A new timeline of when Neanderthals and ancient humans interbred

Hidden in many people’s genetic codes is a mystery that has long intrigued scientists — a tiny slice of Neanderthal DNA that persists tens of thousands of years after the species vanished. 

Most non-African people can attribute around 1% to 2% of their DNA to Neanderthal ancestors.

But the details of that evolutionary history have remained unclear. How often did ancient humans and Neanderthals interbreed? Exactly when did that happen? Why did Neanderthals go extinct, and why did modern humans survive? What does that Neanderthal DNA do for us now? 

Two research groups have separately analyzed collections of ancient genomes and come to the same conclusions about some of those core questions. Studies published in the journals Nature and Science on Thursday suggest that ancient humans and Neanderthals interbred during a limited period of time as the humans left Africa and migrated to new continents. 

The wave of interbreeding took place roughly 43,500 to 50,500 years ago, according to the findings. Then, over the next 100 generations, most Neanderthal DNA got weeded out — but not all. Today, the DNA that remains is linked to traits like skin pigmentation, immune response and metabolism. 

According to the new findings, the interbreeding event happened more recently than some previous estimates suggested, which in turn shifts and narrows the possible range of time when humans spread to places like present-day China and Australia. 

It also clarifies the significance of fossilized remains of humans discovered outside of Africa, like in Europe, that date back more than 50,000 years. The new studies say those populations died off and became evolutionary dead ends. 

“Human history is not just a story of success. We actually went extinct several times,” said an author of the Nature paper, Johannes Krause, a professor at the Max Planck Institute for Evolutionary Anthropology in Germany. “There’s multiple lineages that we have identified now that did not contribute to later people.” 

The findings also demonstrate how skilled anthropologists have become at reconstructing ancient DNA and analyzing it to make inferences about the course of human history.

“It’s just very cool that we can look at these events from the past and really reconstruct what our paths look like,” said an author of the Science paper, Priya Moorjani, an assistant professor of molecular and cell biology at the University of California, Berkeley. “Fifty thousand years ago is a long time ago, but to be able to have genetic data from these samples really helps us paint a picture in more and more detail.” 

The two research groups took different approaches to their work. 

Moorjani’s group built a catalog of genomic information from 59 ancient individuals — who lived between 2,000 years ago and 45,000 years ago — and 275 present-day people. Then the researchers analyzed changes over time in the distribution and length of Neanderthal DNA in those genomes. 

They determined that the flow of Neanderthal genes into humans occurred roughly 47,000 years ago and lasted no more than 7,000 years. Those findings line up with archaeological evidence that suggests Neanderthals and humans overlapped in geography as humans traveled out of Africa. Many scientists suspect the two species crossed paths in the Middle East, but that’s not confirmed.  

After the interbreeding, natural selection kept a few traits from Neanderthals while ditching many more. 

“The majority of selection, positive and negative, on Neanderthal ancestry happened very quickly after the gene flow, within roughly 100 generations,” said a co-author of the Science paper, Leonardo Iasi, a postdoctoral researcher in the evolutionary genetics department at the Max Planck Institute for Evolutionary Anthropology. 

The other new study, in Nature, relied on an analysis of six genomes from remains discovered in Ranis, a cave site in present-day Germany that sits below a medieval castle. The remains date back about 45,000 years, and the DNA suggests two of the six individuals were a mother and daughter. 

“They’re now the oldest nuclear genomes that we have of modern humans,” Krause said. 

The researchers also analyzed the DNA of an individual found in a cave site in present-day Czechia, about 140 miles from Ranis. The two sites date back to roughly the same period. The results indicated that two of the individuals found in Ranis were closely related to the one in the Czechia cave — within five or six degrees in family relation.

They concluded that the individuals found at the two sites were most likely part of a small isolated population of perhaps just 200. From a genetic perspective, they didn’t make it — the population died out. 

“They present a genetic lineage that has no descendants — that actually, later on, got extinct,” Krause said. 

However, those individuals’ DNA shares the same traces of Neanderthal influence as the remains that the other team of researchers analyzed. That strengthens the idea of a single event of “admixture” — or interbreeding.   

“It’s always nice to have two independent studies that are working with independent data using independent methods that come up with basically the same answer. That engenders a lot of confidence,” said Joshua Akey, a professor at the Lewis-Sigler Institute for Integrative Genomics at Princeton University, who wasn’t part of either research group.

Chris Stringer, a professor and research leader on human evolution at the Natural History Museum in London, said pinpointing the interbreeding event helps line up other key parts of the human evolution timeline. The findings constrain “the timing of the arrival of populations in regions like China and Australasia [Australia, New Zealand and Papua New Guinea] that gave rise to present-day people in those areas to less than 50,000 years ago, because their genomes share the same interbreeding event,” he said.

The studies also clarify the time frame in which humans interbred with Denisovans, another extinct species, Stringer added — that took place after the introduction of Neanderthal DNA. 

Akey said questions remain, though. It’s not clear how often humans and Neanderthals mated. And there’s more to be learned about the traits humans got from Neanderthal and Denisovan DNA. Plus, there’s the mysterious disappearance of Neanderthals 39,000 years ago.

Akey said he thinks mating between humans and Neanderthals might have led to the latter’s vanishing. 

“My inclination is to think that mating was pretty frequent,” Akey said. “And that there was enough mating that it contributed to the disappearance of Neanderthals by incorporating them into human populations. But that’s still speculative.”