Timeline, and age of the Y Chromosome

This post will look into the "age" or timeline of our Y chromosome. There are different methods used to estimate how this chromosome changes over time by accumulating mutations (*). This leads to a mutation rate expressed in mutations per site per year. It can be calculated by comparing the Y chromosomes of two different men, or a modern human and an archaic one, or another ape and humans, and count the mutations by which they differ, if we know when their lineages split.

(*) Actually, to be correct, a mutation is a chance change in a base pair, an error in the transcription of our genetic code. A substitution is when a mutation becomes fixed within a population, one that has not been erased by genetic drift, or natural selection. For instance, a chance mutation may lead to a "C" to appear instead of a "G", but and then another chance mutation could flip it to a "T" in that case looking at the original and the final versions we'd see one substitution, and imagine one mutation, but there were 2 mutations. Another example would be a flip back, to "C" (back-mutation or reversion), where we'd see no mutation or substitution, but in fact, there was one mutation.

The formula to calculate the Time to the Most Recent Common Ancestor (TMRCA) is shown below. Where the TMRCA in years; k is the number of base pair differences between both men, 2 is a factor added because the difference corresponds to the divergence in both men, half for each one and we don't want to count them twice, L is the total sequence length sampled in which k was detected; and μ is the mutation rate.

TMRCA (years) = k (mutations) / μ (mutations/site · year) · L (sites)· 2

From which the mutation rate can be calculated by shuffling terms as shown:

μ (mutations/site · year) = k (mutations) / TMRCA (years) · L (sites)· 2

A real life example comparing Chimpanzee and Human base pair divergences found in Shen et al., (2000) is the following: assumed TMRCA: 4,900,000 years, acutal values measured (the length sampled in base pairs) L: 38,568, (the number of divergent base pairs) k: 470, calculation of μ shown below:

μ (mutations/site · year) = 470k (mutations) / 4,900,000 (years) · 38,568 (sites)· 2

μ (mutations/site · year) = 1.25 × 10⁻⁹.

Assumptions and Data

As you can see, the formula is logic, and straightforward, we take a sample of a DNA strand from a Y Chromosome with a length of L base pairs (my intro to Y Chromosome post explains the basic terms) in both subjects, and then count the differences we observe (k), knowing how long ago both individuals shared their last common ancestor (TMRCA) we calculate the mutation rate μ.

The same method can be applied to any chunk of nuclear DNA including the X chromosome and any of the non-sexual chromosomes or autosomal DNA, as well as the mtDNA. The interesting part is that they all mutate at different rates.

Y chromosome mutation rates (μ)

Over the course of the years, different studies using different methods have attempted to calculate the mutation rate of the Y chromosome in humans. The table below shows some of these studies. The values of μ are given in mutations per site per year. For non-scientists, note that expressing a number multiplied by 10^-9 is another way of writing: "divided by 10⁹" and 10 to the ninth power is 1000,000,0000. This means that 1.24 x 10^-9 = 1.24 / 1000,000,000 = 0.00000000124 (very small indeed!).

• 1.240 × 10^-9 Thompson et al., (2000)
• 1.500 × 10^-9 Kuroki et al., (2006)
• 1.000 x 10^-9 Xue et al., (2009)
• 0.617 × 10^-9 Mendez et al., (2013)
• 0.820 × 10^-9 Poznick et al., (2013)
• 0.530 × 10^-9 Francalacci et al., (2013)
• 0.716 × 10^-9 Trombetta et al., (2015)
• 0.871 × 10^-9 Helgason, (2015)
• 0.760 × 10−9 Fu, et al., (2016)

The difference between the first value reported by Thompson et al, and the figure given by Francalcci et al is 2.34 times!

There are big discrepancies in these μ values

Using one or the other to estimate the age of a given specimen would result in one figure being over twice the age of the other one.

The different methods employed to calculate μ involve different assumptions and they all have their shortcomings. In the following commentary I will follow the excellent work of Wang CC, Gilbert MT, Jin L, Li H. (2014) ( Evaluating the Y chromosomal timescale in human demographic and lineage dating. Investig Genet. 2014 Sep 10;5:12. doi: 10.1186/2041-2223-5-12. PMID: 25215184; PMCID: PMC4160915).

The data used for comparing divegencies in the Y chromosome's base pairs can come from different sources: Ancient DNA, samples taken from prehistoric human remains which have been dated by using radiocarbon or other methods. Genealogical, using samples from a certain family for which the genealogy has been confirmed and dated, these usually involve short time spans and few generations. Archaeological Events, taking an estimated date for an event, such as the peopling of America or the settlement in a given region in Europe, and applied to samples from that date.

Confounding Factors

As mentioned in my post on phylogenetic tree branch lengths (a factor that shows that mutation rates are not constant), the value of μ should be considered as an estimation, and not something written in stone. Trombetta et al., (2015) point out that "variants" (mutations) appear at different rates across Y chromosome haplogroups, geographic locations, and time: "... we observed a remarkable heterogeneity in the distribution of variants, not only across different regions, but also across lineages and different times. Hg A00 stands out for showing strong associations with almost all genomic features considered. In the rest of the tree Hg's A0, A1a, A2'3 and B differ from Hg's DE, FC and R, and ancient branches differ from recent ones. The two levels are not entirely independent, as far as recent branches are enriched in lineages belonging to Hg's DE and R. It is possible that different social habits, lifestyles and environmental conditions experienced by populations harbouring different haplogroups resulted in systematic variations of the generation time and average paternal age at conception." They attribute this to older or younger age of the fathers when their children are conceived —older dads have more mutated sperm, and the effects of environment on DNA mutations.

Chimpanzees and Men

When comparing human and chimp Y chromosomes, we are not only separated by a gulf of 5 to 7 million years of separate evoluton, the evolution itself has been different in both species. The chimpanzee Y chromosome is much smaller than that of humans. it lost roughly one-third of its genes in the MSY, or male-specific Y region of their Y chromosomes, compared to men.

Kuroki, Y., Toyoda, A., Noguchi, H. et al. (2006) noted that there is a greater divergence in the sequence of human Y chromosome vs. chimpanzee Y chromosome than between the whole genomes of both species (1.78% and 1.23% respectively).

The reliable dating of the Chimpanzee-Human split is still being debated, and figures range from 4.2 to 12.5 million years ago. A factor of three!

There are also structural differences in the shape of our and the chimp's Y chromosome which complicates the alignment of segments for comparison. Finally, chimpanzees and modern humans have different pair-bonding sexual behaviors (Hughes et al, 2013). Schaller et al., (2010) note that receptive females copulate with multiple male partners creating selective pressure towards the male fertility genes in the chimp's Y chromosome. Monogamous pair bonding in humans lacks this intense selective force. This alters the rate of the mutational clock. The pair bonding in hominins can be seen in the reduced sexual dimorphism in australopithecines and the loss of sperm competition adaptations, suggesting less male-to-male strife, and the growth of cooperation as a means for reproductive success (Gavrilets, 2012).

Genealogical Methods

Pedigree-based studies look at men belonging to the same family, sharing the same paternal lineage, and whose birth dates are known, or at least, how many generations separate them. This provides a well defined dating.

Xue et al., (2009) studied 13 generations of men in haplogroup O3a. However, there are some potential sources of error in this method: Since mutation rates are random, variable, and unpredictable (the statistical term for this is highly stochastic), are we sure that 13 generations (approx. 390 years) is a long enough interval.

Another is the haplogroup itself, we have mentioned that haplogroups accrue mutations at different rates. Is haplogroup O3a a good reference for all other haplogroups?

Finally, if selection and genetic drift act mutations eliminating some of them over longer timescales, the number of mutations found in a genealogical study will be smaller than the actual one detected in longer scales.

Mutation Rates adjusted for autosomal mutation rates

This method was developed by Mendez F., et al., (2013) when they dated the extremely ancient A00 haplogroup Y chromosome, found in the Mbo people of Cameroon, Africa. The μ used by Mendez team was based on a study conducted in Iceland that calculated the autosomal mutation rate by analyzing the divergence between parents and their children. This implies several unverified assumptions: autosomal and Y chromosome mutation rates are similar (they are not), substitution rates and mutation rates are equivalent (they are not). They also used a generation time that spanned from 20 to 40 years when life expectancy for men in Cameroon in 1950 was below 40! (Source). Other authors using genealogical data, like Boattini et al., (2019) found generation lengths of 33.57 years. Hunter-gatherer groups in Equatorial Africa 150,000 years ago probably began mating at the age of 15. How can we know for sure? (See Elhaik E, Tatarinova TV, Klyosov AA, Graur D., (2013) and their critique to Mendez et al.

Older generation times lead to more mutations, and an overestimated TRMCA. A00's age is far shorter than the one put forward by Mendez et al.

Archaeological Data

In my posts, I have mentioned many ancient DNA samples taken from the remains of prehistoric, ancestral human beings and hominins (Yana River, Mal'ta and Ust'-Ishim). They provide a certain age with reliable radiocarbon-dating, and if the DNA is not degraded or contaminated, a reliable count of mutations.

Fu, et al., (2016) compared the remains of the Ust'-Ishim man with those of men alive today, and looked for "missing" mutations, those that appeared in modern men after Ust'-Ishim died. The team calculated a mutation rate of 0.76 × 10^-9

Human Migration approximations

Assuming dates for certain migratory events, like the peopling of America, placed at around 15,000 years ago, the dates for certain haplogroups found exclusively in America can be set close to that event. This has been used to calculate μ for splits between Asian and Amerindian lineages, or between Amerindian groups within America, obtaining a μ of 0.820 × 10^-9 (Poznick et al., (2013)).

A similar method was applied by Francalacci et al., (2013) to men native to the island of Sardinia in Europe, peopled around 7,700 years ago, and using the mutations detected in a sample of Sardinian men to calculate μ for their haplogroup (I2a1a). The value obtained was very low compared to those shown in the Table further up: 0.530 × 10^-9.

Can we be certain that the haplogroup diversified in its current location in Sardinia or America? Could it have taken place earlier (European mainland, or Siberia, respectively). Do the current Sardininans belong to the group that reached the island 7.7 kya? Or did they arrive later?

Implications

The sum of these factors show that environment, generation times, sexuality (pair bonding), natural selection, and genetic drift can promote or reduce mutation rates. Studies have a 2.4-fold variability, ranging from 1.24 × 10^-9 Thompson et al., (2000) to 0.53 × 10^-9 Francalacci et al., (2013), and these are the mean values, the confidence intervals are even wider. Supposing a threefold difference, what some estimate as a divergence taking place between two Y chromosome haplogroups 50,000 years ago during the final Out of Africa migration, may have taken place within Africa 150,000 years ago! And the A00 split instead of taking place 250,000 years ago may reflect one that ocurred 750,000 years ago.

The possibility that our most ancient ancestors had more chimp-like behavior would have implied a faster mutation rate during that period, followed by a slower rate later on. Even pair-bonding during the patrilineal, sedentary, agricultural period of the past 8,000 years may have slowed down mutation rates in comparison to the matrilineal hunter-gatherer period that preceeded it.

Mutation Rates and their impact on TMRCA inference. Copyright © 2026 by Austin Whittall

The image above shows how mutation rates can influence the age of the TMRCA. For the same measured value of "m" mutations marked by the gray line, the use of different mutation rates μ influences the depth or age to the TMRCA. A quick mutation rate like the blue one (μ₁) accumulates mutations quicker and takes less time to reach the detected "m" mutations, so its TMRCA is younger (T1), a slower mutation rate (red line) like μ₂ takes longer to accumulate the "m" mutations and its T2 is longer. Finally, a variable mutation rate like μ₃ (green line) that was faster in the distant past, and slower later on will have an even longer and older timeline (T3).

For those interested in maths, the slope of each curve marks the mutation rate dm/dt = μ(t), steeper curves mean quicker mutation rates. It an analogy of speed as the differential of space over differential of time.

I believe that the μ₃, variable mutation rate is closer to reality, reflecting variable social-sexual-cultural patterns of the small and egalitarian promiscuous hunter-gatherer groups of early hominins and human evolution. Later settled societies with paternal monogamy and private property led to slower mutation rates. This of course would imply an older root for the human Y-chromosome haplogroups, in Africa, prior to our migration into Eurasia.

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Fall has begun here in Buenos Aires, in the Southern Hemisphere! Lucky you who are now entering Spring!

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

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 © 

Short Branch Lengths (Y chromosome)

In my last post I mentioned the issue of shorter branches for contemporary Africans in the Y-chromosome phylogenetic tree. This means that starting from the fork that leads on one side to Africans, and the other to non-Africans, the latter contains more mutations than the former, but we are all the same age and equally distant from our common ancestor. So why do the Africans have fewer mutations? Do Eurasians accumulate more mutations? Are the branches built incorrectly? This post will try to shed some light on this matter.

Y-chromosomes and haplogroups

The accepted haplogroup structure for chromosome Y, just like that of mtDNA, is rooted in Africa, where the most basal lineages are found.

Using the phylogenetic tree analogy, all other variants, found outside of Africa are branches that stem from this African origin. Outlier branches, even closer to the root, include our ancestor-relatives, the Denisovans and Neanderthals.

Back in 2014 I posted about Neanderthal Y chromosomes, and used the following image, which I have updated to add Denisovans.

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 🔒- free access on Biorxiv🔓), which I will comment in depth in a future post. The authors of this paper mention that their Y-chromosome phylogenetic trees display shorter branch lengths for Africans.

This is interesting! They state "Importantly, we discovered that the branch-lengths in Africans are as much as 13% shorter compared to non-Africans (Figure S7.3), which is consistent with significant branch length variability discovered in previous studies and suggested to be a result of various demographic and selection processes."

Below is Figure S7.3 mentioned above. You can see that all these African samples have ratios, except for the S_Mbuti_1 sample, that are lessr than 1, meaning the branches are shorter than the European ones. Furthermore, the most diverged samples (A00) are even shorter :

Original caption:Branch length differences between African Y chromosomes and a panel of 13 non-African Y chromosomes. Ratios were calculated by creating an alignment of chimpanzee, African and non-African Y chromosomes and taking the ratio of the number of derived alleles observed in an African (x-axis) and the number of derived alleles in each of the individual non-Africans (dots, Table S7.1). “A00” represents a merge of sequences of two lower coverage Y chromosomes, A00-1 and A00-2 (Table S4.3). Fig S7.3 in Petr et al. (2020)

The branch lengths refer to the number of accumulated mutations in the branches of phylogenetic-trees. Africans have fewer mutations than non-Africans, so their branches are shorter, yet they are supposedly older! This is an anomaly, because it impliles a slower mutation rate in Africa, or a quicker one outside of Africa. The explanation offered by the authors is a classic one. This explanation is that leaving Africa caused population bottlenecks and forced adaptation to new environments which speed up mutations, or so the theory goes! Below is Fig. S1.7 from this paper.

Branches. Fig. S1.7

The values of the branches a, d, e, and f are given in the paper's Table S7.1 and are the following (I adapted the image and included a new column, a+d the branch leading to non-Africans, which, as you can see, has more mutations than the African ones -compare the values of a+d with f.

Branch lengths. Table S7.1

The difference seems small but it is significant. Furthermore since Ust'Ishim, who died 45,000 years ago, non-Africans added an average of d-e mutations, ~200 of them. Africans added ~180-190 mutations. Hence, the "shorter branch" issue.

Shorter or Longer?

However, an earlier paper that studied Neanderthal and H. sapiens Y chromosomes by Mendez F, Poznik G, Castellano S, Bustamante C, (2016) (The Divergence of Neandertal and Modern Human Y Chromosomes. The American Journal of Human Genetics, 98, 728-734) showed different branch lengths, but with an opposite skew! This work included two figures (Fig. 1B, and Fig. 2) which I have combined and adapted in the image below. (the filters are different regions used to compare the DNA strands, some are more restrictive than others).

The branch lengths leading to the most divergent Africans with haplogroup A00, Mbo people from Cameroon, has a length e, which is longer than the one leading to the Reference (European men), branch d. But both share the same root. Why have the Mbo men accumulated more mutations than Europeans during the same time span?

This paper calculates the split age for both Modern Human branches (Mbo and Europeans) at 280 thousand years ago (kya), and dates the Neanderthals split at ∼588 kya. The Neanderthal man that was analyzed, died ∼49,000 years ago, in El Sidrón, Spain, and is located on branch f. His lineage contains 49,000 years of fewer mutations because we mutated while he remained static, yet, the total line f contains far more mutations than either modern human line: the A00 (a+e) or European lineage (a+d), who, by the way have had an added 50 ky of mutations on them!

This shows that the Neanderthal Y chromosome mutated faster than Homo sapiens Y chromosome, or that the timeline calculated in the paper is inaccurate.

Back and Recurring mutations

The paper noted that "The 17 sites that are incompatible with the tree are principally due to recurrent and back mutations". So these are not as infrequent as imagined.

Reference Bias

Janet Kelso, co-author of Petr et al.'s paper investigated branch lengths and published her research in 2024: Resolving the source of branch length variation in the Y chromosome phylogeny, Yaniv Swiel, Janet Kelso, Stéphane Peyrégne. bioRxiv 2024.07.05.602100; doi: https://doi.org/10.1101/ 2024.07.05.602100.

This paper admits that population size, and reproductive age, accumulated deleterious mutations due to bottlenecks in the out of Africa group, may play a role, but the main cause of branch length differences is the reference human Y chromosome used for comparison, that lacks mutations that appear in more diverged haplogroups: "branch length variation amongst human Y chromosomes cannot solely be explained by differences in demographic or biological processes. Instead, reference bias results in mutations being missed on Y chromosomes that are highly diverged from the reference used for alignment."

Reference bias is an error caused by using a certain benchmark (in this case the reference haplogroup, which is European, known as the Homo sapiens (human) genome assembly GRCh37 (hg19) from the Genome Reference Consortium), that favors genetic "reads" that match it, over those in alternative alleles. The reference Y haplogroup is R1b.

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Comment on A00, the most ancient Y chromosome

For those interested in the deepest root of Y-chromosomes, the one named A00, you can find the original paper describing it by Mendez F., et al., (2013) (An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. AJHG, Vol 92:3 3, 7 March 2013, pp 454-459, https://doi.org/10.1016/j.ajhg.2013.02.002). An interesting critique to the findings, especially the extreme old age of this "basal" root, can be found in this paper: Elhaik E, Tatarinova TV, Klyosov AA, Graur D., (2013). The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome. (Eur J Hum Genet. 2014 Sep;22(9):1111-6. doi: 10.1038/ejhg.2013.303. Epub 2014 Jan 22. PMID: 24448544; PMCID: PMC4135414).

Sometimes the media, and websites mention "the oldest" or "the earliest" people pointing at the Mbo or the Khoisan (San) groups, but in fact nobody alive nowadays is "older" than other populations. We have all been evolving since the first Homo sapiens appeared. We are all equally distant from him or her, nobody is closer or more similar to those original modern humans.

This is why I dislike phylogenetic trees like the one shown below (source) that implies a direct link from the ancient root to nowadays for the San people, and a series of steps to a short fork for Asians and Europeans. (Hss: H. sapiens, Hsnn: Neanderthals, Hsnd: Denisovan)

When I read that the Khoisan separated from all other humans 150,000 years ago, I get the impression that it is a false statement. The Khoisan were not isolated since then, they also have admixture of other humans, but having lived in isolation in the deep past, and admixing with other diverse, divergent, isolated groups, they acquired a higher diversity themselves, as a population, while humans living outside of Africa lost diversity due to bottlenecks and founder effects. But the genes we retained in America, Asia, Oceania and Europe are mostly as old as the ones found in Africans.

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Back to differing branch lengths

Hallast P, Batini C, Zadik D, et al. (2015). (The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Molecular Biology and Evolution. 2015 Mar;32(3):661-673. DOI: 10.1093/molbev/msu327. PMID: 25468874; PMCID: PMC4327154. 🔓) mentioned that "Different clades within the tree show subtle but significant differences in branch lengths to the root." Fig. 3 in this paper (above is part of the figure) gives a clear image on how the branch lengths differ.

The tips of all haplogroups should all align, justified on the right side, as all the tips are contemporary, however, they have different lengths. I took R2 as the reference and drew a black vertical line. This makes the shorter branches stand out: haplogroups A, B, H, I1, Q, and R, and also the longer ones like C, G, J, or T. As you can see in the image above (I recommend visiting Fig 3 following the link, because it has far more detail than the simplified version I included above.)

Replication timing

A very thorough analysis on the causes of branch length differences can be found in Qiliang Ding , Ya Hu , Amnon Koren , Andrew G Clark, (2021). Mutation Rate Variability across Human Y-Chromosome Haplogroups. Molecular Biology and Evolution, Vol 38:3, March 2021, pp 1000–1005, https://doi.org/10.1093/molbev/msaa268.🔓.

The paper used data from over 1,700 men and "uncovered substantial variation (up to 83.3%) [in the] mutation rate among haplogroups. This rate positively correlates with phylogenetic branch length, indicating that interhaplogroup mutation rate variation is a likely cause of branch length heterogeneity."

The authors remarked that "Previous studies suggested that branch length heterogeneity might be caused by nongenetic factors, for example, paternal age variation across populations, acting over many generations. Another possibility is variation in mutation rate among Y-chromosome haplogroups.... [but] It was suggested that variation in Y-chromosome mutation rate across haplogroups was unlikely (Jobling and Tyler-Smith 2017)."

They disagree with the nongenetic factors and with Jobling and Tyler-Smith's dismissal of varying mutation rates, and prove that both are mistaken. This paper confirms that something known as replication timing varies across haplogroups, and this difference is linked to higher mutation rates (later replication causing more mutations than early replication timing).

Replication timing is the sequence in which the DNA of a chromosome is duplicated during cellular division. It involves unwinding and unzipping the DNA strand in a specific orer, in different places, some of them simultaneously.

Due to these differing mutation rates, branch lengths are different, and this impacts on the timing and dating of haplogroups. The paper's supplementary file states that the divergence time of haplogroups E1b, R1a, and R1b may be underestimated, while that of haplogroup B is overestimated, as the former have shorter branches, and the latter, longer ones. See Fig. 3 C and D in the paper.

The explanation sounds good, but why do different haplogroups have different replication timing? Alas, no answer is provided!

Population factors

Nevertheless, Barbieri, C., Hübner, A., Macholdt, E. et al. (2016) (Refining the Y chromosome phylogeny with southern African sequences. Hum Genet 135, 541–553 (2016). https://doi.org/10.1007/s00439-016-1651-0 🔓) attribute branch length in Southern African haplogroups to paternal age: "there is pronounced variation in branch length between major haplogroups; in particular, haplogroups associated with Bantu speakers have significantly longer branches. Technical artifacts cannot explain this branch length variation, which instead likely reflects aspects of the demographic history of Bantu speakers, such as recent population expansion and an older average paternal age. The influence of demographic factors on branch length variation has broader implications both for the human Y phylogeny and for similar analyses of other species." (Sure! it affects the calculation of dates along the branches of phylogenetic trees!).

This paper finds "The shortest branches in the Y chromosome phylogeny are for haplogroups A and B... E1b1a lineages have significantly longer branches than E1b1b or E2 lineages." Taking a look at the mutations marked along the phylogenetic tree shown in the paper's Fig 1, it confirms the comment branch lengths variability (below is the number of mutations from the tip to the root at the A2—T node).

• A2a: 17
• A2b: 7
• A2c:22
• A3b1b: 21
• B2B1: 113
• E1b1a: 208
• E1b1b: 138
• E2: 105

These people, living today have an extremely wide variation in mutation numbers between their common ancestor at the A2—T root and themselves: 7 to 208 mutations!! They are all Africans, and should be equally distant to the R1b reference genome, meaning that Kelso's reference bias does not apply in this case. This could be due to paternity age (older men have more mutations in their sperm as they sire children and pass on mutations in their Y chromosomes to their sons), or to the different replication times of different haplogroups.

T Naidoo et al., (2020) in their analysis of Khoe-San men in South Africa also found the branch issue: " Branch Length Heterogeneity Several earlier studies (Scozzari et al. 2014; Hallast et al. 2015; Barbieri et al. 2016) found evidence of branch length heterogeneity among Y-chromosome haplogroups, and provided possible reasons for its occurrence. We also noted significant differences in branch length heterogeneity among the major African haplogroups (supplementary tables S2 and S3, Supplementary Material online). A reduced mean branch length for haplogroup A, noted previously by Scozzari et al. (2014), was again apparent from our data. Although most major haplogroups differed significantly (with the exception of the E1b1a subclades), we found that haplogroup B did not appear to have as reduced a mean branch length, relative to haplogroup E, as found previously (Hallast et al. 2015; Barbieri et al. 2016). Within haplogroup E, E1b1b1 was found to have the highest mean branch length; though this may have been due to a lower sample size compared with haplogroup E1b1a." It seems to me, as a layman, that the branch length issue perplexes even the smartest scholars.

Closing comments

This post shows that scholars don't agree on why the African branches, the most diverged, and "archaic", leading to the root, and origin of our H. sapiens species, contain fewer mutations than those found in Eurasian people. Since the basis of calculating the splits between modern humans and archaic relatives like Neanderthals and Denisovans is the assumption that there is a "mutation clock" that ticks at a regular pace, so if we know the ticking rate, and the number of mutations, we can calculate when species split from others, and people diverged from others. Short branches on supposedly ancient lineages are incongruent.

We are all equally ancient, Africans, Eurasians, and Americans, yet we have accumulated mutations in our Y chromosome at different rates. This is something that should be clearly analyzed. Software issues, methodology, sampling, reference bias, replication times, older reproductive ages, larger population sizes, bottlenecks, etc. have been put forward to explain this anomaly. None of these answers seems satisfactory. Chromosome Y is peculiar, it is small, and critical; any mutations here can have disruptive effects. We are overlooking something. When we find it, we will know why some branches are longer than others.

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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 © 

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.

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

Siberian Yana people and Native Americans (38-24 kya)

The site at Yana River in Russia is the oldest and northernmost (70°43'N 135°25'E) site discovered, to date in Northeastern Siberia. The people who lived there used a distinct type of stone tools, replaced by later waves of humans who reached the region. It has been dated to 32,000 years ago.

The Yana site was disvovered and studied by Vladimir Pitulko et al., (2004); the team followed up on a discovery that took place in 1993, when a spear foreshaft, crafted from the horn of a wolly rhinoceros was discovered, by chance, on the bank of Yana River by a local scientist named Mikhail Dashtzeren. Dashtzeren led Pitulko's team th the spot, and a methodical search of the area led to the 2001 discovery of the Yana Rhinoceros Horn Site (Yana RHS); Pitulko et al., also found mammoth tusk foreshafts.

The interesting part, is that the wooly-rhino horn foreshaft is very similar to the mammoth ivory foreshafts used by the American natives of the Clovis culture dating back 14,000 years. Foreshafts made of rhino horn were tough and flexible, and not as rigid as the Clovis ones. There were no wolly rhinos in America, so the Clovis had to use mammoth ivory. The foreshaft allowed hunters to replace broken stone points quickly when they broke while hunting megafauna. This implies that there was a shared know-how concerning spear-making, that spanned 18,000 years across two continents. But, as we will see below, the Yana people had vanished in Siberia, replaced by others, long before the Clovis appeared in America. How was this know-how shared?

The people who lived in Yana also shared genes with Amerindians. More recent research (Sikora M, Pitulko VV, et al. The population history of northeastern Siberia since the Pleistocene. Nature. 2019 Jun;570(7760):182-188. doi: 10.1038/s41586-019-1279-z. Epub 2019 Jun 5. PMID: 31168093; PMCID: PMC7617447) noted their specific stone tool technology and that there are no other sites in northeastern Siberia until the final part of the Last Glacial Maximum or LGM: "Following the occupation at Yana RHS, there is an absence of archaeological sites in northeastern Siberia until the latter part of the LGM, when groups bearing a very distinctive stone tool technology appear (~20 kya). It was within that intervening period that the ancestral Native American population emerged, but to date no genomes from individuals of this age have been recovered in northeastern Siberia."

Clearly, the Yana people who had been living there 32 kya had vanished 20 kya. Their stone tool style had also vanished: "by the time of the Last Glacial Maximum (LGM) ~23-19 kya, the Yana-related assemblage had disappeared. LGM and later artefact assemblages are dominated by a distinctive microblade stone tool technology, which spread in a time-transgressive manner north and east out of the Amur region, but did not reach Chukotka or cross the Bering Land Bridge (Beringia) until the end of the Pleistocene, and thus later than the earliest known sites in the Americas." This suggests that those who replaced the Yana came from the southeast, and did not move on, into America until it was already inhabited.

What happened to the Yana? Why did they vanish without a trace? The 2019 paper offers a timeline for the Ancient Siberian population or ANS: "The initial movement into the region represents a now-extinct ANS population diversifying ~38 kya, soon after the basal West Eurasian and East Asian split, represented by the archaeological culture found at Yana RHS... The arrival of people carrying ancestry from East Asia, and their admixture with descendants of the ANS lineage ~20-18 kya, led to the rise of the AP and Native American lineages. In the archaeological record this is reflected by the spread of microblade technology that accompanies the post-LGM contraction of the once-extensive mammoth steppe10. This group was, in turn, largely replaced by Neosiberians in the early and mid-Holocene... We find that, despite the complex pattern of population admixture throughout the last 40,000 years, the first inhabitants of northeastern Siberia, represented by Yana, were not the direct ancestors of either Native Americans or present-day Siberians, although traces of their genetic legacy can be observed in ancient and modern genomes across America and northern Eurasia. These earliest ancient Siberians (ANS), who are known from a handful of other ancient genomes (Mal'ta and Afontova Gora), are the descendants of one of the early modern human populations that diversified as Eurasia was first settled by our species, and thus highly distinct."

The Mal'ta and Afontova Gora remains are much younger, and dated to 25 kya and 17 kya, respectively, and also further south and west from Yana River. They came from central Siberia. The Mal'ta remains carry the U haplogroup (mtDNA) like Yana people, it is rare nowadays in Eurasia and has not yet been detected among Amerindians or ancient Native American remains, Mal'ta's Y-chromosome was haplogroup R, close to its root (Source) so it was also different to the Amerindian Q and Yana River's P haplogroups.

Could the Yana people have moved on, heading east, and entered America? This would explain their sudden disappearance from Siberia, and the transfer of the ivory foreshafts technology used much later by the Clovis people.

In Northwestern Canada 24,000 years ago?

If modern humans were in northern Siberia, 100 km from the frozen Arctic sea, ~71° latitude north, the earliest and northernmost people to have been yet detected in such a northern climate, what stopped them from moving further east and entering America at that time? Nothing.

Research from 2017 (Bourgeon, Lauriane; Burke, Ariane; and Higham, Thomas, Earliest Human Presence in North America Dated to the Last Glacial Maximum: New Radiocarbon Dates from Bluefish Caves, Canada (2017). KIP Articles. 1595. https://digitalcommons.usf.edu/kip_articles/1595), though supporting the Beringian Standstill hypothesis (which I do not agree with), describes radiocarbon dating of bones found in America (Bluefish Caves, Yukon, Canada, 67°09'N 140°45'W, right beside the border with Alaska) which according to the authors "confirm that Bluefish Caves is the oldest known archaeological site in North America ", adding that, "in conclusion, while the Yana River sites indicate a human presence in Western Beringia ca. 32,000 cal BP, the Bluefish Caves site proves that people were in Eastern Beringia during the LGM, by at least 24,000 cal BP" This is an early date for human presence in America.

Y-chromosome Haplogroup P

The 2019 paper on the Yana site (see Suppl. Table 1) mentions that the remains of two men unearthed in the Yana region, dated to ~30 kya, were sequenced. They carried U2 mtDNA (a maternal haplogroup which is not found in among Native Americans). Their Y-chromosome Haplogroup was P1, which is ancestral to two main haplogroups: (1) haplogroup Q, preponderant among Amerindians, and (2) haplogroup R, which very frequent across Eurasia.

These two men from Yana River dated to 31,000 years ago, carried P haplogroup in their Y-chromosome. This variant is not considered a founding lineage in America, where it is found, it is regarded as "imported" after the European discovery in 1492. Only Q, which descends from haplogroup P, is considered a founding Amerindian lineage.

I believe that a deeper look into haplogroup P would be interesting, and that will be the subject of my next post.

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