Researchers Track Down When Neanderthals and Early Modern Humans Interbred Using Ancient Genomes

Though some might be surprised to see Neanderthal DNA in their ancestry test results, people of non-African descent derive 1 to 4 percent of their genomes from this extinct human cousin. This means that at some point, ancient modern humans (Homo sapiens) interbred with Neanderthals. Now, two separate studies published in the journals Science and Nature in December have dated this period of interbreeding more precisely than ever.

“The timing is really important, because it has direct implications on our understanding of the timing of the out-of-Africa migration,” Priya Moorjani, a biologist at the University of California, Berkeley, and co-senior author of the Science study, says in a statement. “It also has implications for understanding the settlement of the regions outside Africa, which is typically done by looking at archaeological materials or fossils in different regions of the world.”

Neanderthals and modern humans descended from a common African ancestor. Some of these ancestors left Africa for Eurasia, and they evolved into Neanderthals roughly 500,000 years ago. Most of our lineage stayed in Africa until about 100,000 years ago, when some Homo sapiens also began to leave the continent—and they ran into Neanderthals in Europe and Asia.

The recent studies independently reached a similar conclusion: that the interbreeding that led to the presence of Neanderthal DNA in our genomes today happened during a sustained period of interaction around 47,000 years ago. According to the Science study, the mingling began about 50,500 years ago and continued for roughly 7,000 years. That estimate is consistent with archaeological evidence that also points to an inter-species coexistence of between 6,000 and 7,000 years, according to the statement.

“It paints a different story than this rare encounter. Whenever you ran into a Neanderthal, it was okay to have a baby with a Neanderthal,” Fernando Villanea, an anthropologist at the University of Colorado Boulder who was not involved in either study, tells the Washington Post’s Carolyn Y. Johnson. “It just paints this story that makes sense to how the real world works. For a long period of time, humans were running into Neanderthals, and they were having babies.”

The team from the Science study analyzed 275 contemporary human genomes and 58 ancient modern human genomes from remains in Europe and Western and Central Asia. They built a catalog of genetic data and used it to pinpoint the times when Neanderthal DNA entered the genomes of our ancestors, finding a “single, shared extended period of gene flow,” per the paper.

Meanwhile, the scientists from the Nature study sequenced the oldest known modern human genomes, which belonged to seven individuals from a 45,000-year-old family from the LRJ culture. The team found that Neanderthal DNA had entered the family’s lineage 80 generations earlier—a timeframe for interbreeding that mirrors the one revealed in the Science paper. But, while this group of people also had Neanderthal ancestry, their population must have died out, because their DNA doesn’t appear to contribute to modern-day genomes.

If all people of non-African descent have Neanderthal DNA from the interbreeding event identified by both papers, it might suggest that Homo sapiens spread to regions like East Asia and Oceania only afterward. That idea, however, conflicts with 100,000-year-old archaeological evidence of modern humans in China and 65,000-year-old evidence from Australia. Pontus Skoglund, a paleogeneticist at the Francis Crick Institute who was not involved in the studies, tells the New York Times’ Carl Zimmer that either the archaeological sites were dated incorrectly, or the modern human lineages that arrived in those regions 100,000 years ago died out later, and thus didn’t contribute to our genetic makeup today.

“Human history is not just a story of success. We actually went extinct several times,” Johannes Krause, a biochemist at the Max Planck Institute for Evolutionary Anthropology and a co-author of the Nature paper, tells NBC News’ Evan Bush. “There’s multiple lineages that we have identified now that did not contribute to later people.”

The Neanderthal genes inherited by Homo sapiens impacted our ancestors’ health. Some areas of the contemporary human genome that are devoid of Neanderthal genes, for example, suggest certain elements of their DNA were deadly to Homo sapiens, and the individuals with those genes would have died out, according to the statement. On the other hand, the scientists also identified high-frequency Neanderthal genes that were likely beneficial to the early Homo sapiens, who were relative newcomers to the region.

Alexander Platt, a geneticist at the University of Pennsylvania who was not involved with either research paper, tells Nature News’ Freda Kreier that the fact that both studies identified a single interbreeding period is “striking” and “eye-opening.”

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Margherita Bassi is a freelance journalist and trilingual storyteller. Her work has appeared in publications including BBC Travel, Discover magazine, Live Science, Atlas Obscura and Hidden Compass.