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Geneticist Joshua Aki states that modern humans and Neanderthals interacted over a period of 200,000 years.

New genetic studies reveal extensive interbreeding and long-term interactions between Neanderthals, Denisovans and modern humans, suggesting a more integrated history than previously understood and supporting theories of Neanderthal assimilation into modern human populations.

After the discovery of the first Neanderthal bones in 1856, curiosity about these ancient hominins grew. How are they different from us? How many are like us? Did our ancestors get along with them? To fight them? Love them? The recent discovery of a group called the Denisovans, a Neanderthal-like group that inhabited Asia and South Asia, added its own set of questions.

Now, an international team of geneticists and AI experts is adding whole new chapters to our shared hominin history. Led by Joshua Aki, a professor at Princeton’s Lewis-Siegler Institute for Integrative Genomics, researchers have uncovered a history of genetic mixing and exchange that suggests a much more intimate relationship between these early human groups than previously thought.

“This is the first time geneticists have identified multiple waves of mixing between modern humans and Neanderthals,” said Liming Li, a professor in the Department of Medical Genetics and Developmental Biology at Southeast University in Nanjing, China, who performed the work as an associate scientist. a researcher in Aki’s lab.

“We now know that for most of human history we have had a history of contact between modern humans and Neanderthals,” Aki said. Hominins, our most direct ancestors, diverged from the Neanderthal family tree about 600,000 years ago, then developed our modern physical characteristics about 250,000 years ago.

Continuous interaction over millennia

“From then until the extinction of Neanderthals – that is, for about 200,000 years – modern humans interacted with Neanderthal populations,” he said.

The results of their work appear in the current issue of the journal Science.

Neanderthals, once stereotyped as slow and dim-witted, are now seen as skilled hunters and tool makers who treated each other’s injuries with sophisticated techniques and were well adapted to thrive in the cold European weather.

(Note: All of these hominin groups are humans, but to avoid saying “Neanderthals”, “Denisians”, and “ancient-versions-of-our-own-species-of-humans”, most archaeologists and anthropologists use the shorthand Neanderthals, Denisovans and modern people.)

Using genomes from 2,000 living humans, as well as three Neanderthals and one Denisovan, Aki and his team mapped gene flow between hominin groups over the past quarter of a million years. The researchers used a genetic tool they designed several years ago called IBDmix, which uses machine learning techniques to decode the genome. Previous researchers depended on comparing human genomes to a “reference population” of modern humans thought to have little or no Neanderthal or Denisovan ancestry DNA.

Aki’s team has found that even the mentioned groups, which live thousands of miles south of the Neanderthal caves, have traces of Neanderthal DNA, possibly carried south by travelers (or their descendants). With IBDmix, Akey’s team identified the first wave of contact around 200-250,000 years ago, another wave around 100-120,000 years ago, and the largest around 50-60,000 years ago.

Rethinking patterns of human migration

This contrasts sharply with previous genetic data. “To date, most genetic evidence suggests that modern humans evolved in Africa 250,000 years ago, remained there for the next 200,000 years, and then decided to spread out of Africa 50,000 years ago and go to the people of the rest of the world,” Aki said.

“Our models show that there was not a long period of stasis, but that shortly after the emergence of modern humans, we were migrating out of Africa and also returning to Africa,” he said. “For me, this story is about dispersal, that modern humans are moving around and encountering Neanderthals and Denisovans much more than we’ve previously acknowledged.”

This vision of humanity on the move coincides with archaeological and paleoanthropological research suggesting cultural and tool exchanges between hominin groups.

Li and Aki’s key insight was to look for modern human DNA in Neanderthal genomes, instead of the other way around. “Most of the genetic work in the last decade has really focused on how mating with Neanderthals has affected modern human phenotypes and our evolutionary history – but these questions are relevant and interesting the other way around,” Aki said.

They realized that the offspring of these first waves of Neanderthal-modern mating must have stayed with the Neanderthals, therefore leaving no record in living humans. “Because we can now include the Neanderthal component in our genetic studies, we’re seeing these earlier dispersals in ways we haven’t been able to before,” Aki said. The final piece of the puzzle was the discovery that the Neanderthal population was even smaller than previously thought.

Genetic modeling has traditionally used variation—diversity—as a proxy for population size. The more diverse the genes, the larger the population. But using IBDmix, Aki’s team showed that a significant amount of this apparent diversity came from DNA sequences that were derived from modern humans, with their much larger population.

As a result, the effective Neanderthal population was reduced from about 3,400 breeding individuals to about 2,400.

Taken together, the new findings paint a picture of how Neanderthals disappeared from the records about 30,000 years ago.

“I don’t like to say ‘extinction’ because I think the Neanderthals were pretty much swallowed up,” Aki said. His idea is that Neanderthal populations slowly shrank until the last survivors folded into modern human communities.

This “assimilation model” was first formulated by Fred Smith, a professor of anthropology at Illinois State University, in 1989. “Our results provide strong genetic evidence consistent with Fred’s hypothesis, and I think that’s really interesting.” , Aki said.

“Neanderthals have been on the brink of extinction for probably a very long time,” he said. “If you reduce their numbers by 10 or 20%, which our estimates do, that’s a significant reduction in an already at-risk population.”

“Modern humans were essentially like waves crashing on the beach, slowly but steadily eroding the beach. In the end, we just demographically overloaded Neanderthals and incorporated them into modern human populations.

Reference: “Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years” by Liming Li, Troy J. Comi, Rob F. Bierman, and Joshua M. Akey, 12 Jul 2024. Science.
DOI: 10.1126/science.adi1768

This research was supported by National Institutes of Health (grant R01GM110068 to JMA).