A team of scientists reported on Thursday that they had recovered the genome from a 4,500-year-old human skeleton in Ethiopia — the first time a complete assemblage of DNA has been retrieved from an ancient human in Africa.
The DNA of the Ethiopian fossil is strikingly different from that of living Africans. Writing in the journal Science, the researchers conclude that people from the Near East spread into Africa 3,000 years ago. In later generations, their DNA ended up scattered across the continent.
“It’s a major milestone for the field,” said Joseph Pickrell, an expert on ancient DNA at the New York Genome Center who was not involved in the new study. For decades, scientists had doubted that ancient DNA could survive in the tropics. The new study raises hopes that scientists can recover far older human genomes from Africa — perhaps dating back a million years or more.
“I would bet it’s not that far in the future,” said Lee Berger, a paleoanthropologist at the University of Witwatersrand who recently announced the discovery of an ancient humanlike species called Homo naledi.
In the 1980s, few scientists would have believed it possible to reconstruct an entire genome from the DNA in a fossil. Once a human or other animal dies, its DNA starts to fall apart. Bacteria swiftly colonize the corpse, overwhelming it with their own DNA.
But by the 1990s scientists were beginning to retrieve fragments of DNA and piece them together into longer segments. In 2010, researchers assembled the genome of a Neanderthal from 38,000-year-old fossils from Croatia.
In many other cases, researchers failed to find ancient DNA in human fossils. Because it was widely suspected that the heat and humidity in the tropics would destroy genetic material, many scientists flocked to places like Siberia to search for ancient DNA.
That skepticism proved to be unwarranted. In recent years, Ron Pinhasi, an archaeologist at University College Dublin, and his colleagues have been surveying different bones to see if any are particularly good for preserving DNA. They found that the bone surrounding the inner ear can hold an abundance of genetic material even when other bones have lost theirs.
As they reported last year, the scientists were able to pull out genomes from the ear bones of hundreds of Europeans who lived thousands of years ago. Their success gave them hope that they might be able to rescue ancient DNA from African skeletons as well.
They got their chance when John W. Arthur and Kathryn Weedman Arthur, archaeologists at the University of South Florida, and their colleagues uncovered the skeleton of a man in the Mota cave, in the highlands of southern Ethiopia. Mota, as the scientists refer to the man, was laid out in a ceremonial burial. His head rested on a pillowlike stone, his hands were folded under his body, and he was surrounded by stone tools.
The researchers sent Dr. Pinhasi a sample of the inner ear bone, hoping that he and his colleagues could fish out some DNA. They succeeded spectacularly, extracting enough DNA to reconstruct Mota’s entire genome.
Dr. Pinhasi and his colleagues also got some clues about what Mota was like by looking at some of his genes. He was probably brown-skinned and had brown eyes, for example. He also had genetic adaptations for living at high altitudes — the same adaptations found in Ethiopian highlanders today.
The scientists then sought to fit Mota into the history of humankind. Ethiopia is home to the oldest fossils of our species, dating back about 200,000 years. Humans later expanded across Africa. Later, sometime between 100,000 and 50,000 years ago, our species began to spread into Asia and Europe.
In recent years, scientists have found segments of DNA in Ethiopians and other Africans that bear a striking resemblance to those found in people from Europe and Asia. They proposed that there was a “backflow” of genes into Africa roughly 3,000 years ago.
Dr. Pinhasi and his colleagues found that Mota, who lived 1,500 years before that time, had no trace of Eurasian DNA in his genome. “It’s an African without this backflow,” he said.
Armed with this early genome, Dr. Pinhasi and his colleagues took a new look at the spread of Eurasian genes into Africa. They pinpointed the source of the DNA to ancient farmers in the Near East. Once those people spread into Africa, their DNA traveled across the continent over the generations.
“The most astonishing thing is there’s quite a lot of backflow in all modern African populations,” said Dr. Pinhasi. He and his colleagues estimate that 7 percent of the genomes of the Yoruba people of Nigeria are of Eurasian origin. In the genomes of Mbuti pygmies who live in the rain forest in the Democratic Republic of Congo, 6 percent of the DNA comes from Eurasians.
Ryan L. Raaum, an anthropological geneticist at Lehman College, part of the City University of New York, called the new study “fantastic” but questioned its conclusions. If people from the Near East moved into Africa, he argued, a drastic shift in the archaeology of the region would logically follow. But no such shift occurred.
It is also possible that Eurasian DNA moved into Africa earlier than 3,000 years ago, Dr. Raaum argued. Mota might have simply lived in an isolated community that never encountered people with those genes.
The best way to test the conclusions of Dr. Pinhasi and his colleagues, Dr. Raaum said, would be to gather more DNA from African fossils of the same age. If the researchers are right, they would also lack Eurasian DNA. “Then the argument starts to seem a lot more plausible,” said Dr. Raaum.
Dr. Pinhasi is ready to look for those skeletons. “We need more genomes across space and time,” he said.