‘A story of contact’: Geneticists rewrite the history of Neanderthals and other ancient humans

Ever since the first Neanderthal bones were discovered in 1856, people have wondered about these ancient hominids. How are they different from us? How are they like us? 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 added its share of questions.

Now, an international team of geneticists and artificial intelligence experts is working to add new chapters to the shared history of hominids. 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 exchange that suggests a much closer connection between these early human groups than previously thought.

“This is the first time that 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 did the work as a research associate in Akey’s lab.

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

“From then 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.

Neanderthals, once stereotyped as slow and stupid, are now seen as skilled hunters and toolmakers who treated the wounds of others with sophisticated techniques and were well adapted to thrive in the European cold.

All of these hominid groups are humans, but to avoid saying “Neanderthals,” “Denisovans,” and “early versions of our own species of humans,” most archaeologists and anthropologists use the abbreviations Neanderthals, Denisovans, and modern humans.

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

The researchers used a genetic tool 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 who were thought to have little or no Neanderthal or Denisovan DNA.

Akey’s team established that even the referenced groups, who live thousands of miles south of the Neanderthal caves, have traces of Neanderthal DNA, probably carried south by travelers (or their descendants).

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

This is in stark contrast to previous genetic data. “Most of the genetic data to date suggest that modern humans evolved in Africa 250,000 years ago, stayed there for the next 200,000 years, and then decided to disperse out of Africa 50,000 years ago and populate the rest of the world,” Akey said.

“Our models show that there was not a long period of stagnation, but that shortly after modern humans appeared, we migrated out of Africa and back into Africa as well,” he said. “To me, that story is one of dispersal, of modern humans moving around and encountering Neanderthals and Denisovans much more often than we previously thought.”

This vision of humanity in motion coincides with archaeological and paleoanthropological research suggesting cultural and tool exchanges between hominid groups.

Li and Akey’s key idea was to look for modern human DNA in Neanderthal genomes, rather than the other way around. “The vast majority of genetic work in the last decade has focused on how mating with Neanderthals impacted modern human phenotypes and our evolutionary history, but these questions are also relevant and interesting in the reverse case,” Akey said.

They realized that the descendants of these early waves of mating between Neanderthals and modern humans must have remained with the Neanderthals, leaving no trace in modern humans. “Because we can now incorporate the Neanderthal component into our genetic studies, we’re seeing these early dispersals in a way that we couldn’t before,” Akey said.

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

Genetic modeling traditionally uses 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 taken from modern humans, whose population is much larger.

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

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

“I don’t like to talk about extinction because I think Neanderthals were largely absorbed,” Akey said. His idea is that Neanderthal populations slowly declined until the last survivors were integrated 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 data that are consistent with Fred’s hypothesis, and I think that’s really interesting,” Akey said.

“Neanderthals were on the brink 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, that’s a substantial reduction in an already threatened population.”

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