Geneticists rewrite the story of Neanderthals and other early humans

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

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

“This is the first time that geneticists have identified multiple waves of modern human and 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 an associate professor in Akey’s lab.

“We now know that for the vast majority of human history, we’ve had a history of contact between modern humans and Neanderthals,” Akey said. The hominins who are our most direct ancestors split from the Neanderthal family tree about 600,000 years ago and then developed our modern physical features about 250,000 years ago.

“From that point until the Neanderthals disappeared, 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.

Once seen as slow and unintelligent, Neanderthals are now viewed as skilled hunters and toolmakers who treated each other’s injuries with advanced techniques and were well adapted to the cold European climate.

All of these hominin groups are humans, but to avoid using the terms “Neanderthals”, “Denisovans” and “ancient versions of our own kind of humans”, most archaeologists and anthropologists use the abbreviations Neanderthals, Denisovans and modern humans.

Using the genomes of 2,000 living humans, three Neanderthals and one Denisovan, Akey and his team mapped the gene flow between hominin groups over the past quarter of a million years.

The researchers used a genetic tool they designed a few years ago, called IBDmix, which uses machine learning techniques to decode the genome. Previous researchers relied on comparing human genomes to a “reference population” of modern humans that were thought to have little or no Neanderthal or Denisovan DNA.

Akey’s team has found that even the aforementioned groups, living thousands of miles south of the Neanderthal caves, have traces of Neanderthal DNA, likely brought by explorers (or their descendants).

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

That’s in stark contrast to previous genetic data. “So far, most genetic data suggests that modern humans evolved in Africa 250,000 years ago, stayed for the next 200,000 years, and then decided to leave Africa 50,000 years ago and populate the rest of the world,” Akey said.

“Our models show that there was no long standstill, but that shortly after modern humans emerged, we migrated out of Africa and came back to Africa,” he said. “To me, this is a story about dispersal, that modern humans moved around a lot more and encountered Neanderthals and Denisovans than we previously thought.”

This view of humans on the move is consistent with archaeological and paleoanthropological research showing that there was cultural and tool exchange between hominin groups.

Li and Akey’s key insight was to look for modern human DNA in the Neanderthal genome, rather than the other way around. “The vast majority of genetic work in the past decade has really focused on how mating with Neanderthals affected modern human phenotypes and our evolutionary history, but these questions are relevant and interesting the other way around as well,” Akey said.

They realized that the descendants of those first waves of Neanderthal-modern matings must have stayed with the Neanderthals, and thus left no trace in living humans. “Because we can now include the Neanderthal component in our genetic studies, we’re seeing these earlier dispersals in ways we couldn’t see before,” Akey 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, Akey’s team showed that a significant portion of that apparent diversity came from DNA sequences inherited from modern humans, with their much larger populations.

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

The new findings paint a picture of how Neanderthals disappeared from history some 30,000 years ago.

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

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

“Neanderthals were teetering on the edge of extinction, probably for a very long time,” he said. “If you reduce their numbers by 10 or 20 percent, which is what we estimate is happening, that’s a substantial reduction in an already threatened population.

“Modern humans were essentially like waves crashing onto a beach, slowly but surely eroding the beach away. Eventually, we overwhelmed Neanderthals demographically and absorbed them into modern human populations.”