Roughly 50,000 years ago, two species of humans met in the shadow of Eurasian ice sheets. One, Homo sapiens, had just embarked on its conquest of the world after leaving Africa. The other, Homo neanderthalensis, had called Eurasia home for hundreds of thousands of years. They looked into each other’s eyes — and then, they did what humans sometimes do: they had children.
For nearly 7,000 years, these two human species shared more than just the same cold landscapes; they shared their genes. That’s according to new research from two independent studies that narrowed down when Homo sapiens and Neanderthals interbred. The findings suggest that this mixing began about 50,500 years ago and lasted until around 43,500 years ago, just before Neanderthals faded into extinction.
Today, those interludes still ripple through our DNA. For non-Africans, between 1% and 2% of their genome comes from Neanderthal ancestors. But the story of how those genes spread, and why some stuck around while others vanished, is far more intricate than previously thought.
When and Where Our Histories Met
In a recent study published in Science, a team led by researchers from the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) and the University of California, Berkeley, analyzed the genomes of 334 humans. Some were modern, while others belonged to ancient individuals who lived between 2,200 and 45,000 years ago. Their findings pinpoint the Homo sapiens-Neanderthal interbreeding period to a window between 50,500 and 43,500 years ago.
“The timing is really important because it has direct implications on our understanding of the timing of the out-of-Africa migration,” said Priya Moorjani, an assistant professor at UC Berkeley and one of the study’s senior authors. “Most non-Africans today inherit 1-2% ancestry from Neanderthals.”
This timeline is consistent with archaeological evidence. Modern humans and Neanderthals likely shared the plains and forests of Eurasia for 6,000 to 7,000 years. As bands of Homo sapiens spread across the continent, they carried Neanderthal DNA with them.
A separate study, published in Nature, corroborates these findings. This research analyzed seven genomes, each around 45,000 years old, and arrived at the same date for the interbreeding event: about 47,000 years ago.
“We created a catalog of Neanderthal ancestry segments in modern humans,” said Manjusha Chintalapati, a former UC Berkeley postdoctoral fellow. “By jointly analyzing all these samples together, we inferred the period of gene flow was around 7,000 years.”
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The Legacy of Neanderthal DNA
But the story of interbreeding doesn’t end here. What mattered most was what happened to those Neanderthal genes. As Homo sapiens spread further, some of the borrowed DNA offered an advantage. Genes linked to immune function, skin pigmentation, and metabolism offered early humans venturing into uncharted territory an evolutionary edge.
“Neanderthals were living outside Africa in harsh, ice age climates and were adapted to the climate and to the pathogens in these environments,” said Leonardo Iasi of MPI-EVA. “When modern humans left Africa and interbred with Neanderthals, some individuals inherited Neanderthal genes that presumably allowed them to adapt and thrive better in the environment.”
Some of those adaptations are still with us today. One variant inherited from Neanderthals boosts resistance to the coronavirus that causes COVID-19.
Yet not all Neanderthal genes were beneficial. Researchers found regions in our genome entirely devoid of Neanderthal DNA, known as “Neanderthal deserts.” These genetic sequences lacking any Neanderthal genes likely formed quickly after the two species interbred, hinting that some Neanderthal variants were harmful to Homo sapiens. “We find that very early modern humans from 40,000 years ago don’t have any ancestry in the deserts, so these deserts may have formed very rapidly after the gene flow,” Iasi explained.
What this means for the story of human migration
These genetic findings also complicate the story of Homo sapiens‘ migration out of Africa. The timing of interbreeding suggests that humans had largely spread through Eurasia by about 43,500 years ago. But not every path out of Africa would have led to Neanderthals.
Bands of sapiens leaving Africa via Sinai might have run into Neanderthals, which was the southern limit of that species’ range. But those crossing via the straits between the Red Sea and the Gulf of Aden — believed by some to have been an important route as well — would not have done.
How did Neanderthal DNA become ubiquitous among non-Africans despite these divergent paths? That puzzle remains.
Previously, researchers found that the likeliest region where modern humans and Neanderthals interbred was the Zagros Mountains, a region stretching across present-day Iran, Iraq, and Turkey.
Looking to the Future, Through the Past
Our Neanderthal inheritance continues to shape us. In some parts of the world, like East Asia, people carry about 20% more Neanderthal DNA than Europeans or West Asians. This difference may reflect the different tangled paths that led to encounters between early humans and Neanderthals .
Researchers like Moorjani are also peering into the genes of another mysterious group: the Denisovans. “It’s really cool that we can actually peer into the past and see how variants inherited from our evolutionary cousins, Neanderthals and Denisovans, changed over time,” she said.