Geneticists are rewriting the narrative of Neanderthals and other ancient humans

Ever since the first Neanderthal bones were discovered in 1856, people have wondered about these ancient hominins. How are they different from us? How much are they like us? Did our ancestors get along with them? Fight them? I love them? The recent discovery of a group called the Denisovans, a Neanderthal-like group that inhabited Asia and South Asia, has added its own set of questions.

Now, an international team of geneticists and artificial intelligence experts are adding brand new chapters to our shared hominin history. Led by Joshua Akeye, a professor at Princeton’s Lewis-Sigler Institute for Integrative Genomics, the researchers found a history of genetic intermingling and exchange that suggests a much more intimate connection between these early human groups than previously believed.

“This is the first time geneticists have identified multiple waves of modern human-Neanderthal admixture,” said Liming Li, a professor in the Department of Medical Genetics and Developmental Biology at Southeast University in Nanjing, China, who conducted the work as a collaborator. researcher in Akey’s lab.

“We now know that for the vast majority of human history we have had a history of contact between modern humans and Neanderthals,” Akey said. Hominins, who are our most direct ancestors, split off from the Neanderthal lineage about 600,000 years ago and then developed our modern physical traits about 250,000 years ago.

“From that time until Neanderthals disappeared — that’s 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.

Once stereotyped as slow-moving and stupid, Neanderthals are now thought to be skilled hunters and tool makers who treated each other’s injuries with sophisticated techniques and were well adapted to thrive in the cold European climate.

All of these hominin groups are humans, but to avoid the words “Neanderthals”, “Denisovans” and “ancient-versions-of-our-own-species-humans”, most archaeologists and anthropologists use the abbreviation Neanderthals, Denisovans and modern humans.

Using the genomes of 2,000 living humans, as well as three Neanderthals and one Denisovan, Akey 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, who were believed to have little or no Neanderthal or Denisovan DNA.

Akey’s team has shown that even these aforementioned groups, which live thousands of miles south of the Neanderthal caves, have trace amounts of Neanderthal DNA, likely carried south by travelers (or their descendants).

With IBDmix, Akey’s team identified the first wave of contact about 200-250,000 years ago, another wave 100-120,000 years ago, and the largest about 50-60,000 years ago.

This contrasts sharply with previous genetic data. “To date, most genetic data suggests that modern humans evolved in Africa 250,000 years ago, stayed there for another 200,000 years, and then decided to disperse out of Africa 50,000 years ago and move into the rest of the world,” he said. Key.

“Our models show that there was not a long period of stagnation, but that shortly after modern humans appeared, we were migrating out of Africa and also returning to Africa,” he said. “To me, this story is about dispersal, about modern humans moving around and meeting Neanderthals and Denisovans much more than we previously realized.”

This vision of humanity on the move coincides with archaeological and paleoanthropological research that suggests cultural and tool exchange between hominin groups.

Li and Akey’s key insight was to look for modern human DNA in Neanderthal genomes, rather than the other way around. “The vast majority of genetic work over the past 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,” Akey said.

They realized that the descendants of these first waves of Neanderthal modern mating must have stayed with the Neanderthals and therefore left no record in living humans. “Because we can now incorporate the Neanderthal component into our genetic studies, we’re seeing these earlier dispersals in ways we weren’t able to before,” Akey said.

The final piece of the puzzle was the discovery that the Neanderthal population was even smaller than previously believed.

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, Akey’s team showed that a significant portion of this apparent diversity came from DNA sequences that had been removed from modern humans with their much larger population.

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

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

“I don’t like to say ‘extinction’ because I think the Neanderthals were largely absorbed,” Akey said. His idea is that Neanderthal populations slowly dwindled until the last survivors turned into modern human societies.

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

“Neanderthals teetered 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 substantial reduction in an already at-risk population.

“Modern humans were basically like waves crashing on a beach and slowly but steadily eroding the beach away. We ended up just demographically overpowering the Neanderthals and incorporating them into modern human populations.”