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 © 

Out of China?

Ye Zhang and Shi Huang ( The Out of East Asia model versus the African Eve model of modern human origins in light of ancient mtDNA findings, bioRxiv, Feb, 10, 2018. doi: https://doi.org/10.1101/546234) have proposed that an "Out of East Asia" (read that as "China") is a better model to explain human origin than the current "Out of Africa" theory.

I invite you to read the paper, which finds fault in the Genetic clock: "...The African Eve model assumes the molecular clock while the Asia model not. Given that the universal molecular clock is widely acknowledged to be unreal" (We have posted about the "clock" several times).

It upholds Huang's Maximum genetic diversity (MGD) hypothesis but does not explain it in this paper, however you can read Shi Huang's detailed explanation here (Shi Huang, New thoughts on an old riddle: What determines genetic diversity within and between species? Genomics, Volume 108, Issue 1, July 2016, Pages 3-10. https://doi.org/10.1016/j.ygeno.2016.01.008).

It also dismisses the Infinite-Sites Mutation Model or ISM, which states that all mutations that have occurred along the sequences since the most recent common ancestor only affect a new site; therefore no single position can mutate twice.

Out of Africa also requires the "Neutral Theory" to be applicable (Mutations can be harmful, and they take place at random and those that are selectively neutral accumulate while those that are deleterious are removed by natural selection). Huang disagrees with this theory (read more here: Genetic equidistance).

The authors find that "Our model furthermore specifically places the least differentiated haplotype R0 or R* as the ancestor of all mtDNA haplotypes, which is in contrast to the African Eve model that puts R downstream of haplotype N (Figure 1). The R0 haplotype is most common today in the Southern Chinese group in the 1000 genomes project, implicating the origin of the modern mtDNA lineage in Southern China [5]."

This is their Figure 1:

The paper concludes that: " the Out of East Asia mtDNA model is inherently more sound and self-consistent than the African Eve model due to stronger theoretical foundations and far more realistic assumptions. "

Readers of this blog are well aware of my anti-sinocentrism, I usually tend to take claims by Chinese scholars lightly, because of their "China is the center of the world viewpoint", however this paper is quite interesting though lacking more sound evidence to fully convince me.

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

Y chromosome Haplogroup R in America

The overlooked lineage

There is a very particular Y chromosome haplogroup in the Americas which is often ignored, overlooked or clumped together with "others" since it is not considered a founding lineage: haplogroup R. with its M173 mutation.

I believe that there are several reasons for this omission, one well founded in common sense, others shielded in political correctness:

• The logical reason is simple: Since modern Eurasian populations are predominantly haplogroup R, the Spaniards and Portuguese, French and British have a high proportion of hg. R in their genes. It was these people who discovered and conquered America so their admixture with the conquered American Native races will surely be reflected in contemporary Native Americans' Y chromosomes by the presence of typically European R haplotypes.
• The politically correct reasons are several: for instance wacko white supremacist claims of European pre-clovis presence in America via a trans-Atlantic Ice Age crossing (Solutrean hypothesis). Then there are some religious beliefs involved (Mormons) with lost tribes reaching America, and things can get even worse: Atlantean migrations... you get it, sci-fi junk. These strange theories are frowned upon by mainstream scholars and even a slight formal support to any of these notions is academically unacceptable. As an example see Stanford and Bradley (2012) who support the trans-Atlantic route [1] and a rebuttal of their theory (Erena et al., 2013) [2].

Then we have the political issues, those involving race, past discrimantion and guilt for the actions of our predecessors regarding their racism and the atrocities that they committed against the natives. It also involves an overly sensitive Native American society, overreaction which is often impeding the course of science and the advancement of mankind's knowledge as a whole. As examples of this I can cite the legal battles at court as allowed by U.S. law (Native American Graves Protection and Repatriation Act - NAGPRA), which have removed from further study ancient remains not even distantly related to contemporary plaintiff tribes.

It is, I believe, for these reasons that any hypothesis that suggests the presence of any kind of Europeans (even the Paleolithic ones) among the ancestors of Native Americans is, to put it mildly, discarded. No wonder the Kennewick man and the Windover Bog remains in Florida did not provide clear evidence of their sexual chromosome haplogroups. I don't believe in conspiracies, but botching up the sequencing twice, especially by a Federal organization of contested remains is indeed rather odd!

But let's get back to our post: we will try to look into this thicket of New World R haplogroup and see what can be made out of it.

Haplogroup R in the World

Officially there are two Y chromosome haplogroups accepted as founding lineages in America: haplogroup Q, which prevails among Amerindians with a 92.9% frequency and a less frequent haplogroup C, which is found at a much lower 7.1% frequency among indigenous American men, mostly in North America, but also with a patchy distribution in South America.

Then we have Haplogroup R which is considered by some to also be another Y chromosome founding Amerindian haplogroups. See, for instance Schurr et al., (2004) who add haplogroups P-M45, F-M89 and R1a1-M17 to hgs. Q and C as founding lineages. [13]

But others such as Zegura et al., (2004) [8] are quite convinced that haplogroup R in Native Americans is of a recent European origin and that it admixed into the local natives during the last 500 years, after the discovery of America in 1492.

This is a reasonable assumption: Hg. R is found among Europeans at very high frequencies. But, it is also found all over the world, so why would it be absent in America?

It is believed to have originated after the OoA (Out of Africa) migration of modern humans some 50 kya, in some part of Western Asia, from where it mutated and spread into Europe, Siberia, India, Eastern Asia, Southern Asia and even Australia. Surprisingly it is also found in Africa, as (according to mainstream science) the outcome of a back-migration from Asia.

Although the presence of hg. R in South eastern Asia and Australia could also be attributed to European colonization (the Spaniards in the Philippines, the French in Indochina, the Dutch in Indonesia, and the British in Australia, etc.), but actually there is no serious academic objections to the notion that these are local Asian haplotypes and not the outcome recent admixture. The table below combines data from three papers to show the frequency of hg. R in certain parts of the Old World and the Americas [14][11][8]:

The table is quite enlightening: the Asian frequencies are relatively low (2.5 to 8.6%), furthermore haplogroup R has not been detected in the highlands or coastal areas of Wests New Guinea and Papua New Guinea, New Britain, Moluccas, Vietnam (surprising since this was actually a French Colony) Taiwan or China.

The American data on the other hand is quite different; the frequencies are much higher among some groups (12.6 to 100%), and lower in others (2.5 to 8.3%), at levels similar to those found in Asians. And, yes, some Amerindians do not carry hg. R: Seminole, Shawnee, Kickapoo, Fox, Omaha, Mixe, Ngobe, Kuna and Emberra. Did they escape this suggested European admixture by some miracle?

This panorama indicates, in my opinion that America has the basic ancient coating of haplogroup R at Asian levels which was later overlain by additional hg. R from the European settlers. There are also some local hotspots with much higher frequencies due to the original peopling and distribution wave of native Americans in the New World and not as we will see below, due to higher admixture with Europeans in those regions. The problem is that mainstream science places all hg. R natives into the "mixed - races" category and dismisses haplogroup R as a founding lineage among Native Americans.

Haplogroup R in America

Haplogroup R is found at very high frequencies in Northern North America and is widely dispersed among most native groups: "In total, 73% percent of the populations analyzed exhibited haplogroup R, which ranges in frequency from 4 to 88%" [12], which is quite significant.

The following map is the one that awoke my interest on haplogroup R among Amerindians, and the reason for it is the very odd distribution gradient of hg. R in North America.

Take a look at the map (and the one below it which compares current population densities and hg. R's frequencies): you would expect a higher frequency of European haplogroup R in the regions where contact took place, that is, within the territories of the European colonies (which basically coincide with those that nowadays have the highest population densities). But the maps show something very different!

Native American frequencies of R haplogroup, From [12]

As you can see the highest frequencies are in the area just south of Hudson Bay in Canada (around lakes Winnipeg and Manitoba), and across N.W. Canada into Alaska. In the U.S., they fall off towards the South West. Mexico in general is a low frequency region with a slight increase among the Maya in Yucatan and the Pima and Seri close to the base of the Californian Peninsula.

The distribution does not coincide with current highs in population density or with those of the past in either Mexico or Canada or the US. So how did this supposedly European haplogroup enter the native genome? Physical proximity with a European for intercourse and baby-making is critical for admixture.

The paper (Malhi et al., 2008) [12] in which this map was published attributes this frequency distribution to : "... the earlier occurrence of European contact in Northeastern North America, which has provided a longer period of time for admixture to occur." [12]. I disagree for several reasons:

1. Hudson Bay and Manitoba of all places, were a zone of pelt trappers not thickly populated regions where Europeans and Natives could have had the chance to admix as for instance in coastal New York state or Maryland.
2. The same can be said about British Columbia and the Northwestern Territories
3. Additionally, long before the founding fathers reached the U.S. during Elizabethan times, Spanish conquistadors had been criss-crossing what is now southwestern US (at that time part of the Spanish Viceroyaty of Nueva España which comprised California, New Mexico, Arizona, Texas, Utah, Nevada and parts of Wyoming, Kansas and Oklahoma) and Mexico (since the early 1500s). These chaps would have definitively left their imprint in the local women... Yet, we can see that this region has an even lower frequency than that of the Canadian wilderness.
4. The whole of Mexico which has a very dense population and a history of admixture (more on this below) of Spaniards with Native Americans and also (but to a lesser extent, African slaves) has a very low frequency of haplogroup R. Why?

The map shows, in my opinion, no correlation whatosever with the European colonies and the quantity of hg. R found in the natives' genomes.

On Mexico, Latin America and Spanish open mindedness

Spaniards have a high frequency of hg. R and were particularly keen on mingling with the locals (natives) and with the African slaves (in Northern South America and Central America mostly), to an even greater degree than the more Puritan New England settlers (which according to Malhi are those who mixed with the natives!).

Admixture was due to a very concrete cause: women did not want to cross the oceans and settle in the New World. The few that did were wives of the Royal government officials. So the only available source of women were the local natives. Initially Spanish colonies were based on exploiting the local natives in mines and smeleters to produce precious metals for export back to the Metropolis. The conquistadors were men whose aim was to make a quick fortune and return home to wife and family. Their relationships in America were basic and obviously had only one outlet: the local women. Only much later would European women migrate to America but again, they would only wed within their social circles.

So quite soon, Spanish American societies had plenty of mixed -race people: Spanish with Indian resulted in Mestizo, Spanish and Mestizo in Castizo, Mestizo and Indian: Coyote, a black and a Spanish woman: Mulato, and so on....

To maintain social order, each group had its privileges and obligations marked out by the Crown's law (for instance Mestizos could not bear arms or have Indians given to them as encomienda -a form of serfdom) [5], these legal inequalities eventually festered into the independence revolutions that began in 1810 and led to the creation of Spanish Americas Republics, ran by Criollos (descendants of Spaniards, but born in America) and Mestizos.

The image below show a Mestizo, the mixture of White European and Native American. According to a Mexican Colonial period painting (1700s).[4] (See more admixture examples, Casta paintings)

Mestizo. Castes in Colonial Latin America

So, why is the prevalence of R haplogroup lower in Mexico and their former Colonial territories in S.W. USA? Do Spaniards have less proportion of haplogroup R than the French (in Canada) or the Britons (in the Eastern Seabord states)?

No they don't. Current Spaniards have between 51 and 85% haplogroup R. [6], similar to the frequencies found among English and French. So this is not the cause of the unequal cline. And we have seen above that there was no reluctance on their part towards mingling with the natives.

What is more, the Spanish colonial system was based on a firm grip over the natives: they replaced the theocratic Aztec, Inca and Maya states with their own bureaucracy (plus the Catholic church), and the lives of the natives remained virtually unchanged (something easy to verify by travelling around rural Latinamerica). Native villages (Pueblos de Indios) in Spanish America would have been very apropriate for admixture, far more better than the nomad camps or N.E. American natives. But the map shows us otherwise...

I believe that the reason for this is that haplogroup R was already present among the natives as a founding clade in America, introgression with Europeans added some percentage points to the mix, and very likely it incorporated new European R haplotypes, but there was a substantial presence of hg. R among North American natives. These appear as we will see below in the joining-network trees as outliers with unique haplotypes not shared with Europeans. The exceptions that confirm the rule.

The issue can be easily settled. An in depth sequencing of native hg. R haplotypes would help distinguish the "American" lines from those haplotypes that are surely "European", however this has not been done. There is a clear preconception - prejudice among scholars that simply ignores the option that hg. R is a founding lineage among Amerindians.

Bias and preconceptions

Since most studies consider haplogroup R as a non-Native American line, it is "often removed from phylogenetic analysis" [10]. As an example I quote a paper (Malhi et al., 2008) which describes the methodology: "All individuals that did not belong to haplogroup Q and C were excluded from the Haplotype data set because these haplotypes are likely the result of non-native admixture" [12]. And that is that; the data that is inconvenient is not even analysed.

In all fairness, some studies have included Amerindian hg. R in their data (to disprove it as a founding lineage) and others have proposed it is a founding lineage, but that was long ago and has not been forwarded lately:

Lell et al., (2002). [9] reported the presence of the R-M173 marker, which indicates haplogroup R1, adding that it was "only found in the M45 Y chromosomes of the eastern Siberians and North and Central American natives and not in those of the Middle Siberians or South Americans". Since M45 is a marker of P haplogroup, and R1 is downstream from P, Lell's comment is correct. Unfortunately his suggestions have been disputed.

For instance [8] assigns a post-1492 origin to 96,2% of the natives belonging to Hg. R. (by the way, R accounted for 13.4% of the total haplogroups). This leaves open the door for the remaining 3.8% as belonging to an ancient non-European R haplotype, but this option is not discussed in the paper.

Network comparisons as the one shown below (Fig. 5 in Zegura et al., 2004) [8] compares Asian, American and European individuals. The paper uses the nomenclature of that time, before marker M343 was discovered and used to identify Hg. R1b, so they refer to SNP P25 to identify R1b (it was used from 2002 to 2004 for this purpose). Since the authors are using a marker close to the root they encompass all of R1b (from the most common European lineages - R1b1a2a - to other Asian ones which are less frequent).

The tree is the following: [8]. It only shows groups that cluster more than two individuals (if it had included those with only one individual, would the picture be different?). Branch length is proportional to the number of one-repeat mutations separating any two haplotypes.

The authors point out that the shared Euro American central node (which includes Sioux, Mixtec, Cheyenne, Wayu, Greek, Italian, Russian, and Briton) has a common haplotype different to the Asian model haplotype in two markers. They also add that "Extensive sharing of haplotypes between Native Americans and Europeans is evident throughout the network".

Based on this and a non published analysis which showed that "five European populations formed a distinct cluster with five of the seven Native American groups. In contrast, none of the four Asian populations were part of the European–Native American cluster" [8], the authors concluded that haplogroup R found in Amerindians was due to European admixture.

Which sounds reasonable but... Looking at the figure, there is a very long exclusively American haplotype on the bottom of the image which has several mutations. Then there are the uniquely American ones on the top (marked with red dots). These are distinct and not "shared" with Europeans. Furthermore, the Euro-Asian group on the right (marked with a blue dot) shows substantial admixture between Asians and Europeans and is also linked to haplotypes shared by Amerindians. This clearly shows an Asian link to America.

The other information that is reported in the paper, (but whose data is not shown) is also curious: it states that 2 out of 5 (or 40%) of the Native American groups do not form a distinct cluster with the European populations. This means that they are "separate" from Europeans...How can that be explained in terms of a uniquely European source for Hg. R? (No wonder the data is not shown).

Finally there is the alleged "modal haplotype" shared bye Europeans and Native Americans mentioned in the paper [8], actually, the following table, from [10] indicates a wide variety of haplotypes and not one of them (they are from Central America and Chibchan natives) belongs to this "modal haplotype" yet all of them are R1b haplotypes. For comparison I added the "modal haplotype" as the first row, in red:

The paper [10] also includes a joining-network for hg. R1b among Mesoamerican natives and finds it similar to that of hg. Q3 (a recognized founding lineage) interestingly it shows "better segregation among male lineages" but the haplotype diversity (which can be seen in the table above) is attributed to "over 500 years of European contact in the region". Interestingly, one population did not have any R1b, the Maléku. (Why? were the Maléku reclusive? their women ugly or unfriendly towards Europeans? or simply because they were a distinct ethnic group that did not have this haplotype) Remember the Seminole mentioned at the beginning of this post? They had no haplogroup R either. How can that be explained in the framework of the Euro-admixture-model?

Another paper [7] also compares haplotypes (and does not including the data either) and finds "exact or near matches between the haplotypes of nonindigenous lineages and those haplotypes of Europeans. Hence, although these men are Aboriginal, some of their genetic ancestry traces back to Europe", once again these "near matches" should be interesting since it is in the differences where we will learn something. Furthermore the paper overlooks something very interesting: 28.3% of the populations sampled belonged to hg. R., the majority were R1b1a2, but 2 individuals out of the 40 belonging to hg. R, were typed as being R1a1a1*. This is an uncommon paragroup identified by the mutations M17 (for R1a1a) and M417 (for R1a1a1), both are very basal and are found in men living in a vast area: Northern India, Slavic countries, Siberia, and, evidently America. This is not the typical R1b Western European haplotype, it is a rare variety.

Of course, the authors [7] do not analyse the R hg. samples at all. They declare it foreign and then focus on the accepted Amerindian lineages (Q and C).

Getting back to network comparisons, Bolnick et al., 2006, [11] find hg. R present in 31.0% of their sample and openly admit that "Haplogroup R-M173 likely represents recent (post-1492) European admixture, as may P-M45*", they point out that the median-joining network (their Fig. 6, which I include below, colored to highlight some points) "shows no clear-cut patterns. Haplotypes in this network do not cluster by population, culture area, language family, or geography. This lack of structure is consistent with the hypothesis that haplogroup R-M173 represents recent (post-1492) European admixture in eastern North America rather than a founding Native American lineage" [11].

Actually the fact that they are not linked to any other variable is similar to that of Hg. C in its pan-global range and may have a similar ancient origin that predates culture or language barriers among Amerindians.

Image caption: (b) Pink circles represent haplotypes shared with Europeans, striped circles represent haplotypes that are one mutational step away from European R-M173 haplotypes, and red circles represent haplotypes not shared with Europeans. TMC, Turtle Mountain Chippewa; WC, Wisconsin Chippewa; Sio, Sisseton/Wahpeton Sioux; CA, Cheyenne/Arapaho; Mic, Micmac; OC, Oklahoma Red Cross Cherokee; SC, Stillwell Cherokee; Chic, Chickasaw; Crk, Creek; Sem, Seminole.

It is clear as the authors point out that the most common American haplotypes are shared with Europeans (pink circles) but there are also those (red circles) that are uniquely American. They are not shared with Europeans and do not conform to geographic restrictions either (see Fig. 6 a in [11]).

The authors support the Euro-admixture theory stating that a total of 62 R haplotypes found in Eastern North America are "rare or absent in Asia" or that "the most common R-M173 haplotype in eastern North America is also the most common R-M173 haplotype in Europe, but this haplotype is rare in Asia (and therefore unlikely to be a founding lineage)" [11]. But this overlooks the devastating effects of Old World disease on the native Americans which may have selected negatively against those Asian-American haplotypes while favoring the Euro-American ones. Not because of the haplotypes themselves, but to other genes received from European fathers.

Sequencing the Y chromosome hg. in remains of Amerindians will also let us glimpse the variety and frequency distribution present among pre-discovery natives. I fortell that we will be surprised by those studies.

We should always remember that we are looking at those who survived and not the millions who perished and took their haplotypes with them to their graves.

The authors dismiss the "14 [haplotypes that] are one mutational step away from known European haplotypes [and the] Five haplotypes [that] are 4–8 mutational steps away from European haplotypes... they probably also stem from recent European admixture: the median-joining network suggests that they derive from separate European haplotypes." [11]. This is because they do not cluster together (maybe they did - pre conquest genocide, evidence erased from current populations).

Yet it is remarkable that 14 haplotypes differ from the purported European sources while 5 are even more mutated still! The reasons for this are not given and no explanation is attempted. For instance: they are older and therefore had more time to diversify; they arrived via Asia, and are different to those that came via Europe.

But, having said all this, the authors are not too emphatic against an Asian origin: "Thus, few, if any, R-M173 haplotypes in eastern North America are likely derived from founding lineages of the Americas." [11], they leave the window open.

Closing comments

Having looked at the frequency distribution map in North America and the academic interpretation of European admixture, I am surprised at how "active" the British and French settlers were in their socializing with the natives. Their degree of admixing with them is well above that of the Spanish in the rest of Latin America (and South Western US) as well as the Portuguese in Brazil.

Which seems highly unlikely due to the nature of the Puritan British in the North which would have precluded such introgression and the well documented Spanish - Native mixing in the South.

Why is this admixture so strong around the Great Lakes and the vast empty forests of Central Canada? Those places are far away from the densely populated regions where introgression would have been easier... something is not right with the orthodox explanation. While the obviously simple explanation is very reasonable: that was where these people carrying hg. R settled after reaching America.

Though R haplotypes detected in the very limited studies conducted so far are "rare" in Asia and "identical" or "near matches" to European ones, there are unique Amerindian haplotypes which are not shared with Europeans. Furhtermore "rare" does not mean absent, and additionally, haplogroups that do not exist in Eastern Siberia are found in America and nobody is concerned about it. Lets use the same scales to measure our theories.

So this makes it probable that R1 reached America via Beringia in the wave that peopled America over 25 kya.

R and Q appeared in a similar region in Central Asia, descended from Hg. P., why would R spread across Siberia eastwards and remain on the brink but not enter America? (yes, there is an explanation, but I do not agree with the Bergingian standstill theory and the isolation of America). Add to this the rare high frequencies of mtDNA haplogroup X which are found precisely among the Northeastern North American natives, where R is preponderant! and it makes you ask: did mtDNA hg. X and Y chromosome R reach America together, carried by the pople who settled N.E. America? Maybe they did.

For those looking for other logical explanations here are some interesting ones:

• Escaped Slaves. An interesting suggestion was put forward by Clyde Winters (2011) [15], and suggests that the high frequency of R-M173 among Seminole and Ojibwa (groups with the highest values for R hg.) is due to admixture, but not with Europeans, instead it was the outcome of intimate contact with African males (escaped slaves). The logic behind the paper is that white Europeans were at war with the natives and would not have mixed with native women, but escaped slaves would have, as they found a safe haven to rebuild their lives.
• Pre Discovery contact. Perhaps the source of European genes were the Portuguese and Galician (Spain) who fished cod during the Middle Ages on the Terranova banks, just off the Eastern Seabord. We can imagine some castaways melting into the local natives and sowing their seed. Another option is the Vikings: they founded a village (L'Anse aux Meadows, Newfoundland) and may have raided and raped their way along the Northeastern shores of America...

Sources

[1] Stanford D. and Bradley B., (2012). Across Atlantic ice: the origin of America's Clovis culture. Berkeley: University of California Press
[2] Metin I. Erena, Robert J. Pattenc, Michael J. O'Briend and David J. Meltzer, (2014). Refuting the technological cornerstone of the Ice-Age Atlantic crossing hypothesis. Journal of Archaeological Science 40 (2013) 2934 - 2941 http://dx.doi.org/10.1016/j.jas.2013.02.031
[3] U. S. Census Bureau Maps of population density
[4] See more Images, Casta paintings, Lasalle University
[5] Norma Angélica Castillo Palma, (2001). Cholula, sociedad mestiza en ciudad india: un análisis de las consecuencias demográficas, económicas y sociales del mestizaje en una ciudad novohispana (1649-1796). Plaza y Valdes
[6] Carlos Flores et al., (2004). Reduced genetic structure of the Iberian peninsula revealed by Y-chromosome analysis: implications for population demography. European Journal of Human Genetics (2004) 12, 855–863. doi:10.1038/sj.ejhg.5201225 Published online 28 July 2004
[7] Matthew C. Dulik, et. al., (2012) Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations. www.pnas.org/cgi/doi/10.1073/pnas.1118760109
[8] Stephen L. Zegura, Tatiana M. Karafet, Lev A. Zhivotovsky, and Michael F. Hammer, (2004). High-Resolution SNPs and Microsatellite Haplotypes Point to a Single, Recent Entry of Native American Y Chromosomes into the Americas. Mol. Biol. Evol. 21(1):164–175. 2004 DOI: 10.1093/molbev/msh009
[9] Jeffrey T. Lell et al., (2002). The Dual Origin and Siberian Affinities of Native American Y Chromosomes. Am. J. Hum. Genet. 70:192–206, 2002
[10] Phillip Edward Melton, (2008). Genetic history and pre-Columbian Diaspora of Chibchan speaking populations: Molecular genetic evidence. Dissertation, Univ. of Kansas.
[11] Deborah A. Bolnick, Daniel I. Bolnick, and David Glenn Smith, (2006). Asymmetric Male and Female Genetic Histories among Native Americans from Eastern North America. Mol. Biol. Evol. 23(11):2161–2174. 2006. doi:10.1093/molbev/msl088
[12] Ripan Singh Malhi, (2008). Distribution of Y Chromosomes Among Native North Americans: A Study of Athapaskan Population History, AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 000:000–000 (2008)
[13] Schurr TG, and Sherry ST, (2004). Mitochondrial DNA and Y chromosome diversity and the peopling of the Americas: evolutionary and demographic evidence. Am J Hum Biol 16:420-39.
[14] Manfred Kayser, et al., (2003). Reduced Y-Chromosome, but Not Mitochondrial DNA, Diversity in Human Populations from West New Guinea, Am J Hum Genet. Feb 2003; 72(2): 281–302. doi: 10.1086/346065
[15] Clyde Winters, (2011). Is Native American R Y-Chromosome of African Origin?. Current Research Journal of Biological Sciences 3(6): 555-558, 2011

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