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.

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