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In search of Denisovans: Genetic tools identify lost human relatives from fossil records

Using new genetic tools to identify lost human relatives from fossil record
Predicted phenotypic differences between AMHs, Neanderthals, and Denisovans. Credit: Proceedings of the National Academy of Sciences (2025). DOI: 10.1073/pnas.2513968122

New genetic techniques are shedding light on a mysterious part of our family tree—ancient human relatives called the Denisovans that emerged during the Pleistocene epoch, approximately 370,000 years ago.

Little is known about them because so few fossils have been found. The group was discovered by accident in 2010, based solely on DNA analysis of what was thought to be a Neanderthal finger bone found in the Denisova Cave in Siberia. However, it turned out to belong to a previously unknown lineage closely related to Neanderthals.

Since then, only a few additional fragments have been found, so David Gokhman from the Department of Molecular Genetics, Weizmann Institute of Science in Israel and colleagues developed a new genetic tool to go through the fossil record identifying potential Denisovans. Their starting point was the Denisovan genome.

The research is in the journal Proceedings of the National Academy of Sciences.

The research team's innovative technique detects subtle changes in how Denisovan genes are regulated. These changes were likely responsible for altering the Denisovan skeleton, providing clues to what they looked like.

Using this technique, the scientists identified 32 physical traits most closely related to morphology. Then they used this predicted profile to scan the Middle Pleistocene fossil record, specifically focusing on skulls from that period.

Before applying this method to unknown fossils, the researchers tested its accuracy. They used the same technique to successfully predict known of Neanderthals and chimpanzees with more than 85% accuracy.

Next, they identified 18 skull features they could measure, such as head width and forehead height, and then measured these traits on ten ancient skulls. They compared these to skulls from reference groups, including Neanderthals, modern humans and Homo erectus. Using sophisticated statistical tests, they gave each ancient skull a score to see how well it matched the Denisovan blueprint.

Of these, two skulls from China, known as the Harbin and Dali specimens, were a close match to the Denisovan profile. The Harbin skull matched 16 traits, while the Dali skull matched 15.

The study also found that a third skull, Kabwe 1, had a strong link to the Denisovan-Neanderthal tree, which may indicate that it was the root of the Denisovan lineage that split from Neanderthals.

Are there even more human relatives in the fossil record?

In their study, the team states that their work may help with the identification of other extinct human relatives.

"Our work lays the foundation for future efforts to infer phenotypes of other extinct hominin groups and to refine the taxonomic classification of the using genetic data."

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More information: Nadav Mishol et al, Candidate Denisovan fossils identified through gene regulatory phenotyping, Proceedings of the National Academy of Sciences (2025).

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Citation: In search of Denisovans: Genetic tools identify lost human relatives from fossil records (2025, September 1) retrieved 1 September 2025 from /news/2025-09-denisovans-genetic-tools-lost-human.html
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