2 Neanderthals present at same Siberian cave 10,000 years apart were distant relatives, 110,000-year-old bone reveals
Two Neanderthals present at the same cave site, 10 millennia apart, were distant relatives, a tiny 110,000-year-old bone fragment from Siberia’s Altai Mountains reveals. The fragment also produced the fourth complete genome of a Neanderthal to date, shedding light on the small size and isolation of Neanderthals long before their disappearance around 34,000 years ago.
Researchers found the bone fragment in Denisova Cavewho at the same time Neanderthals and the Denisovans lived there off and on for almost 300,000 years. In a study published Monday March 23 in the journal PNASThe researchers compared the genome of the 110,000-year-old male Neanderthal (called D17) with three other complete Neanderthal genomes to better understand the structure of the Neanderthal population.
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“But it is likely that Denisova Cave was part of a larger landscape used repeatedly by these Neanderthal populations over time, rather than a site occupied by a single, continuous group,” explains the first author of the study. Diyendo Massilaniprofessor of genetics at the Yale School of Medicine, told Live Science in an email.
The study results also revealed that Neanderthals in the Altai region lived in very small, highly isolated populations of 50 people or fewer, as shown by stronger genetic markers of inbreeding. Specifically, the researchers found that the individuals analyzed had large sections of identical DNA, indicating that their parents were very closely related – as close as first cousins, for example.
The new research complements previous studies that showed Neanderthals lived in smaller, more isolated groups than our own species. A 2022 study indicated that a Neanderthal community in Altai numbered about twenty peoplewhile another study provided evidence that one group was isolated for approximately 50,000 years. Many researchers have pointed out inbreeding and isolation as the causes of the disappearance of the Neanderthals around 34,000 years ago. But the latest findings suggest that Neanderthals also survived for long periods in extreme conditions of isolation and small population sizes.
Massiliani and his colleagues also found that Altai Neanderthals were very different from later European Neanderthals. In their genetic analysis, the researchers found that D17 from the Altai Neanderthal was more closely related to D5 than to Neanderthals in Europe or later populations in the Altai region. This suggests that Neanderthal populations in eastern and western Eurasia became genetically different from each other in a relatively short time and within a fairly small geographic area.
“Even though the individuals whose genomes we have have only been separated for about 50,000 years on average, they have reached levels of difference similar to those we see today between some of the most distinct human populations, such as the people of central Africa and Papua New Guinea who separated about 300,000 years ago,” Massilani said.
We’re starting to have enough Neanderthal genomes to make real claims about their population structure. Populations are groups of individuals, so the more data the better.
Léo Planche, population geneticist at the Interdisciplinary Digital Sciences Laboratory at Paris-Saclay University
Probably because they were small and isolated, Neanderthal populations genetically distinguished themselves much more quickly from one another, Massilani said. This may be because, in small, isolated groups, a process called genetic drift can result in a greater frequency of random genetic changes over time.
“We already knew that Neanderthals were not a single, homogenous population distributed across Eurasia, but a patchwork of groups shaped by complex demographic processes, including divergence, migration, local extinctions and replacements,” he said. “What is striking about our results is how differentiated these populations could become.”
The high degree of genetic separation and differences between groups may have limited Neanderthals’ ability to adapt to environmental changes, Massilani said.
The study provides new details about how Neanderthal populations were structured, an expert said.
“Having two Neanderthals sequenced in such a close geographical location provides a new and finer vision” of their population, Leo Planchepopulation geneticist at the Interdisciplinary Digital Sciences Laboratory at the University of Paris-Saclay who was not involved in the study, told Live Science in an email. “We’re starting to have enough Neanderthal genomes to get a sense of their population structure. Populations are groups of individuals, so the more data the better.”
Massilani, D., Peyrégne, S., Iasi, LNM, De Filippo, C., Mafessoni, F., Mesa, AB, Sümer, AP, Swiel, Y., Popli, D., Silverman, S., Boyle, MJ, Kozlikin, MB, Shunkov, MV, Derevianko, AP, Higham, T., Douka, K., Meyer, M., Zeberg, H., Kelso, J. and Pääbo, S. (2026). A high-coverage Neanderthal genome from the Altai Mountains reveals the population structure of Neanderthals. Proceedings of the National Academy of Sciences123(13). https://doi.org/10.1073/pnas.2534576123
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