mtDNA C1 haplogroup and Neanderthals

In today's post we will let the Y chromosome take a rest for a while because we will be looking into the female contribution to our ancestry, our mitochondrial DNA (mtDNA), and in particular, the interesting distribution of the C1 haplogroup in America and Eurasia.

While I was writing my previous posts on the Y chromosome Q haplogroup in Scandinavia, I came across a paper on the presence of mtDNA haplogroup C1 in Iceland, and recalling that it was considered -until now- an almost exclusively Amerindian haplogroup (with very low frequencies in Asia), I was intrigued, and decided to research the matter. This post is the result.

C1 haplogroup in America

The Native American people belong to five mtDNA haplogroups, which are almost exclusive to America (there have been some minor back-migrations from America into Asia): A2, B2, C1, D1 and X2a.

Of these, haplogroup C1 is widespread across the Americas, from Tierra del Fuego to central northern Canada (it is absent among the Innuit in northernomost Canada and Alaska).

A Map showing the mtDNA C1 haplogroup current and probable archaic range
Copyright © 2014 by Austin Whittall

C1 hg has in mutated in America and originated four subclades (C1a, C1b, C1c and C1d), of which C1b to C1d are found exclusively in America, and C1a is found in Asia where it back-migrated from the New World. These subclades, in turn have branched into other sublineages.

The Age

The coalescent age of these subclades is shown below [1]:

• C1a: 7.7 +⁄- 1.9 kya (Siberian Branch)
• C1a: 18.0 +⁄- 7.9 kya (Founder age)
• C1b: 17.9 +⁄- 2.3kya
• C1c: 22.2 +⁄- 3.3 kya
• C1d: 20.1 +⁄- 4.4 kya

C4 is also present, in Asia and has been recently been detected in two individuals North and South America [1], (C4c) it has a similar age (20 to 25 ky).

I have already written about my doubts regarding the age and coalescence calculations which are based on estimated mutation rates and mtDNA clocks, which I believe are not too reliable (see my post mtDNA clock ticks out of time).

These mutation rates are fit "by hand" by geneticists to coincide with the data provided by the archaeological scientists, which firmly believe in a late peopling of America. So this is a self-fulfilling-prophecy where the mutations found in populations obviously coincide with the arrival dates of those populations in their current territories, since one is based on the other and no external corroboration is provided.

As an example see a criticism againt an "old" age proposed by Fagundes et al., 2008 [4] which states: "The older dates also require additional explanation for the absence of archaeological evidence in the Americas during this phase and for why populations should beshowing significant signals of expansion under such unfavorable climatic conditions" [3], where the unfavorable climate is the last Ice Age however the previous beningn periods are not even considered because they are too old and the archaeological evidence, when provided is not even taken seriously because it is too old!.

Interesingly, C1 has a high values for nucleotide diversity indices, and show a South to North cline (with most variations in South America), indicating that it has deeper roots in the southern part of the New World or that bottlenecks reduced its diversity in the North. In my opinion in points at an older date of entry into America than those mentioned above.

But back to orthodoxy: Just before entering America, there already was intra-haplogroup variation originating the C1b, C1c and C1d subclades [1]. Regarding C1a, it is also found in diverse populations in Asia, but is quite rare there: Southern Siberia where it is found among the Daurs (2.2%), Ulchi (1.1%), Bashkirs (1.5%), Kazakhs (0.8%), Kirghiz (0.5%), Buryat (0.7%), Kalmyk (0.9%), Orok (11.5%), Mongolians (1.3%), Nanai (1.2%) and Japanese (0.3%) [8]. This presence in Asia is the result from a back migration from America [1] or from "the same ancestral population" that originated the Amerindian haplotypes. [7] As additional proof, you will find that several groups mentioned above figure in my post on a back migration of Y chromosome Q hg into Asia, maybe clans with Q and C1a moved back to Asia.

mtDNA C1 haplogroup in Iceland

A Thesis written in 2010 (Sigríður Sunna Ebenesersdóttir) [5], followed by a paper (Sigríður Sunna Ebenesersdóttir et al., 2011) [2] disclosed the presence of a novel C1 haplogroup in Iceland; it was named C1e.

• It is not the result of recent gene flow from Native Americans or Asians. [2][5]
• It does not belong to any of the four known Native American (C1b, C1c, and C1d) or Asian (C1a) subclades of haplogroup C1. [2]
• The Viking settlers in Iceland had brief and bellicose contact with the Native Americans but could have kidnapped women and taken them to Iceland thus originating the local haplogroup C mtDNA lineage, but the differences between Amerindian C1 lineages and the Icelandic one are considerable.
• Since Aleut, Inuit and Eskimos are not carriers of C1 hg, they are not the vector. [2]
• C1 is quite infrequent among the North American Na-Dene speaking Native-Americans (Apache, Navajo, Haida and Tlingit). [2]
• Amerindian haplotypes are very rare in post 1492 Europe, suggesting limited Euro-Amerindian admixture. [2]
• It is found at very low frequencies in Iceland: about 0.3 %

An Eurasian origin for Iceandic C1e

The likely source arrived in Iceland with the original Viking settlers ca. 900 CE; since these were Europeans, it is possible "that C1e is a very rare European branch". [2] This is corroborated with another line of evidence: "one of the thirteen HVS1 sequences that potentially belong to sub-clade C1e was found in Germany" [2] and that the female settlers brought by the Scandinavian men were women from the British Isles and as "the vast majority of mtDNA lineages observed in contemporary Icelanders are descended from the original set of mtDNA lineages present in the female settlers" [2], this haplogroup was surely present in the X^th century Great Britain.

mtDNA C1 haplogroup in Northern Europe

Only recently was the C1 hg found in the remains of a prehistoric North European (Clio Der Sarkissian et al., 2014) [6], reinforcing the theory of a European source for the Icelandic haplotype. But, surprisingly, it belongs to yet another distinct clade, named C1f, distinct from all other haplotypes.

It was detected in the remains of three individuals retrieved from a Mesolithic site in North Western Russia, on the Kola Peninsula, at the Yuzhnyy Oleni Ostrov site.

This places C1f in Europe 7,500 years ago. But, it has not been detected in current population mtDNA data-bases.

The apparent absence in modern populations may be due to its extinction and replacement by other mtDNA haplogroups introduced by more recent migrations into Europe or a very low frequency among contemporary Europeans leading to its non-detection in the samplings that have been made.

Though C1f has not been found, "HVR-I diversity has revealed extremely low frequencies of hg C1, with very few haplotypes found in Germans, Canarians, Icelanders and Bashkirs. These sequences lack HVR-I Single Nucleotide Polymorphisms (SNPs) diagnostic of the sub-clades C1a (T16356C) and C1d (A16051G)." [6] Meaning that they do not belong to the current East Asian or Amerindian groups (C1a and C1d Hg.)

Comment: The Bashkirs are surely C1a and the Icelanders C1e; the Canarian C1 may be Amerindian: it was a port of call on the way to Southern South America, and had very strong links to the New World during the Spanish colonial period. The German C1 is very probably archaic.

The most widespread haplogroup

So here we have a very interesting mtDNA haplogroup spanning the globe: Northern Europe, Iceland, East - Central Asia ⁄ Siberia and the Americas. What does this tell us?

It apparently entered America via Beringia from Siberia, but it is virtually absent there, where it is believed to have originated as a back-flow from America or an expansion from the ancestral population. It is found in Iceland but the source is apparently European.

It is reasonable to assume that the source for C1 is located in Eurasia (or maybe in America?).

Let's look a the C1f from the Yuzhnyy Oleni Ostrov site. Did they arrive via the invasions of Asian hordes? (we have already seen this hypothesis when we analyzed the Y chromosome Q haplogroup in Europe): Mongols, Huns, Cimmerians (100 BCE to 1,295 CE). It seems unlikely because "the common Asian C1a clade is characterised by the HVR-I transition T16356C, which has not been found in any European C1 haplotype" [6].

The age of these remains (7,500 ya) means that they could not have arisen from European - Native American admixture post-discovery of America in 1492. This clade is definitively an Old World one.

This leaves us with only one option: C1f is very old and has been in Europe at least since Mesolithic times. Its age and location could imply that it is ancestral to the C1e taken by the Vikings (actually by the British women they wed) to Iceland. It also means that C1f and C1a (the East Asian) branches split long ago from the C1 tree, evolving along separate routes. [6] This is shown in the map above where C1f splits from the one leading into America (C1b, C1c, C1d) in Central Asia, and C1a is a back flow from the New World. The pale blue area is the possible range once occupied by the primitive basal C1 root in Eurasia, which later disappeared.

As mentioned above, it has not found in the modern populations in Europe or Asia where it may still exist but has not yet been detected in genetic samplings of the populations. In depth and large scale samples may be required to find it because its originally low frequency may have been further diluted it making it even more uncommon now than it was in the recent past.

To get an idea of its rarity, C1 has appeared only once in Germany, and its presence in Siberia is very low (4 individuals among 1,432 tested) [9]. Interestingly, "The Baltic coast of Europe and Poland also contains a unique C lineage, which may have expanded north from the Black Sea" [9], unfortunately no details are given about it.

The other Mesolithic remains that have been sequenced in Europe did not yield any C1 haplogroup samples [6], this means that even at that time it was quite rare or restricted to certain geographical locations, perhaps as part of relict groups of Paleolithic populations.

And this brings us to... yes! the Neanderthals.

Europe and Central Asia, Western Siberia were the homeland of Neanderthals for hundreds of thousands of years. The Amerindians carry the highest proportion of Neanderthal ancestry suggesting an intimate admixture with them in the New World. The region covered by C1 haplotypes coincides with the range of the Neanderthal people. They were later incorporated by cross-breeding into the modern humans that left Africa 70 kya, this effectively eliminated them by absorption.

But, for this to be true, C1 would have to be a Neanderthal mtDNA haplogroup, and we know (mainstream version) that this is not possible because Neanderthal mtDNA that we have sequenced is too different from ours, furthermore, it would lie on separate branches of the tree, not in one that sprouts from the first modern humans in Africa.

The "Wild" theory

Since this is just a blog and not a peer-reviewed paper and I have no academic career to protect, I can concoct wild ideas and post them here for further criticism and analysis. This is one of them:

The persistence of archaic hominins in modern human genomes

I have already given exactly the same explanation for the Neanderthal's Y chromosome haplogroups which are expected to be different branches, joined at the root by Neanderthal and H. sapiens common ancestor but actually may not be so.

I have expressed my doubts about the ages of the lines and the mutation rates employed to calculate coalescence: maybe mtDNA and Y chromosomes mutate far slower than assumed and the apparent African Modern Humans at the root of the haplo-trees are not human at all, they are H. erectus or H. habilis (the A, B Y chromosome hgs. and the L and M mtDNA lineages within Africa are not the oldest mordern men, they are our ancestors).

This means that the notion of branches splitting like roads and ending in dead-ends is mistaken. Branches criss-cross and mutate and the individuals carrying the mutations change along the branches.

The "tree" below tries to show this, by Analog evolution in (b) I mean many hues and colours due to admixture and introgression, not only discrete lineages that mutate like clocks and die out or survive in a "digital" or binary (black and white, yes - no) fashion, but instead with a full range of options in between).

An approach to the admixture in human evolution. "Analog" evolution
Copyright © 2014 by Austin Whittall

So the paths we see now out of Africa into the rest of the World are not that of H. sapiens, it is the first Hominids to leave Africa and occupy Asia (the Y chromosome C hg, in India and SE Asia and... maybe even into America) or Europe (H. antecessor, Homo heidelbergensis) and later Neanderthals as they spread out across the Middle East, and Western Eurasia.

Only later do the haplogroups (both female and male) follow the trail of Modern Humans, perhaps the Y Chromosome hg is the into Africa path of the modern Humans that originated out of Africa.

I will polish this theory a little and post on it soon.

The point is that both the Y chromosome Q haplogroup and the mtDNA C1 haplogroup span the same region, are found in low frequencies across Northern Eurasia and America, have been detected also at very low frequencies among Mesolithic people and are now rare in the Old World. Both are absent in Africa. Q is found in Oceania (I have no data regarding C1 there). So both display a similar behavior and (orthodox) time frame hinting at a common origin and source population. Both were later overlain by more recent arrivals, diluting them to near oblivion in the Old World.

To me that spells: Neanderthal admixture and dismissal after encountering modern Humans.

It also means: Neanderthals did reach America and were probably present there at the time of arrival of modern humans (within the last 40 - 50 ky), the encounter led to myths regarding ogres and wid men that persist until nowadays among Native American people.

Sources

[1] Satish Kumar et al., (2011), Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins. BMC Evolutionary Biology 2011, 11:293
[2] Sigríður Sunna Ebenesersdóttir et al., (2011). A new subclade of mtDNA haplogroup C1 found in icelanders: Evidence of pre-columbian contact?. Am. J. Phys. Anthropol., 144: 92–99. doi: 10.1002/ajpa.21419
[3] Simon Y.W. Ho and Phillip Endicott, Letter. The Crucial Role of Calibration in Molecular Date Estimates for the Peopling of the Americas. The American Journal of Human Genetics 83, 127–147, July 2008 pp. 142
[4] Fagundes, N.J., et al., (2008). Mitochondrial population genomics supports a single pre-Clovis origin with a coastal route for the peopling of the Americas. Am. J. Hum. Genet. 82, 583–592.
[5] Sigríður Sunna Ebenesersdóttir (2010). Faculty of Social Science. MA-thesis, Anthropology. The origin of Icelandic mtDNA lineages from haplogroup C
[6] Clio Der Sarkissian et al., (2014). Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub-Clade within the Broadly Distributed Human Haplogroup C1. PLoS One. 2014; 9(2): e87612. Feb 4, 2014. doi: 10.1371/journal.pone.0087612
[7] Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, et al., (2007). Beringian Standstill and Spread of Native American Founders. PLoS ONE 2(9): e829. doi:10.1371/journal.pone.0000829
[8] Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Rogalla U, et al., (2010). Origin and Post-Glacial Dispersal of Mitochondrial DNA Haplogroups C and D in Northern Asia. PLoS ONE 5(12): e15214. doi:10.1371/journal.pone.0015214
[9] Jeremy R. Newton, (2011). Ancient Mitochondrial DNA From Pre-historic Southeastern Europe: The Presence of East Eurasian Haplogroups Provides Evidence of Interactions with South Siberians Across the Central Asian Steppe Belt. Master Thesis Paper 5.
 

On the 70^th anniversary of D-Day. Long live the heroes of that glorious day, who layed down their lives for freedom.

---

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

On the Q haplotypes in Europe (Part 2)

My previous post looked into the three theories that explain how the Y chromosome Q hg, with a clearly non-European origin, managed to get into the heart of Europe from its supposedly archaic homeland in Central Asia. We saw how the Huns, Cimbrians and Mongols may have been the human vectors bearing this haplogroup in their "Asian" Y-Chromosomes and carrying it with their invasions into the heart of Europe.

But, could there be another explanation for the presence of Q hg in Europe? To be able to address the issue, we have to look at the facts and the haplotypes of current and past Europeans. Today's post will do just that.

The Ancient Dispersal theory

As an alternative to the alleged historical dispersal that supposedly took place between 103 BCE and 1245 CE, it is probable that the Q haplogroup is actually very ancient and spread across Europe long before the Huns, Mongols or Cimmerians appeared on its eastern borders.

In fact, the genetic imprint of the repeated invasions of Asian nomads on the Y chromosome haplogroups in Moldavia, on the main route used by most of these hordes, was minimum which is in ".. good agreement with earlier studies on Y-chromosome variation in eastern and central Europe, asserting a minimal impact of gene flow from Siberia/central Asia". [1]

The European genetic data shows that Q hg found at very low frequencies: between 0.2 and 2% in most of Europe (except a few hot spots with higher frequencies). This may show the ghost outline of a population that once occuped a vast swath of Europe, but was later replaced and watered down, to its current low frequencies by other Y chromosome haplogroups during the Neolithic (as happened to I haplogroup during that same period [2]). And, once again I am thinking of our Neanderthal predecesors, who lived in this region and were replaced by modern humans (more on this below).

In other words, what we currently see are the relicts of an archaic dispersal of haplogroup Q.

Since haplogroup Q branches off from P hg much earlier than the R hg that nowadays prevails in most of Europe, it would be a reasonable assumption to find Q underlying R in the European continent, that is: widely spread out, but at lower frequencies as successive migrations incorporated other haplogroups into the continent with varying success rates in their new habitats.

In fact, Paleolithic migrants introduced R (xR1a) -the x stands for "excluding"- haplogroup into Europe from the East, and it is the most frequent (37%) haplogroup on the continent, mainly in its Western regions. The other high-frequency haplogroups are E2b (which came from the south), J (from the Southeast) with the introduction of farming, and N, among the Uralic speakers (Northeast). [3]

Could they have spread over an earlier European population?, one with hg Q? Do we even have evidence of an archaic hg Q presence in Europe? Let's see what the sequencing of ancient Europeans tells us:

The Motala remains

The remains of several persons were found at the Kanaljorden site at Motala in Central Sweden in 2009. They were deposited in a small lake, during rituals which included displaying skulls on stakes and placing human bones inside skulls. They have been dated to between 6,212 and 5,675 Cal BC, making them about eight thousand years old.

Recently the genes of six of the Motala remains were sequenced, and the Y-chromosomes of all but one of them, were classifeid as belonging to I hg; the remaining one was probably a Q1a2 hg.

This is remarkable since, as seen above, today hg I is not found at high frequencies among Europeans; yet it was prevalent among Mesolithic hunter-gatherers. This "suggest[s] an old origin" [2]. (Currently it is found in Sardinia, North Germany, Moldavia, Scandinavia and the Western Balkans, probably due to recent expansions and not to archaic settlements).

The Q element in Motala

So we have a doubtful Q1a2 haplotype found in Motala [6]; why is it questioned?

The doubts surrounding the haplogroup of Motala [6] are due to the fact that it carried the marker L55, that is: L55+ (19413335 G>A). This marker is only found in Y-haplogroup Q's haplotype Q1a2a (and branches that arise from it) and in no other haplogroup. But... and this is perplexing, it is L232 -, that is, it does not carry marker L232 which is necessary to make it part of haplogroup Q1.

These are phylogenetically inconsistent findings and the authors of the paper that describe the remains state, quite reasonably, that they "are unable to assign a haplogroup to this individual [2].

A review of all global haplotypes listed at the website www.semargl.me [4], does not show one single person with a L232- marker (that is, lacking it but belonging to Q hg). So it is either very rare or, it is not tested for unless the individual is known to belong to the Q hg, in which case it is then tested for to define the haplotype.

Afontova Gora 2

Genetic tests were also done on remains uncovered at the Afontova Gora 2 site in Siberia, within the city of Krasnoiarsk on the banks of the Yenisei River (56° N 92&deG;51' W). These are also old (17 kya) human remains, and inital information on it indicated that it was Q1a1 [5][6]; these were later retracted and it was classified as R1 (perhaps due to contamination during handling).

If confirmed as carriers of Q hg, both men could point at hunter-gatherers belonging to minor lineages such as Q1a and its downstream branches in both Europe [7] and Siberia between 17 and 8 kya.

Amerindians in this context

Motala [6] if Q1a2 and Afontova Gora 2, if Q1a1, would both be closer to the root of the Q hg tree, more basal, than the Amerindians (with M3 marker) and other Scandinavians (L804 lineage). Meaning that they split earlier from the branch that later led to contemporary Scandinavians and American Natives.

The data on most of the Scandinavians (which lacks detail in many cases regarding haplotype markers) places them downstream from Q1a2 (further away from the root) together with some Siberian groups. Even further away from the root we find the Native Americans with M3 and a specific haplotype found in Scandinavians (those carrying L804, L807). [8][9][20] See the tree below.

Since the split originating the two haplotypes found in America: L54 (Q1a2a1) and M3 (Q1a2a1a1) has been dated to roughly 22 kya (see my previous post), then these other European haplotypes from Motala and Krasnoiarsk, which are closer to the root should then be much older than 22 kya. (and therefore older than the remains that have been sampled - 17 and 8 kya). This pushes far back in time, to a period contemporary with Neanderthals in Eurasia.

Link between Scandinavia and America

So we have two populations, one in America and another in Scandinavia which derive from a common root, Q1a2a1a, and which are separated by thousands of kilometers of "Siberia"; this suggests that they share a common origin in Siberia [10] and that they each moved on from this source into the areas where we now find them.

Since an earlier (closer to the root) split (L54) is also found in America, we could suppose that it reached the New World first, however (see my previous post) these L54 derived haplotypes are actually younger than the M3 ones!

Then we have the more basal Scandinavians, closer to the root, whose haplotypes are closer to those found in India, Pakistan and the Middle East (Q1a2*) as well as Afghanistan, Central Asia, Russia, Georgia and Germany (Q1a2b). These haplotypes have been dated as being only 2,200 - 2,150 years old, [11], far too young in my opinion and which clearly do not fit the tree! (perhaps the dates were adjusted so they could justify the Cimbrian theory -see my last post.

So, leaving the dates alone for the time being, let's follow the mutational trail: a mutation once acquired should not be lost, but as we have seen, Motala [6] has the L55 mutation of Q1a2a, which would place it at the same level as the two mutations mentioned in the previous paragraph (Q1a2 and Q1a2b), making it older than the other Scandinavian and Amerindian haplotypes mentioned further up (M3 and L804).

But it lacks the M232 mutation which is found in all Q haplogroup members. Why? Was it lost in a back mutation?

Probably: although back mutations (or reversions) are not common, they are known to happen [12], for instance in marker P25 which has mutated at least twice [13]. Are other markers similary unstable? Most likely. A reversion would explain why the M232 marker is absent in Motala [6] and place him in the Q1a2a hg. See tree below:

Q haplogroup tree, based on [20]. Copyright © 2014 by Austin Whittall

Dispersal

We know, as per mainstream orthodox theories, that the Q haplogroup first appeared in South Central Siberia (yellow star on map below) where it sprung from P hg. It then spread (red arrows) east and west (the pink regions are the current areas where it is found in high frequencies); it also spread southeast and southwest into India and the Middle East. Those going towards America took a northern route, close to the retreating glaciers, perhaps enticed by the good hunting grounds of the Siberian tundra.

Dispersal of Haplogroup Q. Copyright © 2014 by Austin Whittall

In this context then, we can envisage a split in the ancestral Q1a2a1 hg group, into two populations:

1. The future Scandianvian Q1a2a2 with the L804 mutation
2. The future Amerindian Q1a2a1 with the M3 mutation only found in America (and some Bering Asian natives - result of a back-migration from America into Asia).

This ancestral lineage Q(xM3) -the x stands for excluding- is found among the Khakass people in Siberia, south of Krasnoyarsk, with an average frequency of 4.8% (with maxima of 28% among the Butrakthy Sagais), clearly indicating that Q hg "is the most ancient one in Siberia... mark[ing] the Paleolithic human migration along the Boreal pathway... constitut[ing] a major part of the chromosome Y pool of the first migrants to Siberia in the early stages of human expansion to North Eastern Asia." [14]

Its eastern range extended into Europe, where it is found at relativley low frequencies:

Current frequencies of Q haplogroup in Europe

Notice that some studies yield 0% frequency while others show a higher rate (i.e. among Icelandic and Khantys), perhaps due to sampling bias. Also, some studies have not dug deeper into the different haplotypes so there are many blanks in the data:

• 0.0% Serbian, Croatia, Bosnia, Kosovo, Albania, Macedonia, [5] Greece, Bosnia -Croats, Bosnia-Serbs, Slovenia, northeast Italy, Hungary, Czech Republic, Poland, Georgia and Balkaria [15] Ireland, [16], Russia (Eastern European part - Arkhangelski, Kursk, Tver, Izhemski Komi, and Priluzski Komi) [17]
• 6.10% Hvar Island, Croatia (Q*-M242) [18]
• 0.71% Herzegovina. [5] (mentioned as Q-M242 only)
• 1.10 % Ukraine (Q M242) [15]
• 0.80% Moldavia (Q M242) [1]
• 0.10 - 1.60% Bulgaria Depending on the region: 0.1% Q-M25 and Q-M346; 0.2% Q-M378. Peaks of 1.6% and 1.3% Q-M378, in Lovech and Montana on the south shores of Danube River [19]
• 0 - 3.70% Russia, Siberia (Khanty) (Q1a2...) [17][21]
• 3.00% Faroe Islands [16] Matching Norweigan haplotypes
• 2.00% Norway [16]
• 0 - 7.00% Iceland [16][22]
• 3.00% Sweden [16], but has regions with higher frequencies -up to 22.2%- (See the map [9]
• Denmark, Haplotype distribution: [9]
  
  • 10%   Q1a2b
  •  8%   Q1a2*
  •  8%   Q1a2a1a2 (with L804 - 807)
  • 60%   Q1a2 60% (unspecified haplotype)
• 0.08% Sardinia (Q1a3c) [8]

The Amerindian link revisited

We tend to imagine Q haplogroup moving towards the West, into Scandinavia and from there, dispersed widely by the Vikings to the Faroe Islands and Iceland. But could it have reached Iceland and Europe from the West? That is, from America, and spread East?

The Icelandic sagas of the Vikings mention the hostile encounters between the Norse and the "Skraelings" (Native Americans), making it unlikely that they mixed. However, in the Greenland colony the ancestors of the Innuit (Thule people) may have wed widowed Viking women, incorporating their Q hg into the local population which later reached the Scandinavian mainland and Iceland after their return in the XV^th century when they abandoned Greenland.

We would have to screen Innuit for the Q haplotypes found among Scandinavians to answer this. It is a possible explanation. Perhaps it is even older than the Vikings, and reflects the admixture of small party of archaic Innuit paddling across the fringes of the Arctic ice cap and reaching Scandinavia, where they mixed with the locals. But this would be unlikely due to the small size of the kayaking Innuits in comparison to the locals and would have minimized the impact of their Y chromosome in the Scandinavian population.

By the way, there is also a circumpolar C1 mtDNA haplogroup prevalence, one that links America (where it is found at very high frequencies), Siberia, Iceland and Northwestern Eurasia... which may be tied to the archaic Innuit Y chromosomes, or may indicate that those who carried them, once lived in this area surrounding the Arctic, but prevailed in the Americas.

The Neanderthal link

But, going full circle and returning to my opening comments, after looking at the map above I keep on thinking that there must be some link between Neanderthals and haplogroup Q.

The map is shaded with a yellow color in the territory once occupied by the Neanderthal at the time modern humans began their supposed Out Of Africa migration. The Altai source for hg Q in one of Neanderthal's known sites, is intriguing.

It would also explain its presence at low frequencies in Europe, its predominance in America, where Native Americans carry a high proportion of Neanderthal ancestry, and account for its very old age and wide range across Eurasia, underlying more recent "modern human" lineages. It may also account for the mtDNA C1 haplogroup found in the same regions.

But this will be the subject of another post.

Sources

[1] Varzari A, Kharkov V, Nikitin AG, Raicu F, Simonova K, et al. ,(2013). Paleo-Balkan and Slavic Contributions to the Genetic Pool of Moldavians: Insights from the Y Chromosome. PLoS ONE 8(1): e53731. doi:10.1371/journal.pone.0053731
[2] Lazaridis, I. et al. (2013), Ancient human genomes suggest three ancestral populations for Europeans. biorxiv.org, pre-print online 23 December 2013.
[3] Mark Jobling and Chris Tyler-Smith., (2003) The Human Y chromosome an evolutionary marker comes of age. Vol 4. Aug. 2003, p598 www.nature.com/reviews/genetics
[4] www.semargl.me
[5] Y-SNP calls for Afontova Gora 2. Genetiker. May 2014
[6] Source: See first column under AF2
[7] Europedia. Geographic spread and ethnic origins of European haplogroups.
[8] Paolo Francalacci et al., (2013). Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny. Science 341, 565, DOI: 10.1126/science.1237947
[9] Svenska Haplogruppdatabasen
[10] Danish Demes, A Regional DNA Project for Danish Americans and Danes around the World
[11] I. Rozhansky, (2010). Riddle of the Cimbri. Experience the historical and genealogical investigation. Proceedings of the Russian Academy of DNA Genaology, v.3., p. 545 (Russian language)
[12] Jennifer F. Hughes and Steve Rozen, (2012). Genomics and Genetics of Human and Primate Y Chromosomes. Annu. Rev. Genom. Human Genet. 2012.13:83-108. 10.1146/annurev-genom-090711-163855
[13] Adams SM, King TE, Bosch E, Jobling MA., (2006). The case of the unreliable SNP: recurrent back-mutation of Y-chromosomal marker P25 through gene conversion. Forensic Sci Int. 2006 May 25;159(1):14-20. Epub 2005 Jul 18.
[14] V.N. Khar’kov et al., (2011). Genetic Diversity of the Khakass Gene Pool: Subethnic Differentiation and the Structure of Y Chromosome Haplogroups. Molekulyarnaya Biologiya, 2011, Vol. 45, No. 3, pp. 446–458.
[15] Battaglia V, Fornarino S, Al-Zahery N, Olivieri A, Pala M, et al. (2009) Y-chromosomal evidence of the cultural diffusion of agriculture in Southeast Europe. Eur J Hum Genet 17: 820–830. doi: 10.1038/ejhg.2008.249
[16] Allison Mann., (2009). Vikings, Merchants and Pirates at the Top of The Wold: Y-Chromosomal signatures of recent and ancient migrations in the Faroe Islands, Thesis Univ. of Louisville. Table 3, pp. 27
[17] Sheyla Mirabal et al., (2009). Y-Chromosome distribution within the geo-linguistic landscape of northwestern Russia. Eur J Hum Genet. 2009 October; 17(10): 1260–1273. doi: 10.1038/ejhg.2009.6
[18] Saric T, An Asian trace in the genetic heritage of the Eastern Adriatic Island of Hvar. International Society for Applied Biological Sciences Abstract number: ABS-282-ISABS-2013
[19] Karachanak S, et al,. (2013). Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry. PLoS ONE 8(3): e56779. doi:10.1371/journal.pone.0056779
[20] Y-DNA Haplogroup Q and its Subclades - 2014. The International Society of Genetic Genealogy.
[21] Ville N Pimenoff et al., (2008)., Northwest Siberian Khanty and Mansi in the junction of West and East Eurasian gene pools as revealed by uniparental markers. European Journal of Human Genetics (2008) 16, 1254–1264; doi:10.1038/ejhg.2008.101
[22] The Shetland Y-DNA Surname Project www.davidfaux.org

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

On the Q haplotypes in Europe (Part 1)

Y chromosome haplogroup Q is always mentioned as being prevalent among Native Americans and used as proof of their Asian origin because some minor Asian groups also carry the same haplotypes found in America. With this incorrect generalization one would assume that it is the most recent haplogroup as it is carried by the latest group of humans to people a continent: Amerindians.

Actually Q is found not only in America, but also in Southeastern Asia, Papua New Guinea, the Indian subcontinent, the Middle East, Western Asia, the Middle East and all across Europe. This is rather striking since it is portrayed as a relatively young haplogroup but has the most extended global dispersion: from Cape Horn in Tierra del Fuego on the southernmost tip of South America, to Scotland and Iceland in Europe, to Sri Lanka, Sicily, Sweden and Israel.

This post will look into the European Q haplotypes since some of them are closely related to those of Amerindians.

The origin of European Q haplogroup

The map below shows that hg Q is found in central Europe between an imaginary line that joins Marseille with Hambourg and another joining the Black Sea with Finland. It encompasses large portions of Scandinavia with in pockets in the UK, Iceland, Sicily, South Western Iberia, Cotentin, Dalmacia and South Sardinia. The voids are interesting too, it is absent from most of Western France, Spain, Italy, the Balkans and Slovenia, Belarus and central-western Poland.

Map showing the frequencies of Q haplogroup in Europe. Copyright © europedia.com

The "hot spots" are found in Scandinavia, South Sicily and the Rhone Valley in France. Why?

Several theories have been put forth to explain the distribution of an "Asian" haplogroup in European soil, and all must somehow explain how the Q hg got from Asia to Europe, to do so different dispersal "agents" originating in Asia are proposed:

• The Huns
• The Cimmerians - Cimbrii
• The Mongols

Let's look into the different options

Huns

The only contemporary written record on their origin was penned by Ammianus Marcellinus (IV^th century CE), who reported them [1] in Ukraine, clashing witht the Alans along the Don and then uniting them into a coaliton to invade Western Europe.

The Huns were nomads which came from beyond the Sea of Azov and moved towards the Danube around 150 CE.

After defeating the Alns, they raided the Roman Empire and the territories of the Barbarian Germanic nations that surrounded it (territories of the Goths, Taifalia and Sarmatae).

Their conquests spanned the Danube and their most known leader Attila was defeated in the battle of Catalunian Plains (or Battle of Chalons) in 451 CE, bringing an end to the hunnic "empire".

The descriptions that the Romans made of them clearly point to a prevalent Mongoloid strain, but how strong it was, is a mystery.[2] Furhtermore, the scant 300 years (roughly 10 generations)during which they dominated central Europe would not admit great admixture into their vassals or enemies. Furthermore, many of their soldiers were exterminated [2] after their defeat by the Romans, during the two Goth wars that ensued, and those that survived would have quickly melted into the original inhabitants of the lands they had formerly conquered, admixing into them.

The argument behind the Hun Q haplogroup admixture in Europe goes like this: as they were Asians, from central Siberia, apart from other haplogroups, they also carried the Q hg in them. This explains the presence of Q hg in the areas formerly occupied by the Hunnic Empire (central Europe); it is also found in Provence / Burgundy because many huns settled there after their defeat at Chalons. Furthermore, the Huns supposedly employed Scandinavian (i.e. Goth and Heruli) warriors and many Huns marched north with them after being beaten by the Romans, dispersing their Y chromosomes in that area.

The Norse peoples (Vikings, Normans) descended from this admixture later spread the hunnic Q hg widely when they raided Europe (ca. 900 CE): this explains its presence France (Cotentin - Normandy), Great Britain (Danelagh), Sicily (conquered by Normans in 1091 CE) and, as they went across the Atlantic, in Iceland, the Shetland and Faroe Islands.

Another theory is outlined below:

Cimmerians or Cimbri

The Cimmerian culture was centered in Crimea (a current Russian -Ukrainian hot spot) and Kerch, on the northern coast of the Black Sea, and around the Sea of Azov about 3,000 years ago. It was born from different ancestral roots: One was local, Ukranian, originating in the Belozerka culture; another was the Koban culture of Caucasian origin, and yet another, linked with the Ananino Culture from the Volga - Kazhan area. Finally people from further East (Ordos region). [3]

Remains of their bimetallic daggers, horse bits and arrowheads have been found across a vast region of Eastern and Central Europe (see the brown area in the map below).

Dispersal of the Cimmerian - Cimbri in Europe. Copyright © 2014 by Austin Whittall

The oldest written record on them, is from Homer, in his Odyssey (ca. 8^th century BCE), [4], he imagines their territory as wild: "where is the land and city of the Cimmerians, wrapped in mist and cloud...", set on the northern shores of the Black Sea.

Greek historian, Herodotus, [5] (ca. 484–425 BCE) also wrote about the savage Cimmerian invasions in Asia: reporting that the Cimmerians were forced to migrate from their homeland, pushed by the Scythian nomads (pressed in turn by the Massagetai).

The Scyths were Asians, which after crossing the Araxes (Volga) River invaded Cimmeria ca. 713 BCE, causing them to flee in two directions: One group invaded Asia Minor (Phrygia) and settled in Sinope on the northern coast of Turkey. Another marched west after a fratricide battle on the shores of the Dniester (Tyras) River and then entered Thrace.

Herodotus reports their plundering raids on Ionia (675 or 695? BCE) during the reign of Ardys; and they also captured Sardis. It was later, ca. 600 BCE, that they were repulsed from Asia Minor by Ardys' son. [5]

Despite the Scyths, some Cimmerians remained in their homeland, by the Sea of Azov (Lake Maeotis). Pliny [6] quotes Greek poet Philemon (362 – ca. 262 BCE) when he says that they called their "ocean" Mori Marusa or, "Dead Sea" (either Azov or Black Seas). Some sources [7] incorrectly assume that this is the Baltic Sea, but, as we will see below, they are mistaken.

These Cimmerians from the Chersonesus (Crimea) several centuries later, sent an embassy to Emperor Augustus in Rome with gifts, to ask for pardon for their raids one century before (Plutarch [8] and Strabo [9]).

But the largest part of these people, had migrated from their Crimean home and lived in the wooded lands of Central Europe, along the Danube River and at the sources of the Elbe and the Vistula rivers, which they settled long before the appearance of the Germanic tribes. [10] They were considered Celtic people and they took part in the attack upon Delphi in Greece (279 BCE) allied with the Illyrians, but were defeated. [12]

After five centuries in central Europe and Thrace, they moved once again invading the Roman Republic in 113 BCE.

The Romans at that time occupied the coastal areas around the Mediterranean sea (green in map below), they ignored the homeland of these barbarians who " sallied forth against Italy, being called at first Cimmerians, and then, not inappropriately, Cimbri." [8]. Their twelve year campaing ended in defeat, and they retreated to the north, deep within the forests, into Jutland, which is now Denmark, where, according to Strabo [9] they occupied the country west of the Elbe. A map by Claudius Ptolemy (ca. 90 – ca. 168 CE) that is, roughly 220 years after their invasions, places the land of the Cimbri at the northernmost tip of Jutland.

Their campaign would explain the presence of their Q hg across the central parts of Europe. Its later dispersion from Denmark into Scandinavia and the rest of Europe would be identical to the "Hun's Q hg dispersal" already mentioned above. The presence of Cimbrian Y Chromosomes in the Valley of the Rhone belonged to the refugees escaping the defeat at Vercelli, crossing the Alpine passes into current Savoy and Haute Rhone. Or (chose your option): (1) the survivors of the Cimbri garrison that remained in Belgium (who later became the Aduatuci), after their defeat by Julius Caesar in 57 BCE (most were killed or sold as slaves). (2) Later moves towards the south (400 CE) of the Burgundians from Scandinavia, to current Poland, and finally to France, bearing Cimbrian admixture in their genomes.

An interesting paper (I. Rozhansky, 2010) [11] views the Cimbrians as carrying different haplogroups in their genome, but after being subjected to a bottleneck (the battles against Rome), male lineages were reduced and only a small part of it reached the Jutland refuge after a 1,700 km march. Their long settlement there (100 BC - 400 CE) subjected them to further genetic drift yielding two haplotypes of Q1a3 unique to Scandinavia which date back to a common ancestor 2200 - 2150 ya. (coincidental with the date of the Cimbrian Invasions).

Next, the least likely origin for Q hg in Europe:

Mongolians & Tartars

The Mongol hordes employing cavalry and gunpowder advanced West (1235) and occupied the Russian principalities. They continued their advance into Poland, Hungary and Serbia, defeating all forces of armored knights that faced them. The death of the Great Khan and perhaps the dense forests and fortified castles of Western Europe stopped their advance in 1242. They conducted ther invasions until 1295 into Thrace and Poland, but finally retreated East. Their "Golden Horde Empire" later declined and fell prey to civil war.

The recency of this invasion (800 years ago) and the lack of penetration into areas where we currently find Q hg (Scandinavia, England, France), makes it an extremely unlikely vehicle for the introduction of it in Europe. Furthermore, they did not settle the land, they returned back to their Asian homes.

Above I have outlined the theories that try to explain how Asian Q haplogroup ended up in Europe. Personally none of them satisfy me. I find them too recent in comparison with the "sister" branch that entered America over 15 kya. Furthermore the low frequency but wide coverage of Q hg in Europe hints at an ancient origin: the other "latecomers" (in the sense of their later branching-off the P hg root), such as Hg N and R - with all its haplotypes, have covered the same territory with a higher frequency, overlaid on the archaic Q hg substrate. But this will be the subject of my next post.

Read the second part: An Ancient Dispersal

Sources

[1] Ammianus Marcellinus XXXI, 2, 12 The Roman History of Ammianus Marcellinus
[2] Otto Maenchen-Helfen, (1973). The World of the Huns: Studies in Their History and Culture. University of California Press
[3] Gocha R. Tsetskhladze, Ed., (2001). North Pontic Archaeology: Recent Discoveries and Studies. Brill, 2001
[4] Homer, Odyssey 11:14
[5] Herodotus, History, Translated by Rawlinson, George, Blakeney, Edward Henry. London, Dent. 1919. [1:1,6] [1:8,15][4:9,11 - 13]
[6] Pliny, 4:13
[7] David K. Faux, (2011). The Cimbri of Denmark, the Norse and Danish Vikings, and Y-DNA Haplogroup R-S28/U152 - (Hypothesis A)
[8] Plutarch, The Parallel Lives . Vol. IX, 11, Loeb Classical Library edition, 1920
[9] Strabo Vii. 293. 294 pp
[10] Anthon Charles, 1872. A classical dictionary... Harper. pp. 539.
[11] I. Rozhansky, (2010). Riddle of the Cimbri. Experience the historical and genealogical investigation. Proceedings of the Russian Academy of DNA Genaology, v.3., p. 545 (Russian language)
[12] Appian's Roman History. Vol II, pp 59

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

Y Chromosome mutation rates

In my previous post I pointed out the differences found between the ages of different branches of the Y chromosome's Q haplogroup, and how papers tend to date Native American lineages so that they coincide with the date that mainstream science considers the correct one for peopling America: ca. 15 kya.

This made me wonder what certainty do we have of their accuracy, or how precise are these dating methods. The answer is surprising!: not very precise.

The complexity encountered in dating Y chromosome lineages is summarized very well by Chuan-Chao Wang and Li Hui (2014): "... Different time estimation methods use different algorithms and assumptions, thus alternative methods probably fit more or less well with sequence data in time estimations. In addition, the best-fit mutation model might vary for different STRs... some specific lineages might have their own unique best-fit STR mutation rates for time estimation." [4]

In other words, it is extremely fuzzy. Today's post will look into the issue of "dates", the calculations of haplogroup ages, of TMRC, and the fallacy of a "clock" behind Y chromosome mutations.

The complexities behind the Y chromosome

The Y chromosome is particular because it is passed along from father to son, basically unchanged -excepting random mutations- in a long line that links all modern men to an "ancestral Adam" who lived in Africa in the distant past of mankind and from which all Y chromosome haplogroups derive.

Y is one of the sex chromosomes found in mammals, and obviously, humans; the other is the X chromosome. An X chromosome and a Y chromosome ("XY") pair detrmine a male, a double X ("XX"), a woman.

Just like all other chromosomes, the Y chromosome also mutates: chance mutations and natural selection act upon it and create small differences that, if not negative (that is, killing its carrier), are passed on to the next generations.

Y chromosome's high mutation rates

The Y chromosome mutation rate is much higher than that of autosomes because it is restricted to the male germ line, and there, most cell divisions occur by meiosis [1]: Sperm is formed in a process of cellular division known as gametogenesis, inside the testis, and it is during this process, where mutations may take place in a way that can affect the future generations (if a Y chromosome in any other cell of the body mutates -i.e. a cell in the liver-, it will have no impact on the offspring of the bearer of the mutation).

Men produce sperm from pubrerty to death, while women are born with a given number of ovum one of which matures monthly from puberty till menopause. This means that sperm are subjected to many more rounds of cell divisions and may accumulate more chance mutations. If the men are older, the chances are even higher.

Unlike the X chromosome, excepting small regions at the telomers (tips), the Y chromosome cannot undergo recombination (where mutated parts are replaced with other "healthier" ones). This means that most of the Y chromosome (95% of it) forms a non-combining region where Single Nucleotide Polymorphisms (SNP) mutations accumulate without being "repaired".

This non-recombining situation arose because X and Y chrmosomes do not recombine among each other (as do the X chromosome pairs in women), to preserve them from gaining harmful genes from the opposite sex. Allowing Y chromosome to preserve male-specific genes.

These mutations allow geneticists to trace lineages and paternity by comparison. They would also allow calculating the age of lineages by comparing differences that accumulated in each line and the rate at which they accumulate. But this is easier said than done.

Calculating ages of Y-chromosome lineages

The key element in dating lineages or haplogroups is to know the mutation rate, and there are basically two methods for calculating it:

I. Direct Measurement or Pedigree estimates: Take two individuals, related by descent and identify the mutations in their Y-chromosome. As the time span that separates them is known (either in years or in generations), the mutation rate can be calculated directly. (it is a value given in: mutations per nucleotide per generation).

The direct measurement (Yali Xue et al., 2009) [1] of the substitutions in the Y chromosome of two related men, separated by 13 generations gave a "mutation-rate measurement of 3.0 × 10^-8 mutations/nucleotide/generation... 1.0 × 10^-9 mutations/nucleotide/year " [1].

The published human-chimpanzee comparisons are "2.3 × 10^-8 – 6.3 × 10^-8 mutations/nucleotide/generation... depending on the generation and split times assumed" [1].

The uncertainty is highlighted by the very ample confidence interval values (95% CI) 8.9 × 10^-9 – 7.0 × 10^-8 mutations/nucleotide/generation obtained.

II. Evolutionary estimates: they use STR polymorphisms or Microsatellites (defined by SNPs). These can be easily genotyped. So taking the microsatellite variation within Y chromosome lineages and knowing the historical dates of certain key events in these lineages history, a mutation rate can be calculated.

As an example, I will folllow the very cited paper by Zhivotovsky et al., (2004) [2], which has a lot of assumptions, plenty of formula and maths. I am an engineer and love maths, but I will spare you the details. Those interested can check the paper (see Statistical Analysis in [2]).

The calculated average "effective mutation rate" (w), was between 0.000312 and 0.000454 per 25 years for Polynesians and Gypsies respectively, however (and these are the things that surprise me!), these values are "adjusted" because they were considered underestimates. The correcting factor ASD₀ or average squared difference was applied and voilá, a mutation rate w of 0.000705±0.000332 and 0.000725±0.000187 is obtained for Maori - Cook islanders and Bulgarian Gypsies respectively.

As can be seen the "adjustment" roughly doubled w (it increased 2.25 times in Polynesians and 1.59 times in Gypsies). Furthermore, the error bars are enormous (47% and 26% for each population).

These two values and another one estimated for "global" loci were then averaged resulting in the "magic number" most quoted, cited and used in current genetics papers: "an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9×10-4 per 25 years" [2].

Different mutation rates

As we can see the values calculated with each method (Pedigree and Evolutionary) are very different, and applying them to calculate ages of lineages will give very differing results.

Being an engineer with a scientific point of view, I believe that the real values are those that are measured, and that the theory should provide a good model that explains reality and sets of equations or formulae that can be applied with some simple parameters to obtain results that are very similar to reality.

The "laws" of mechanics are used because they are a reasonable model that fit the every day world and gives accurate predictions and practical results (you can design a car or a plane to withstand stress and accelerations, calculate the trajectory of a missile with precision, etc). But when it comes to "laws" in genetics, it seems things are much more blurred and lack precision.

Let's look at possible factors that may explain these differences in mutation rates:

• Frequent mutations might occur within the few generations used in pedigree studies, while slowly mutating loci only become significant over a longer time interval. [2]
• Evolutionary calculations use statistics of current variation which include reverse mutation of old alleles as well as forward mutation to new alleles; and these reverse mutation would reduce the number of alleles. On the other hand, Pedigree estimates count mutations on a per-meiosis basis so reversals are counted as new alleles. [2]

I would add that the mechanisms working here are not clearly understood so the model fails to replicate reality.

Factors that distort the estimations

Software and assumptions

Another factor to take into account when calculating the age of different haplotypes are the assumptions behind the calculations.

Modern geneticists employ software that runs simulations (i.e. rho statistics with Network, Bayesian analysis with Batwing), which are fed with these assumptions: weight assigned to different STR variants, exclusion of certain loci (those considered ambiguous or with multi nucleotide repeats), generation time, population sizes, mutation rates (which as seen above are also shrouded in uncertainties), and "others". [3]

Among these "others" are the assumptions that, after populations split, no further migration occurs between them, [3] or, for instance, that there is an exponential growth from an initally population with a constant size "N" [4]. These may not be true, as we will see below, together with other causes

Evolutionary Rate and Repeat unit size

Evolution rate is lower for STRs that have an increased repeat unit size (that is, "n" has more nucleotides).[6][7] In other words, penta or hexa nucleotides mutate slower (3.45 x 10^-4 per 25 year generation) than tri or tetra markers (6.9×10^-4 per 25 years -the figure given by Zhivotovsky et al., (2004) [2]). [7]

This is because (Dupuya et al., 2004) [8] there are "relatively more gains in short alleles and more losses in long alleles.". [8]

These mutation rates yields different coalescence dates for haplogroups; for instance the age estimate for haplogroup CF clade based on tri/tetra marker results is 42.2 ky which is much lower than 64.7 ky estimated with penta/hexa markers. [7]

The fact that mutation rate depends on allele size means that the different haplogroups (which are characterized by different and specific STRs) will mutate at different rates when compared to each other. [8] Yielding incorrect coalescence dates when compared.

More Factors that influence Y chromosome estimates

When comparing mtDNA timelines (these are based on women) and the male Y chromosome datings, differing patterns appear. These are due to:

1. Genetic drift. It acts strongly upon Y chromosomes: many males don't have sons (they may have only daughters, or die before reproducing) so their Y chromosome is not passed on, and is lost from the gene pool, reducing diversity. [9]

2. Polygyny (having more than one wife at a time) This custom would lead to a small number of males to spread their genes (including their Y chromosome) among a disproportionately large number of children. While others are excluded from the reproductive cycle and their Y chromosomes are lost. [9]

In our recent evolutionary past, humans lived in polygynous, extended families. Where male longevity (>50) would allow them to reproduce up to high ages via younger women, situation which is not found in monogamous societies where menopause effectively cuts off older men's reproductive cycle. Older male sperm may also accumulate more mutations than younger sperm, adding more diversity to the gene pool.

3. Lower effective Male Population Size. The higher Male mortality Rate and the reproductive sucess of males (i.e. due to polygyny) are factors that reduces Y chromosome diversity in populations compared to mtDNA and autosomes. [9] This is seen in the higher level of X chromosome (females) variability compared to that of Y chromosome (males). [10]

In their estimate, Zhivotovsky et al., (2004) [2] consider male and female population as equal, but they are not. And this influences the data on ratio of variance at Y chromosome STRs to that of autosomal STR loci. This ratio varies from 1.14 in "sub-Saharan African hunters" to 0.51 among "American farmers" (the global average is close to 1); and this is due to less males per female in the latter population. This lower ratio leads to a lower mutation rate.

4. Migration. Is an important cause of gene flow within a population. It will lead to overestimation of the accumulated STR variance used in evolutionary calculations.

If migrants admixing with a population are of the same haplogroup they cannot be told apart from the original population, so mutation rates would be overestimated for the admixed population.

The gender mix is also important: if more men migrate than women, this will influence the Y to autosomal STR variance as discussed above. [2] Patrilocality (the residence of a newly married couple with the husband's family or tribe) and Matrilocality (the opposite situation) also alters mtDNA to Y chromosome variance.

5. Generation times. "In present-day hunter-gatherer societies generation time is estimated to be approximately 32 and 26 years for males and females, respectively" [11] which is different to the 25 years postulated by Zhivotovsky et al., (2004) [2]. It may seem trivial but if a generation is 32 years instead of 25, the estimates will vary considerably 10 ky can actually mean 12.8 ky. Historical generation times as calculated by pedigree estimates may be very different from those of our evolutionary past.

My next post "Generation time is not 25 years", gives some sources and data to prove it is at least 30 years for males.

6. Variation in founding populations. The Y-STR variation of the founding population at time of arrival in a geographic region is taken into account in evolutionary estimates [2], if variation is lower, the mutation rate will increase and, for higher variation mutation rate will be lower. So if the founding male population has a substantial diversity it will lead to an incorrect (lower) divergence time calculation. [2]

7. Positive Selection. Natural selection also acts upon men, and will increase frequency of a given lineage if it is more benefical for those carrying it. [9] Or, may I add, it will also benefit Y chromosomes piggybacking on individuals with some other allele favored by selection.

8. Expansion and bottlenecks. Genetic diversity between two populations that shared the same original genetic structure may be due to expansion of one of them: because random mutations will arise more frequently in a larger population simply because there are more sperm cells in which they can arise. This will increase the diversity of the larger population. [9]

A bottleneck will have exactly the opposite effect: a paucity in genetic diversity of the decreasing population as lineages become extinct. [11]

Amerindians

When considering Native Americans we must look back towards their Paleo-Indian ancestors and see how some of the assumptions mentioned above apply to them:

They were not small isolated groups with a closed-shared ancestry. Instead they were dinamic groups that had fluid contacts and exchange between each other and their ancestral populations back in Asia. [12]

They were not a "neutral" system where mutations accrete regularly, they were instead subject to positive selection, war, disease, famine which modified the clock's rate of ticking. [12]

Last but not least is the sampling bias when studying populations. Most are not drawn in a random manner from large populations. Instead they come from tiny samples from small villages where the groups are mostly composed by relatives with shared ancestry. This of course modifies the basic premises of coalescent methods and leads to shorter coalescence times than the actual ones.

Another factor is that the current genes found in a population may not actually represent the historic or even the prehistoric mix of that population [12]. Amerindians suffered a severe bottleneck after the discovery and conquest of America (after 1492 CE) which wiped out many lineages (who knows how many Y chromosome or mtDNA haplogroups disappeared during this period?).

Anzic-1 remains

The remains of a Clovis youth from Montana, US (Anzic-1), which are 12.6 ky old, were typed (Rasmussen et al., 2014) [5] and found to belong to Q-L54*(xM3).

The paper indicates that they then calculated the date of divergence between haplogroups Q-L54*(xM3) (Anzic-1) and Q-M3 of contemporary Native Americans. It is a simple rule of three calculation:

They notice that Anzic-1 had 12 traversions (mutations) while modern ones have on average 48.7, then these 36.7 additional traversions must have arisen during the 12,600 years that elapsed between Anzic-1's death and today: so 12.6 x 48.7 ⁄ 36.7 = divergence date, which happened 16.72 kya.

Of course, to make it statistically neater for the paper, they then "implemented a Poisson process model for mutations on the tree and used the constrOptim() function in R to compute a maximum likelihood TMRCA estimate of 16.9 ky. We then repeated this for 100,000 bootstrap simulations to yield a 95% confidence interval of 13.0–19.7 ky." [5]. The outcome ratified their previous simple calculation.

Below is part B of their Extended Data Figure 2: [5]

Fig 2. Adapted from [5]

The figure's original caption reads: "Each branch is labelled by an index and the number of transversion SNPs assigned to the branch (in brackets). Terminal taxa (individuals) are also labelled by population, ID and haplogroup. Branches 21 and 25 represent the most recent shared ancestry between Anzick-1 and other members of the sample. Branch 19 is considerably shorter than neighbouring branches, which have had an additional ~12,600 years to accumulate mutations."

Cross checked and doubts

I checked this value using the transversions indicated in their figure.

So I took the values in brackets and added them up for each individual, the sum is shown on the far right in green (Q-M3 individuals) and red (Q-L54 ones). At the top is an example of the calculation. The sum is referred to the split that takes place at branch 26 (marked with the vertical green line).

As an example individual at branch 0, MXL NA19682, has 8 + 2 + 8 + 3 + 21 = 42 transversions.

For Q-M3 individuals I calculate an average of 40.33 extra transversions in moderns vs. Anzik-1 and an age of 17.96 ky. Using only the Q-L54 individual's values the average is 44.3 transversions and the age is 17.29 ky, using all modern values the figurs are 41.54 transversions and 17.72 ky. They differ slightly from the 16.9 calculated in [5].

Weird Maths or incorrect assumptions

The odd thing is that when the same methodology is applied to the Saqqaq remains (Branch 27), the age estimation goes awry!:

The paper mentions the Palaeo-Eskimo Saqqaq "sequence had a relatively high missing rate of 0.24 and is divergent with respect to the other hgQ lineages in the sample, its singleton branch should more properly be considered to be of length 71 (54 / 0.76) transversions" [5].

So when we take the age of Saqqaq (4 ky), its transversions from the root at the split of branch 28 (which are 71), and calculate the amount of transversions for modern samples (by adding the 31 that correspond to branch 26, to the previously calculated figures), we obtain an average for all moderns of 72.93 transversions, so the difference that accumulated over 4,000 years is only 1.93 transversions, which leads to: 4.0 x 72.93 ⁄ 1.93 = divergence happened 152 kya! Yes, one hundred and fifty two thousand years ago.

Furthermore the distance in transversions from the baseline (the green line in the figure above) ranges from 26 (on branch 3) to 52 (on branch 12), that is, twice the amount. But all belong to modern human populations, why would one group accumulate twice the quantity of transversions than another? the difference of 26 is 26/36.7 = 70.8% of those accumulated by Anzic-1, and if we apply the same criteria 0.708 x 12,600 y = 8,926 years should separate these populations. But no, they are contemporary. In other words, the amount of transversions does not reflect age as a direct proportion.

This clearly indicates that better calculation methods for Y chromosome lineage dating are necessary.

Subjects for future posts: no Y chromosome from Neanderthals is found in modern humans. Did Q haplogroup originate in America?. Where did the Q hg found in UK and Scandinavia come from?

Sources

[1] Yali Xue et al., (2009). Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree. Curr Biol. Sep 15, 2009; 19(17): 1453–1457, doi: 10.1016/j.cub.2009.07.032
[2] Lev A. Zhivotovsky, et al., (2004). The Effective Mutation Rate at Y Chromosome Short Tandem Repeats, with Application to Human Population-Divergence Time. Am J Hum Genet. Jan 2004; 74(1): 50–61. doi: 10.1086/380911
[3] Matthew C. Dulik, et al., (2012). Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet. Mar 9, 2012; 90(3): 573. doi: 10.1016/j.ajhg.2012.02.003
[4] Chuan-Chao Wang and Li Hui, (2014). Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates. bioRxiv posted online May 3, 2014. doi: http://dx.doi.org/10.1101/004705
[5] Morten Rasmussen, et al., (2014). The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (13 February 2014) doi:10.1038/nature13025
[6] Mari Järve, Lev A. Zhivotovsky, et al., (2009). Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit. PLoS One. 2009; 4(9): e7276. doi: 10.1371/journal.pone.0007276
[7] Järve M, Zhivotovsky LA, Rootsi S, Help H, Rogaev EI, et al. (2009). Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit. PLoS ONE 4(9): e7276. doi:10.1371/journal.pone.0007276
[8] B. Myhre Dupuya, M. Stenersena, , A.G. Flønesa, T. Egelandb and B. Olaisena, (2004). Y-chromosomal microsatellite mutation rates: differences in mutation rate between and within loci. International Congress Series 1261 (2004) 76 – 78 doi:10.1016/S0531-5131(03)01791-6
[9] Cuan-Chao Wang, Li Jin, Hui Li1, Natural selection on human Y chromosomes. arxiv.org
[10] Michael F. Hammer, Fernando L. Mendez, Murray P. Cox, August E. Woerner, Jeffrey D. Wall, (2008). Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity. PLoS Genetics doi:10.1371/journal.pgen.1000202
[11] Labuda D, Yotova V, Lefebvre J-F, Moreau C, Utermann G, et al., (2013). X-Linked MTMR8 Diversity and Evolutionary History of Sub-Saharan Populations. PLoS ONE 8(11): e80710. doi:10.1371/journal.pone.0080710
[12] Peter N. Jones, American Indian mtDNA, Y Chromosome genetic data and the peoping of North America, Bauu Institute, 2004.

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

Out of America (into Asia)? Part 2

On the Y-Chromosome Q haplogroup

 

TThis is the second part (See First Part here) of my ramblings on a possible Out of America migration back into Asia.

I will carry on from where I left off: (Summary) some Asian (specifically Northern, Central and Northeastern Asians - from Siberia, NE China and Mongolia) have a small but noticeable content of specific genes of Amerindian content. Mainstream science has it that these Asians descend from the people that were also the ancestors of Amerindians therefore they do carry some of the same genes.

I posted that the Turkic people moved out from the Altai spreading West towards Europe and North, Northeast into Siberia (Sakha or Yakuts, Kets and Selkups) and that they probably admixed there with aboriginal Siberians who in turn had an American admixture due to an Out of America gene flow.

I pointed out tha the Kets have the highest frequency of Y chromosome haplogroup Q (Q hg) in all of Asia (93.7%), which is only found among Amerindians; The Selkups have the second-highest frequency of haplogroup Q (Q hg) in Asia (66.4%).

Other groups, Tuvans, Oroqen, Mongols, Hadza and Daur carry a much lower Amerindian content and is very likely due to admixing with the other Siberian peoples.

The Y-chromosome Q haplogroup (Q hg) mentioned above is very interesting due to its strong preponderance in the Americas. Could it be a signal of an Out of America back-migration into Asia?

The Y-Chromosome haplogroups in America

Global distribution of Q Y-Chromosome haplogroups

A paper analyzing American and Asian lineages of Y-Chromosome (Battaglia V., et al., 2013) [2] notes that of the two founding lineages of Y-chromosome found in America, (C and Q), Q is the oldest and most widespread (with 75% frequency), while C, is limited to North America and found at a lower frequency . This means that Q haplogroup (Q hg) reached America first and spread from Alaska to Tierra del Fuego, C hg is a later arrival.

Q haplogroup is found in two main lineages in America: Q1a3a1a-M3 (76.8%) and Q1a3a1-L54* (16.7%). It is however interesting to point out the great diversity of Q hg in America: another 8 haplotypes have been discovered, mainly found among Peruvians and Mexicans, and they add up to 6.4% frequency, much greater than the diversity found in Siberia. [2]

The M3 part of Q1a3a1a stands for the M3 marker which is believed by mainstream geneticists to have arisen in Beringia, except for some extant Far Eastern Siberians (it appears among Koryaks at a frequency of 40%) [2] it is only found among Native Americans. Its presence among Koriaks (see image below for Q1a3a1a* red and blue square) is believed to be "... the result of a back migration rather than be direct M3 Beringian descendants... [and] could also be due to recent contacts (gene flows) with modern northern Native Americans." [2] .

An alternative explanation could be that M3 originated in Asia and those that took it into America survived, while the Siberians that carried it, passed away without descent.

The other marker L54, is definitively American (with a higher frequency in Mexico and Central America and lower elsewhere), none were found in the "populations living along the entry route to the Americas" [2] , and "only a potential Q-L54* has been observed in one Chukchi from Northern Siberia" [2], the paper cautiously points out that "any interpretation of this result (new Asian lineage, remnant of an ancestral state, trace of forward or back-migration) is premature..." [2].

Eastern and Southern Siberian peoples, Mongolians from the Altai Region in Western Mongolia and southern Ataians are definded by the Q1a3a1c sub-clade defined by the L330 marker. Asian upstream intermediate is L53* is found in Northern-Altai and Mongolia, at very low frequencies.

The paper concludes that the Altai Mountains were the southern barrier for these people who carried an ancestral form of L54, which "in prehistoric times and long before the peopling of the New Continent, moved eastwards during the Beringian standstill." [2]

This is reasonable, but the dating of the different branches is very strange:

The Odd phylogenetic tree

What I find perplexing are the dates of the branches of Battaglia et al.'s Phylogenetic tree of Y-chromosome Q hg; where some branches are older than their roots!:

Below is my adaptation of Battaglia et al.'s figure 1; in red I shaded the American haplogroups (M3), and in blue the Asian ones. The number on the right is the age of each haplogroup, (kya). The branches that are "American" are shaded red. All other branches are fully Asian.

Phylogenetic tree of Y-chromosome haplogroup Q. From [2]
The ages are on the right. Blue= Asian, Red= Amerindian

We see an incongruity in the "main" branch MEH2 whose branches M120, MEH2* and M25 (with ages that range from 2.7 to 15.4 kya) are all younger than the offshoots of branch M346 which is at their same level.

Furthermore, M346 (dated by Zhong et al., [3] at 17.77 +⁄- 4.4 ky, then branches succesively into branch L53 which then branches into L54 and this one then branches into M3 which is the oldest in the tree with maximum ages between 21 and 23.6 kya.

Lets look at the details:

Dates (I round off the dates from Tables 2 and 3, in [2]):

• America
  
  • Q1a3a1a-M3*. Most (from 66 to 100%) Amerindians belong to it: 22 kya for Central and Southern Americans, 3.4 kya for Na-Denes and 7.4 kya for Eskimo-Aleuts. Which is reasonable since the last two populations belong to a more recent migratory wave into Northern North America.
  • Q1a3a-L54*. The remaining American Natives belong to it: 23.6 kya old, except Na-Dene which, again, are younger: 5.6 kya.
• Asia
  
  • Q1a1-M120 and Q1a2 - M25. Mongols were not dated in [2], however Table 1 in [3] gives 15.4 and 2.7 ky respectively.
  • Q1a*-MEH2. Koryaks = 3.5 kya and also the remains of the "Saqqaq" man from Greenland (Morten Rasmussen et al., 2009) [1] which are about 4,000 years old but belong to a later wave into America.

  • Q1a3a1c-L330. Mongols = 6.5 kya and Altaians: 2.9 kya.
  • Q1a3a*-M346, is dated at 17.77 +⁄- 4.41 kya [3]

Below I reproduce the data from Table 3 [2], showing the "average" ages for all Q haplogroups:

Average age Q lineages. From [2]

Once more, American Q hg are between 21.1 and 23.4 ky old. The Asian ones range from 10.3 to 22.4 ky with a decreasing age cline as you move East to West from America into Siberia.

This would suggest that these Asian Q lineages originated in America and dispersed West, diversifying (mutating) along the way since the youngest are deeper in central Asia.

But that assumption is apparently wrong, because the markers follow the opposite order (that is, Americans have markers that Asians don't, implying that these markers appeared later, in Americans).

I guess I am going to have to do some deeper research into specific Haplogroup markers, but first, let's look into the Siberian Q haplogroups.

Siberian ancestors (?)

The presence of haplogroup Q (Q hg) among Siberians was pointed out in 2002 (Karafet et al., 2002) [4] at relatively low frequencies of 18.8% (when compared to Native Americans). Two populations concentrate 79.5% of the ocurrences: the frequency reached 93.8% among Kets and 66.4% among Selkups. The age of haplogroup Q was estimated at 17,700 +⁄- 4,800 years [4], in tune with the mainstream theory (it is just a bit older than the 15 kya date for entry into America).

These high frequencies were due to "intergenerational genetic drift coupled with founder effects... supported by very low levels of Y-STR diversity associated with haplogroup Q in both populations (0.149 and 0.159, respectively)..." [4]

In other words it was not natural selection, but chance that acted upon the small population sizes and their high mobility allowing Q hg to become predominant; therefore its frequency grew (intergenerational genetic drift), add to this the fact that small groups with Q hg survived while other haplogroups just died out (bottleneck); outcome: Thus the Q hg became the prevailing line among these people.

Different to Americans and different to each other

But, as we have already seen, these haplotypes are not the same as those found in Native Americans; a Russian language paper (Volkov, 2013) [5] provides an interesting phylogenetic tree, reproduced below:

Phylogenetic tree of haplogroup Q1a3. From [5]

At the split between Americans and Asians (Q1a3a-L53), two branches appear, one leading to all Siberian groups in blue. Another one, in orange one leads to American Natives (red branch M3) while another (yellow) leads to the Q haplogroup found in certain Europeans: Q1a2a2 L804, L805 (Sweden, Norway and via Vikings: UK) - this is worth looking into! [6]

The Q frequency (L330) among Siberians is in agreement with Karafet et al: Kets: 84%, Northern Selkups: 66.4% (and drops to: Evens: 4.2%, Nenets: 1,4%, Kanthy: 1%). [5]

But they are not the same Q haplotypes: Selkups, who originally lived in the Urals, share the same haplotype with the Chechens of the Caucasus (which is close by). On the other hand, the remaining Siberian populations and among them the Kets belong to another haplotype, with other downstream mutations: DYS347=14, and DYS437=13, DYS390=23 ("DYS" stands for DNA Y chromosome Short Tandem Repeat, with a lenght of "n").

Considering that Altai was the source of Amerindian Q haplogroup, Dulik at al., (2012) [7] explored the differences between the Q hg of Southern and Northern Altaian's (this is also reflected in the image above). They found that the latter were quite recent (Bronze Age) the former older -early Bronze Age or late Neolithic.

Then they calculated the divergence times between Southern Altaians and Native Americans, but their TMRCA ages fluctuate widely; from a too recent 7.74 kya (Pedigree Based) to a more reasonable 21.96 ky (Evolutionary-Based); the Split Time values were 4.95 and 13.42 kya for Pedigree based and Evolutionary based, respectively.

Seeing this 3 fold difference between the ages and taking into account that America was peopled more than 8 kya, the authors dismissed the Pedigree based values arguing ("that the evolutionary rate provided a more reasonable estimate.... making the use of the pedigree-based mutation rate questionable." [7]).

These "average" values are to young (even more recent than the 23 kya age estimated further up for the M3 and L54 haplotypes found in America. And, in my opinion it is due to the fact that the 95% confidence intervals for the Bayesian analyses are extremely broad: they range from 12,260 to 42,690 ya. for TMRCA and 5,220 to 30,430 ya. for Splilt Time.

Taking the oldest figures would mean that the ancestors of Americans could have shared a common ancestor with Altaians 42,690 years ago, which is really much more reasonable and consistent with the earliest dated Upper Paleolithic industries from Altai: 43.3 kya [4].

Dating and TMRCA values: Are they reliable?

Looking at these disparities it seems that a key issue is the dating, the timeline, the estimation on when groups split or when they shared a common ancestor.

As seen above, Pedigree estimations differ substantially from those based on evolutionary estimations. And these depend on the mutation rates adopted.

When reading the papers that deal with this subject, my doubts intensify. For instance, a paper by Poznik et al., (2013) [8] estimates mutation rates by adopting, as a "calibration point, the initial migration into and expansion throughout the Americas", based on the dates of known archaeological sites (Paisley Cave and Buttermilk Creek in the US and Monte Verde in Chile) they find Goebel et al. estimation that " humans colonized the Americas around 15 kya” acceptable, and use it for calibration purposes. [8]

But what if instead of 15 kya the date was really 30 kya or 45 kya? This would introduce a strong bias in their estimations. Once again we see how a "recent date" for the peopling of America impacts upon other branches of formal science.

The authors then use the Y haplogroup Q for their calibrations and assume that M3 arose "shortly subsequent to initial entry to the Americas", and in doing so, underestimate the impact that an earlier divergence (Between L54 and M3) in Siberia, prior to the entry into the New world could have had on their calibration. [8]

The strange dates produced by these estimations are higlighted by the case I mentioned in a Previous post on the useless mtDNA clock, where the dating of a novel Y-chromosome haplogroup (Mendez et al, 2013) named A00, 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..." [9], strangely old date indeed. The clocks need to be checked.

Another example can be found in a paper on a Q hg sublineage (Q5) detected in India (Sharma et al., 2007) [10]; the ate estimated for it was 47.1 kya (34.2 – 75.6 ky), but the authors believe that it is "an over estimate than the age of haplogroup Q (15,000–18,000 Years Before Present)" and try to explain the distorted "old" age they calculated as caused by "enhanced diversity, probably as an effect of population expansions and severe bottlenecks or might be due to later migrations and admixture" [10], they then recalculate it as 14.4 ky old! (fitting it nicely into the assumed age range).

Summary

Y chromosome Q hg predominates in America, most of it belongs to the M3 subtype, the rest is L54. There is a very small presence of these two subtypes in East Beringia (Asia), most likely due to a back migration into Siberia from America.

Greater diversity within Q hg is found in America than in North East and central Siberia, this hints at a deeper and more ancient origin for the American lineages.

However the ages of the oldest Amerindian haplotypes are quite recent and have been calculated as being 22 -23 kya. Asian strains contrary to what would be expected from the theory of a trans-Beringian peopling of America appear to be much younger. Suggesting instead a migration Out of America and into Asia, carrying Q hg. We will see in a future post that there is additional proof from mtDNA and language of a migration from America into Eastern Siberia.

Despite doubts regarding age calculations, the oldest mainstream date of 43 kya for a split between the ancestors of Altaians and Americans seems to allow for an early peopling of America.

There is something with the ages that I find strange. But that will be the subject of another post, where I will deal with the dating methods (in particular after reading how Anzic-1 remains from Montana US were dated. By the way, he was a Q-L54*(xM3) 12,600 years old.

I will review the markers that indicate splits in Q hg, because a radiation out of America seems highly probable. I will also take a look at those odd Q hg found in Europe which some attribute to the Huns, but may have more ancient roots, the same ancient roots that Amerindian Q hg has... (I am thinking about Neanderthal here... however Neanderthal Y chromosome would be even older than the A00 haplogroup mentioned above, and quite different from the current Q hg that descends from A00).

Sources

[1] Morten Rasmussen et al., (2010). Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762 (11 February 2010) | doi :10.1038/nature08835
[2] Battaglia V, Grugni V, Perego UA, Angerhofer N, Gomez-Palmieri JE, et al., (2013). The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q.. PLoS ONE 8(8): e71390. doi:10.1371/journal.pone.0071390
[3] Hua Zhong et al., (2010). Extended Y-chromosome investigation suggests post-Glacial migrations of modern humans into East Asia via the northern route. Oxford Journals.
[4] Tatiana Karafet et al., (2002). High Levels of Y-Chromosome Differentiation among Native Siberian Populations and the Genetic Signature of a Boreal Hunter-Gatherer Way of Life, Human Biology, December 2002, v. 74, no. 6, pp. 761–789.
[5] VG Volkov, (2013). Ancient Samoyeds of Yenisey, and migration in light of Genetic Data. Tomsk magazine Ling. and Antropo. 2013. 1 (1) 79-96
[6] International Society of Genetic Genealogy
[7] Matthew C. Dulik, et al., (2012). Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet. Mar 9, 2012; 90(3): 573. doi: 10.1016/j.ajhg.2012.02.003
[8] G. David Poznik et al., (2013). Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females. Science 2 August 2013: vol. 341 no. 6145 pp. 562-565 S. Inf. page 13. DOI: 10.1126/science.1237619
[9] 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.
[10] Swarkar Sharma et al., (2007). A novel subgroup Q5 of human Y-chromosomal haplogroup Q in India. BMC Evol Biol. 2007; 7: 232. doi: 10.1186/1471-2148-7-2327
[11] Morten Rasmussen, et al., (2014). The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (13 February 2014) doi:10.1038/nature13025

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