In a new study powered by artificial intelligence, researchers have identified three major waves of interbreeding between humans and Neanderthals over the past 250,000 years.
The close relationship between modern humans and Neanderthals has a much longer history than previously believed. According to the findings of this new research, Neanderthals and Homo sapiens repeatedly interbred, shared genes, and merged populations over a span of nearly 250,000 years.
Using an AI-powered genetic tool called IBDmix, which employs machine learning techniques to decode genomes, scientists traced gene exchanges between modern humans and Neanderthals. Their findings suggest that Homo sapiens interacted and interbred with Neanderthals much earlier and more frequently than previously assumed.
The new research identifies three primary waves of interbreeding: the first around 200,000 to 250,000 years ago, the second around 100,000 to 120,000 years ago, and the largest wave occurring approximately 50,000 to 60,000 years ago.
These findings challenge many contemporary theories about human migration. It is commonly believed that modern humans evolved in Africa about 250,000 years ago, remained there for around 200,000 years, and only migrated out of Africa roughly 60,000 to 50,000 years ago, at which point they encountered Neanderthals and Denisovans—who had evolved much earlier in Eurasia.
However, the new study indicates that, contrary to the previous belief that modern humans and Neanderthals interbred only once around 50,000 years ago, multiple instances of genetic exchange occurred over 200,000 years—up until Neanderthals went extinct about 40,000 years ago.
Joshua Akey, a professor at the Lewis-Sigler Institute for Integrative Genomics at Princeton, explains that their models show modern humans did not remain in a prolonged period of isolation after emerging, but instead began migrating out of Africa relatively early—and even returned to Africa later on.
There is little physical and archaeological evidence suggesting that Homo sapiens spread across Eurasia before 50,000 years ago. A fossilized skull found in southern Greece, estimated to be at least 210,000 years old and believed by scientists to belong to a modern human, stands as a rare and exceptional case.
Typically, researchers search for traces of Neanderthal DNA in the genomes of modern humans. But this time, they took the reverse approach: searching for modern human DNA in Neanderthal genomes. This different methodology yielded new insights into the genetic exchange between the two groups.
Akey noted:
“Most genetic studies over the past decade have focused on how interbreeding with Neanderthals influenced the physical traits and evolutionary history of modern humans. But these questions are equally intriguing when viewed in reverse. Our study shows that Neanderthals didn’t vanish completely—they were genetically absorbed into the modern human lineage and became part of our genetic structure.”
The study also reveals that Neanderthal populations were much smaller than previously thought. When modern humans entered Neanderthal-inhabited regions about 50,000 years ago, their larger population size gave them a competitive edge. Eventually, they outcompeted, absorbed, or merged with Neanderthals, preventing the continuation of a distinct Neanderthal genetic lineage. Akey explains:
“Neanderthals were probably teetering on the edge of extinction for a long time. In such a vulnerable state, even a 10 to 20 percent decline in population—as our models estimate—would have been enough to drive them to extinction.”
The study has been published in the journal Science.
