Some West Africans may have genes from an ancient ‘ghost’ hominid

An ancient, humanlike population still undiscovered in fossils left a genetic legacy in present-day West Africans, a new study suggests.

These extinct relatives of Homo sapiens passed genes to African ancestors of modern Yoruba and Mende people starting around 124,000 years ago or later, say UCLA geneticists Arun Durvasula and Sriram Sankararaman. Surviving DNA of those ancient hominids is different enough from that of Neandertals and Denisovans to suggest an entirely different hominid was the source.

Yoruba and Mende groups’ genomes contain from 2 to 19 percent of genetic material from this mysterious “ghost population,” the scientists report February 12 in Science Advances. Some DNA segments passed down from the mysterious Homo species influence survival-enhancing functions, including tumor suppression and hormone regulation. Those genes likely spread rapidly among modern West Africans, the investigators suspect.

DNA from Han Chinese in Beijing as well as Utah residents with northern and western European ancestry also showed signs of ancestry from the ancient ghost population, Durvasula and Sankararaman found. But DNA from those two groups was not studied as closely as that from the Yoruba and Mende people.

The report adds to recent evidence that interbreeding of ancient people with various Homo species played a bigger role in the evolution of modern Africans than has generally been assumed. For instance, after leaving Africa around 60,000 to 80,000 years ago, H. sapiens groups interbred with European Neandertals before taking Neandertal DNA back to Africa starting around 20,000 years ago, another team has concluded (SN: 1/30/20). That study found that Neandertal DNA accounts for, on average, about 0.5 percent of individual Africans’ genomes, far more than reported in earlier studies. Most present-day people outside Africa carry about three times as much Neandertal DNA as Africans do.

Ghost hominid DNA and Neandertal DNA appear to have made separate inroads among African H. sapiens at around the same time, says geneticist Iain Mathieson of the University of Pennsylvania Perelman School of Medicine, who did not participate in the new study.

Although ancient humans trekking back to Africa already might have mated with members of the ancient ghost population, “it is more likely that interbreeding happened in Africa,” Sankararaman says. That possibility is supported by the fact that several late Stone Age African H. sapiens fossils — some dating to as late as around 16,000 years ago — display traits like those of much older Homo species, including Neandertals, he says.

Precisely how these genetic exchanges played out is hard to know because researchers lack any fossils from the ancient ghost population from which to extract examples of its DNA, says geneticist Pontus Skoglund of the Francis Crick Institute in London. But the new study makes a good case for DNA transmission from a poorly understood hominid population to ancestors of West Africans today, he says.

Durvasula and Sankararaman compared genomes of 405 West Africans — more than half either Yoruba or Mende — with ancient DNA from a roughly 44,000-year-old Eastern European Neandertal fossil and a Denisovan fossil from Siberia dating to at least around 51,000 years ago. Patterns of single DNA unit changes, or SNPs, enabled the researchers to identify areas across Yoruba and Mende genomes that were inherited from a line of ancient hominids other than Neandertals and Denisovans. That ghost population diverged from direct ancestors of present-day Yoruba and Mende more than 1 million years ago, the scientists estimate.

A 2012 investigation suggested that 15 modern African hunter-gatherers had inherited about 2 percent of their DNA from an unknown hominid species that split from ancestors of people today around 1.1 million years ago (SN: 7/31/12). It’s unclear whether ancient DNA identified in that study and in the new report trace back to the same hominid species, Sankararaman says.