Neanderthal Genome Reveals Small, Isolated Populations in Siberia

The story of human history, and prehistory, is constantly being rewritten. Recent analysis of a remarkably well-preserved bone fragment discovered in Denisova Cave in Siberia reveals a modern layer of complexity in the relationships between Neanderthals, and underscores just how small and isolated these populations could be. Researchers have extracted a complete genome from a 110,000-year-old Neanderthal male, designated D17, and compared it to other Neanderthal genomes, revealing he was a distant relative of another Neanderthal who lived in the same cave 10,000 years earlier.

Denisova Cave: A Crossroads of Ancient Humans

Denisova Cave, located in the Bashelaksky Range of the Altai Mountains in Russia, is a site of immense archaeological significance. As Wikipedia details, the cave has yielded evidence of habitation by Denisovans, Neanderthals, and Homo sapiens, sometimes concurrently. This makes it a unique location for understanding the interactions between these different hominin groups. The cave itself is found 700 meters (2,297 feet) up in the hills, and has been a site of archaeological interest for decades, but it was the discovery of the Denisovans in 2010 that truly cemented its place in the history of paleoanthropology. IFL Science notes the cave contains remains of dozens of animal species, including extinct ones, and at least four major periods of hominin occupation.

A Glimpse into Neanderthal Population Structure

The recent study, published in the journal PNAS, provides a detailed glance into the genetic makeup of Neanderthals who inhabited the Altai region. By comparing the genome of D17 with three other complete Neanderthal genomes, and specifically with the genome of a female Neanderthal (D5) from the same cave dating back 120,000 years, researchers were able to piece together a picture of their familial relationships. While D5 wasn’t a direct ancestor of D17, the analysis showed they belonged to closely related lineages, indicating a long-term Neanderthal presence in the area. This suggests that, despite periods of isolation, there was some degree of genetic connection between Neanderthal groups in the region over time.

Though, the study also revealed a surprising degree of genetic isolation. The researchers found evidence of significant inbreeding within the Altai Neanderthal population, with individuals exhibiting large sections of identical DNA. This suggests that these groups were likely very small, numbering 50 or fewer individuals, and that mating between close relatives was common. This level of inbreeding could have had detrimental effects on the health and viability of the population, potentially contributing to their eventual decline.

Small Populations and Genetic Drift

The findings align with previous research indicating that Neanderthals generally lived in smaller, more isolated groups than modern humans. A 2022 study, for example, suggested that one Altai Neanderthal community consisted of around 20 individuals, while another study indicated a group was isolated for roughly 50,000 years. Live Science explains that in small, isolated groups, a process called genetic drift can cause random genetic changes to become more common over time. This can lead to a loss of genetic diversity and potentially reduce a population’s ability to adapt to changing environmental conditions.

Léo Planche, a population geneticist at Paris-Saclay University, who was not involved in the study, emphasized the importance of having more Neanderthal genomes to understand their population structure. “We start to have enough Neanderthal genomes to actually have some claim about their population structure. Populations are groups of individuals, so the more data the better,” he told Live Science.

Divergence Between Eastern and Western Neanderthals

The study also uncovered evidence of genetic divergence between Neanderthals from the Altai region and those from Europe. The analysis showed that D17 was more closely related to D5 than either was to Neanderthals in Europe or to later populations in the Altai region. This suggests that Neanderthal populations in eastern and western Eurasia became genetically distinct from one another relatively quickly, even within a relatively small geographic area. This rapid divergence may have been due to limited gene flow between the groups, further highlighting the degree of isolation experienced by these populations.

Researchers believe that this genetic separation could have limited the Neanderthals’ ability to adapt to environmental changes. The study’s first author, Diyendo Massiliani, a genetics professor at the Yale School of Medicine, noted that even though the individuals analyzed were separated by only about 50,000 years, they exhibited levels of genetic difference comparable to those seen between modern human populations that diverged 300,000 years ago.

What Comes Next: Expanding the Neanderthal Family Tree

The ongoing work at Denisova Cave, and similar sites, continues to yield valuable insights into the lives and relationships of our ancient ancestors. Future research will likely focus on extracting and analyzing more Neanderthal genomes, particularly from different geographic regions, to build a more comprehensive picture of their population structure and genetic diversity. This will help scientists better understand the factors that contributed to their eventual extinction, and shed light on the complex history of human evolution. Further analysis of the archaeological record at Denisova Cave, combined with advances in genetic technology, promises to reveal even more about the interactions between Neanderthals, Denisovans, and early modern humans.

Study Citation: Massilani, D., Peyrégne, S., Iasi, L. N. M., De Filippo, C., Mafessoni, F., Mesa, A. B., Sümer, A. P., Swiel, Y., Popli, D., Silverman, S., Boyle, M. J., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Higham, T., Douka, K., Meyer, M., Zeberg, H., Kelso, J., & Pääbo, S. (2026). A high-coverage Neandertal genome from the Altai Mountains reveals population structure among Neandertals. Proceedings of the National Academy of Sciences, 123(13). https://doi.org/10.1073/pnas.2534576123