A few days ago, in my post about Y-chromosome haplogoup P (the root from which Eurasian R, and Amerindian Q haplogroups arose) I mentioned that the source of P (haplogroup K), which has been said to be located in Indonesia, Island South East Asia. This is interesting because this region is also a hotspot for people carrying a high frequency of Denisovan alleles. I wonder if Denisovans and haplogroup P are connected. This post will look into that possibility.
Archaic Y-chromosomes
The Denisovan and Neanderthal Y-chromosomes were studied by Martin Petr et al. (2020) in their paper The evolutionary history of Neanderthal and Denisovan Y chromosomes (Science 369, 1653-1656 (2020). doi:10.1126/science.abb6460 🔒). The following image is adapted from the paper's Figure 2.
The tree shows Denisovans, Neanderthals, and modern humans; the oldest haplogroup A00 is in Africa, and the others are non-African. The authors comment this figure as follows: "Unlike the rest of the nuclear genome, which puts Denisovans and Neanderthals as sister groups to modern humans, the Denisovan Y chromosomes form a separate lineage that split before Neanderthal and modern human Y chromosomes diverged from each other (Fig. 2A). Notably, all three late Neanderthal Y chromosomes cluster together and fall outside of the variation of present-day human Y chromosomes."
A more recent paper by Peyrégne et al., (2025) added the specimen known as Denisovan 25 to the tree, in the upper green branch. (See Fig. 2 C in that paper).
Petr et al., (2020) also defined the dates of the splits between the branches after calculating a mutation rate and dating the oldest A00 human haplogroup [249 ka ago (bootstrap CI 213 to 293 ka ago)]: "The two Denisovan Y chromosomes split from the modern human lineage around 700 ka ago (Denisova 8: 707 ka ago, CI 607 to 835 ka ago; Denisova 4: 708 ka ago, CI 550 to 932 ka ago) (Fig. 2B and table S12). By contrast, the three Neanderthal Y chromosomes split from the modern human lineage about 370 ka ago: 353 ka ago for Spy 94a (CI 287 to 450 ka ago), 370 ka ago for Mezmaiskaya 2 (CI 326 to 420 ka ago), and 339 ka ago for El Sidrón 1253 (CI 275 to 408 ka ago)."
This study found that, unexpectedly, the Y-chromosomes of Neanderthals was closer to modern humans than to Denisovans (puzzling, because the autosomal DNA of Denisovans and Neanderthals is closer between those two groups than either group to modern humans). To explain this incongruent finding, the authors suggest "that the Y chromosomes of late Neandertals represent an extinct lineage closely related to modern human Y chromosomes that introgressed into Neanderthals between ~370 and ~100 ka ago." ↺
In other words, a first and oldest "Out of Africa" event of modern humans that took place some 100,000 to 370,000 years ago resulted in mating between human men and Neanderthal women. The male hybrid offspring of these trysts carried human Y-chromosomes (these pass from fathers to sons) and these human Y-chromosomes spread among the Neanderthal groups. These first-out-of-Africa modern humans then went extinct in Eurasia, and for that reason they are not related to the final Out of Africa wave of modern humans who mixed for a second time with Neanderthals in Eurasia 50-70 ka. Complicated? Far-fetched? Possibly.
Comment: The authors of this paper noticed different branch lengths in their phylogenetic trees, suggesting that mutations accumulate at different rates. This subject discussed in my previous post.
No surviving Neanderthal Y-chromosomes
The final mating episode (~100 to 50 kya) between modern humans and Neanderthals led to hybrids, and the male offspring of Human males and Neanderthal females carried modern human Y-chromosomes. However, the Neanderthal Y-chromosomes became extinct, meaning that the sons born from Neanderthal men and human women may have had some incompatibility due to the Neanderthal Y-chromosomes. Could this have triggered stillborn or miscarried sons in modern human mothers?
Neanderthal Y-chromosomes carry proteins that can provoke a immune response from mothers during pregnancy "Such effects could be important drivers of secondary recurrent miscarriages and might play a role in the fraternal birth order effect of male sexual orientation... It is tempting to speculate that some of these mutations might have led to genetic incompatibilities between modern humans and Neandertals and to the consequent loss of Neandertal Y chromosomes in modern human populations." (Source).
Another explanation is that the small size of Neanderthal populations compared to those of Modern Humans, and their isolation, led to an accumulation of damaging mutations in their Y-chromosome, and this affected male fertility while modern humans coupling with Neanderthal women had more offspring (boys carrying the human Y-chromosome). Over several thousands of years of intermingling, the Y-chromosomes of the Neanderthtals died out, extinct for good, replaced by those of Modern humans.
Another theory wass put forward by Juraj Bergman and Mikkel Heide Schierup (2022) who study an area of the human sex chromosomes X, and Y, known as the pseudoautosomal region 1 (PAR1). PAR1 is involved in the male meiosis process (where the 46 human chromosomes in testis cells are split in half to form sperm cells with 23 chromosomes — including a Y or an X, sexual one, so that when the sperm fertilizes an egg to form a complete cell, it will contain 46 chromosomes). PAR1 is subject to mutations and recombination (a shuffling of DNA). This paper found that even though the Neanderthals received human Y chromosomes, they retained their PAR1 sequences. The human PAR1 was not passed on to the Neanderthal offspring, only the part of Y that determines sex, and it is likely that this part was under the pressure of selective forces, which favored the modern human Y component.
Extinction
Regarding selection Aaron Ragsdale (2025) wrote that "if human-related haplotypes carried fewer deleterious alleles due to their larger long-term effective population size, human-introgressed DNA would have been favored in Neanderthal genomes. The replacement of Neanderthal mitochondrial and Y chromosomes by early human haplotypes appears to support this model of post-admixture positive selection in the Neanderthal lineage... haplotypes that have accumulated more deleterious mutations, e.g., from a population with small long-term effective population size, will be selected against under either direction of gene flow. Introgressed ancestry at a given selected locus will decrease in frequency in one introgression scenario and increase in the other. This may explain the replacement of MT and Y chromosome DNA in Neanderthals by human haplotypes after early human-to-Neanderthal introgression and the absence of such Neanderthal haplotypes in modern humans."
But not only lack of fitness can lead to loss of the archaic Neandrthal Y chromosomes, David Reich (2026) argues that "Males have more variation in reproductive success than females, and if females prefer mates whose fathers were from the modern population, this would rapidly remove introgressing archaic Y chromosomes without there having to be reduced biological fitness associated with archaic Y chromosomes. In fact, a model of a matrilineal human range expansion has some empirical support based on estimates of more Neandertal introgressed segments on the X chromosome than the autosomal average." My recent post commenting a paper about Neanderthal men preferring human women is in line with this assumption regarding X chromosomes. It seems then, that Neanderthal women preferred human males and that the male offspring of Modern human-Neanderthal matings were less successful than the opposite progeny.
Back in 2016, Mendez FL, Poznik GD, Castellano S, and Bustamante CD. (The Divergence of Neandertal and Modern Human Y Chromosomes. Am J Hum Genet. 2016 Apr 7;98(4):728-34. doi: 10.1016/j.ajhg.2016.02.023. PMID: 27058445; PMCID: PMC4833433) noted that Neanderthal Y chromosome was very different from that of modern humans: "The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups." This also explains why hybrids would miscarry or be stillborn. The Neanderthal Y chromosome are an outgroup to modern human Y chromosomes. This team analyzed the ∼49,000-year-old Neandertal man from El Sidrón site in Spain. But, these conclusions contradict the findings of Petr: who suggested an introgression of Anatomically Modern Humans into Neanderthals long before the El Sidrón man existed! Petr wrote (see further up): "the Y chromosomes of late Neandertals represent an extinct lineage closely related to modern human Y chromosomes that introgressed into Neanderthals.".
These incongruences are a signal that further research is needed to clarify the picture.
Regarding Denisovans, as mentioned at the beginning of this post, they lie on an even more distant branch, and are quite distinct from Modern Human Y chromosomes.
There is the remote chance that someone out there, a man, carries a Neanderthal or a Denisovan Y chromosome. The number of people who have had their full genome sequence is around 2 million, globally, out of 8 billion people, roughly 0.025%, a very small sample. Those who have had these tests are mainly urban people in develped countries. So there is the possibility that a man in the wilderness in Turkmenistan carries a yet undetected Y chromosome of a Neanderthal or a Denisovan.
Denisovans and haplogroup P?
Getting back to the question that led me here, could the Haplogroup P be linked to Denisovan Y chromosomes? I believe the answer is no. The only possible way a Denisovan could belong to this haplogroup is that his father was a modern human carrying the haplogroup, and his mother Denisovan, he'd be a hybrid. Haplogroup P is the outcome of a long line of mutations from an original, ancestral basal lineage, i.e. the root linking A00 and other A haplogroups, in Africa. Another alternative is that the timelines of Y chromosome haplogroups is completely wrong. This option will be the subject of a future post.
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