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.

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

An intro to Y chromosome haplogroups

My last post mentioned the possibility of Denisovans being linked to Haplogroup P of the Y chromosome, and the possible presence of haplogroup P in America. I thought that it would be straightforward to associate Denisovans with haplogroup P. But after giving it some thought, it isn't. So I decided to recap and go back to the basics and try to find out if it is feasible to associate Denisovans with any human Y chromosome haplogroup.

Transmission and Mutations of Chromosome Y

Chromosome Y is inherited in a patrilineal manner. All men carry one chromosome X and one chromosome Y, they inherit the X from their mothers and the Y from their fathers. In human beings, carrying a pair of X and Y means you are a man. If you inherit the X from both parents, you are a woman.

Base Pairs

Like all chromosomes, Y is made up of DNA (Deoxyribonucleic acid) a molecule that is made up of two counter-spiraling helicoids (like a winding circular stairway), both strands are made up of sugar-phosphate and are the backbone onto which four different compounds (bases) attach. These are Adenine (A), Cytosine (C), Guanine (G), and Thymine (T); these are the steps of the stairway. The bases bind in a particular way, A with T and G with C.

DNA carries the instructions that the cells can read and use it as a template to build proteins.

The bases are laid down in a certain sequence along the spirals, for instance one strand could have: A T G C C T A G T... and the opposing one would have the complementary bases (a T for every A, a C for each G, and viceversa): T A C G G A T C A...

Each pair of linked bases (the rungs of the stairway) is a base pair, for instance A—T. There are 60 to 300 million base pairs in each of our 46 chromosomes, a total of around 3 billion of them in our genome.

Chromosome Y is the smallest in terms of base pairs: roughly 60 million on average.

Genes

Genes are a specific sequence of aligned base pairs in one chromosome. They are the basic unit of heredity. A gene has the codes required to produce special molecules known as RNA or specific proteins.

When cells replicate, or in the case of our sexual gametes (ovarian eggs and sperm), the chromosomes undergo a process of splitting and the DNA strands unwind and replicate. With 3 billion base pairs, copying the new strands can lead to alterations in the base pairs: mutations.

Some base pairs are lost (deletions) others are copied twice (duplications). This alters the blueprint and may have an impact on how the gene that contains these mutations functions. Mutations can be negative (deleterious), neutral, or even positive. As we will see below, mutations in chromosome Y are problematic, as they accumulate.

Hominin Evolution

Our closest primate relative is the common ancestor that we share with chimpanzees, who lived between 6 and 8 million years ago.

This distant ancestor evolved, through a series of mutations into our homo ancestors: Homo habilis and Homo erectus, and others, reaching the common ancestor of Neanderthals, Denisovans, and Homo sapiens.

The original male hominins living 3 or 4 million years ago, carried certain base pair sequences in their Y chromosomes. We can imagine a small population with a few hundred males sharing identical base pairs (this is of course an over simpification, they differed). These "men" then passed their Y chromosomes with these same sequences to their sons. Some of them probably died in their childhood and did not mate, others only had daughters, so their Y chromosomes were lost, only those who had sons passed them on to the next generation.

Mutations

Each generation went through the same process, but the sequences that were passed on, changed over time as chance and external factoes introduced random mutations in the base pairs of the DNA strands of the Y chromosome.

Below are some of the factors that cause mutations:

• Chance, random mutations.
• Age of conception, those men who reproduce later will have more male germ-cell divisions, and each division entails the risk of a failed copy in the sequence. Formation of sperm (or spermatogenesis) implies constant cellular division over a man's lifespan. Female oocytes that result in eggs are all produced at birth, in one go.
• Methylation, the addition of a methyl group (—CH₃) to the DNA strand due to epigenetic (lifestyle or external) factors such as stress, famine, or toxins (alcohol, chemicals, smoking).
• Oxidative stress. Sperm are also modified by inflammation, heat, radiation (cosmic rays) which can produce free radicals which are oxidants and degrade the DNA.
• Inadequate repair systems, although the Y chromosome has limited repair mechanisms as it is mostly non-recombining (it has no partner like the other non-sexual chromosomes and does not recombine with the X chromosome). It has limited ability to fix glitches due to its high content of repeat sequences called palindromes.

Unlike other chromosomes, mutations can't be purged in Y chromosomes, so if they are harmful, they will accumulate and lead to genetic malfunction (sterility, illness, death, stillborn boys, and miscarriages). The chromosome will not work as expected. Mutations can reverse, undoing the original variation, but it is an unusual event.

The hominins evolved, but the basic structure of their Y chromosomes was similar, only the accumulated mutations, those that had allowed viable offspring survived, the others vanished as those who carried them died.

The whole genome is subjected to mutations, the X chromosome, and the other chromosomes, and natural selection acts, promoting the survival of the mutations that provide an advantage to those carrying them. It is possible that certain Y chromosomes, even though they were fit and possibly provided survival benefits, were eclipsed by deleterious mutations in other chromosomes. This led to the loss of many Y chromosome variants that had evolved over millennia.

The image Below shows an extremely oversimplified version of a Y chromosome. The original, ancestral version is (1) it has 50 million base pairs (not shown), but one mutated, say an A for a T (shown with the red band). It survives in the following generation and after many generations during which othe over the years, and today, when we look at the global population and sample the men, we find the variants marked (2) to (8), each one carries the original "red" mutation but have added others, each identified with a different color (blue, black, orange, green, violet, and gray).

Y Chromosome markers explained. Austin Whittall ©2026

Haplogroups

Here is where modern geneticists and anthropologists use their computer software tools, algorithms, and theory to build phylogenetic trees. They choose certain base pair mutations known as SNPs as "markers" that define "haplogroups" that split populations into branches from a main trunk (the basal one). Assuming that there are no back-mutations, and that repeat mutations are extremely uncommon, they propose that each marker (a mutation at a given base pair) that is fixed in a given population arose in a sequential manner.

In the example shown above, the phylogenetic tree would be the one shown below, assuming that mutations accumulate and don't reverse:

Caveats

We could argue that (8) resulted from (4) that lost its "blue" mutation, but as mentioned further up, orthodoxy considers that back mutations are rare so they ignore them. Problems also arise when we ask which mutation came first, (2), (7), or (8) they are all just one mutation away from the ancestral root.

In the real world, this is far more complicated, especially when we sequence the Y-chromosome of Neanderthals and Denisovans, which have degraded, decayed, and are incomplete. The strands of DNA of ancient remains are full of voids, and bases that have switched, or flipped. Comparing them with modern strands is done with software that "matches" them and points out the differences.

Toomas Kivisild (2017) highlights the complexity of analyzing haplogroups in ancient Y-chromosome samples: "it can be challenging to distinguish true mutations from those induced by damage, particularly in case of C to T and G to A substitutions", contamination is another factor, and the errors caused by low quality readings caused by "coverage" (how many sites were measured in a sample for comparison with a reference genome) and "sequencing depth" (how many reads covered the sample). All of them can lead to incorrect branch lengths, tree inferences, and dating.

SNPs

And mutations can appear in markers leading to mistaken identifications, like the ones reported by A.T. Fernandes, R. Goncalves, and A. Brehm (2004), in the Azores, where "It was found that some individuals share the same haplotype but belong to different Y-chromosome haplogroup suggesting that SNP mutations may occur frequently." SNPs are Single Nucleotide Polymorphisms (a switch in one base, like an A for a T). This paper notes that "The human Y-chromosome haplogroups are characterized by several mutations according to the phylogeny and nomenclature proposed by the Y-chromosome Consortium. Haplogroups are considered to be stable due to the very low mutation rate of most binary markers (SNPs), around 10⁻⁹ per base per generation, showing evidence of recurrent mutation at only 6 of 240 SNPs." This study involved 240 unrelated men and found "three individuals that share an haplotype with a double duplication suggest[ing] that a recurrent mutation occurred in SNP M78 because the duplication event is rare and it is unlikely to occur twice. For the individuals sharing the same haplotype but belonging to different haplogroups two explanations can be possible: recurrent mutations in several SNP namely in M78 and M81 (E3b1/E3b2) and M172 (J/J*) or several STR mutations may have occurred." So much for haplogroups and the assumptions that they are based on! 6 in 240 may seem a low frequency but it is high, 2.5%.

STR, mentioned above is a Short Tandem Repea, a snip of 2 to 6 base pairs long that is repeated two or more times in a location along the DNA strand.

The Branches of the Haplogroup tree

Another factor to consider when looking at ancient and modern DNA is that a man who died 50,000 years ago shows us a picture of a lineage that stopped accumulating mutations then. During the following 50,000 years all other lineages continued adding mutations to their DNA strands at a rate of 10^-9 per base per generation (I am using the SNP haplogroup marker value given above). So assuming generations of 25 years, in 50 ky, there are 2000 generatons, and with 50 million base pairs in a Y chromosome, we can calculate 50 x 10⁶ x 2 x 10³ x 10^-9 = 100 mutations.

When we look at our last shared common ancestor with the Denisovan group who lived ~550,000 years ago, if we assume no mixing with these people since then. After 500 ky, when we met them again in Asia during the Out of Africa migration, each branch, ours, and theirs would have accumulated an average of 1000 mutations (1000 in 50 million base pairs is a very low proportion: 0.002%). With Neanderthals from who we split later, around 350 kya, and met during our first Out of Africa 150 kya, only 400 mutations would have accumulated during the 200 ky we remained apart.

Intra Homo sapiens comparisons like the ones that compare a modern Chinese or a Native American from the Amazon, with an African San, are comparing lineages that have accumulated mutations since they split, probably 60 ky (Chinese and Amerindian) ago from the African line, accumulating mutations separately since then ~120 mutations in each line. And Native Americans with a 30 ky split from Chinese would have added 60 mutations.

Branch Shortening

Finally, and this will be the subject of my next post, mutations do not accumulate at the same rate. Africans have "shorter branches" on the phylogenetic trees. A paper by Petr et al, (2020) using data from an ancient man found in Siberia, Ust’-Ishim, 45,000 years old and modern humans noticed that the number of mutations from the root of each "branche" that leads to Africans and Non-Africans differed, implying different mutation rates (or, in my opinion, incorrect dating of the root, or fork): "Importantly, we discovered that the branch-lengths in Africans are as much as 13% shorter compared to non-Africans, which is consistent with significant branch length variability discovered in previous studies and suggested to be a result of various demographic and selection processes. Notice how they attempt to explain the issue away with "various" processes.

Further reading. Though old and dated, it is short, clear, and comprehenisive. Mark A. Jobling and Chris Tyler-Smith, (2003). The human Y Chromosome an evolutionary marker comes of age, Nat Rev Genet. 2003 Aug;4(8):598-612. doi: 10.1038/nrg1124.

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

The Y chromosome of Neanderthals

A paper published in Science (The evolutionary history of Neanderthal and Denisovan Y chromosomes by Martin Petr et al. SCIENCE 25 SEP 2020 : 1653-1656), reports that "interbreeding between early humans and Neanderthals and selection replaced the more ancient Denisovian-like Y chromosome and mitochondria in Neanderthals".

The paper includes this tree:

Caption for image: "A) Neighbor-joining tree estimated from the Y chromosome genotype calls, excluding C-to-T and G-to-A polymorphisms, rooted with a chimpanzee as the outgroup (14). Numbers show bootstrap support out of 100 bootstrap replicates. Terminal branch lengths are not informative about the ages of specimens (Fig. 1A), owing to differences in sequence quality. (B) Estimates of TMRCA between Y chromosomes along the x axis and a panel of 13 non-African Y chromosomes. Each dot represents the TMRCA with a single non-African Y chromosome, with error bars showing 95% CI from a resampling of branch counts (14). Black horizontal lines show the mean TMRCA calculated across the full non-African panel (dashed lines) with resampling-based 95% CI (solid lines) (14).".

I have written about Neanderthal Y chromosome in two posts (May 2014 and May 2018), so I found this paper really intersting.

It suggest that:

• Denisovans, Neanderthals and Humans lie on three separate phylogentic branches ("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"). This is what one would expect.
• Split dates: "The two Denisovan Y chromosomes split from the modern human lineage around 700 ka ago ... By contrast, the three Neanderthal Y chromosomes split from the modern human lineage about 370 ka ago". Which also seems quite normal to me.
• They conclude that "The Denisovan–modern human Y chromosome TMRCA estimates agree with population split times inferred from autosomal sequences, suggesting that the differentiation of Denisovan Y chromosomes from modern humans occurred through a simple population split"
• And find the 370 ky TMRCA too recent for the Neanderthal Y chromosome. They authors write: "By contrast, the young TMRCA of Neanderthal and modern human Y chromosomes and mtDNAs suggest that these loci have been replaced in Neanderthals through gene flow from an early lineage closely related to modern humans."

So they concluded that a line of modern humans admixed into Neandethals, and they completely replaced Neanderthal Y chromosomes and that is why the split seems so recent. Instead of reflecting the older age they expected. This is summarized as "Autosomal genomes show that Neanderthals and Denisovans are sister groups that split from modern humans between 550 thousand and 765 thousand years (ka) ago. By contrast, the mtDNAs of Neanderthals and modern humans are more similar to one another [time to the most recent common ancestor (TMRCA) of 360 to 468 ka ago] than to the mtDNAs of Denisovans."

They add: "We conclude 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. The presence of this Y chromosome lineage in all late Neanderthals makes it unlikely that genetic changes that accumulated in Neanderthal and modern human Y chromosomes before the introgression led to incompatibilities between these groups".

Now, they only sampled 3 male Neanderthals. Perhaps a larger sample may result in a different outcome. An introgression 370 ka would mean that these humans "closely related" modern humans left Africa -assuming the Out Of Africa theory is correct- 370 ka in an ancient migration and mated with Neanderthals. Since their Y chromosome is distinct from ours, these "closely related" people must have died out in Eurasia.

But looking at the tree and the dates, why conclude an admixture from "closely related" humans into Neanderthals? An admixture that erased old Neanderthal Y chromosomes?

Occam's razor approach suggests: the Neanderthals have a different Y chromosome to us and to Denisovans (fig. above, B) it lies on a different branch. Which ratifies the conclusion. So is the age an issue? 370 ka is too recent?

Why not look into the assumptions that lead to this date? Such as the mutation rate (they estimated 7.34 × 10⁻¹⁰ per base pair per year) or the age they adopted for the "oldest Y lineages" (A00): ~249 ka ago.

I am agree with the authors when they state " Furthermore, we predict that the ~400-ka-old Sima de los Huesos Neanderthals should carry a Y chromosome lineage more similar to that of Denisovans than to that of later Neanderthals", it is reasonable, and does not impact on their supposed Y chromosome replacement theory. Sima de los Huesos chromosomes may also have evolved into what we find in later Neanderthals.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall © 

Haplogroups of Humans and Neanderthals and Denisovans: mtDNA and Y chromosomes)

I have just read a paper that refutes my closing comments of this 2014 post: A shared Y chromosome lineage Neanderthals and Modern Humans but it does support the image I posted in it, pictured below:

Hypothetical Y chromosome phylogenetic tree for humans and Neanderthal. Copyright © 2014 by Austin Whittall

I explained the image as follows: "the ancestral population of both humans and Neanderthals, split into two groups: one that would later evolve into modern humans, and another that would evolve into Neanderthals. Each would carry, in the beginning, the "original" archaic Y chromosome of the ancestral population, which, as each lineage accumulated mutations due to chance and positive selection would begin to grow in different directions, forming two distinct branches, which then in turn would continue branching as more mutations appeared."

And that is what the paper states (Reconstructing the genetic history of late Neanderthals by Mateja Hajdinjak et al., 652 NATURE VOL 555 29 march 2018, doi:10.1038/nature26151.) Figure 2 in the article is shown below, and it agrees with the Y chromosome tree that I proposed back in 2014:

Phylogenetic trees for mtDNA, autosomal DNA and Y-chromosome of humans, Neanderthals, Denisovans and Sima de los Huesos hominin. From Hajdinjak et al.

The Human haplogroups are on distinct branches, well away from those of the older hominins.

See this Sept. 2020 update.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall ©