethiopian who lived some 4500 years ago—has shed little light on this mystery.   

Pontus Skoglund knew there had to be more to the story. So the Harvard University evolutionary geneticist and his colleagues obtained DNA from 15 ancient Africans from between 500 and 6000 years ago, some before the Bantu expansion. In addition, Skoglund’s team got DNA data from 19 modern populations across Africa for comparison, including from large groups like the Bantu and smaller ones like the Khoe-San and the Hadza.

For the most part, the ancient DNA was most similar to that of people living in the same places where the bones were found, Skoglund reported. But some interesting exceptions showed intermingling among various groups. “It’s really exciting to see in Africa that there was already this ancient admixture,” says Simon Aeschbacher, a population geneticist from the University of Bern who was not involved with the work. “There must have been population movements in early Africa.”

The ancient genomes indicate that Southern Africans split off from Western Africans several thousand years ago, and subsequently evolved key adaptations that honed their taste buds and protected them from the sun. Around 3000 years ago, herders—possibly from today’s Tanzania—spread far and wide, reaching Southern Africa centuries before the first farmers. But modern Malawians, who live just south of Tanzania, are likely descended from West African farmers rather than local hunter-gatherers, Skoglund says. Indeed, the analysis suggests that West Africans were early contributors to the DNA of sub-Saharan Africans. But even these DNA donors were a hodgepodge of what are now two modern groups—the Mende and the Yoruba. And one ancient African herder showed influence from even farther abroad, with 38% of their DNA coming from outside Africa.  

Another study focused on Southern Africa, where some researchers think modern Homo sapiens evolved. Evolutionary geneticist Carina Schlebusch and her colleagues at Uppsala University in Sweden partially sequenced seven ancient genomes: three from 2000-year-old hunter-gatherers and four from 300- to 500-year-old farmers. They also included modern DNA in their analyses.

The more modern farmers did have Bantu DNA in their genomes, but the ancient hunter-gatherers predated the spread of the Bantu, she and her colleagues reported last month on the preprint server bioRxiv. Their other findings parallel Skoglund’s discoveries: Nine percent to 22% of the DNA of these farmers’ modern descendants—including the southern Khoe-San—comes from East Africans and Eurasian herders.

Schlebusch’s analysis reaches even deeper into human history than does Skoglund’s, as her team used the ancient and modern genomes to estimate that the hunter-gatherers she studied split off from other groups some 260,000 years ago, about the age of the oldest H. sapiens fossil. Having that date “lets us start to think about questions like where, and how, anatomically and behaviorally modern humans evolved,” says Iain Mathieson, an evolutionary geneticist at Harvard. Whether this date survives peer review after publication is yet to be seen.  

Aeaschbacher has a simple solution to resolve such uncertainties: sequencing more ancient African genomes. “There’s a deep-seated need to understand this,” he says. How ancient Africans divided into groups and when and how they moved around “could have a strong impact on what shapes present-day humans.”