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45,000-year-old human genomes reveal extent of Neanderthal interbreeding

Two new genetic studies have shed light on just how often our ancestors got frisky with Neanderthals. Scientists analyzed the genomes of 45,000-year-old human remains found in caves in Czechia and Bulgaria, including the oldest known genome of a modern human, and found that they all had relatively recent Neanderthal ancestors.

Today, modern humans, or Homo sapiens, are the only living species of human, but that wasn’t always the case – for hundreds of thousands of years we shared the planet with a whole family of related species. While there was no doubt conflict, and we may have even contributed to the extinction of some species, we also got along very well at times.

Genetic studies have long shown that modern humans interbred with archaic species, including Neanderthals, Denisovans, and mysterious “ghost” species that we haven’t even identified. As a result, all non-African human populations have up to two percent Neanderthal DNA in their genomes, while people of Melanesian, Aboriginal Australian and Papuan descent have between three and eight percent Denisovan DNA.

Now, a pair of new studies has delved deeper into when exactly this interbreeding occurred and how common it might have been. One examined the skull of a woman nicknamed Zlatý kůň, found in Czechia, while the other study analyzed the remains of three individuals found in Bacho Kiro Cave in Bulgaria. All four specimens were dated to around 45,000 years ago.

The skull of Zlatý kůň, which the researchers suggest represents the oldest known modern human genome
The skull of Zlatý kůň, which the researchers suggest represents the oldest known modern human genome

Martin Frouz

The teams conducted genetic analyses on the bones to investigate their ancestry, and the extent to which they contributed genes to present-day human populations. All five genomes contained substantial Neanderthal DNA and, intriguingly, it seemed that the interbreeding had happened relatively recently in the family histories.

When species interbreed, the most immediate offspring not only have the highest levels of Neanderthal DNA, but these segments appear longer in the genome. The more generations down you go, without more of that DNA being added into the mix, the shorter these segments become. With that in mind, the teams were able to determine how far back the admixing had taken place.

”We found that the Bacho Kiro Cave individuals had higher levels of Neanderthal ancestry than nearly all other early humans,” says Mateja Hajdinjak, an author of one of the studies. “Crucially, most of this Neanderthal DNA comes in extremely long stretches. This shows that these individuals had Neanderthal ancestors some five to seven generations back in their family trees.”

Zlatý kůň, meanwhile, was found to have been about 2,000 years removed from her Neanderthal ancestors – still not all that long, in the grand scheme of things. From the length of her Neanderthal segments, the researchers estimate that she represents the oldest known modern human genome found so far.

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Modern human molars found in Bacho Kiro Cave in Bulgaria
Modern human molars found in Bacho Kiro Cave in Bulgaria

MPI-EVA/ Rosen Spasov

The scientists were also able to learn more about the descendants of these people and, curiously, none of them seemed to have contributed genetically to the local European populations. The three Bacho Kiro Cave individuals were found to be more closely related to ancient and present-day populations in East Asia and the Americas than they were to Europeans. Zlatý kůň was also found to not have any genetic continuity with the modern human populations in Europe after around 40,000 years ago.

These kinds of studies can help us piece together the puzzle of ancient human migrations and evolution. Previous work has even managed to identify a first-generation hybrid between a Neanderthal and a Denisovan.

The study focusing on Zlatý kůň was published in the journal Nature Ecology & Evolution, while the study on the Bacho Kiro Cave specimens appeared in Nature. Researchers discuss the Zlatý kůň find in the video below.

A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia – publication video

Sources: Max Planck Institute [1],[2]

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