Ilaria Rosella Pagliaro An international team of geneticists has discovered new evidence of genetic mixing between Neanderthals, Denisovans and modern humans, revealing a much more complex and fascinating history of interactions
©Princeton University
Since the discovery of the first Neanderthal remains, humanity has always wondered: who were these ancient hominids? How similar were they to us? How did they interact with our ancestors? The recent discovery of the Denisovans, a group similar to Neanderthals that inhabited Asia and Oceania, has added further questions.
Now, an international team of geneticists and artificial intelligence experts is rewriting our shared history. Under the leadership of Joshua Akey, a professor at the Lewis-Sigler Institute for Integrative Genomics at Princeton, researchers have found that interactions between ancient human groups were much more frequent than previously thought. The results of their work were published in the journal Science.
Multiple waves of interaction
Liming Li, a professor at Southeast University in Nanjing, China, who conducted this research in Akey’s lab, stated:
“For the first time, we have identified several waves of mixing between modern humans and Neanderthals. Today we know that for most of human history, we had contact with Neanderthals.”
Hominids, our direct ancestors, separated from the Neanderthal lineage about 600,000 years ago, evolving modern physical characteristics around 250,000 years ago. Modern humans interacted with Neanderthals for about 200,000 years until their disappearance.
Tracing genetic flow Between hominids
Using the genomes of 2,000 living humans, along with those of three Neanderthals and one Denisovan, Akey and his team traced genetic flow between hominid groups over the last 250,000 years.
The researchers used an innovative genetic tool called IBDmix, which leverages machine learning techniques to decode the genome. Previous studies relied on comparing human genomes with a “reference population” of modern humans considered to have little or no Neanderthal or Denisovan DNA.
Akey’s team discovered that even those reference groups, located thousands of miles south of Neanderthal caves, have traces of Neanderthal DNA, likely carried by travelers or their descendants.
With IBDmix, Akey’s team identified an initial wave of contact around 200,000-250,000 years ago, another wave 100,000-120,000 years ago, and the largest about 50,000-60,000 years ago. These data starkly contrast previous genetic findings:
“Until now, most genetic data suggested that modern humans evolved in Africa 250,000 years ago, remained there for the next 200,000 years, and then decided to disperse out of Africa 50,000 years ago to populate the rest of the world.”
“Our models show there was no long period of stasis, but that shortly after the emergence of modern humans, we began to migrate out of Africa and return. To me, this story is about dispersion, that modern humans moved around, encountering Neanderthals and Denisovans much more than we previously recognized.”
A revolutionary view of human-Neanderthal interaction
The key discovery by Li and Akey was to look for modern human DNA in Neanderthal genomes, instead of the reverse:
“The vast majority of genetic work over the past decade has focused on how interbreeding with Neanderthals impacted modern human phenotypes and our evolutionary history, but these questions are relevant and interesting in the opposite case as well. Now that we can incorporate the Neanderthal component into our genetic studies, we are seeing these early dispersals in ways we couldn’t before.”
They realized that the descendants of the early waves of interbreeding between Neanderthals and modern humans must have stayed with the Neanderthals, leaving no traces in living humans. The final piece of the puzzle was discovering that the Neanderthal population was even smaller than previously thought.
Genetic modeling traditionally used variation – diversity – as a proxy for population size. More diverse genes indicate a larger population. But using IBDmix, Akey’s team showed that a significant amount of that apparent diversity came from DNA sequences taken from modern humans, with their much larger population. Consequently, the effective population of Neanderthals was revised from about 3,400 reproductive individuals to about 2,400.
The disappearance of Neanderthals
Piecing together the new findings paints a picture of how Neanderthals disappeared about 30,000 years ago. Akey’s idea is that Neanderthal populations slowly dwindled until the last survivors were integrated into modern human communities.
This “assimilation model” was first articulated by Fred Smith, a professor of anthropology at Illinois State University, in 1989, as highlighted by Akey:
“Our findings provide strong genetic data supporting Fred’s hypothesis, and I think it’s really interesting. I don’t like to say ‘extinction’ because I think the Neanderthals were largely absorbed. The Neanderthals were probably on the brink of extinction for a long time. If you reduce their numbers by 10 or 20 percent, as our estimates suggest, that’s a substantial reduction for an already at-risk population.”
Modern humans were essentially like waves crashing on a beach, slowly but surely eroding the shoreline. Eventually, we demographically overwhelmed the Neanderthals and incorporated them into modern human populations.
Source: Princeton University
