New research published last week revealed the genetic makeup of a Neanderthal man (Denisova 17) who lived in the Denisova cave in Altai, 110,000 years ago. The paper reached some surprising conclusions.
This is the paper: D. Massilani,S. Peyrégne, et al. A high-coverage Neandertal genome from the Altai Mountains reveals population structure among Neandertals, Proc. Natl. Acad. Sci. U.S.A. 123 (13) e2534576123, https://doi.org/10.1073/pnas.2534576123 (2026).
Key findings:
- Population Replacement. The Denisova 17 Neanderthal man was closer to the older (~120 kya) Altai Neanderthal from Denisova (a woman known as Denisova 5) than to more recent European Neanderthals (the Vindija Cave woman, from Croatia and the Goyet female) and to the Neanderthal woman from Chagyrskaya Cave in the Altai region (80 kya, called Chagyrskaya 8 (Chag 8 for short). Suggesting that more recent Neanderthals replaced the older population in Altai.
- Denisovan admixture. The 120 and 110 kya Neanderthals from Denisova Cave (Denisova 17 and Denisova 5) had Denisovan admixture. This is not seen in the later Neanderthals of Western Europe or Chagyrskaya Cave.
- The estimated age of the common ancestor of the Y chromosome of Denisova 17 and modern human beings is ~395 ± 44 kya.
- The Eastern Neanderthals lived in groups of less than 50 individuals, these were smaller, and also more isolated than those of Western Eurasian Neanderthals.
- Replacement. The Western Neanderthals moved eastwards across Eurasia and replaced the older Eastern Neanderthals. But there was no admixture so the authors conjecture that both populations never met "perhaps because the older Neandertal population disappeared before the younger population from the west appeared in the Altai Mountains... Western-derived Neandertals are thought to have replaced the Eastern Neandertals in the Altai Mountains, and presumably elsewhere, sometime between ~110,000 and ~70,000 y ago."
- Interaction with modern humans: comparing non-African modern human genes with Neanderthal genes and counting the matches, the authors find that Western Neanderthals, especially the Vindija type were closest to the Neanderthals who admixed with humans. Those matching Eastern Neanderthals were four-times smaller. I wonder if modern humans leaving Africa mated with Western Neanderthals, who may have carried Eastern alleles? or perhaps they also intermingled with Eastern Neanderthals.
Mutation Rate and Divergence
The most interesting part is how divergent both Western and Eastern Neanderthal were, when compared to modern human beings. The paper states that:
"... it is striking that the allele frequency differentiation between Eastern Neandertals (D5 and D17) and Western Neandertals (Vi33.19 and others) (FST = 0.30, 95% CI: 0.29 to 0.31) exceeds that of even the most differentiated pairs of present-day populations, such as the Mbuti of Central Africa and the Papuan Highlanders of New Guinea (FST = 0.27, 95% CI: 0.26 to 0.27). The divergence between Mbuti and Papuan is estimated to have occurred 130 to 220 kya, resulting in separate genetic drift along the two lineages over 260 to 440 ky. The divergence between Eastern and Western Neandertals occurred about 35 ky before D5 and D17 and about 80 ky before Vi33.19 lived resulting in separate genetic drift along the two Neandertal lineages over about 115 ky. This suggests that Neandertal populations reached greater levels of differentiation over shorter timescales than modern humans did. This is also illustrated by the modest differentiation between a ~45,000-y-old modern human genome from Siberia (Ust’Ishim) and present-day populations (FST = 0.052, 95% CI: 0.049 to 0.056)."
The authors suggest that the small bands of Neanderthals underwent higher genetic drift, that led to high frequencies of different alleles in the two populations. So even though they were not far apart in Eurasia, they were, nevertheless isolated from each other. The point is that "Neandertal populations accumulated allele frequency differences more rapidly than the ancestors of present-day human groups." So much for the molecular clock and its regular ticking rate.
In my previous posts on the MUC19 allele that introgressed into humans from Denisovans via Neanderthals wo were not related to the Altai Neanderthal (Denisova 5), I wondered if the Neanderthals who were ancestral to the Chagyrskaya and Vindija individuals but not to Denisova 5, the Altai Neanderthal were the ones who had admixed with modern humans. This paper seems to suggest it was them.
If there was an Early peopling of America by Neanderthals, it was surely done by the Older Eastern Neanderthal Group.
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