Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall

Tuesday, July 15, 2014

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]:

R haplogroup frequencies

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!

R haplogroup America map
Native American frequencies of R haplogroup, From [12]

R haplogroup map in America

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 mix indian and spanish
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.

R haplogroup tree

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:

R haplogroup mesoamerica

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.

R haplogroup network

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...


[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
[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.
[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

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


  1. If you disagree the way the dna tests have been done, why bothering testing ancient remains that eventually will make people jump into wrong conclusions? They are completly right in not allowing to explore their blood. Also, this is mostly where racism and bigotry is rampant like the US. South American natives have given their samples several times with rare objections to it.

    "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."
    From what I know there is genetic continuity of modern and ancient amerindians even when you have phenotypical discontinuity with the ainu-polynesian-australian-melanesian remains.

    And also, what's with the unchanged amerindian lifestyle in rural latin america thing? Most are christians, don't speak their languages, wear different clothes - or just wear clothes since many did not, live in different territory, go to school or hospital... And this are the ones who say they are amerindians, let alone the ones who say they're mestizo (even if they look east asian LOL) which is what most rural latinos say they are. Ummm... I think I might travel to Peru and watch some child sacrifice. you know, for the fun.


    1. Christians? yes, and incredibly, they still maintain (Argentina) their older beliefs, I have seen their offerings to Pachamama, some food, the stub of a cigarette,
      some coca leaves, an act of appeasement to the mother Earth goddess. The apachetas (or stone cairns serve) the same purpose, they are very ancient,
      and can be found from the south of Patagonia to the Andean Plateau next to Bolivia. So do the ribbons or strips of cloth tied to the branches of certain trees.
      Very very old customs.
      Peppers and corn drying on the ground as a source of food for the winter, different varieties of Andean potatoes some red, others purple, some the
      size of an olive, others like a wallnut. They still cook their ancient foods and maintain their ancient traditions and ancient customs. Llama jerky (sometimes replaced by
      goats -which were introduced by the conquistadors) is seen drying in the cold dry mountain air.

      They still till the soil and use the irrigation channels built before the Spaniards arrived.

      Yes, now they have schools and medical care, there is a church in each village and a sattelite dish on many adobe huts. The twentyfirst century does
      find its way into their lives, but the women still weave and knit the wool of llamas and alpacas in the way their ancestors did, by hand. Dyed with
      local plants...
      The imperial serf systems of Mita, Yanacona, Encomienda (to mention some) of enforced labor for the state were quickly adopted by the Spaniards and used
      to exploit the natives. The aldeas de Yndios sprung up on the sites of the fomer native villages, and close by, the Spanish lord built his Villa and chapel.
      One master replaced another. The official religion was replaced by Catholicism.

      Children sacrifice in Perú was not all that frequent (It was known as capacocha), it took place on the summits of certain volcanos. But heart plucking seems to have been more common, among
      the Aztecs. But that was nothing compared to the catastrophe caused by discovery.

      Genocide. The population of local natives dropped catastrophically due to contact with the Europeans. War as well as disease took its toll.
      Look at the Kilmes of the Calchaqui River valley in Tucuman, Argentina. They held out in a mountain fortress against the Spaniards for years during the
      century long Calchaqui Wars (1560 - 1666), they defeated in an unexpected mid-winter raid and were disbanded, transplanted to Buenos Aires, forced to walk there -1,200 km or 746 mi-
      hundreds died on the way. They were "reducidos" (restrained) in what is now a suburb of Buenos Aires, the town of Quilmes until 1812, when the remaining three descendants of the Kilmes were
      set free. Thousands had died.
      This took place all over America, take the epidemic of 1518 in the Caribbean: "There occurred an epidemic of smallpox so virulent that it left Hispaniola, Puerto Rico, Jamaica and cuba desolated of Indians"
      (1518) Oviedo y Valdes G. F. (1851-1855), Historia General y Natuarl de las Indias... , Vol 1. 105.

      The dreadful impact of discovery and conquest on the genome of the original people of America is often overlooked: Bernardo Veksler in his "Una Vision Critica de la conquista de America", states that out of the "
      the American Indians were at least seventy million or maybe more when the foreigners showed up on the horizon. One and a half centuries later, they were
      reduced to only three and half million". That is one big bottleneck, only 1 out of 20 natives survived, 95% of the genetic diversity of America died out. What is left today is just a pale shadow of what
      it once was. That is why I emphatically suggest that the remains of Amerindians should be sequenced, they hold the variety that has been lost.
      The Black death which only wiped out 33% of Europeans impacted in its genetic diversity, reducing it ( and
      Imagine the impact of a 95% population drop!

    2. Well, so good that your rural latin america is just the aymara, a drop of water in an mestizo ocean!! How many rural argies will ever say they are "indios" or that they care of what their great great grandparents believed? They are rather ashamed of it and deny it that they have redskin blood in them - meaning the mentality changed aka not the same. The vast majority of the region is westernized - and in fact they are considered part of the west for the most because no indian culture has been left unchanged.In Brazil, perhaps half of south america in territory and population alone, you can count straight haired people who maintain significant amerindian believes with your left hand. Same thing in Panama, Carribean or whatever. I can't believe that you come with this rural latin americans are amerindians with milennial culture. LOL Racially, there will be many in Mexico to be fair with you. I guess we have to leave this with 99% of scholars who say LatAm culture is western = not amerindian and that includes the rural areas.
      And the ones who are really amerindians are very different from their pre-colombian times too. Changing religion, language and ethinic clothing is a SIGNIFICANT difference. It's pretty much a big loss, yet there you are.

      As for the 95%, firstly the nnumber is highly debatable. Secondly, I don't deny that the pre-colombian natives could have more lineages, BUT there is no significant changes which means continuity. There are a lot of remains in the Andes that has been tested and no surprise. There are even studies on the continuity of ancient quechuas and aymaras and the modern ones, from what I know. I admit I'll have to look this up to know it in detail, but overall I maintain strong continuity between ancient amerindians and modern ones even with the australoid discontinuity of past indians and modern Guaranis or Botocudos.

    3. Guaraní in Paraguay keep their ancient language as well as the Bolivians, both countries have many speakers of their "official" native languages.
      Brazil is a peculiar case. They kept on killing the natives especially in the southern part well into the 1700s. They raided the Jesuit Missions there. No wonder they had to import millions of African slaves to make up for the natives that were virtually exterminated. The only thing left of the Tupi culture in Brazil is the place names. Brazilians have a high Afro admixture and of course the pre-1700s native Tupi-Guaraní stock. So the half continent may be there but not the culture.
      I suggest visiting the highlands in Ecuador, Bolivia and Perú or visit some locals in Castro, Chile, Aluminé, Argentina. Those are natives with little admixture of Europeans.
      Argentine admixture with Europeans is very interesting indeed. A population of 500,000 in 1860 grew to 5.5 Million by 1900, and due to the influx of Europeans, mainly from Spain and Italy, Admixing in the coastal areas, but not so in the interior. There is a large proportion of Amerindian mtDNA and Y chromosmes in Argentina ( despite this influx of Europeans.
      The Amerindian civilizations despite being decimated by the Spaniards had a much larger population than the prairie indians in the US or the Amazonian slash and burn natives.
      The impact of natives in Spanish speaking Americas was more significant than in the US, Canada or Brazil. African populations and Native Americans have an inversely proportion more of one less of the other (US, Brazil high, rest of America: low). The Taino were exterminated so Cuba, Haiti, Republica Dominicana have a large Afro population.
      The Botocudos are an interesting case. See this paper:
      Their Polynesian genes came via slave trade from Africa!
      and this reply closes posts on the subject.
      Thanks for your comments.

  2. A contact with viking or ibearians would have killed the natives from deseases since you find the haplogroup in a rather big geographical area... that would mean, to me, that some wide contact would have taken place. And, well, the puritan british left no pure blooded north american natives, actually, you can see they are very very mixed. The thing in Latin America is that they could move to the villages and cities, reproduce and increase their number and then mix to whites while leaving some pure people behind in tribes or the cities. If you spoke poruguese and wore clothes, you were civilized by lusitanian standard (perhaps the most open minded whites ever). By british standard your very physical appearence was an issue, and therefore you should be erased from this land or put in concentration camps to eat rations and get lazy.

    For me a common source for R and X is reasonable, though.

  3. "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."

    I agree that it's possible that Native American Rs is a mix of pre-Columbian and post-1492 variants and I agree that labs need to spend more time teasing it out. However there are a few considerations that make the mainstream position understandable. 1) Unlike mtDNA hg X, Y-DNA hg R hasn't been confirmed in pre-Columbian ancient remains for the simple reason that we don't have any ancient Y-DNA samples yet. The discovery of mtDNA hg X in pre-Columbian remains was a decisive factor in vindicating this lineage as an indigenous one; 2) mtDNA hg X is a rare (albeit pervasive) lineage in Europe. If it originated from post-1492 contacts then more common European markers such as hgs H and U would have been widely found in Native Americans. Y-DNA hg R is widely found in Europe and finding it in America fits the model of post-Columbian admixture well; 3) Asymmetric sex-based gene flow (no common European mtDNA markers but plenty of European Y-DNA markers in America) fits well with the colonization mode of admixture when European men married into tribes, but the opposite process was rare; 4) Ancient Mal'ta DNA in Siberia is mtDNA U and Y-DNA R. mtDNA U is not found in the Americas, while its sister clade B is. In Siberia, hg B is rare to non-existent. Y-DNA R is not found in the Americas but it's sister clade Q is. Hg Q is rare in Siberia as well. There seems to be a meaningful pattern here.

    I'd like to bring your attention, Austin, to the presence of "underived" Y-DNA hg P* lineages in America. They, too, tend to be more frequent in North America, although more among Na-Dene than among non-Na-Dene populations. The fit with hg X is not perfect but with more data from tribes it may become better. Y-DNA hg P* is upstream from most common European R and Amerindians Q haplotypes just like mtDNA X is upstream (in most mtDNA phylogenies) from European U, H and Amerindian B haplotypes.

    1. German, yes what is needed is to find hg R in pre-Discovery remains, that should settle the issue.
      I also noticed that there are references to P, F (in Seminole and some Costa Rican natives, the Boruca), which will be the subject of another post. And may not be Founding Lineages.
      Thanks for the link.

  4. Interesting post. I agree that there is too much R among northeast North America Native Americans to all be from post Columbian males. But the origin near Hudson Bay makes it look to me that it came from Europe. More on

  5. Interesting post. I agree that there is too much R among northeast North America Native Americans to all be from post Columbian males. But the origin near Hudson Bay makes it look to me that it came from Europe. More on

  6. The two explanations don't count for the Ojibwa, I mean how many Spanish explorers got to the Wisconsin/Minnesota area. Those states are not know for having slaves either.

  7. I took two DNA tests. One said I was European the other test said I was Pehuenche (Mestizo) Indian. Lets hope I never have to have a paternity test in North America.


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