Into Africa: Ancient skeleton sheds light on reverse migration

4,500-year-old Ethiopian provides baseline for measuring Eurasian DNA in modern Africans

Mota Cave

HOME SWEET GENOME  A 4,500-year-old man’s skeleton found in Ethiopia’s Mota Cave has yielded the first ancient human genome from Africa. Rocks placed over the man’s burial were cleared away before excavating the skeleton.

Both: Kathryn and John Arthur

DNA from a man who lived about 4,500 years ago in what’s now Ethiopia has illuminated a surprisingly influential migration of Eurasians into Africa 1,500 years after his death.

That back-to-Africa trek occurred around 3,000 years ago and left a substantial genetic imprint on populations now living throughout sub-Saharan Africa, say University of Cambridge evolutionary biologist Marcos Gallego Llorente and his colleagues. The East African man’s genome, the first map of ancient human DNA from Africa, helped to determine that a population closely related to Europe’s first farmers made major inroads in Africa, the researchers report online October 8 in Science.

DNA was extracted from a man’s skeleton excavated from Ethiopia’s Mota Cave in 2012 and radiocarbon dated to about 4,500 years ago. Dry, cool conditions in the cave helped to preserve DNA in the skeleton. Genetic material was taken from a thick bone at the base of the skull. DNA survives best in dense, thick bone.

The ancient African genome provides a reference for estimating what human DNA looked like on that continent shortly before Eurasians showed up. It also shines a light on Africans’ genetic makeup before speakers of an early Bantu language spread from West Africa into central and southern regions around 3,000 years ago. The Bantu expansion reshaped Africa’s population genetics and may have helped spread Eurasian gene variants throughout the continent, Llorente’s team suspects.

The new study was inspired by an analysis of DNA from modern populations suggesting that Europeans or West Asians reached East Africa roughly 3,000 years ago and passed on genetic variants that populations in all three regions now share (SN Online: 5/16/13). Evolutionary geneticist Joseph Pickrell, now at the New York Genome Center in New York City, led that effort. “It’s quite plausible that a population related to early Neolithic farmers of Europe migrated into eastern Africa sometime after 4,500 years ago,” Pickrell says.

Other DNA comparisons among modern populations show genetic contributions from Eurasians in East and West Africa, says Harvard University geneticist Pontus Skoglund. But armed with the first ancient African genome as a baseline from a time before migration into Africa, Llorente’s team finds a “very surprising” contribution of Eurasian ancestry — even in Central Africa’s Mbuti people, a pygmy group, Skoglund says.

About 6 percent of Mbuti DNA comes from Eurasians, the new study finds. West Africa’s Yoruba people carry a 7 percent genetic contribution from Eurasians. That figure reaches 18.5 percent in South African groups and as high as 47 percent in East African populations.

“My guess is that these [Eurasians] were farmers who left the Near East [in or around modern-day Turkey] and perhaps colonized the Arabian Peninsula before migrating into East Africa,” speculates study coauthor Ron Pinhasi, an archaeologist at University College Dublin.

Agriculture had already spread into Europe from the Middle East starting about 7,000 years ago, during what’s known as the Neolithic period. Investigators don’t know where in Africa the roving outsiders first made their genetic mark.

Genetic links to ancient Eurasian farmers also appear in present-day descendants of the 4,500-year-old Ethiopian man, Llorente’s team reports. DNA from today’s Sardinians and a roughly 7,000-year-old Central European farmer display close connections to DNA from living Ethiopians, who share the most gene variants with the ancient African individual. Sardinians have previously been identified as the closest modern relatives of early European farmers.

The new evidence of Eurasian farmers’ genetic legacy in Africa “tells us about the power in the innovations that drove the agricultural revolution in Europe,” says evolutionary geneticist Mattias Jakobsson of Uppsala University in Sweden.

Why Eurasian farmers migrated into Africa 3,000 years ago is unclear. But around that time, Eurasian crops such as wheat and barley appeared in East Africa, perhaps brought by the newcomers.

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