A new study by researchers from the Department of Anthropology at the University of Utah shows that over 700,000 years ago, the ancestors of Neanderthals and Denisovans interbred with their Eurasian predecessors — members of a ‘superarchaic’ population that separated from other humans about 2 million years ago.

“We’ve never known about this episode of interbreeding and we’ve never been able to estimate the size of the superarchaic population,” said University of Utah’s Professor Alan Rogers, the lead author of the study.

“We’re just shedding light on an interval on human evolutionary history that was previously completely dark.”

Professor Rogers and colleagues studied the ways in which mutations are shared among modern Africans and Europeans, and ancient Neanderthals and Denisovans.

The pattern of sharing implied five episodes of interbreeding, including one that was previously unknown.

The newly discovered episode involves interbreeding over 700,000 years ago between a distantly related ‘superarchaic’ population which separated from all other humans around 2 million years ago, and the ancestors of Neanderthals and Denisovans.

The superarchaic and Neanderthal-Denisovan ancestor populations were more distantly related than any other pair of human populations previously known to interbreed. For example, modern humans and Neanderthals had been separated for about 750,000 years when they interbred.

The superarchaics and Neanderthal-Denisovan ancestors were separated for well over a million years.

“These findings about the timing at which interbreeding happened in the human lineage is telling something about how long it takes for reproductive isolation to evolve,” Professor Rogers said.

The researchers used other clues in the genomes to estimate when the ancient human populations separated and their effective population size.

They estimated the superarchaics separated into its own species about 2 million years ago. This agrees with human fossil evidence in Eurasia that is 1.85 million years old.

The scientists also proposed there were three waves of human migration into Eurasia.

The first was 2 million years ago when the superarchaics migrated into Eurasia and expanded into a large population.

Then 700,000 years ago, Neanderthal-Denisovan ancestors migrated into Eurasia and quickly interbred with the descendants of the superarchaics.

Finally, modern humans expanded to Eurasia 50,000 years ago where we know they interbred with other ancient humans, including with the Neanderthals.

“I’ve been working for the last couple of years on this different way of analyzing genetic data to find out about history,” Professor Rogers said.

“It’s just gratifying that you come up with a different way of looking at the data and you end up discovering things that people haven’t been able to see with other methods.”

The results were published in the journal Science Advances.

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Alan R. Rogers et al. 2020. Neanderthal-Denisovan ancestors interbred with a distantly related hominin. Science Advances 6 (8): eaay5483; doi: 10.1126/sciadv.aay5483