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  and a rebuttal of their theory (Erena et al., 2013) .
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. 
But others such as Zegura et al., (2004)  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 :
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%" , 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!
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)  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." . I disagree for several reasons:
- 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.
- The same can be said about British Columbia and the Northwestern Territories
- 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.
- 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) , 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). (See more admixture examples, Casta paintings)
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. , 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" . 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" . 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).  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  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)  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: . 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" , 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 , actually, the following table, from  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  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  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  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,  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" .
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 ).
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)" . 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." . 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." , they leave the window open.
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) , 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...
 Stanford D. and Bradley B., (2012). Across Atlantic ice: the origin of America's Clovis culture. Berkeley: University of California Press
 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
 U. S. Census Bureau Maps of population density
 See more Images, Casta paintings, Lasalle University
 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
 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
 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
 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
 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
 Phillip Edward Melton, (2008). Genetic history and pre-Columbian Diaspora of Chibchan speaking populations: Molecular genetic evidence. Dissertation, Univ. of Kansas.
 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
 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)
 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.
 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
 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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