Two Neanderthals who lived in the same Siberian cave 10,000 years apart were distant relatives, found in 110,000-year-old bones

A small 110,000-year-old bone fragment from Siberia’s Altai Mountains reveals that two Neanderthals, who lived in the same cave 10,000 years apart, were distant relatives. The fragment also produced the fourth complete Neanderthal genome to date, revealing just how small and isolated Neanderthals were long before they disappeared around 40,000 years ago.

Researchers discovered bone fragments in Denisova Cave, where Neanderthals and Denisovans lived intermittently for nearly 300,000 years. In a study published Monday (March 23) in the journal PNAS, researchers compared the genome of a 110,000-year-old Neanderthal man (called D17) with the genomes of three other complete Neanderthals to better understand Neanderthal population structure.

The researchers compared D17’s genome to that of a 120,000-year-old female Neanderthal (called D5) taken from the same cave. They found that although D5 was not a direct ancestor of D17, the two Neanderthals belonged to closely related lineages linked by a common ancestor. This distant biological relationship suggests that Neanderthals had a long presence in the Altai region, the researchers said.

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“However, Denisova Cave was not a site occupied by a single continuous group, but was likely part of a broader landscape that was used repeatedly over time by Neanderthal populations,” Diendo Masirani, lead author of the study and professor of genetics at Yale School of Medicine, told Live Science in an email.

The findings also revealed that Neanderthals in the Altai region lived in very small and highly isolated groups of fewer than 50 individuals, as indicated by stronger genetic markers of inbreeding. Specifically, the researchers found that the individuals they analyzed had much of the same DNA. This indicates that their parents are very closely related, for example, close cousins.

This new study complements previous research showing that Neanderthals lived in smaller, more isolated groups than our own species. A 2022 study showed that the Neanderthal community in Altai had a population of about 20 people, and another study showed evidence that one group had been isolated for about 50,000 years. Many researchers point to inbreeding and isolation as causes for the disappearance of Neanderthals about 40,000 years ago. However, new research suggests that Neanderthals also survived for long periods of time under extreme conditions of isolation and small population size.

Massiliani and his colleagues also found that the Altai Neanderthals were very different from later European Neanderthals. Through genetic analysis, the researchers found that Altai Neanderthal D17 was more closely related to D5 than to European Neanderthals or later populations from the Altai region. This suggests that Neanderthal populations in eastern and western Eurasia became genetically distinct from each other within a relatively short time frame and within a fairly narrow geographic area.

“Even though the individuals whose genomes we have have been separated for only about 50,000 years on average, we have reached levels of divergence similar to those seen today among the most disparate human groups, such as the peoples of Central Africa and Papua New Guinea, who separated about 300,000 years ago,” Masirani said.

Perhaps because Neanderthal populations were small and isolated, they became genetically distinct from each other much earlier, Masilani said. This may be because random genetic changes can become more common over time in small, isolated populations, a process called genetic drift.

“We already knew that Neanderthals were not a single homogeneous population spread across Eurasia, but a patchwork of populations shaped by complex demographic processes such as divergence, migration, local extinction, and replacement,” he said. “What is surprising about our results is how differentiated these populations can be.”

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Masirani said the degree of genetic separation and differences between populations may have limited Neanderthals’ ability to adapt to changes in their environment.

One expert says the study provides new details about how Neanderthal populations were structured.

“The sequencing of two Neanderthals in such close geographical proximity provides new and more detailed insights into their population,” Leo Planche, a population geneticist at the Interdisciplinary Institute for Digital Sciences at the University of Paris-Saclay, who was not involved in the study, told Live Science via email. “We’re starting to have enough Neanderthal genomes to actually make some claims about Neanderthal population structure. A population is a group of individuals, so the more data we have, the better.”

Editor’s note: This article was updated on March 27, 2026 to note that the majority of Neanderthals became extinct 40,000 years ago, not 34,000 years ago as previously stated.

Neanderthal quiz: How much do you know about our closest relatives?