Genomes reveal timing of Homo sapiens interbreeding with Neanderthals

Neanderthals went extinct roughly 39,000 years ago, but in some sense these close cousins of our species are not gone. Their legacy lives on in the genomes of most people on Earth, thanks to interbreeding between Homo sapiens and Neanderthals.

New research is providing the most precise estimate to date of when this mixing occurred — with the height of the interaction around 47,000 years ago — and showing how Neanderthal components have shaped the human genome in functions such as skin pigmentation, immune response and metabolism.

One group of scientists examined genomes from three female and three male Homo sapiens individuals who lived around 45,000 years ago based on bones found in a cave at the German town of Ranis, and one genome from a woman from about the same time whose skull was found in a cave at Zlaty kun mountain in the Czech Republic. The study, published in the journal Nature and involving the oldest Homo sapiens DNA ever sequenced, gave a date range for the mixing of about 49,000 to 45,000 years ago.

A second group of researchers examined the genomes of 300 present-day and ancient Homo sapiens individuals, including 59 who lived between 2,000 and 45,000 years ago. The study, published in the journal Science, gave a date range of the mixing of about 50,500 to 43,500 years ago.

The scientists described the interbreeding, found to have been more recent than previous estimates, as a single extended period of gene flow lasting for numerous generations.

It is difficult to know the nature of the interaction between Homo sapiens and Neanderthals based on genome data beyond being able to say they mixed and had children together. The researchers could not pinpoint geographically where this interbreeding occurred but saw the Middle East as likely.

Neanderthals, formally called Homo neanderthalensis, were more robustly built than Homo sapiens and had larger brows. They lived from around 430,000 years ago until their disappearance relatively soon after Homo sapiens — a species that arose roughly 300,000 years ago in Africa — trekked into areas Neanderthals inhabited in the Middle East, Europe and Asia. Previous research has shown that Neanderthals were intelligent, creating art and using complex group-hunting methods, pigments probably for body painting, symbolic objects and perhaps spoken language.

Most people today have genes inherited from Neanderthals, roughly 1-2% of their DNA.

“Neanderthals were living outside Africa for thousands of years before modern humans arrived, and they were presumably adapted to the climate and pathogens outside Africa. Thus, some of their genes may have been beneficial to modern humans,” said University of California, Berkeley population geneticist Priya Moorjani, one of the research leaders.

For instance, an immune gene variant inherited from Neanderthals protects against coronaviruses like the one that caused the COVID pandemic. Some Neanderthal genes involved in the immune system and skin pigmentation increased in frequency in Homo sapiens over time, suggesting their value to survival.

“In contrast, some genomic regions are nearly devoid of Neanderthal ancestry,” Moorjani said.

That indicates that some Neanderthal gene variants proved lethal to Homo sapiens and were not passed down through generations.

Among the Ranis individuals, a mother and daughter were identified. The Zlaty kun woman, about 145 miles (230 km) away, turned out to be distantly related to two of the Ranis people.

The genomes revealed their physical appearance.

“These early Europeans numbered just a few hundred and had dark skin, dark hair and brown eyes, reflecting their arrival from Africa,” said one of the researchers, zooarchaeologist Geoff Smith of the University of Reading in England.

These early Homo sapiens pioneers in Europe faced harsh Ice Age conditions. The genome data from the Ranis and Zlaty kun individuals showed they have no descendants alive today, indicating their population died out – a lost branch of the human family tree.

Zlaty kun’s remains illustrate a hazardous landscape.

“Marks on the skull hint towards predators, possibly hyenas, to have either attacked her or gnawed on the skull after her death,” said evolutionary geneticist Arev Sümer of the Max-Planck-Institute for Evolutionary Anthropology in Germany, one of the research leaders.

The fate of the Neanderthals has been long debated.

“There are different ideas of what role modern humans played in the extinction of Neanderthals. We find it at least plausible that the relatively small incoming modern human population may have incorporated a substantial part of the likely even smaller Neanderthal population in the region at the time. Since their DNA persists in present-day humans’ genomes, they are — in a way — alive and well and more successful than ever,” Sümer said.