Modern Humans May Have More Neanderthal DNA Than Previously Thought

Neanderthals and early humans share a common ancestor that originated in Africa, but they evolved as separate species hundreds of thousands of years ago. By the time Homo sapiens emerged in Africa about 300,000 years ago, Neanderthal ancestors had already been living in Europe and Asia for some 100,000 years.​

Groups of Homo sapiens didn’t leave the African continent in large numbers until about 60,000 years ago, although smaller migration events to Eurasia took place long before. Scientists suspect populations of Homo sapiens could have traveled back-and-forth to the African continent several times, but evidence of such returns are scarce.

Thousands of physical artifacts and fossils—from tools to near complete skeletons—now tell us that early humans eventually lived near their Neanderthal cousins in Europe and Asia for at least a few thousand years. In the last decade, a growing body of genomic evidence shows that the species interbred—even as recently as 37,000 years ago—before Neanderthals went extinct. Scientists previously estimated that Neanderthals contributed anywhere from one to four percent of the DNA in people with European or Asian ancestry.

Because Neanderthals evolved outside of Africa, scientists assumed their DNA would not show up in the genomes of modern African populations. Previous studies have found only about 0.02 percent of Neanderthal DNA in modern African genomes.

However, new research published last week in Cell turns that assumption on its head with a groundbreaking new finding: People with African ancestry actually have close to 0.5 percent Neanderthal DNA in their genome. The study also found that Neanderthal DNA makes up roughly 1.7 and 1.8 percent of the European and Asian genomes, respectively.

This surprising discovery of heritage, however, does not show that Neanderthals and ancient Africans directly interbred, reports Maya Wei-Haas for National Geographic. Rather, it may provide evidence that populations of early humans went to Europe, mated with Neanderthals and then returned to Africa, mating with African populations that had never left.

“Our work highlights how humans and Neanderthals interacted for hundreds of thousands of years, with populations dispersing out of and back into Africa,” study author Joshua Akey, a geneticist at Princeton University, tells Bruce Bower at Science News.

Akey and his colleagues weren’t the first to propose the idea of Neanderthal heritage in African populations. Other groups have hypothesized that early migrations in and out of Africa might have mixed Neanderthal DNA into the continent’s human populations, explains Svante Pääbo, a geneticist at the Max Planck Institute for Evolutionary Anthropology who wasn’t involved in the study, in an interview with Gizmodo’s George Dvorsky. But these theories were difficult to uphold when the first Neanderthal genome was published in 2010 and no such signatures were found in modern African genomes, according to National Geographic.

However, African genomes have long been understudied. The overwhelming majority of genetics research continues to be conducted in people of European descent, a bias that scientifically ignores vast swaths of the modern human population. African lineages are so poorly understood that geneticists may have unintentionally compromised their results with incorrect assumptions, Akey explains in an email interview with Gizmodo. Previous methods to find Neanderthal sequences in modern human DNA, he says, would compare genomes against those from African populations, which were believed to have little to no Neanderthal content, to look for discrepancies. This method likely biased the final estimates of Neanderthal DNA in modern African populations.

To uncover traces of Neanderthal DNA in modern genomes in a more comprehensive fashion, Akey and his colleagues developed a new method to identify past instances of interbreeding, in part by directly comparing modern genetic sequences to those from Neanderthal remains. They then applied their technique to the genomes of 2,504 individuals from around the world, including people of East Asian, European, South Asian, American and African descent.

The method identified 17 million base pairs in African genomes as Neanderthal, while finding European genomes to contain 51 million base pairs of Neanderthal DNA and Asian populations with 55 million. (The human genome is made of 3 billion base pairs.) And when the team compared the three broad groups, they found that the Neanderthal signatures in the African genomes more closely resembled those of Europeans than East Asians.

The ultimate picture that emerges is one of multiple migrations between Africa and Eurasia, with early humans making the intercontinental hop possibly several times over. As University of Buffalo geneticist Omer Gokcumen, who was not involved in the study, tells Carl Zimmer of the New York Times that the results reshape our current perception of human history.

“[It’s] almost as a spider web of interactions, rather than a tree with distinct branches,” Gokcumen says.

David Reich, a geneticist at Harvard Medical School who was not involved in the study, isn’t quite sold on the web theory just yet, noting that the flow of genes back into Africa looks like “a really weak signal,” he tells the New York Times.

When migration out of Africa hit its peak between 10,000 and 60,000 years ago, subsets of this group then trickled back into Africa in the last 20,000 years, mixing Neanderthal heritage into the continent’s human genomes, Akey suggests.

But it’s also possible, Akey proposes, that an even earlier group of modern humans left Africa 200,000 years ago and mated with Neanderthals when they got to Europe, reports the New York Times. Therefore, when modern humans left again during the peak of migration, Neanderthals already had a little Homo sapiens DNA in their genome. (This hypothesis is perhaps backed up by a controversial study published in 2019 regarding a skull that would place modern humans in Greece some 210,000 years ago, notes National Geographic.)

However, the new study makes Reich think an earlier departure from Africa was possible, he tells the New York Times. “I was on the fence about that, but this paper makes me think it’s right,” he says.

Could we find out later that modern humans have even more Neanderthal ancestry than we think? The University of Wisconsin-Madison’s John Hawks, a paleoanthropologist who was not involved in the study, tells National Geographic that he certainly thinks so. He explains that the Neanderthal genome used in this analysis was from a specimen found in Siberia, which was likely not part of the population directly intermingling with modern humans leaving—or returning to—Africa.

Additionally, the team sampled only a limited number of modern African populations, and they can’t conclusively say whether their results apply to all people with African ancestry. As such, the new findings call for more studies in these populations, which remain neglected by most genetic research, says Sarah Tishkoff, a geneticist at the University of Pennsylvania who wasn’t involved in the study, in an interview with Science News.

More research will inevitably add even more complexity. But as Akey tells National Geographic, results like these—though not always simple—still point to humankind’s shared history. That message, at least, is easy to understand.

Katherine J. Wu | | READ MORE

Katherine J. Wu is a Boston-based science journalist and Story Collider senior producer whose work has appeared in National Geographic, Undark magazine, Popular Science and more. She holds a Ph.D. in Microbiology and Immunobiology from Harvard University, and was Smithsonian magazine's 2018 AAAS Mass Media Fellow.