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First DNA extracted from an ancient African skeleton shows widespread mixing with Eurasians

Africa is the birthplace of our species and the source of ancient migrations that spanned the globe. But it has missed out on a revolution in understanding human origins: the study of ancient DNA. Although researchers have managed to sequence the genomes of Neandertals from Europe, prehistoric herders from Asia, and Paleoindians from the Americas, Africa’s hot and humid climate has left little ancient DNA intact for scientists to extract. As a result, “Africa was left out of the party,” says anthropological geneticist Jason Hodgson of Imperial College London.

Until now. A paper published online this week in Science reveals the first prehistoric genome from Africa: that of Mota, a hunter-gatherer man who lived 4500 years ago in the highlands of Ethiopia. Named for the cave that held the remains, the Mota genome “is an impressive feat,” says Hodgson, who was not involved in the work. It “gives our first glimpse into what an African genome looked like prior to many of the recent population movements.” And when compared with the genomes of living Africans, it implies something startling. Africa is usually seen as a source of outward migrations, but the genomes suggest a major migration into Africa by farmers from the Middle East, possibly about 3500 years ago. These farmers’ DNA reached deep into the continent, spreading even to groups considered isolated, such as the Khoisan of South Africa and the pygmies of the Congo.

Anthropologists John and Kathryn Arthur of the University of South Florida, St. Petersburg, discovered the skeleton in 2012 at Mota Cave in southwest Ethiopia after local Gamo elders led the pair to the cave, a hiding place for the Gamo during wartime. The Arthurs unearthed the skeleton of an adult male beneath a stone layer and dated it to 4500 years ago using radio-carbon. The researchers analyzed the petrous bone of the inner ear, which can sometimes preserve more DNA than other bones.

DNA had indeed survived in the ear bone, perhaps aided by the cool temperatures in the highland cave. Researchers were able to sequence each DNA base more than 12.5 times on average, considered a high-quality genome. When population geneticist Andrea Manica and graduate student Marcos Gallego Llorente at the University of Cambridge in the United Kingdom analyzed the sequence, they found that the Mota man had brown eyes and dark skin, as well as three gene variants associated with adaptation to high altitudes; some peaks in the highlands reach 4500 meters, as high as the Matterhorn.

  	Researchers sequenced the genome of a 4500-year-old skeleton found in Mota Cave in the Horn of Africa.

Researchers sequenced the genome of a 4500-year-old skeleton found in Mota Cave in the Horn of Africa.

By comparing 250,000 base pairs from Mota’s genome with the same sites in individuals from 40 populations in Africa and 81 populations from Europe and Asia, the team found that Mota was most closely related to the Ari, an ethnic group that still lives nearby in the Ethiopian highlands. They zeroed in on the DNA that the Ari carry but Mota doesn’t, which was presumably added during the past 4500 years. They found that Mota lacks about 4% to 7% of the DNA found in the Ari and all other Africans examined. This new DNA most closely matches that of modern Sardinians and a prehistoric farmer who lived in Germany. Hints of these early farmers’ DNA previously had turned up in some living Africans, but Mota helped researchers zero in on the farmer’s genetic signature in Africa, and to establish when it arrived.

Manica suggests that both the European farmers and living Africans inherited this DNA from the same source—a population in the Middle East, perhaps Anatolia or Mesopotamia. Some of these Middle Easterners headed into Europe and Asia starting 8000 years ago, and were the first farmers of Europe. But other descendants of this population migrated into Africa, likely after Mota lived. This fits with traces of Middle Eastern grains found in Africa and dated to 3000 to 3500 years ago.

Because so many far-flung Africans still carry the farmers’ DNA, the study suggests a “huge” migration, Manica says. Farming had already been established in Africa by this time, but the newcomers likely had some advantage that explains why their genes spread. “It must have been lots of people coming in or maybe they had new crops that were very successful,” Manica says.

Population geneticist David Reich of Harvard University is struck by the magnitude of the mixing between Africans and Eurasians. He notes that “a profound migration of farmers moving from Mesopotamia to North Africa has long been speculated.” But, he says, “a western Eurasian migration into every population they study in Africa—into the Mbuti pygmies and the Khoisan? That’s surprising and new.”

Migrations into and out of Africa were likely complex and ongoing. “This study is significant on its own,” Hodgson says. “But hopefully it is only just the beginning of ancient African genomics.”

*Update, 1 February, 7:50 a.m.: The authors of the paper reported in this story have identified an error in their analysis and now conclude that the prehistoric “back migration” of West Eurasian farmers to Africa was less extensive than initially reported; it did not reach central and western Africa, such as the Mbuti pygmies or the Yoruba people of western Africa.

The error was spotted by researchers at Harvard University, who could not replicate the results and notified the authors, who then checked their analysis. Co-author Andrea Manica, a population geneticist at the University of Cambridge in the United Kingdom, has posted a note online explaining that incompatibility between two software packages used to compare Mota’s genome with the reference human genome led the software program to simply drop certain DNA variants, with the result that all living Africans seemed to have inherited more “Eurasian” DNA than they actually did.

“There is no longer any West Eurasian ancestry inferred in West and Central African populations,” says Harvard population geneticist Pontus Skoglund, who alerted Manica to the problem. “The genome sequence is otherwise beautiful … and the link between Mota and some East African populations [remains] robust. … This is how the scientific process goes sometimes.”