Neanderthals and humans mated for thousands of years : NPR

Humans once had a way smaller footprint.

“Homo Sapiens, modern humans, evolved in Africa,” says Arev Sümer, a paleogenetics PhD student at the Max Planck Institute for Evolutionary Anthropology in Leipzig.

For millennia, humans stayed in Africa. But then, roughly 100,000 years ago, humans started leaving the continent in waves. “We don’t know exactly when ” says Sümer, but “sometime about 50,000 years or so, there was a group that migrated into Europe and Asia.”

Scientists know something crucial happened to those who dispersed. “They met Neanderthals,” says Sümer.

To be more direct, prehistoric sparks flew. These early modern humans and the Neanderthals had babies. “Most people that live today outside of Africa have about 1 to 2% of their genome inherited from a Neanderthal ancestor,” says Benjamin Peter, a population geneticist at the University of Rochester.

The timing of this ancient interbreeding has been somewhat fuzzy. Now, in two papers released in the journals Nature and Science, Sümer, Peter, and their respective teams clarify that ancestral timeline, pinning the period of interbreeding to sometime between 43,500 and 50,500 years ago. The results provide a better picture of humanity’s origin story.

Two approaches with a similar conclusion

The challenge of studying early hominids is that specimens from that period are scarce and in rough shape. “Ancient DNA samples are very often poor quality,” says Peter. “If a fossil is in a cave or other site for tens of thousands of years, its DNA tends to degrade a lot.”

Peter and his colleagues got around the problem with a new computational approach. They took the beat-up DNA sequences from 59 ancient humans living thousands of years ago, primarily in Eurasia, and compared them to good quality DNA sequences from a few Neanderthals and 275 people today with very little Neanderthal ancestry.

“We looked at people that lived over the last 45,000 years and detected which parts of their genome come from a Neanderthal,” he says. “So what we did that’s novel is we traced Neanderthal ancestry through time.”

Meanwhile, Sümer and her team were also trying to clock when early humans and Neanderthals interbred. They worked with rare well-preserved early human remains from Germany and the Czech Republic, including the best preserved paleolithic bone from an early modern human ever found.

“We were able to get high quality genomes from two of them,” Sümer. She analyzed those two genomes, along with lower-quality DNA from five other individuals at the site in Germany.

Sümer found that this group of early modern humans was related and living in a small population of 200 to 300 individuals. In addition, they lived at least 45,000 years ago. It turns out, “we just identified the oldest modern human family ever sequenced and ever known actually,” says Sümer.

She also found that 3% of the DNA of these early humans, arrayed in fairly long stretches, came from Neanderthals — the result of that earlier interbreeding, and pointing to more recent Neanderthal ancestry.

“In each generation, you can imagine the Neanderthal DNA getting broken into smaller pieces and getting shorter and shorter,” says Sümer. “So we can estimate how many generations must have passed since this event happened.”

Adding that number to the age of the specimens, Sümer calculated a more refined timestamp for when the ancestors of this early group of humans likely interbred with Neanderthals over multiple generations. The answer is between 45,000 and 49,000 years ago.

Peter and his colleagues used their computational method and got a similar time estimate: 43,500 to 50,500 years ago. Both intervals are “on the later side from what people think,” he says.

That means that when the descendants of those who interbred with the Neanderthals ultimately fanned out across Europe, Asia, and eventually Oceania and the Americas, it would have been on the more recent side of what researchers have believed. “It’s really important because it does constrain quite a few other things about human migration patterns,” says Peter, including not just when early humans migrated but who these communities were and how they diversified.

Peter was also able to show that selection on Neanderthal genes in early humans happened within a couple thousand years of interbreeding. That is, “there were some regions in the genome that rose in frequency quickly,” says Peter. “And there were other regions of the genome where Neanderthal ancestry was relatively quickly purged.”

Less uncertainty, more questions

“These new papers are significant,” says Joshua Akey, a genomicist at Princeton University. “They are much more of a direct estimate compared to the previous inference, which involved fitting a fairly complex statistical model that had a lot of uncertainty.” This uncertainty meant that researchers were using a longer time interval for the interbreeding. That window has now narrowed.

The constrained, more recent timeline “also means that any evidence of H. sapiens fossils or archaeology older than 50,000 years in places like western Europe, China and Australasia probably represents populations that subsequently died out without giving rise to any contemporary populations,” says Chris Stringer, a paleoanthropologist at the Natural History Museum in London. That’s because early humans in these places had no Neanderthal DNA before the interbreeding event. But the people today who are descendants of those who once lived there do.

He says that this suggests there were “numerous pre-50,000 year dispersals of H. sapiens from Africa, which were by small pioneering groups that were unable to establish a longer-term foothold.”

Still, plenty of unanswered questions remain.

“Human history is really complex,” says Sümer. “But we are trying to make sense out of it with every result we are getting.”