Y chromosome C-BY63635 in America

Y-chromosome haplogroup C is widespread and it can be found across the globe (outside of Africa). It is also present among American Natives in different variants. However, it isn't the most predominant haplogroup in the New World, that honor goes to haplogroup Q, exclusive to the American continent. But, Hg. C has some interesting surprises for us.

An article by Miguel Villar published in July 2024, mentions a subtype C-P39 in North America, which is 8,500 years old, and another special ancient haplogroup, C-BY63635, found among the Lapa do Santo site (of the Lagoa Santa people):

"In South America, a separate, older, and lesser-known haplogroup C lineage has also been discovered. Haplogroup C-BY63635, more recently identified in 10,000-year-old remains from Brazil’s Lapa do Santo site, has living relatives among the people of Colombia, Ecuador and Mexico today. This lineage, a completely different branch of haplogroup C than C-P39, seems to have split into its South American and North American counterparts more than 13,000 years ago. It then proceeded to survive independently in both continents for millennia while in the shadows of the dominant haplogroup Q. This evolutionary split likely occurred early in the prehistory of the Americas, an account supported by its occurrence among South America’s oldest remains."

This haplogroup is found in extant people with Native American ancestors. I must point out that it is also known as C2a2b, which is part of Haplogroup C2 (also known as C-M217, and formerly C3) -confusing nomenclature!!

Geoffrey Sea posted on Aug. 1, 2025, an entry in a Facebook group titled Correlating Haplogroups and Migration Routes, in it he states " Y-haplogroup C-BY63635 is most interesting because it has been found in an ancient sample in Primorsky Krai, the far southeastern province of Russia, and is also found in specific tribal groups in Peru, Ecuador, and Paraguay. It has therefore been linked to a suspected early migration across the South Pacific."

The post includes a map of this proposed South Pacific migratory route:

Migrations that peopled America. Source

The 2019-2020 Haplogroup C Tree by the Copyright 2020, International Society of Genetic Genealogy, reported the C2a2 as a newly confirmed group in 2020, with the captions:

"C2a2 - BY63635/MPB374, BY74777, BY100887, BY104139/MPB378, BY106469/MPB380, BY112376, BY118088/MPB385, BY134626, BY135393, BY142506, Z12675.3
Texas (USA), Ecuador (Kichwas, Waoranis)"

If you wonder how it reached Texas, Villar's article mentioned further up, explained more about the BY63635 found in Mexico: "Members of the Arrendondo family from Mexico, some of which are FamilyTreeDNA participants, carry this unique haplogroup C lineage and can trace their ancestry to the 1700s in the state of Nuevo Leon. Eighteenth-century records suggest that the Arredondo lineage was part of the Alazapa Indian group and lived and fought in northern Mexico as the country gained its independence from Spain and fought against the United States to maintain its sovereignty.." And Mexicans remained in Texas since it became part of the US in the mid 1800s, with their Native American genes.

---

Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall © 

The link between Negritos, Papuans and Amerindians!

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

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

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

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

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

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

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

---

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

Kennewick Man, Ainus and Sunda

Two men were walking along the bank of the Columbia River in Washington, U.S. on July 28, 1996 when they came across a human skull, they quickly notified the autorities who inspected the area and, after a thorough search, managed to recover an almost complete skeleton, belonging to a man. This is how the "Kennewick Man" remains were discovered.

An initial inspection by an archaeologist [3] concluded that the man was not a Native American because the skull had a "caucasoid" appearance. A bone sample was sent to a laboratory and dated. We now know that these remains are between 8,000 and 9,500 years old. Which, by American standards is very ancient.

An act of Congress, The Native American Graves Protection and Repatriation Act (NAGPRA) was passed in 1990 with the goal of redressing the evils of the past, when Native American graves were profanated and their bones stolen and placed in Museums. The good intentions behind this legislation (which sought to return these remains to their original resting places in their tribal communities), has been distorted by the very extreme view held by some Native groups which are against any studies conducted on Paleo-Indian remains.

Actually most "modern" Native communities are relativley recent arrivals to their traditional tribal territories none go back more than one or two thousand years at most. Yet, they will go to court and in most cases succeed to get remains that date back thousands of years returned to "their homeland". In many cases the only link between the Paleoindians and the modern natives is the land where the remains were found.

Kennewick man was no exception, in 1996 some native groups took a hard stand and went to court to stop any further studies on his remains. Native American groups and the Federal Government of the U.S. combined their resources against the scientists who wanted to learn as much as possible from these extremely valuable ancient remains.

The legal battle took 8 years. In 1998 Kennewick man's bones were sent to the Burke Museum (Washington state) to protect them until the lawsuit was settled. They are still safeguarded at the Museum. [1]

The case was heard by a U.S. District Court which found that the remains could not be classified as "Native American". His ruling was appealed and the 9^th Circuit Court of Appeals upheld that decision in 2004. So the remains, which were found on Federal land, are now in custody of the U.S. Army Corps of Engineers and will remain so indefintely unless the Natives can somehwo prove in the future that Kennewick was a Native American. [1]

What have we learnt from the remains?

The remains comprise an almost complete skeleton (only some bones from hands and feet and the sternum are missing) which belonged to a tall man (about 1.73 m - 5.67 ft.) between 40 and 55 years old.

Although his DNA was intact, the tests were done on two samples but were inconclusive! (more on this below).

He had the broken off remains of a flint leaf-shaped serrated projectile stuck in his right ilium (hip bone). The wound was partly healed and the stone spear tip was quite large: 20 x 54 mm (0.78 x 2.12 in), [2] however, "The extensive amount of bone that has grown around the stone point suggests that the point was in place for a considerable amount of time and was not the cause of death." [3]

The surprising part is the skull, the cranial index marks it as dolichocephalic (long and narrow skull) instead of bracycephalic (short and wide skull) as found among the modern Natives. His face was narrow instead of broad and had a pronounced chin. This and other features gave him a "caucasoid" appearance. Yet, surprisingly his teeth were Sundadont like those found among South Asians. [2]

A clay facial reconstruction gives him a very "Caucasian" look indeed, [6] below is another view of this Kennewick man's face: [7]

Facial reconstruction of Kennewick Man. From [7]

Sundadonty is not a Caucasian trait, it is part of the "Mongoloid dental complex" [4], which evolved locally in Sunda Land (insular Indonesia); very similar teeth are found among Aboriginal Australians which "are also generally like those of Jomonese and some Ainus, suggesting that members of the late Pleistocene Sundaland population could have initially colonized Sahulland as well as the continental shelf of East Asia northward to Hokkaido" [4].

Map showing the Asian Range of Sundadonty (blue) and Sinodonty (yellow).. Copyright © 2014 by Austin Whittall

East Asians to the north of Sunda (i.e. Chinese, Japanese, Koreans, Mongolians) all have Sinodonty (dental shoveling). In general people belonging to Mongoloid groups (North Eastern Asians and, also American Indians) have the highest frequency of shoveled incisors while the rest of the world has chiseled ones. Shoveling is caused by the Ectodysplasin receptor gene (EDAR), also associated with hair thickness and the size and quantity of sweat and mammary glands. It is frequent in Asian populations and absent in Europeans, Africans, Denisovans and the Mal'ta remains from Siberia who carry the ancestral allele. The mutation or introgression (admixed through direct contact with H. erectus) is believed to have appeared in central China >30 Kya, a late date in my opinion since it was obtained by simulations restrained by a 15 Kya date for peopling America, which is far to recent. [5]

His teeth

The sundadonty of Kennewick man is an interesting find because it links him to Sunda (Insular Southeast Asia) and the archaic population of Japan, the Ainus.

The map above shows a discontinuity in the Sundadont range (blue). It is the intromission of Sinodonty (yellow) which cuts off Sunda in the south from Taiwan, Hokkaido, the Kuril Islands, Sakhalin and the tip of Kamchatka in the north.

This gap is currently occupied by sinodont populations (Chinese, Koreans and Japanese).

A simpe explanation for this discontinual distribution is that the sundadonts were the original people inhabiting the coastal areas of Oriental Asia and were later overlain or displaced to their current insular ranges by sinodonts in the central region (China, Korea, Japan).

Another option is that the Sundadonts moved from Sunda northwards, along the coastal areas in boats, or walked along the now submerged continental shelf alll the way to Hokkaido -the current Ainu territory (yet they seem to have failed occupying the main southern Japanese islands, or were later displaced from there by sinodonts).

Map showing a hypothetical route from Sunda to America for sundadont dental morphology. Copyright © 2014 by Austin Whittall

Did a branch of these migratory sundadonts reach America before the sindonts whose dental pattern now prevails among Amerindians? or, since sinodonty is a Homo erectus trait, did the admixture leading to Amerindian sinodonty take place in America, between an early arrived sundadont H. sapiens population and the ancient H. erectus settlers in America?

Turner [8] proposes a theory where "Sundadonty or more likely proto-Sundadonty, [is] the ancestral pattern for all modern humans". He bases this on the "generalized" appearance of Southeast Asian population: "they possess various external physical features of many geographic races, although usually in relatively low frequency". Interestingly "when South Siberian teeth are compared with those of Sundadonts, they show remarkable similarities. Because South Siberian [...] hybrid condition retrodicts the probable dental pattern of the common ancestors of Europeans and Asians before these derived groups drifted to their distinctive patterns by late Pleistocene times..." [8].

So Sunda would be the source of this dental morphology, coinciding with the place from which Y chromosome Haplogroup C radiated into New Guinea, Australia, India, China and Northeast Asia. see my post on haplogroup C. South Siberians also have hg. C at low frequencies.

The Ainu

Regarding the Ainu people of northern Japan, their similarity to Sunda populations such as the Bataks of Sumatra and the Dayaks of Borneo (shee photos below) was reported back in 1872 [9]. More recently, Genetic studies link the Ainu to Amerindians, and one should reread those studies within the hypothesis mentioned above. Perhaps both groups (Amerindians and Ainu) share a common sundadont ancestor which is the main reason for the similarities detected in these genetic studies.

Ainu people (Notice their curly hair in the top image and the clearly non-Mongolian look of the bearded man in the bottom one)
The impression I get is that they are two different kinds of Ainu.

Batak from Sumatra and Dayak from Borneo

His DNA

The DNA samples taken from the Kennewick man did not give any conclusive results. The tests were botched (since I don't believe in conspiracy theories, I can only guess that they were done in an inadequate manner or that the technology used was rudimentary, perhaps the samples were unwittingly contaminated, etc.). Below is the conclusions by the National Parks Service [3]:

"Thus, two separate amplifications from two different extractions suggested that Kennewick Man does not belong to haplogroup D (because the fragment was at least partially digested at np 5176 by Alu I restriction enzyme) while a single amplification from one of the two extractions suggests he might belong to haplogroup D. Given that at this point it was still unclear whether or not either of the two extractions were clean (i.e., uncontaminated), amplifications from the extracts had given conflicting information and neither extract had been successfully tested for the diagnostic markers for haplogroups B, C or X, it was impossible to determine to which, if any, of the common modern American Indian mtDNA haplogroups the Kennewick remains belong. At very most, our results provided, at this point, no evidence that the Kennewick remains belonged to haplogroups A, B or C [3]

In other words he does not belong to mtDNA haplogroups A, B or C. And the two tests gave differing results for hg. D (one was positive, the other negative). So he may or may not belong to haplogroup D. He may belong to X or M or any of the other haplogroups for which he was not tested.

I have not found any records regarding his Y chromosome analysis.

Closing Comments

Despite the theories put forth by some blogs and forums regarding a European origin for Kennewick man and the links they try to build between him and the Solutreans and Cro-Magnons of Europe, I am inclined towards an Asian origin for the Kennewick man

His sundadont teeth clearly set him apart from any modern Europeans. He is closer to the more ancient modern human migrants that reached Sunda, Sahul and what is now insular Eastern Asia in the Out of Africa initial migration some 70 kya. He probably represents this basic and most archaic line of modern humans who may have reached America not long after their departure from Africa. They do not, in my opinion, represent the more recent "white Europeans" as some propose (many of these forums have some white supremacist viewpoints, which I abhor).

A clear typing of his mtDNA and Y chromosomes will settle the issue of this man and lead us to ask interesting questions regarding why are there no contemporary Caucasoid-looking Native Americans? and maybe clarify what is the exact link between these Sundadont populations, perhaps some other gene similar to the EDAR of the sinodonts?

I will dig deeper into the Ainu, they intrigue me and I want to learn more about them.

Sources

[1] Burke Museum, Kennewick Man - The ancient one
[2] James C. Chatters, (2004). Kennewick Man. Smithsonian Institution.
[3] U.S. National Parks Service Article 1, and Article 2
[4] Turner C. G., et al., (1990). Major features of Sundadonty and Sinodonty, including suggestions about East Asian microevolution, population history, and late Pleistocene relationships with Australian aboriginals. Am J Phys Anthropol. 1990 Jul;82(3):295-317
[5] My post on an Early Peopling of America
[6] Sciencephoto.com, Clay reconstruction of the Kennewick Man
[7] Chelbea Fair, The Desert Town Right Around the Riverbend
[8] G. Richard Scott, Christy G. Turner, (2000). The Anthropology of Modern Human Teeth: Dental Morphology and Its Variation in Recent Human Populations . Cambridge University Press, pp. 303.
[9] Vivien de Saint-Martin, (1872). L'ethnologie du Grand Archipel d'Asie... races humaines. L'Anée Géogr. 9:90-97

---

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

A special Y chromosome marker

The Y chromosome has a "male-specific region" or MSY; it is the sector of the Y chromosome that differentiates sexes (females and males). It spans roughly 95% of the chromosome's length and is is made up of different sequences, one of which is known as "X-degenerate".

Despite its name, its sequences are the relicts of the ancient autosomes which later evolved into our current X and Y human sexual chromosomes.

A paper (Rozen et al., 2009)[1] analysed the human MSY region and reached some interesting conclusions.

An interesting mutation

The researchers sequenced a global sample of Y chromomes (belonging to haplogroups: A, B, C, D, E, G, H, I, J, T, L, M, N, O, P, Q and R) and found that they were all extremely similar in the X-degenerate protein sequences: any two chromosomes selected in a random draw only differ in one aminoacid; and in 50% of the cases, the differences are due to one particular mutation.

This special mutation switched Aspartic Acid for Glutamic Acid at a certain spot of the MSY region ( mim400005). It happened quite some time ago: the authors calculate that this mutation took place roughly 50 kya - 95% CI 37.7 - 55.7 kya (my comments on this date can be seen below).

They also found out that natural selection seems to be operating as a factor that preserves amino acid sequences in this part of the Y chromosome therefore raising doubts about the assumed "neutrality" of mutations taking place in the Y chromosome: they are assumed to be random but apparently are not.

The image below, (from [1]) shows the Y chromosome's haplogroups that were tested. The red dots mark nonsynonymous nucleotide substitutions, the other dots (blue and gray) mark other kinds of substitutions. The arrow indicates the particular mutation mentioned in the text above. I added a red sector indicating those haplogroups that do not carry this mutation, the "oldest" haplogroups A, B, C, D and E.

Y chromosome tree hgs. and mutations.. From [1]

Its location, at the root of branches leading to all the other haplogroups from G to R, makes it the oldest of the twelve mutations that the study found, as well as the closest one to the root of MSY genealogy.

The African haplogroups A and B, plus the most ancient Eurasian ones C and D as well as the East African E hg., do not carry this mutation, all other sampled haplogroups do. So this suggests that it originated in Asia After the Out of Africa migration of modern Humans.

The issue of the dates

The date assigned to this ancient mutation (37.7 to 55.7 ky) was not calculated directly. Instead the paper is based on another study (Karafet et al., 2008) [2], which provides the usual mainstream accepted dates for an OoA event of 50 to 60 kya.

I have already given my critical opinion on these dates and the assumptions on which they are based on, so I will not repeat them again here, but one of the objections is that mutations used to time the "molecular clocks" used to date human events (either using mtDNA or Y chromosome substitutions) may not be random, due to pure chance (or neutral), but may be selected for by evolutionary forces.

And, as mentioned above, this very paper [1] includes a comment which impacts directly on one of the basic assumptions of the "genetic clock": since Natural Selection is acting, then "the assumption that all MSY SNPs—as well as any structural polymorphisms in the Y chromosomes marked by these SNPs— are selectively neutral." is false. The paper adds (bold mine):

" [our] data contradict this simplifying assumption. The MSY does not undergo sexual recombination with a homologous chromosome, so it is subject to natural selection as an indivisible unit. Even if the particular MSY SNPs employed in a population study are functionally inconsequential, they may have been coupled to detrimental or beneficial SNPs or structural variants elsewhere in the MSY... Taken together, these studies of structural polymorphism and coding sequence variation in the MSY highlight the role of natural selection in human MSY lineages. This new awareness means that we can no longer assume selective neutrality in the MSY when drawing conclusions from population genetic studies." [1]

This mutation is selected for in a positive manner, it appeared and was conserved intact in the MSY region. It may have appeared a long time ago, 80 ky or 100 ky or even 300 ky ago. Which brings me to the reason for my post.

An ancient Eurasian mutation

If it appeared and was not obliterated by natural selection and it is not neutral, then it must provide an advantage to its carriers. The paper [1] points out that the substitution of Asp. for Glu. "may be of little functional consequence", and that 11 out of 12 mammals and birds studied have glutamic acid in this locus like men belonging to hgs. G to R.

The only one with aspartic acid instead of glutamic acid is the mouse and of course the "ancestral sequence of humans" found only among those men belonging to haplogroups A to D.

In other words it is absent among contemporary Africans (hg. A, B) and the oldest haplogroups (C, D, E), so it evidently originated in Eurasia. Since I distrust the 50 ky age, and believe the mutation to be much older, I ask: Was it a Neanderthal Trait? Did it admix back into H. sapiens from the Neanderthal?

Or if the date is correct, it may even be a Homo sapiens mutation that is not found in older Y chromosome lineages that, as I have suggested in other posts, date back even further than Neanderthals.

A closer look at the tree above shows that the mutation took place just after the split of C and the ancestor of all the other groups G to R. Perhaps the mutation marks the spread of Modern Humans out of Africa and even more interestingly, it spreads overlying the more ancient non-mutated haplogroups, which in turn reflect those of archaic humans. Which as I have suggested in previous posts (i.e. C hg.) mark the presence of H. erectus in Eurasia.

Sources

[1] Steve Rozen, Janet D. Marszalek, Raaji K. Alagappan, Helen Skaletsky, David C. Page, (2009). Remarkably Little Variation in Proteins Encoded by the Y Chromosome's Single-Copy Genes, Implying Effective Purifying Selection. Am J Hum Genet. 2009 December 11; 85(6): 923–928. doi: 10.1016/j.ajhg.2009.11.011
[2] Karafet TM1, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF, (2008). New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 2008 May;18(5):830-8. doi: 10.1101/gr.7172008. Epub 2008 Apr 2.

---

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

Another anomaly in the OoA cline

Always on the lookout for genetic markers that contradict the mainstream assumption that America was populated by some very small bands of migrants that had remained in splendid isolation in Beringia for several millennia until the end of the last Ice Age, I came across a paper (Pereira, dos Santos and Junho Pena, 2006) [1] which looks into the human X chromosome (interesting because all of us carry at least one copy - women carry two). The global pattern of a marker they identified is quite odd; please read on below:

A new marker DXS225

The paper describes how the authors found a region with a low recombination rate and within that region they identified a novel polymorphic Alu insertion which was later named DXS225.

The insertion allele is the mutation, and the archaic ancestral form, found in our distant chimpanzee relatives is the "pre-insertion allele".

Interestignly, there are some specifc groups that lack the modern mutation, (well, modern is not the best word for it, because it appeared 100 kya) shown in the table below [1]:

DXS225 has two allelic states, one is the "archaic pre-insertion (marked as 0 or -) and the other is the "mutated or modern" Alu insertion allele (marked as 1 or +). [2]

Table showing only those populations in each region that only carry the archaic pre-insertion allele and not the "modern" insertion.

It is interesting because the "ancient" African groups San, Bantu and Yoruba don't carry the modern mutation, but it is also found among the Dai in Yunnan, China, the Northern Italians, the Papuans and four out of five Amerindian groups! The other African, European, Middle Eastern, Central Asian and East Asian as well as Oceanian populations carried both alleles at different ratios.

What is necessary is to explain why the "ancient" Africans, Dai, Papuans, Northern Italians and Amerindians do not carry the modern allele.

The map below shows the global distribution, the populations lacking the modern allele are marked: [1]

Analysis

1. Antiquity

The polymorphic nature of DXS225 (poly: many, morph: kinds; there are two variants of it: with and without insertion) and its absence in chimps, is taken by the authors as having taken place after our split from the other non-hominids; since it is "found in polymorphic frequencies all over the world..." [1] they conclude that it took place among modern humans some time before the Out of Africa (OoA) event some 100 kya.

The same team wrote a second paper on this allele (2007) [2] where they estimate the time of the most recent common ancestor as 182 ky (56.7 to 479 ky)* and the date that the DSX225 mutation took place: 94,4 ky (24,3 to 310 ky)*. [2] Which the authors find "compatible" with the OoA dates*.

* Comment. Just look at the error bars on this calculation! it spans from a putative OoA date to the split with Neanderthals! The mutation date also ranges from the time the world was fully peopled to a date 300 kya which possibly predates modern humans. This goes to show all the uncertainties that exist in the models used -see my post criticising models.

2. Amerindian singularity

Regarding its pan-global distribution there is a glaring exception: Native Americans: "among the five Amerindian populations [...] only the Karitiana showed presence of the Alu insertion". [2] So the "modern" allele is found all over the world but is absent in America except for only one group, the Karitiana... why?

The authors explains this singularity as follows:

• Karitiana are not pure Amerindians, they admixed with Europeans and Africans (former slaves) in the early 1900s and these introduced the Alu insertion into their genome, add to this that it is a small inbred tribe. [2][1]
• All other Native Americans lost the inseriton in a pre-hispanic founder effect. So the people who entered America did not carry this allele.[2]

They then eliminated the Karitiana from further analysis in their study!

But what about the Papuans, Dai, Northern Italians and the African groups. Nothing is said about them, no explanations are offered, but I would expect them.

Maybe the Karitiana are an admixture of extra-American genes, but the "founder effect" should be justified. As we will see below, statistically a 25% of a given population carry the mutated allele. Are we to expect that these people died out while migrating into America, (not only that, the founder effect spans Y chromosome hgs., mtDNA hgs, etc. it is indeed a fantastic excuse to explain away what is unexplainable!).

Diversity. DXS225 has a "low level of genetic structure" [1] suggesting that it is neutral to natural selection and that "the variations in insertion allele frequencies among populations result from genetic drift" [1], which is true if you look at the data for all groups except the Native Americans and Papuans, because these other groups have a very small degree of variability.

But when you look at Papuans and Native Americans, the situation is different. The authors' second paper delved in this matter when they combined DXS225 with other markers and defined several haplotypes which were analyzed using AMOVA, and, again found two regional exceptions to the general lack of genetic variation: Oceania and America (sans the Karitiana of course).

A strange finding because the variation is very large: Oceania had a 14.95% and the American Natives a 15.29% of "among-populations within-regions variation"; as a reference, the values were -0,59 in East Asia 1,06 for Eurasia and 1.99 Africa. That is almost a difference of an order of magnitude (tenfold).

This is exactly the opposite you'd expect in the American population which orthodoxy (and the paper [2] itself) have defined as subjected to "a significant bottleneck that led to a large reduction of haplotypic diversity" [2], it is a situation which does perplex the authors:

They find it "difficult to ascertain the meaning of this relatively elevated component" in Oceania because only two populations were studied. Well, why didn't they add more populations to the study to elucidate the matter?

Of course, American diversity is easily explained with the usual excuse: the"high levels of genetic drift" [2] that characterize its populations. They are excused from having to justify anything.

I believe however that the high diversity (note that these haplogroups they defined combines several markers and not only DXS225) is due to admixture with archaic hominins which carry long evolved mutations which have had plenty of time to evolve: both in Oceania (New Guinea) and the Americas... I am thinking Homo erectus here.

Speculation

The facts of these two papers are that there is a mutation (DXS225) in modern humans' X chromosomes, that ~25% carry and the other roughly 75% do not carry. Averages that make sense:

The following image shows how a man develops a chance mutation in his X chromosome and after 2 generations it appears in 4 of his 16 grandchildren: 4⁄16 = 25% carrying the mutation.

Statistically a 75% of the people would not carry the mutation and 25% would. But (see the table further up), the numbers show a different panorama:

• 75.0% Theoretical average statistical value
• 74.4% Africa
• 74.3% East Asia
• 81.0% Oceania
• 64.0% Europe
• 90.7% America
• 59.3% Middle East
• 65.3% Central Asia
• 70.6% Global Average

Further down we look into the transmission of the allele: it is matrilineal, those with more daughters will transmit more of the allele to future generations. But is this the cause for Europeans, Central Asians and Middle Eastern populations in having a much lower "archaic allele" value? (i.e. they had more daughters?) while Amerindians and Oceanians have a higher ratio of the archaic allele because they had more sons?.

Maybe the differences are due to admixture with archaic populations that did not have the modern mutation: Amerindians and Oceanians admixed with, say, H. erectus in their respective territories and took up their X chromosomes with the archaich pre-insertion variant, diluting the modern allele that they carried with them...

Getting back to DXS225, the archaic form is the lack of this insertion: chimpanzees do not carry it.

Neither do several populations within Africa, 100% of their members do not have the mutation. Since genetic diversity is highest accepted as being highest in Africa [3], this should not surprise us. An archaic form could be conserved in some groups which do not carry the "modern" mutation that appeared almost 100 kya, maybe it appeared in others that migrated out of Africa and many that stayed behind lacked the mutation or even admixed with archaic African populations (Mendez et al., 2013 [5]) and therefore had a higher influx of the archaic pre-insert variant.

It is not found among the Papuans either. These people (see my most recent post on haplogroup C, C2 haplotype) reached their territory in New Guinea very soon after leaving Africa their Y chromosome haplogroup C2 is unique to them and very old. They could have retained the non-mutated allele too.

The Dai in South China, Thailand and Myanmar are intriguing. These people are either indigenous to their territory or originated in South China and moved there [4]. This region is probably the homeland of the C* Y chromosome paragroup, the point it split into its haplotypes (C1 to C5), including the C2 found among Papuans and the C3 found in America.

What role do the Northern Italians from Bergamo have in this plot? I am at a loss. Maybe these people have C6 (the European branch of hg. C)?

Amerindians have haplotype C3 (North America) at very low frequencies and C3* in Soth America. And all have DXS225.

I mention the C hg. because in my previous post I conjectured a link between haplogroup C and Homo erectus. As we see the allele also follows the pattern of hg. C, but not because of the haplogroup itself -see below- but because it is the rang e once occupied by Homo erectus

No link between DXS225 and Y chromosome haplogroups

Unfortunately I can not make a link between a mutation in the X chromosome and Y chromosome haplogroups. The explanation is below:

The image further up shows us that the men (Man 1) carrying the X mutation (green X chromosome) do not pass it on to their sons (male descent) or his grandchildren born from those sons, so there is no link between Y chromosome haplotype of men carrying the mutated allele and the allele. The boys born from Man 1 do not carry the Allele. This is interesting, it is transmitted via women: Man 1's daughters.

His daughters will receive the mutation (green colored X), and they will of course carry the same haplogroup as their mother, Woman 1, (pink squares). Their children if boys, will have the Y chromosome haplogroup of their fathers (which may or may not be the same as that of their grandfather). So this shows there is no link between Y chromosome hgs. and the allele.

Regarding the descent via Man 1's daughters: Half of the granddaughters born from his daughters will carry the mutation and so will half of his daughters' sons; all of them will carry the mtDNA of their mother, Woman 1.

Conclusions

The most interesting scenario is the one that suggests that a non-human archaic homin left Africa long before this allele evolved (I am thinking H. erectus). They took the coastal route to New Guinea, South East Asia and onwards into America. Y chromosome haplogroup C marks their course (yes, some spread into Europe, where some Northern Italians still carry it).

It remained back in Africa too among H. erectus or related groups. Later with the evolution of modern Humans, the mutation appeared and spread globally, overlaying the C hg archaic allele carriers with other more recent haplogroups and modern populations carrying the allele at a 25% ratio. It did not erase the archaicn pre-insertion mutation however: three out of every four modern humans carry the archaic type. Some groups remained isolated from the mutation and suffered no admixture. Maybe it is not neutral (we have seen that it is found at very high frequencies in N. Guinea and America) and is subject to natural selection and this contributes to its survival despite the presence of the mutation.

America peopled by H. erectus received waves of H. sapiens with this insertion mutation, but the archaic form prevailed. Were the erectus better adapted to the New World conditions?

Sources

[1] Rinaldo Wellerson Pereira, Simone Silva dos Santos Lopes and Sérgio Danilo Junho Pena, (2006). A novel polymorphic Alu insertion embedded in a LINE 1 retrotransposon in the human X chromosome (DXS225): identification and worldwide population study. Genet. Mol. Res. 5 (1): 63-71
[2] Ibid. (2007) A Worldwide Phylogeography for the Human X Chromosome. PLoS ONE 2(6): e557. doi:10.1371/journal.pone.0000557
[3]Brenna M. Henn, (2011). Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. vol. 108 no. 13 5154–5162, doi: 10.1073/pnas.1017511108
[4] Sun H, Zhou C, Huang X, Lin K, Shi L, et al. (2013). Autosomal STRs Provide Genetic Evidence for the Hypothesis That Tai People Originate from Southern China. PLoS ONE 8(4): e60822. doi:10.1371/journal.pone.0060822
[5] Mendez et al., (2013). An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet. 2013 Apr 4;92(4):637.

---

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

Helicobacter Pylori and Homo Erectus

I am posting once again on the Helicobacter Pylori bacteria, because I came across a paper while researching on Homo erectus in Southern Asia for my recent series on Y chromosome C haplogroup.

My previous post in case you are interested is this one: Ulcer causing bacteria and Neanderthals in America.

H. Pylori and Homo erectus

H. pylori are a type of bacteria that is found in the stomachs of roughly 66% of mankind. Its name "helicobacter", comes from its shape ("Helico" means "spiral").

People usually pick it up during childhood and in general it lives in its host unnoticed but, in certain people it causes disease (ulcers, inflamation or gastritis and in some cases, cancer).

It spreads from one person's mouth to another, so it quickly passes from parents to children and is exchanged between siblings as well as between couples. Another form of transmission is through contact with feces due to lack of hygene (a person who does not wash his or her hands after using the toilet). It can also be picked up from contaminated water or food.

Risk is higher in developing countries, but in the past, overcrowded conditions, lack of access to clean water and poor hygene allowed for an ample transmission within geographic localities and the people inhabiting them.

For this reason, it spreads rapidly within a population and is also affected by natural selection however this does not completely erase its origin.

Comment on Natural Selection.
The original American variety of H. pylori (known as hspAmerind) was specialised in infecting Native American hosts, when Europeans arrived (1492), the dramatic drop in native population due to war and disease plus the increase of Europeans and their "mestizo" mixed Amerind-European offspring allowed the more generalised European H. pylori (hspEurope) to outcompete it and greatly replace it.

This familial transmission keeps the different varieties of H. pylori within certain social groups (obviously those who live, share food, toilets, water and have sex together). This allows it to be used to study the prehistoric migrations of human beings with H. pylori in their stomachs.

Our most distant ancestors carried it in their gut, and as H. habilis evolved into our archaic ancestors (Neanderthals, H. erectus, H. heidelbergensis, etc.), H. pylori was in their stomachs, evolving too and passing along the evolving line of hominins till it reached us and (as orthodoxy states), left Africa some 60 kya in the wave of H. sapiens that would people the world and replace any other hominins out there. These human migrants settled in different regions and their H. pylori also evolved separately from those in the bellies of other humans in other places.

This is attested by the fact that there are different varieties of the bacteria specific to different geographic locations: [1]

• hpNEAfrica, from Northeast Africa.
• hpAfrica1, found in Western and Southern Africa.
• hpAfrica2, only found in South Africa.
• hpEurope, found in Europe, Western Asia, the Middle East, India and Iran.
• hpAsia2, from Northern India, Bangladesh, Thailand and Malaysia.
• hpEastAsia, found in Japan, Korea, Taiwanese Chinese, China and Vietnam.
• hpSahul, carried by natives in Papua New Guinea and the Australian Aboriginals.
• hspMaori, found among Melanesians, Taiwanese Aboriginals and Polynesians.
• hspAmerind, carried by Native Americans.

This is interesting and points out closed groups moving with their own bacterial strains into the territories they peopled. But it also shows links between them that are not so clearly revealed by the human genome studies (mtDNA or Y chromosme sequencing). Below is Figure 2., from [1], the interesting part is not the map, but the trees:

H. pylori Asian strain, in Asia and tree. From [1]

The captions from the original text are: "(A) Map of sampling locations of hspEAsia haplotypes in Southeast Asia... (B) Neighbor-joining tree from pair-wise FST values of hpEastAsia haplotypes rooted with haplotypes of the population hpSahul. (C) Neighbor-joining tree of pair-wise FST values of the subpopulation hspEAsia. doi:10.1371/journal.pone.0022058.g002" [1].

Look at B and C, the hspAmerind is completely separate from all the Asian and Melanesian - Polynesian branches. Very distinct indeed. They split off long ago, close to the split with hspSahul.

Looking at it from the perspective of my last post NRY haplogroup C, Eurasia and Homo erectus It is clear that hspMarori does not reflect the ancient C2 Y chromosome hapoltype of NG, instead it reflects the later arrivals from Taiwan. hspSahul on the other hand does reflect the archaic people that occupied Sahul with the C4 and C2 haplotypes. HspEAsia reflects C1 (Japan), C3 and C*. So clearly hspAmerind is the ancient C haplotypes found in America.

What about the Indian C5? and C-M130 marker, or the archaic European C6?

Let's look at the other figure from [1]:

hspEurope in Asia, map and Tree. From [1]

European varieties split into two main branches North Europe (top) and France - Spain (bottom). The La Braña remains (7 ky old) with C6 haplotype were found in Spain.

The hspEurope is also found in Asia: in India and S.E Asia. This is what the paper (Breurec S., et al., 2011) [1] deals with in detail, trying to find out how did a specifically European variety of H. pylori reach the heart of South East Asia. The conclusions are remarkable:

Since it is found at high frequencies among Khmer (52%) and the variety was similar to the one found among Thais, but different to the French type, it is clear that it was not introduced into those populations due to Colonial contact with the French in Indochina (Vietnam, Laos, Cambodia), it is far older, and the paper suggests that "hpEurope bacteria in Southeast Asia might be a marker for an old human migration that predated the European colonial history." [1]

The link, as can be seen in the neighbor-joining tree (based on these pairwise FST values), shown above clusters the S.E. Asian and Indian varieties in a distinct group linked to the European types.

Recent introduction by Indians into S.E. Asia is also discarded because Malays, Thai and Khmer are closer to each other than to the Indians (from India or those that migrated to Malaysia).

Once again the paper concludes that this "suggest[s] a common origin of these strains and argu[e] against an exclusively recent acquisition of Malaysian hpEurope strains from Indian immigrants..." [1]. I fully agree, these are ancient strains that somehow were introduced into the region and prevailed despite the introduction of the hspEAsia.

The question is when did they reach Southeast Asia. The paper supports a two stage arrival: one to India and another onwards, into S.E. Asia: "an old introduction of hpEurope strains into the Indian subcontinent by Indo-Aryan migration (4000–10000 BP) as previously described. This was followed by subsequent eastward migrations of their descendants into Southeast Asia, carrying hpEurope strains in their stomach, probably within the last 3000 years." [1].

I disagree with both dates; they are too recent. Furthermore, allow me to quote another paper on H. pylori in the region (Tay et al., 2009): "there is no evidence that ancestral Malays migrated from India [or evidnece that] supports Malays sharing direct common ancestry with Indians." [2].

The paper adds: "Therefore for the Malay population, the ancestry of H. pylori does not reflect human ancestry as in other populations." [2]. I fully agree, it does not reflect the human ancestry of these people but their archaic ancestral Homo erectus ancestry.

Tay et al., are at a loss to explain the Indian - Malaysian link, and bogged down by the constraints of orthodoxy overlook the most parsimonious explanation. I will quote the paper (bold is mine):

"Another potential source of H. pylori for non-aboriginal Malays is the Orang Asli population, who originated from early human migration out of Africa.
The Orang Asli is likely to have taken the "Southern Route" into South East Asia to reach Malaysia by traveling along the Indian Ocean Coast line 50–65,000 years ago.
Therefore the Orang Asli H. pylori, if it exists, may share common ancestry with the Indian H. pylori, leading to the observed similarity of Malay isolates to Indian isolates."
So far so good, that is exactly the correct explanation, but then they dismiss it!.
"However given that other earlier H. pylori populations such as the Maori and American Indian populations can be readily identified, one would expect that the Orang Asli H. pylori population would be unique and identifiable after such a long period of separation, arguing against acquisition from Orang Asli population and in favour of acquisition from the Indian population." [2]

Actually the Orang Asli H. pylori and that of all S. E. Asians as well as the Indians, is the original archaic hspEurope in its "Asian Clade" as shown in the figure above.

Proof of the ancient origin of the Indian clade of hspEurope is found in S Manjulata Devi et al., (2007) [3], who were cited by [2] above, and who wrote: (bold mine)

"we suggest that H. pylori might have arrived in India probably at the same time when Indo-European language speaking people crossed into India (~4000–10,000 years before present). Alternatively, the unquestionable common origin of Indian strains with the European ones could be actually more ancient, following the upper Paleolithic spread of Homo sapiens in Eurasia, as suggested by mtDNA variability, and our data on H. pylori MLST do not rule out this possibility." [3]

This is where Breurec S et al., picked their date of 10 - 40 ky, but it is clear that S Manjulata Devi admits that an earlier date is possible, the actual OoA event into Asia.

The uniform dispersal within distinct geographic locations is in my opinion a clear indicator of an extremely ancient relationship between H. pylori and hominins, one that reflects, in my opinion, the most ancient dispersal of humans from Africa, the OoA event of H. erectus and their migrations.

The African diversity reflects perhaps even more ancient roots. But in Eurasia and the Americas the H. pylori lineages mirror the Y chromosome C haplogroup regions. As I conjectured in my previous post:

Current C hg. distribution reflects the migration of Homo erectus out of Africa 1.8 Mya. A band of a few hundreds of people walking into Asia with the CF haplogroup, splitting in the Persian Gulf by acquiring the M130 marker, and thus forming C haplogroup. They moved across South Asia keeping their C hg. identity during their long trek (note that since mutation rates are slower than accepted, no mutations arose during this period).

Finally reaching the Homeland from which it differentiated into its current haplogroups, in the North of S. E. Asia. From there they spread out. Some moved into NG, Australia mutating (slowly) into C2 and C4. Others went back into India and mutated to C5. The core in S.E. Asia evolved into C* while others went north forming C1 and C3.

A group did not take the Eastern route and went West into Europe forming C6 there. Maybe it will be sequenced someday from the bones at Sima de los Huesos...

Erectus entered America long ago, and the patchy C3* distribution in South America is what remains of a once widespread coverage of H. erectus in the New World...

So we see the correlation: hpEurope = C6, hpAsia2 = C5 - C* hpEastAsia = C3 - C1, hpSahul = C2, C4, hspMaori = C2 (Polynesia), hspAmerind = C3 (America).

Sources

[1] Breurec S, Guillard B, Hem S, Brisse S, Dieye FB, et al., (2011). Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast Asia. PLoS ONE 6(7): e22058. doi:10.1371/journal.pone.0022058
[2] Tay CY, Mitchell H, Dong Q, Goh KL, Dawes IW, et al., (2009).Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population. BMC Microbiol 9: 126. doi:10.1186/1471-2180-9-126
[3] S Manjulata Devi, et al., (2007). Ancestral European roots of Helicobacter pylori in India. BMC Genomics 2007, 8:184 doi:10.1186/1471-2164-8-184

---

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

NRY haplogroup C, part 2. Eurasia and Homo erectus

Y chromosome Haplogroup C is perhaps the oldest and therefore earliest indicator of the presence of modern human males in Eastern Asia. It is found at a relatively low frequencies across most of Asia, reaching its highest frequencies in North Eastern Asia (Mongolia, Siberia); it declines in Japan, Korea, China, India, Southern Asia, but risies in Eastern Indonesia, Polynesia and Australia. It is absent in Africa, found at moderate frequencies in North America and very low frequencies in Europe and South America. [1] (see map below)

As we will see below, it has distinct geographically-specific haplotypes of which C3 is the most widespread one spanning Asia and America.

Map showing global distribution of C haplogroup, frequencies and official dispersion routes. Adapted from [2]

This extended range and low frequency coverage underlying more recent Eurasian haplogroups clearly indicate that it arose very early in Asia, among first humans that left Africa, during their trek across Western Asia and before they reached Eastern Asia.

In today's post I will summarize its regional haplotypes and frequencies and, close the post with a discussion on their origin and dispersal. I will go over the data and the "orthodox" point of view and later will suggest some non-orthodox ideas regarding C hg. and its origin. To skip the region by region information click here to go to the analysis part of this post.

A Regional Analysis of NRY Haplogroup C

We will detail the C haplogroup's haplotypes and their frequencies of in the following regions:
Australia, Melanesia, Polynesia and Papua New Guinea, Indonesia, Indian subcontinent, China, Japan, Korea, Northwest Asia and Siberia, Persian Gulf, Europe, North America, (South America was discussed in a previous post.

C haplogroup across Southeastern Asia, Australia and Polynesia

To get your bearings in our regional analysis, the following map will come in handy. It shows the frequencies of the different C haplotypes in East and Southeast Asia, PNG, N. Zealand, Polynesia and Australia:

Y chromosome C haplogroup, Range and frequencies in Asia, Australia and Polynesia. Adapted by A. Whittall from [3]

The map clearly shows how hg. C is present in the region at noticeably differing frequencies and with very distinct haplotypes in the each of the geographic locations:

• C3 (M-217). North Asia (Mongolia, Korea, China) and the Americas
• C1 (M-8). Only found in Japan and Ryukyu
• C*. In South China and S.E. Asia, but this is a Paragroup and may conceal yet unknown haplotypes.
• C2 (M-38). From East Indonesia and across Melanesia, Polynesia and New Zealand, but with two distinct haplotypes in the West and the East of this vast region.
• C4 (M-347). Unique to Australia
• C5 (M-356). Not shown in the map, but unique to India, Nepal and Pakistan

As you can see, there is a clearly geographic distribution of haplotypes with little or no overlap.

The following table gives some numerical data for the whole of Asia (including Greater India, not shown in the map above and North America):

Table with C haplogroup frequencies Asia and America. Adapted from [4]

This of course mirrors what we have mentioned above: discrete regional distributions and an overlaid C* paragroup at low frequencies (highest in South East Asia) which will have to be resolved into other new haplotypes once their markers have been identified.

Below we will review each region in detail and then try to reach some conclusions.

The Australian Aboriginals - C4

Austrailian natives have their own unique haplogroup, C4, defined by SNP M347; C4 has two haplotypes: C4a (with STR DYS390 deleted) and C4b with M210.

This is the original, ancient haplogroup that arrived in Australia during its peopling wave, which took place some 50 kya and was followed by "considerable isolation after the initial arrival" [4].

The original migrants came from the southern tip of mainland Asia: "Sunda" (encompassing the main Indonesian islands and Malaysia). The "Wallace Line", a strip of sea with many minor islands forming "Wallacea" (Sulawesi, Lombok, Sumbawa, Flores, Sumba, Timor, Halmahera, Buru, etc.) separated it from the other landmass of "Sahul", which was formed by Australia and Near Oceania -New Guinea (NG) and Melanesian Island. The migrants trekked across this now submerged land (sea levels rose after deglaciation c. 9 kya) and rafted across the Wallace Line, reaching Australia.

Interestingly, the other C haplogroups and paragroup C* did not enter Australia (one study detected some C* in Arnhem which may reflect modern arrivals), or if they did, disappeared without a trace.

Despite my hopes that Homo erectus admixed with this Paleolithic migratory wave that peopled Australia and New Guinea (NG), the mainstream science does not support this notion: ""local H. erectus or archaic Homo sapiens populations did not contribute to the modern aboriginal Australian gene pool" [4].

One thing that surprised me is that the time it took the human groups to move across Sahul and Sunda was so long in comparison to what orthodoxy attributes to the peopling of America event:

• Australia. "...the migration from southwestern Asia to Australia would have taken <5,200 years ... This migration speed is in the same order of magnitude as estimated for other prehistoric continental settlements" [4]
• Americas. " the Paleo-Indian spread along the entire longitude of the American double continent might have taken even <2000 yr." [5]

Note that to cross America from Alaska to Cape Horn is about twice the distance compared to the trek from Malaysia to Tasmania yet we must believe that they did it in less than half the time. Did the Paleoindians move four times faster than the Australian Aboriginals' ancestors? Something is not quite right with these numbers. Most likely the American peopling event is far too short, but since orthodox science has to have people in Monte Verde, Chile c. 13 kya and they supposedly entered the New World 15 kya., the absurdly short 2 kya figure appears... Another example of fiddling with the dates to make them fit with preconceptions.

C2: Melanesia, Polynesia and New Guinea (NG)

Melanesia and New Guinea (NG) were settled in the same wave that peopled Australia over 42 kya [6], but later waves of humans reached this area and account for over half the Y chromosome haplogroups in the Region. Nevertheless, haplogroup C is widespread and found at a ㅏ% frequency in Indonesia, indicating its ancient origin [3]. It is found with different haplotypes:

• C* [C-RPS4Y*(xM38, M217, DYS390.1del]. This paragroup is the oldest (50 kya) lineage in Sunda and Sahul [6]. It is very rare in Melanesia and only appears in some coastal NG samples.
  It is "notably absent from the NG Highlands and Taiwan and the Philippines" [6], reaching only 3.4% in the latter (Taiwan and Philippines are mentioned because they are apparently the ancestral home of many Melanesians, but seemingly not the C* carriers). [8]
• C2.
  
  • C2-M38*(xM208). It is almost absent west of the Wallace Line, its highest frequencies are found in East Indonesia, Moluccas Nusa Tenggara (51 - 44%) [9], coastal NG and Cook Islands.
    It is the most common haplogroup in Northwestern NG (34.6%) and the second most frequent haplogroup in New Guinea (avg. 12.8%). Since its STR diversity his highest in NWNG (Bird's Head region) it very likely originated there (or in Wallacea as the oldest hg. (42 - 61 kya) [6] , expanding east across Melanesia and NG into Polynesia (although rarely observed there); and also West, into Eastern Indonesia. [10][8]
  • C2b-M208. Found at high frequencies in the West Papua highlands and among Cook Islanders, it is old: mean age 46.2 ky [6] but had a much more recent expansion into Polynesia (5 - 2.2 kya) [8], where it is found at high frequencies (34%) and also among the New Zealand Maori (77%). [11] [10]
    Is a low frequency hg. in Northwest NG (2.5%) and NG (avg. 6.8%). [10]

A variety (originally named C6) with the P55 marker was reported [6] but is now considered as a Private SNP due to lack of positive testers [2] or a familial group of related males [12] so the C6 haplotype has been dropped and reassigned to European lineages. Three other haplotypes are absent in the region : C5, C3 and the Australian Aboriginal C4 [6].

Rest of Indonesia

• C*. Has a patchy distribution across the Asian region, it is found at high frequencies in East Indonesia (29.2% in Flores and 22.8% in Lembata) and, as mentioned above, is absent in Melanesia and Polynesia. Further north it appears in China (Yao, 20%). [3]
• C2-M38*, is absent in Western Indonesia but grows to an average of 33.5% in Eastern Indonesia (from 11% in Sulawesi to 57% in Sumba); it is found at very low frequencies in Polynesia and Melanesia. [3]

The Indian Subcontinent and the C5 clade

Haplogroup C was detected in India and had been initially classified as C* until Sengupta S. et al., (2006) [14] analysed the paragroup and identified a new haplotype, C5-M356. Almost 85% of the Indian C* individuals were assigned to the new subclade. Which is only found in the Indian subcontinent. [14]

Ancient and autochthonous

C5 is a pan-Indian lineage, absent in the rest of the world yet found at very low frequencies in India (1.4%) where it is widely distributed: It "occurs in all linguistic groups and in both tribes and castes. It also occurs in one Dravidian Brahui in Pakistan" [14]. For this reason, it "is an ancient hg... most plausibly arose in situ within the boundaries of present-day India" [14].

Unsurprisingly, The C3-M217 hg. frequent in Eastern and Central Asia has not been detected in India (it did appear in Pakistan though) [14], neither have C2 or C4.

The data regarding C hg. in India and Pakistan is the following [14] (notice the very low frequencies):

• India
  
  • C*-M216 (RPS4Y) 0.27%
  • C5-M356 1.51%
• Pakistan
  
  • C3-M217 6.82%
  • C5-M356 0.57%

Tamils of Southern India

The Tamil people inhabit southern India and northern Sri Lanka. A study [15] that sampled tribes, some of which are still foragers, found that haplogroup C was present in 19 out of the 31 groups sampled at relatively high frequency of 4.4% (avg). 90% of them were C5 and the remaining 10% were C*. C hg exhibited a high variance (0.80) suggesting a local origin for its prevailing haplotype.

China

C haplogroup is unevenly spread across China, it is scarce along the eastern coast and more frequent in the North, South and West. The C* paragroup is common in the South and East, and C3 in the North and West.

• Southeast. (Yao, 20% - C*). [3]
• Northeast. Heilongjiang (Manchu, 44.0%) and Hezhe 6.7%, Inner Mongolia (Mongolian, 52.2%; Oroqen, 61.3%), Outer Mongolia (52.8%) [2]
• Northwest. Xinjiang (Hazak, 75.5%) [2]
• Center. Miao 1.7%, Hui 6.7%, Tujia 8.2% (C-RPS4Y*), Han 6% (C-M217), Tujia 18,3% (C-M217)[7] [2]
• South. C*: Mulau 9.1% and Shui 6.9% [2]

Neolithic archaeological remains 6.5 - 2.7 kya from West Liao River valley in Northeast China carried the C3e - P53.1 haplotype. These people are believed to have originated in the northern China steppe, a region where extant populations still carry C3e at a 23.8% frequency. [[17]]

Japan and its C1

C haplogroup is found in Japan at low frequencies, and it has a local haplotype, C1 exclusive to Japan. The values are: [18]

• C1 - M105, the local haplotype, 1.5%
• C3 - M217, originated in the mainland, 2.2%

Korea - C3*

The prevalent C haplogroup in Korea is C. The values differ according to the source: [20] indicated a 12.6% frequency of C-RPS4Y (that is C*, very likely C3*). Another [7] indicated a 16.2% frequency of C3* (xC3c) and yet another [14] 9.6% of C3*.

C3* is also found in neighboring Manchuria at moderate frequencies: higher than in Southeast Asia yet lower than Northeast Asia suggesting an expansion from Mongolia or Siberia into Korea.

Siberia and Northwest Asia

The North Asian haplotypes are (always from the orthodox point of view) relatively recent: C3 as a whole (4.1 to 14.9 ky), and its subclusters are even younger still: C3c (1.6 to 5.9 ky) and C3d (0.5 to 2.0 ky). Notice how wide spread these dates are, which shows the uncertainty originated by the mutation rates used in the calculations. [14]

These are the C lineages found in Northern Asia:

• C3c. (M-48) Prevails among Manchurians, Evens, Kalmyks and Evenks. All of which are Mongolic-Tungusic peoples. [19]
• C3d. Is frequent among Mongol speaking peoples: Mongols, Khamnigans and Buryats.
• C3*. Paragroup with high frequencies (+30%) among Koryaks and Mongols it is also found in North America.

Trivia: history

There is a Genghis Khan "star cluster" (part of paragroup C3*) which is said to have originated 1 kya ago in Mongolia and spread by the Khan's relatives due to their "social status" (a neat sinophylic way of saying that the Mongol hordes raped their way across Eurasia). It now ranges from 35% among Mongols to between 3 and 8% among Buryats, Kazaks, Tuvinians, Shors and Altaians. It is between 0.27 to 2.8 ky old, so it may be related to Genghis Khan and his male relatives. [14][19] Nevertheless, the Kereys tribe in Kazakhstan have the highest frequency (76.5%) of this C3* star cluster and it is unlikely that it is due to Genghis Khan's clan. [19] So maybe these people are the original source of it.

Persian Gulf region

This in Southwestern Asia, the region where haplogroup C first appeared in Asia after leaving Africa. It is found at very low frequencies:

Iran [21]:

• C*. 0.1%. Only appears among the Zoroasterians of Yazd province (2.9%).
• C3. 0.4%, is found in 4 out of 20 ethnic groups, from 0.8% (Bandari) to 2.9% (Zoroasterian).
• C5. 0.5%, appears in 3 groups, From 1.5% (Bandari) to 2.8% (Mazandarani). This is the Indian clade, did it back-migrate into Iran recently or is this a relict?

No apparent pattern, just a patchy distribution: C3 and C5 in the north cicum-Caspian area; C3 and C* in central Iran, C3 and C5 by the Persian Gulf. Perhaps the remnants of the ancient dispersal or are they recent movements of people? [21]

Other Gulf Countries: we also have C* (C-M216) at low frequencies in: Oman 3.3%, Saudi Arabia 1,3% and the UAE 1,2%. [21]

European C6

There is a very rare Southern European haplotype within C hg. The nomenclature for this European C-V20 haplotype has changed: it is now named C6 (originally named C7, but since the NG P-55 became a private marker, C6 was reassigned to Europe). It is characterized by markers V20, V7, V86. V182. V184, V219, V222.

Very few samples were known, a recent study [22] found 1 (one) person carrying C6 out of a sample of 1965 individuals! The paper indicates that "Further studies are needed to establish whether C7 [they use the old notation] chromosomes are the relics of an ancient European gene pool or the signal of a recent geographical spread from Asia.". If the latter, the C6 hg. has yet to be identified in Asia; I am inclined towards an ancient origin in Europe.

Archaic La Braña C6 individual

C6 has been identified in the 7,000 year old remains of a Mesolithic man, discovred at the La Braña site in Spain, supporting its ancient origin. However, with the usual caution of a scientific paper, the authors indicate that: (bold mine):

"... La Braña 1 sample belongs to either haplogroup C or F. When mutations defining those haplogroups were checked, only ancestral alleles were found in the haplogroup F-defining mutations, whereas seven C-defining mutations (M130, M216, P255, P260, V183, V199 and V232) showed only derived alleles. Thus, La Braña 1 most likely belonged to haplogroup C [...] The fact that we found ancestral alleles in mutations defining C1, C2, C3 and C4 (Table S9), together with their actual phylogeographic distribution restricted to Asia, Oceania and the Americas suggests that our individual does not belong to any of these branches. Rather, a new branch within haplogroup C (C6, originally named C7) has recently been identified in several men from Southern Europe, suggesting this could be an ancient European clade. Importantly, mutation V20 showed one read with the derived allele (A), which points to C6 as the most probable sub-clade for La Braña 1 sample. It could also be possible that this G to A mutation is a result of DNA damage. Other less likely haplogroup affiliations are C* and C5 (no read covered SNP M356), both found mainly in present-day India." [23]

North American C3b

Haplogroup C is present in North America at moderate frequencies in a unique haplotype found only in that part of the New World: C3b (P39). The details of the frequencies among the native people: [24]

Tanana (Alaska): 41.7%, Cheyenne: 15.9%, Sioux: 11,4%, Apache: 14.6%, Navajo: 1.3%. It was not detected among any other population across North or Central America.

See my previous post on C3* in South American natives.

Analysis and Discussion

Above I pointed out that Y chromosome hg C is absent in Africa; this means it originated outside of Africa. Conventional mainstream science will therefore place this origin after the OoA (Out of Africa) migration of Modern Homo sapiens some 60 kya.

1. Origin

The accepted theory is that Haplogroup C originated with the split from the hypothetical Haplogroup CF -or CF(xDE). Its marker is SNP P143, which is ancestral to F and C hgs. This split took place somewhere in Southwestern Asia, perhaps on the shores of the Persian Gulf 60 kya.

2. Dispersal across Asia

Men carrying hg. C are believed to have taken an eastern "coastal" route along the coast of the Arabian Sea, reaching the mouth of the Indus River. I see no objections to the possibility that they also advanced inland along the main rivers of this area, but the official dispersal theory sticks to a coastal route (perhaps to tie in the timing of the OoA event and the peopling of Australia, a quick march along the coasts of Asia is required).

2.a. India

From the Indus, C entered the Indian subcontinent, we can suppose that the typically Indian C5 arose later, from those who stayed behind in India, because it is unlikely that C mutated and only those with the C5 marker stayed in India and all the rest, with the non-mutated version kept on moving. Another option is that the mutations arose later from some other region and back- ispersed into India, where it is now prevalent. But this needs us to explain why it became lost in its point of origin.

2.b. Into Austronesia

These migrants pushed on south towards Cape Comorin and Sri Lanka, and then north along the Bay of Bengal and across modern Bangladesh, Myanmar and down into Malaysia, till they reached the edge of the emerged continental shelf in Indonesia: (during the Ice ages sea level was lower so all East Indonesian islands were joined into the Sunda landmass). They boated across the Wallace Line, a stretch of deep seas that blocked access of placental mammals southwards into Australia and New Guinea (NG) -as well as marsupial migrations towards the north. They finally reached Sahul the joined continent of NG and Australia.

Peopling of Sahul and Southeast Asia. Adapted from [25]

The map above shows the current continental area and the emerged continental shelves (in grey), the red arrow shows the migration into Sahul.

It was during these moves that C2 appeared in Wallacea (Western Indonesia and NG) and stayed there while C4 appeared in Australia and also stayed there... why? what kept them from expanding and overlapping in a unified landmass?

The answer: Culture and Topography. Swamps, jungle, valleys and mountain ranges, deserts, rugged shores have kept NG people physically isolated. Tribal societies with their cultural imprint also kept them separated. Current language diversity is a clear indicator of isolation in NG. It is likely that these factors plus population bottlenecks may have kept PNG and Australian natives isolated after the initial single-wave peopling event allowing them to develop their own specific haplotype mutations without any furhter admixture. (Further reading on the peopling of Sahul, McEvoy et al., 2010).

Only much later did another migratory spasm take C2 across the vast Pacific Ocean to people Polynesia and New Zealand but this was a new C2 subclade (C-M208).

2.c. Northwards

We have not considered that these people may have crossed India via the Narmada (by this river, remains of H. erectus were unearthed) and Ganges Rivers or advanced upstream and inland along the Indus, Sutlej, Brahmaputra, Irrawaddy or Saleween rivers, reaching Tibet and Central China or that they may have gone across the continent from Dhaka (Bangladesh) to Hanoi (Vietnam) along the Tropic of Cancer (yellow arrow in map above) and from there advanced inland too (Mekong and Pearl rivers).

No, we have supposed that they took the long tortuous coastal route proposed by orthodoxy, which, in an Ice Age World is shown above (red arrow along Sunda and Blue one northwards towards S.E. Asia). Don't ask me why we must stick to the coast.

I bet that if populations in the interior, in North of Myanmar, Thailand, Yunnan and Laos are sampled, C* and maybe C5 will appear at low frequencies.. maybe this is the homeland of C* from which all others radiated and C5 back-migrated into India.

The following map shows all these possible routes (actually these make more sense than the coastal route for the North Asian populations):

Entry and dispersal routes of C haplogroup in Asia. Copyright © 2014 by Austin Whittall. Data from [13]

The Green route is the official route. In blue, my suggested change, following the rivers (this explains why it is not so frequent along the East China Sea), a radically different route but also feasible is the Red route, across the Indus, Tian Shan, Altai and Southern Siberia into Manchuria.

I will cite a very interesting paper by Derevianko and Shunkov (2011) [27] which deals with the OoA theory it is worth reading it:

"Early human migration was a slow process, not a relay race. It is hard to conceive why the migrants should have moved directly to the east along the narrow coastal line rather than exploring the banks of the rivers which flow into the ocean and thus moving far to the north, where favorable ecological niches were available." [27]

Having said this, we will assume that, as per Zhong et al., [19] they moved in a "single coastal northward expansion route... in China about 32 to 42 thousand years ago."

2.d. China

They reached Southern China, and the paragroup C* formed here some 36 kya; the migrants continued along the coast (once again we must explain why C* stayed behind and the others moved on), part entered Taiwan (and from there Japan), the others and kept on towards North China leaving barely a trace in the coastal areas of Eastern China (now isn't that strange?).

In North China (Liaoning, Heilongjiang) the C3 haplotype appeared (33 to 20 kya) and dispersed widely: Eastwards, from Manchuria into Korea and Japan. West into Mongolia and South-Central Siberia, Western China, Altai, etc. (20 to 8 kya), and finally as the ices receeded at the end of the last Ice Age, (15 kya) Northwards into Northeast into Eastern Siberia, Beringia and... finally, America.

Another group entered Japan via Ryuku from Taiwan and originated the local C1 haplotype there.

And this is the end of the Orthodox dispersal version.

3. Sub-haplogroups

We have seen above that C hg. has various discrete subhaplogroups (C1, C2, C3, C4, C5 and C6 plus a paragroup C*) each with a specific geographical distribution. Common sense indicates that they "have undergone long-time isolation" [2]. But little is said about how they originated without spreading into other regions.

Below I adapted Fig. 2, from Redd A., et al., (2002) [26]; at that time the C5 haplotype from India was not known and the C4 among Australians was not shown in the tree, so I added the C4 dotted line around the yellow Aboriginal dots; I also wrote C5? around the green Indian dots within C* paragroup (top part). C3 in this figure does not include Native Americans and surely contains a lot of paragroup C3*. So I included on the right hand side, the C3* data for Asia and America from Roewer et al., (2013) [19], correlating the regions to the color code of Redd et al. (I added the South American natives in pink), but I maintained the individual data dots with their original colour (key is on upper right corner).

Also see C3* phylogenetic tree in my previous post.

C haplogroup unrooted tree. Adapted from [26] and [19]

The tree is quite revealing as it shows a central core of C* from which the other branches appear. Actually, a closer look at the tree reveals that this central C* as per Redd et al., is Indian, and it is linked to the probable root in the form of the branch joining it with haplogroup B (on the left).

The most central branches of the tree are the Australian C4 (left-center) tightly gathered in the middle, and Indian C5 (center and top-center) with the other branches located further apart:

• C2. (bottom left). Is diverse as can be judged from its spread branches, and it arises from C4
• C1. (upper left). Is quite diverse and arises from C*
• C3. (upper right). Is diverse and is also born from C*
• C*. (middle and bottom center). Is diverse. The main branch on the bottom is mainly South East Asian, but there are also some Indian in it. It is very spread and closely linked to the root of C2 and C4, which suggests that this South Asian C* and the Austronesian lineages C2 and C4 are the very old lines of the C hg. peopling wave.

Comments:

The bottom clusters are basically a widely divergent C2 sprouting from the Australian C4, and C* in S.E. Asia

The top clusters are C1, C5 and C3 all sprouting from the archaich core.

Redd's original root from Hg. B, anchors in Indian C* (green dots). I have no way of telling apart the C5 and the C* of (See data above: Indian origin), my guess is that the upper cluster is genuine C5 while the green dots in the central part of the tree and the bottom are actually C*.

The core from which C1, C5, C3, C* and C4 sprout from are green Indian subcontinent dots... surely C* from India. Only C2 is clearly rooted in one line of C4

1. Origins

C2. Arose in Wallacea from an ancestral lineage of C (which must be the original C M-130 variety) carried by the group that would move into Australia and Melanesia. Part of them moved on into Australia forming C4, the other proto-C people remained in Wallacea and formed derived clades: paragroup C-M38* and haplogroup C-M208, which remained in this territory located East of the Wallace Line and much later moved into Polynesia. Topography, tribal structure and bottlenecks kept C2 and C4 apart.

C4. See above, the "ancestral C stock" from Wallacea entered Australia and remained there in isolation.

Of course the ancestra C line is ancestral to current C* in S. E. Asia, and the C4, C5, C1 and C3 lines. C* is still found in India and other parts of S.E. Asia, it is represented by the green dots in the central part of the image. These will prove to be a new haplotype (H7?) when their marker is found. This is the ancestral lineage, from which all others sprout, it is Indian.

This may help explain some of the questions we posed during the haplotype analysis:

C5 originated from this ancestral C in India, the ancestral C people are the original peopling wave, they moved north and became C3 and C1, they moved south and became C4 in Australia and C* in S.E. Asia, a yet to be discriminated haplogroup (H8?) It

The European C6 is not placed in the tree but it is surely a group that split early in Asia and marched West into Europe.

Clearly further analysis is necessary to breakdown C* into newer sub-clades.

C* in Indonesia has a very high STR variance: this means that it has had plenty of time to mutate; it is very old. In Indonesia it is more frequent in the East, because a "continual eastward migration of the initial settlers (i.e., settlements were not permanently established in western Indonesia) or later waves of (partial) replacement." overlaid it. [3] This corroborates is antiquity.

As we can see in the Table of C haplotype distribution, above, haplotype C3 is concentrated in Northern Asia and has a decreasing cline towards the south (absent in Australia, NG and Polynesia) and west, it is found in North America at relatively high frequencies (C3b - P39, unique to the New World) and in South America in a patchy C3* distribution (see my previous post on C3* in South America.

A sinophile paper [19] proposes that this cline is due to its Chinese origin some 42 to 32 kya, and a coastal north route of expansion, it adds that the highest STR diversity for C3 is found in Southeast Asia. This, in my opinion corrobrates its origin from the ancestral C group, but not in China; it appeared in a region that is central to the other Haplotypes:

The region currently occupied by Myanmar, North Thailand, East India and Yunnan in China.

From there it irradiated and became the current regional haplotypes.

Some Crazy ideas

Having given the official story and facts, allow me to let my imagination fly and suggest an alternative scenario based on these same facts.

The area where C hg. is found with a highest diversity in Asia is precisely the area where Homo erectus lived for over 1.5 million years: Southern and Eastern Asia (from China and Korea in the North, to India and Indonesia in the south).

Haplogroup C's coastal route is precisely the one supposedly taken by our distant H. erectus ancestor.

The OoA theory with H. sapiens originating in Africa and peopling the world, totally replacing previous extant populations (if they existed), is so widely accepted that it dealt a death blow to the multiregional theory (H. sapiens evolved in different regions from a common archaich ancestor). But recent genetic discoveries of admixture with Neanderthals, Denisovans and mysterious "X" hominins as well as some remains in China with a mosaic of archaic and modern features have put fresh wind in the sails of the Multiregional theory.

For instance, Derenko and Shunkov (2011) question the OoA theory and support the Multiregional hypothesis in which an "independent formation of anatomically modern humans occurred", this took place in three regions with four subspecies all of which merged into modern humans:

• East and South East Asia, with Homo sapiens orientalensis
• Rest of Eurasia, with Homo sapiens neanderthalensis and Homo sapiens altaiensis (Denisovans)
• Africa, with Homo sapiens africanensis

Among other things, they also use the evidence of a distinct post-Middle Paleolithic South East Asian lithic industry that was different to that of Europe and Asia, with an "autochthonous development of the Upper Paleolithic,"[27]

They go a step further and suggest a Homo erectus evolution into modern humans in Asia:

"...population of anatomically modern humans descended from Homo erectus locally. .... progressive biological traits are due to parallel evolution. Both in East Asia and in Africa, anatomically modern humans apparently originated from the same ancestral species – Homo erectus sensu lato. ...The totality of evidence speaks in favor of a progressive in situ evolution of Homo erectus in East Asia over a span of more than one million years. This does not preclude the immigration of small populations from adjacent regions, small-scale gene flow, or admixture." [27]

If this is the case, then the C haplogroup found among South East Asians is in fact the one carried by H. erectus from Africa into Asia and later mutated in situ in Asia.

But this would contradict the accepted notion that our Y chromosomes are exclusively human, and that our ancestors (and their Y chromosomes) split from those of H. erectus long ago. Their genes disappeared with them and therefore do not appear in us.

But a study has already suggested an ancient origin for human Y chromosome: (Mendez et al, 2013) it reports the discovery of a novel Haplogroup named A00, which gave a very old age: "338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils..." [16]. In other words this "human" Y chromosome haplogroup is older than humans!

Which of course has been criticised by OoA proponents as using incorrect mutation rates that pushed the dates too far into the past.

I wonder, (read my previous posts criticising the mutation rate calculations) if actually the mutation rates for this (and All other) haplogroups is not underestimated by a factor of three or four, which would mean that the dates could be 711 - 2,381 ky, more than enough to accomodate H. erectus in the picture.

This means that Y chromosomes mutate far slower than currently accepted. And that when we look at the current distribution of NRY hgs. we are seeing the ancient migrations of pre-sapiens men across the globe.

Current C hg. distribution reflects the migration of Homo erectus out of Africa 1.8 Mya. A band of a few hundreds of people walking into Asia with the CF haplogroup, splitting in the Persian Gulf by acquiring the M130 marker, and thus forming C haplogroup. They moved across South Asia keeping their C hg. identity during their long trek (note that since mutation rates are slower than accepted, no mutations arose during this period).

Finally reaching the Homeland from which it differentiated into its current haplogroups, in the North of S. E. Asia. From there they spread out. Some moved into NG, Australia mutating (slowly) into C2 and C4. Others went back into India and mutated to C5. The core in S.E. Asia evolved into C* while others went north forming C1 and C3.

A group did not take the Eastern route and went West into Europe forming C6 there. Maybe it will be sequenced someday from the bones at Sima de los Huesos...

Erectus entered America long ago, and the patchy C3* distribution in South America is what remains of a once widespread coverage of H. erectus in the New World, and not a recent transpacific junk with Jomons from Japan shipwrecked on the shores of Ecuador.

Of course this could be proved or rejected if DNA could be sampled and sequenced from H. erectus remains (maybe impossible due to DNA decay). Maybe in the future it could be done, who knows?

Sources

[1] Chuan-Chao Wang and Hui Li, (2013). Inferring human history in East Asia from Y chromosomes. Investigative Genetics 2013, 4:11 doi:10.1186/2041-2223-4-11
[2] Hua Zhong et al., (2010). Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. Journal of Human Genetics doi: 10.1038/jhg.2010.40
[3] Tatiana M. Karafet et al., (2010). Major East–West Division Underlies Y Chromosome Stratification across Indonesia. Mol Biol Evol (2010) 27 (8): 1833-1844. doi: 10.1093/molbev/msq063 First published online: March 5, 2010
[4] Georgi Hudjashov et al., (2007). Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. vol. 104 no. 21, 8726–8730, doi: 10.1073/pnas.0702928104
[5] Martin Bodner, Ugo A. Perego et. al., (2012). Rapid coastal spread of First Americans: Novel insights from South America's Southern Cone mitochondrial genomes. Genome Res. May 2012; 22(5): 811–820. doi: 10.1101/gr.131722.111
[6] Laura Scheinfeldt, (2006). Unexpected NRY Chromosome Variation in Northern Island Melanesia. Mol. Biol. Evol. 23(8):1628–1641. 2006. doi:10.1093/molbev/msl028
[7] Yali Xue, et al., (2006). Male demography in East Asia: a north-south contrast in human population expansion times Genetics 172:4 (April 2006): pages 2431-2439.
[8] Stephen Oppenheimer, (2006). The 'Austronesian' story and farming-language dispersals: Caveats on timing and Independence in Proxy Lines of Evidence from the Indo-European Model, from "Uncovering Southeast Asia's Past: Selected Papers from the 10th International Conference of the European Association of Southeast Asian Archaeologists : the British Museum, London, 14th-17th September 2004" European Association of Southeast Asian Archaeologists. NUS Press, Jan 1, 2006
[9] Kayser M, Underhill P, et al., (2003). Reduced Y-chromosome, but not mitochondrial DNA, diversity in human populations from West New Guinea. Am. J Hum Genet 72:281–302
[10] Stefano Mona et al., (2007). Patterns of Y-Chromosome Diversity Intersect with the Trans-New Guinea Hypothesis. Mol Biol Evol (2007) 24 (11): 2546-2555. doi: 10.1093/molbev/msm187 First published online: September 10, 2007
[11] Underhill PA, Cavalli-Sforza LL., et al., (2001). The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations. Ann Hum Genet 65:43–62
[12] Y-DNA Haplogroup C and its Subclades - 2014. International Society of Genetic Genealogy
[13] Asian Ancestry based on Studies of Y-DNA Variation: Part 1 Early origins – roots from Africa and emergence in East Asia. Genebase Tutorials. http://www.genebase.com/learning/article/21
[14] Sanghamitra Sengupta., et al., (2006). Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists. Am J Hum Genet. Feb 2006; 78(2): 202–221 Dec 16, 2005. doi: 10.1086/499411
[15] Ganesh Prasad Arun Kumar et al., (2012) Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System. PLoS ONE 2012. doi:10.1371/journal.pone.0050269
[16] Mendez et al., (2013). An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet. 2013 Apr 4;92(4):637.
[17] Yinqiu Cui et al., (2013). Y Chromosome analysis of prehistoric human populations in the West Liao River Valley, Northeast China. BMC Evolutionary Biology 2013, 13:216
[18] Nonaka, I., Minaguchi, K. and Takezaki, N., (2007). Y-chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms. Annals of Human Genetics, 71: 480–495. doi: 10.1111/j.1469-1809.2006.00343.x
[19] Roewer L., et al., (2013). Continent-Wide Decoupling of Y-Chromosomal Genetic Variation from Language and Geography in Native South Americans. PLoS Genet 9(4): e1003460. doi:10.1371/journal.pgen.1003460
[20] Soon Hee Kim, Myun Soo Han, Wook Kim, and Won Kim, (2010). Y chromosome homogeneity in the Korean population. International Journal of Legal Medicine 124:6 (November 2010): pages 653-657.
[21] Grugni, V. et al., (2012). Ancient Migratory Events in the Middle East: New Clues from the Y-Chromosome Variation of Modern Iranians. PLoS ONE 7(7): e41252. doi:10.1371/journal.pone.0041252
[22] Scozzari R, Massaia A, D’Atanasio E, Myres NM, Perego UA, et al. (2012) Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree. PLoS ONE 7(11): e49170. doi:10.1371/journal.pone.0049170
[23] Iñ,igo Olade, et al., (2014). Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European, Nature (2014) doi:10.1038/nature12960
[24] Stephen Zegura, Tatiana M. Karafet et al., (2004). High-Resolution SNPs and Microsatellite Haplotypes Point to a Single, Recent Entry of Native American Y Chromosomes into the Americas. Molecular Biology and Evolution, vol 21(1), pp 164-75
[25] Moss, S. J. & Wilson, E. J. 1999. Biogeographic implications of the Tertiary palaeogeographic evolution of Sulawesi and Borneo. In Hall, R. & Holloway, J. D. (eds) Biogeography and Geological Evolution of SE Asia. Backhuys Publishers, Leiden, 133-155. [26] Redd, Alan J., et al., (2002). Gene Flow from the Indian Subcontinent to Australia: Evidence from the Y Chromosome. Current Biology, Vol. 12, Issue 8, 16 April 2002, Pages 673–677. doi: 10.1016/S0960-9822(02)00789-3
[27] A.P. Derevianko and M.V. Shunkov, (2011) Anthropogenesis and colonization of Eurasia by Archaic Populatoins. Formation of anatomically Modern Human. From Proceedings of the International Symposium “Characteristic Features of the Middle to Upper Paleolithic Transition in Eurasia: Development of Culture and Evolution of Homo Genus” (July 4–10, 2011, Denisova Cave, Altai). Edited by A.P. Derevianko, M.V. Shunkov. pp 50 - 74.

---

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