Denisovan, Neanderthal, and modern humans: the Y-chromosomes

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.

Figure 2 A in Petr et al., (2020). Source

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.

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

Y-Chromosome Haplogroup P in America

<>In yesterday's post about the Yana River site in northern Siberia, I mentioned that the remains of two men discovered there, dated to ~30 kya, who carried haplogroup P as a marker in their Y-chromosomes. This is a rare variant, and is not considered a founding lineage of Native American people. This means that when found in America it is considered as a later arrival, after the 1492 discovery of America by Europeans.

Y-chromosome Haplogroup P

These two men from Yana River dated to 31,000 years ago, carried P haplogroup in their Y-chromosome. This variant is not considered as a founding lineage in America.

Amerindian men are almost 100% haplogroup Q (Y-chromosome), with some rare C3 haplogroup individuals. No P haplogroup is ever mentioned in any of the studies involving Native Americans, so, if the Yana people moved to America and carried P haplogroup with them, it is nowhere to be seen. It has vanished, or, the lack of it is probably proof that they never reached the New World.

However, a thesis discussing the peopling of Patagonia from a genetic point of view (Poblamiento de la Patagonia: una aproximación genética en poblaciones indígenas actuales de Chile y Argentina, Michelle de Saint Pierre Barrera, p. 146), has an interesting entry: IV.5.2 P haplogroup: an Amerindian marker?, argues that "it is peculiar that the native populations of all America have one main Amerindian haplogroup, Qla3al, and only two rare haplogroups, Qla and C3b... So the question is if the low diversity observed could be due to an undertypification of rare haplogroups, assign them erroneously in non-Amerindian category haplogroups. Since for most of Amerindian tribes have between a 5-25% of non-Amerindian haplogroups, it is not difficult to assign erroneously. In this work we show an average of 3.6% for the marker M45 in Amerindian samples both M242 and M207 negatives, which discards them belonging to the Q or R haplogroups and assigning them to P. The fact that we had not found the P marker in any of rural populations and only found the marker in natives populations with high level of Amerindian haplogroups, together with Asiatic provenance of P (Mitchell et al., 1997), allow us to put in the category Amerindian haplogroups."

This is thought provoking. Samples that can't be assimilated to the native Q or to R, which is Eurasian, and brought to America by the European discovery) are roughly 3.6% of the total, and to make matters worse, samples from Amerindians that don't conform to the Q haplogroup are assigned to non-native introgression!

The author suggests that "The information showed here allows us to propose a revision of this lineage and it reassignation like a proper haplogroup, analog to Q1a-M242 description by Seielstad et al. (2003). We show the presence of this haplogroup only in northern Chilean native samples with high levels of the other Amerindian haplotype, Q1a3al. Like P marker is the ancestry of two lineages very common in Europe (R) and Asia (Q), a more carefully revision on P it is necessary to determine its real presence in both continents."

The paper cites some authors who have studied the presence of P haplogroup among South American natives:

Bortolini et al. (2003) "They obtained variable percentage of P haplogroup in several populations.". Bolnick et al. (2006) "found P positive samples in Cheyenne and Cheroke in percentages between 2-4%". Blanco-Verea et al. (2010) "found P positive in Colla, Diaguita and Mapuche" but Toscanini et al. (2010) failed to confirm this among Colla and Tobas. Bailliet et al. (2008) "found possible P (assign it within K haplogroup) in Ayoreo, Lengua, Wichi, Mocovi, Huilliche and Tehuelche".

Regarding the latter study, Baillet et al. (see p. 299 in their article) consider P as allochtonous (imported, originated in some other, non-American location) and found it at high levels: "K(xQ,R) did not exceed values of ~7%" they place P withing K excluding Q and R haplos. As usual, any genetic markers that don't fit into the expected Q haplogroup for Amerindian males is considered as having been brought to America after is European discovery in 1492!

Baillet et al. also argue that "K(xQ,R) is a minor haplogroup among South American samples and involves subhaplogroups of Asian origin (Su et al. 2000; Hammer et al. 2001; Su et al. 1999; Underhill et al. 2001"

Looking into other P-haplogroup studies in America, I found a paper by M. Saõ-Bento et al., (2009) reported P haplogroup at 1.23% frequency in a Brazilian study in the interior of Sao Paulo state, but remarked that it could be a mistaken identification: "the presence of the haplogroup P(xR1,T) is most probably due to the Native American haplogroup Q, which cannot be identified with the chosen Y-SNPs, even though it may also be related to the Asian input."

The ISOGG website from their now obsolete 2018 webpage on P haplogroup, states that "appearance. Haplogroup P is best represented by its two immediate subclades, haplogroups Q and R, which expanded to become the dominant haplogroups in, respectively, the Americas and Europe. P1-M74 or M45 has been found in n. Philippines, India, China (Maks, Ai Cham, Biao, Then, Uygurs, Tibetans, Hans), Taiwan (Pyuma), Indonesia (Batak, Malay, Minangkabau, Kaili, Alor), Romania (Szeklers), Scandinavia, Iran (Bakhtiari, Arabs) Pakistan (Burushos), Melanesia, Jordan, It is not clear that all these men were verified negative for the haplogroup Q subgroup. P2-B253 was identified in the Philippines (Agtas)" This is a wide geographic range, spanning many people of different ethnic origins, from Romania and Scandinavia, across the Middle East, Southern, Eastern, and Southeast Asia, Siberia, and Melanesia! This is a clear hint of antiquity, an original group that was widespread in that area, and possible presence elsewhere at low frequencies. The ISOGG 2019-2020 current version repeats this information. But no values for prevalence frequencies are provided.

I dug a bit deeper into some of the groups mentioned above. Interestingly, it includes dark skinned, short statured Negrito people like the Agta, where P is found at frequencies of 4.62% (Source), white Indoeuropeans like the Pakistani Burushos, and Asian people like the European Romanian Szeklers, who are said to descend from Atila's central Siberian Huns (as stated by Csány et al., (2008): "...the presence of the haplogroup P*(xM173) in Szekler samples, which may reflect a Central Asian connection".

An interesting point is to look at the distribution of haplogroups Q and R and try to figure out the location of their source (the root is haplogroup P). The map is from Chiaroni J, Underhill PA, Cavalli-Sforza LL. (2010) (Y chromosome diversity, human expansion, drift, and cultural evolution. Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20174-9. doi: 10.1073/pnas.0910803106. Epub 2009 Nov 17. Erratum in: Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13556. PMID: 19920170; PMCID: PMC2787129.)

Haplogroups R and Q, distribution and frequency maps. Adapted from: Source

Below are two images showing R and Q haplogroup distribution in Eurasia (it did not include America for haplogroup Q) it is four years newer than the previous image; they appear in the Supplementary information files of Raghavan, M., Skoglund, P., Graf, K. et al. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505, 87–91 (2014). https://doi.org/10.1038/nature12736.

Haplogroups R and Q, distribution and frequency maps (excl. America) Source

It would seem that R originated in Central Asia (somewhere between Afghanistan, Pakistan, and Tajikistan and moved west across Western Asia, Europe, and into northern Africa. Q, on the other hand could have originated in North-Central Asia, and moved east into America. But if that was the case why is it absent in Western Siberia? Could Q in Asia be a backflow from America?

Where is the geographic location for haplogroup P, the root of both Q and R? The maps in Chiaroni, Underhill, and Cavalli-Sforza (2009) don't show P or the root from which P originated (haplogroup K), neither does the 2014 paper.

However, I found a non-scholarly online source posted in 2013, that says:

"Haplogroup K... was the parent of haplogroup P which is the parent of both haplogroups Q and R.
It has always been believed that haplogroup R made its way into Europe before the arrival of Neolithic farmers about 10,000 years ago. However, that conclusion has been called into question, also by the use of Ancient DNA results... in a nutshell, he said that there is no early evidence in burials, at all, for haplogroup R being in Europe at an early age. In about 40 burials from several location, haplogroup R has never been found. If it were present, especially in the numbers expected given that it represents more than half of the haplogroups of the men of Europe today, it should be represented in these burials, but it is not. Hammer concludes that evidence supports a recent spread of haplogroup R into Europe about 5000 years ago. Where was haplogroup R before spreading into Europe? In Asia.
It appears that haplogroup K diversified in Southeast Asian, giving birth to haplogroups P, Q and R. Dr. Hammer said that this new information, combined with new cluster information and newly discovered SNP information over the past two years requires that haplogroup K be significantly revised. Between the revision of haplogroup K, the parent of both haplogroup R, previously believed to be European, and haplogroup Q, known to be Asian, European and Native, we may be in for a paradigm shift in terms of what we know about ancient migrations and who is whom. This path for haplogroup R into Europe really shouldn’t be surprising. It’s the exact same distribution as haplogroup Q, except haplogroup Q is much less frequently found in Europe than haplogroup R."

This is quite revealing, (see Dr. Hammer's conference and its map showing K, P, R and Q, here).

Other maps found online show R and Q splitting from P somewhere in Central Asia: see the map below (source) where I added the "P" in red to highlight it. Notice however, how this map shows K splitting in Northern Iran (?) and not in Southeast Asia, P spits into R and Q somewhere close to the Altai region west of Lake Balkhash.

There does not seem to be a consensus for the location of K or P roots of the Q and R lineages. The information from yfull.com shown below (online here), shows the two samples mentioned at the top of this post, from Yana River, and modern ones from Malaysia, the Andaman Islands in India, the Philippines, and an ancient one ~1100 BP from Austria (maybe a remnant of Huns?). The tree then splits into Q and R.

This tree seems to confirm a contemporary prevalence in Southern and Southeastern Asia.

A paper by Karafet TM, Mendez FL, Sudoyo H, Lansing JS, Hammer MF. (Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia. Eur J Hum Genet. 2015 Mar;23(3):369-73. doi: 10.1038/ejhg.2014.106. Epub 2014 Jun 4. PMID: 24896152; PMCID: PMC4326703), suggests an origin in that area. It also (See Table 1), gives the following frequencies (all other locations in Asia, Europe, and America have 0%) for haplogroup P-P295*: Aeta, 28%; Sulawesi, 0.6%; Sumba, 3.2%; Timor, 10.8%. This study calls Haplogroup P-P295, K2b2, and mentions its "sister clades Q and R" adding that "The P295 mutation, previously assumed to be equivalent to 18 other mutations defining the haplogroup P, is derived in a broader group of chromosomes. In our worldwide sample of 7462 Y chromosomes, we observe the newly defined paragroup P-P295* in 83 chromosomes from Island Southeast Asia (Timor, Sumba, Sulawesi) and the Negrito Aeta population from Philippines." Clearly a lineage set in the insular part of Sundaland! The paper continues:

"...This pattern leads us to hypothesize a southeastern Asian origin for P-P295 and a later expansion of the ancestor of subhaplogroups R and Q into mainland Asia. An alternative explanation would involve an extinction event of ancestral P-P295* chromosomes everywhere in Asia. These scenarios are equally parsimonious. They involve either a migration event (P* chromosomes from Indonesia to mainland Asia) or an extinction event of P-P295* paragroup in Eurasia. However, given the geographic distribution of the P331 mutation, the immediate predecessor of P lineage and its likely origin in Southeast Asia/Indonesia, the existing evidence favors the first scenario."

The P lineage originated in Indonesia and migrated into Asia. This paper mentions that the K haplogroup "arose somewhere in the Middle East shortly after anatomically modern humans dispersed from Africa" It then split into two families, one leading to Haplogroups T and L, with limited geographic distribution, and the other, characterized by the M526 mutation which leads to several sublineages of K named a to d. By far, K2b is the largest, and it comprises two sub-groups, K2b1 and K2b2. The first leads to haplogroups M, S, K-P60 and K-P79. The second is the one that we are interested in, because it leads directly to haplogroup P and its branches Q and R. This paper says: "the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania."

Karafet et al. suggest a rapid diversification, just 3,000 years between the appearance of K and its split into K2b1 and K2b2, and another 2,000 years to the split leading to P-P295. Then another 12,300 years to the root from which Q and R split (95% CI: 6.6–20 ky). So if K originated after the OOA event some 70 kya, the appearance of P was very early.

Denisovans

Anomalies in geographic distribution open the door to new questions. In this case, why does P have such a strange distribution? Interestingly, the Australasian signal detected in Native Americans is shared with people living in Island Southeast Asia!

I think that the answer may lie with our ancestor-cousins, the Denisovans.

They lived in this region, and admixed with modern humans as they crossed Asia to the north, and also and in this area. Furthermore, there were different groups of Denisovans exchanging body fluids with humans. At least two Denisovan lineages, D1 and D2 interbred with humans here in Southeast Asia, the Negritos of the Philippines may have met another Denisovan group that lived there (source).

The rapid spread of the mutation leading to P →Q, R, may have been induced by this intermixing with Denisovans. But, considering the "tree" of human Y-chromosome haplogroups, Denisovan Y-chromosome should have split off from the branch leading to H. sapiens long ago, and it would have different markers. A Denisovan man would not belong tho haplogroup P, his markers would differ.

In a future post I will look into the Y-chromosomes of Denisovans and Neanderthals.

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall ©