Genealogical research, some interesting thoughts

For several years I have been exploring my family tree, building on the work of my maternal grandfather and my father who pieced toegether information they had into two branches of ancestors.

It is far easier now than when my grandfather did his research in the 1980s, and my dad did his in the mid 1990s. In those days you had to go to the sites where the records were preserved (Register Office, cemeteries, churches — for baptism, burial, and marriage records). Now, online websites, offer free or paid services that let you browse document collections online. Government offices have searchable data (census, weddings, births, deaths, migration, etc.)

So, building on the work of my predecessors, I have added more information and found interesting data about my family.

It also helped me put in perspective things like generation times, the size of families, the terrible mortality rates of past ages, and the effects of these factors on the genetic mixup that I carry.

Each generation dupicates my direct ancestors (two parents, four grandparents, eight great grandparents, sixteen great great grandparents, and so on), by the time you have gone back seven generations to, say, James Whitehall, born in 1741, you have 128 great great great great great grandparents. Each of them contributed genes to their offspring, but even though you'd reckon that you received 1/128th of their genetic material (or 0.78%), it is very likely that you did not get any!

This is because genetic material is sliced into chunks, and recombined. Although on average a child gets 50% of its genes from each parent it may not be exactly 50 percent because these chunks aren't equal. So, alleles are passed on in a random way. So as you go further back in time, the chances are that a given ancestor's genes may have got lost on their way to you. Below I quote Bird, 2025 to clarify this fact:

"For example, while each of a person's four grandparents is expected to contribute to 1/4th of their autosomal genome, ten generations (~250–300 years) ago, a person can have at most 2¹⁰ = 1024 ancestors. Thus each of these more distant ancestors is expected to contribute to < 1/1000th of their autosomal genome, with a ∼58% chance of no detectable relationship at all. At fourteen generations ago (∼420 years), this probability goes up to <95% (Donnelly 1983; Ralph and Coop 2013). For this reason, our genome is necessarily only a snapshot of a fraction of a person's complete set of ancestors and carries no information about the ancestors that did not contribute any DNA to this particular descendant."

I am certain that my mother's mtDNA is in my body's cells, and that it came from her mother, and so forth, along that matrilineal line. But, many mothers' mtDNA never got a chance to pass on because they only had sons, their daughters dying before they managed to reproduce.

Regarding the man, I am also certain that I carry the Y chromosome along a patrilineal line which may or may not be that of those who passed on the Whittall surname given the proclivity to stray that we humans have when it comes to making babies. A study by Guerrini, 2022 published in Cell, found that "3% of the total sample learned that the person who they thought was their biological parent is not." So, who provided your Y chromosomes may not be too certain.

My X chromosome came from my mom, but... which of her two X chromosomes did I inherit? The one she got from her Dad, and therefore, originating in his mother, or the one that came from my maternal grandmother, which in turn could have come from either of her parents... Complexity increases as we move deeper into the past.

Regarding the autosomal DNA, I carry a cocktail of alleles in my chromosomes, passed down from past generations, but, as mentioned further up, some ancestors are not represented, and their signature has been lost. This is like a bottleneck. Genes got lost despite the fact that there is a continuous line of descent between those ancestors and me.

Generation times vary. For instance James Whitehall, is 7 generations from me, and this spans 218 years between our birth dates: 31.14 years per generation. Taking another random ancestor on my maternal line is James Paterson, born in 1781, seven generations away, 178 years, 25.42 years per generation. I didn't average all 128 ancestors of those seven generations ago, but as you can see, the spread is large; roughly 28 ± 3 years.

A study published in Science by Wang et al., 2023 found "an average generation time of 26.9 years across the past 250,000 years" which seems more or less similar to the one of my family tree. However, the paper states that "The average human generation interval was at a recent minimum of 24.9 ± 3.5 years at ~250 generations ago (6.4 ka ago), roughly concurrent with the historic rise of early civilizations. Before this, it had declined from a peak of 29.8 ± 4.1 years at ~1400 generations ago (38 ka ago), just before the beginning of the Last Glacial Maximum." So, bearing this in mind, my family seems to have a longer generation time, roughly 10% longer than this paper's value for the recent past.

Finally, I was surprised at how people died at a young age. Women bore children from age 20 to their mid 40s, as many as 14 children, and most died in their youth. Women and men lost their spouses and remarried in their 30s and 40s, some did so even twice! The world was deadly in those days before vaccines, antiseptics and antibiotics. These deaths also erased many genes that my distant cousins and great great uncles and auntes carried.

So, just looking back at my family, I wonder how can we be so certain about the genetic diversity of some populations, generation times, admixtures, bottlenecks, when chance and probabilities rule how genes are passed down from our distant ancestors, even in a healthy population in Modern Scotland, England, and Ireland.

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

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).

San, the oldest humans?

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 © 

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 © 

The complex Human tree in Africa...

A new paper published in Nature (Ancient West African foragers in the context of African population history, Mark Lipson, Isabelle Ribot, David Reich. Nature 577, 665–670 (2020). https://doi.org/10.1038/s41586-020-1929-1) tells us about the admixture going on in Africa some thousands of years ago:

The paper's highlights are:

• They sequenced the DNA of four children from Shum Laka in Cameroon buried on two separate occasions (two of the children were buried 8,000 years ago, the other two, 3,000 years ago).
• One of them carried the oldest and most divergent Y chromosome haplogroup: A00
• Their model implies that these children belong to the fourth group that originated modern human lineages. There were three more groups: (i) from which modern Khoisan people descend from. (ii) Ancestral group to the East Africans. (iii) An exinct "ghost" population. These groups are some 250 ky old.

Science tells us more about the extinct group (iii): "Another two-thirds of children’s DNA came from an ancient "basal" source in West Africa, including some from a "long lost ghost population of modern humans that we didn’t know about before" says population geneticist David Reich of Harvard University, leader of the study."

And even more interesting is that "...the Shum Laka individuals are most related to present day rainforest hunter-gatherers [pygmies] and not ancestors of Bantu-speakers is surprising given that Shum Laka was long considered by archeologist[s] as the site where Bantu-speaker culture [was] developing in situ" (from LiveScience).

These four children are therefore not related to the modern Africans living in Cameroon or to the Bantu speakers who spread out across Africa. Instead they are closer to the pygmies of Central Africa!

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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 © 

An old paper with Amerindians as ancestral to Europeans and Asians

Just a very short post. I came across an old paper (A view of modern human origins from Y chromosome microsatellite variation, Ibrahim, Muntaser E.; Seielstad, Mark), which gave an "old" origin date for African Y chromosomes, which by the way were the "most diverse". The funny part are Fig. 1 and 2. Shown below:

Trees showing the relationship of Y chromosome among humans. Americans seem to be the oldest after Africa.. From Ibrahim and Seielstad.

These figures have Asians and Europeans further from the root than Amerindians...

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2014 by Austin Whittall © 

The link between Negritos, Papuans and Amerindians!

At last a paper that sheds some light on the origin of Native Americans. I was pleasantly surprised to see a paper today that postulates that America had two distinct founding populations and that the older one, found in South America, is linked to Negrito people of the Andamans, Papuans, New Guineans and Australian Aboriginals.

This is the paper: Pontus Skoglund, Swapan Mallick, Maria Cátira Bortolini, Niru Chennagiri, Tábita Hünemeier, Maria Luiza Petzl-Erler, Francisco Mauro Salzano,Nick Patterson,David Reich. Nature (2015) Genetic evidence for two founding populations of the Americas doi:10.1038/nature14895 Received 05 February 2015 Accepted 14 July 2015 Published online 21 July 2015,

The paper is here LINK; the following image is the map that portrays that similarity between those groups:

Just in case you are expecting a post-discovery of American admixture of Asian genes with Amerindian ones... the paper on page 3 shows that they are closer to South East Asians Onge than to Polynesians. The closing paragraphs hint at a very ancient origin for these Amerindian ancestors and this is because though they are similar to the Andaman Negrito-Papuan group they "are not particularly closely related to any of them" and the original population that later led to these Amerindian ancestors became extinct in Asia. By the way, the Andaman natives and the Negrito people are believed to be among the oldest humans out of Africa.

Allow me to throw a wild idea: how can we be sure the flow was from South east Asia to America and not the other way round? an Out of America move from a basal archaic population that lived in the Americas?

And I recall my post on Y chromosome Haplogroup C, which is present in America at low frequencies and... also found in SE Asia.

It is indeed an interesting discovery and is I believe related to the recent paper on the Botocudos, which I wrote about a few weeks ago: "Put together we could conjecture that the old human lineage that peopled Asia reached the New World long before later East Asian or Siberian waves got there. That they are found in some secluded parts of America. They are old, and linked to Melanesia, Australia (whose inhabitants recently moved across the Pacific peopling Polynesia)."

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall ©