A new analysis of DNA from ancient modern humans (Homo sapiens) in Europe and Asia has determined, more precisely than ever, the time period during which Neanderthals interbred with modern humans, starting about 50,500 years ago and lasting about 7,000 years — until Neanderthals began to disappear.

That interbreeding left Eurasians with many genes inherited from our Neanderthal ancestors, which in total make up between 1% and 2% of our genomes today.
A more precise timeline for modern human interactions with Neanderthals can help scientists understand when humans emigrated out of Africa and peopled the globe, while understanding the DNA that Neanderthals shared with our ancestors provides information on the role Neanderthal genes play in human health.
The genome-based estimate is consistent with archeological evidence that modern humans and Neanderthals lived side-by-side in Eurasia for between 6,000 and 7,000 years. The analysis, which involved present-day human genomes as well as 58 ancient genomes sequenced from DNA found in modern human bones from around Eurasia, found an average date for Neanderthal-Homo sapiens interbreeding of about 47,000 years ago. Previous estimates for the time of interbreeding ranged from 54,000 to 41,000 years ago.

This allowed us to build a more complete picture of the past
Manjusha Chintalapati

The new dates also imply that the initial migration of modern humans from Africa into Eurasia was basically over 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, as most non-Africans today inherit 1-2% ancestry from Neanderthals,” said Priya Moorjani, an assistant professor of molecular and cell biology at the University of California, Berkeley, and one of two senior authors of the study. “It also has implications for understanding the settlement of the regions outside Africa, which is typically done by looking at archeological materials or fossils in different regions of the world.”
The genome analysis, also led by Benjamin Peter of the University of Rochester in New York and the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) in Leipzig, Germany, will be published in the Dec. 13 print issue of the journal Science. The two lead authors are Leonardo Iasi, a graduate student at MPI-EVA, and Manjusha Chintalapati, a former UC Berkeley postdoctoral fellow now at the company Ancestry DNA.
The longer duration of gene flow may help explain, for example, why East Asians have about 20% more Neanderthal genes than Europeans and West Asians. If modern humans moved eastward about 47,000 years ago, as archeological sites suggest, they would already have had intermixed Neanderthal genes.
“We show that the period of mixing was quite complex and may have taken a long time. Different groups could have separated during the 6,000- to 7,000-year period, and some groups may have continued mixing for a longer period of time,” Peter said. “But a single shared period of gene flow fits the data best.”
“One of the main findings is the precise estimate of the timing of Neanderthal admixture, which was previously estimated using single ancient samples or samples from present-day individuals. Nobody had tried to model all of the ancient samples together,” Chintalapati said. “This allowed us to build a more complete picture of the past.”

Neanderthal deserts in the genome

In 2016, Moorjani pioneered a method for inferring the timing of Neanderthal gene flow using often incomplete genomes of ancient individuals. At that time, only five archaic Homo sapiens genomes were available. For the new study, Iasi, Chintalapati and their colleagues employed this technique with 58 previously sequenced genomes of ancient Homo sapiens who lived in Europe, Western and Central Asia over the past 45,000 years and the genomes of 275 contemporary humans worldwide to provide a more precise date — 47,000 years ago. Rather than assuming the gene flow occurred in a single generation, they tried more complex models developed by Iasi and Peter to establish that the interbreeding extended over about 7,000 years, rather than being intermittent.

The timing of the interbreeding between Neanderthals and modern humans was corroborated by another, independent study conducted by MPI-EVA researchers and is scheduled to be published Dec. 12 in the journal Nature. That study, an analysis of two newly sequenced genomes of Homo sapiens that lived about 45,000 years ago, also found a date of 47,000 years ago.
“Although the ancient genomes were published in previous studies, they had not been analyzed to look at Neanderthal ancestry in this detailed way. We created a catalog of Neanderthal ancestry segments in modern humans. By jointly analyzing all these samples together, we inferred the period of gene flow was around 7,000 years,” Chintalapati said. “The Max Planck group actually sequenced new ancient DNA samples that allowed them to date the Neanderthal gene flow directly. And they came up with a similar timing as us.”
This content is taken from University of California - Berkeley

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"A new timeline for Neanderthal interbreeding with modern humans", MachPrinciple, September 10, 2025, https://machprinciple.com/post/A-new-timeline-for-Neanderthal-interbreeding-with-modern-humans