Ghost DNA Hints at Africa’s Missing Ancient Humans

Ghost DNA Hints at Africa’s Missing Ancient Humans

Scientists reported on Wednesday that they had discovered evidence of an extinct branch of humans whose ancestors split from our own a million years ago. The evidence of these humans was not a fossil. Instead, the researchers found pieces of their DNA in the genomes of living people from West Africa.

Arun Durvasula and Sriram Sankararaman, two geneticists at the University of California, Los Angeles, described this so-called ghost archaic population in the journal Science Advances. Their discovery may shed light on human genetic diversity in Africa, which has been hard to chart until now because the fossil record is sparse.

The new study builds on a decade of research into ancient DNA extracted from human fossils. In 2010, a team of researchers published the first genome of a Neanderthal. Later, they found DNA from fossils in a Siberian cave called Denisova. That genetic material belonged to a second lineage of humans, called Denisovans, who proved to be closely related to Neanderthals.

The ancestors of Neanderthals and Denisovans split from our shared ancestor about 600,000 years ago, quite likely in Africa. They expanded into Eurasia, where the Neanderthals moved west while the Denisovans moved east. By roughly 40,000 years ago, both populations became extinct.

As that occurred, modern humans evolved in Africa. They later expanded into Eurasia, where they interbred with both Neanderthals and Denisovans. Today, all living humans carry some Neanderthal DNA. In addition, Aboriginal Australians as well as people in New Guinea and neighboring regions carry Denisovan DNA.

For the new study, Mr. Durvasula and Dr. Sankararaman carried out a large-scale comparison of genetic diversity in living humans, Neanderthals and Denisovans.

The researchers tracked how new variants of genes arose in each branch of humans. For the most part, the data fit the current thinking about human evolution. But in a few populations in West Africa, such as the Yoruba of Nigeria and the Mende of Sierra Leone, some of the DNA contained variants not found in other living humans, or even in Neanderthals or Denisovans.

“What it told us was that this was not a simple story,” Dr. Sankararaman said.

A few percent of the DNA in the living West Africans seemed to have arisen in a distant branch of humans that were not Homo sapiens, or other species in our genus known from their genes. Mr. Durvasula and Dr. Sankararaman’s model suggests that this ghost archaic population split as long as a million years ago from the lineage that led to modern humans, Neanderthals and Denisovans.

They estimated that the ancestors of West Africans and the ghost archaic population interbred roughly 50,000 years ago — intriguingly, around the time that modern humans in Eurasia also interbred with Neanderthals and Denisovans.

The scientists could not say what species of human the ghost archaic population belonged to. The fossil record in Africa offers only a few hints. A million years ago, Africa was home to a species known as Homo erectus. The oldest fossils of Homo sapiens date back 300,000 years, in Morocco. But researchers have also found a remarkable range of other fossils from our genus in Africa during that period of time.

One of the most intriguing is a human skull dating back just 11,200 years ago at a site in Nigeria called Iwo Eleru.

The first researchers who studied the remains linked them to living West Africans. But in 2011, a team of scientists took a more careful look at the Iwo Eleru skull and concluded it was an intermediate form between modern humans and Homo erectus.

Mr. Durvasula and Dr. Sankararaman speculate that fossils like Iwo Eleru might belong to the archaic ghost population.

“It is indeed possible,” said Isabelle Crevecoeur, a paleoanthropologist at the University of Bordeaux in France. But she cautioned that scientists still needed to learn a lot about the physical and genetic diversity of Africans before jumping to such a drastic conclusion. “I would favor a conservative approach,” she said.

The best test of the new study would ultimately be to get DNA out of a fossil, like the one at Iwo Eleru, and find a match to the segments identified by the scientists. Scientists have yet to succeed at that effort, because DNA quickly degrades in the tropics. But scientists have recently managed to get DNA from modern human remains in Africa dating back thousands of years, so there’s reason for hope.

“That’s the gold standard,” Dr. Sankararaman said. “I can’t wait for that to happen.”

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