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Tuesday, February 4, 2014

New subclade of mtDNA haplogroup C1 from Mesolithic Northeastern Europe


A paper at PLoS ONE describes the discovery of a new, but possibly now extinct, mtDNA C1 lineage from the Yuzhnyy Oleni Ostrov Mesolithic archaeological site in far Northwestern Russia. The enigmatic lineage, classified as C1f, is the bridge between the various C1 subclades carried by modern-day Native Americans, Siberians and Icelanders.



Abstract: The human mitochondrial haplogroup C1 has a broad global distribution but is extremely rare in Europe today. Recent ancient DNA evidence has demonstrated its presence in European Mesolithic individuals. Three individuals from the 7,500 year old Mesolithic site of Yuzhnyy Oleni Ostrov, Western Russia, could be assigned to haplogroup C1 based on mitochondrial hypervariable region I sequences. However, hypervariable region I data alone could not provide enough resolution to establish the phylogenetic relationship of these Mesolithic haplotypes with haplogroup C1 mitochondrial DNA sequences found today in populations of Europe, Asia and the Americas. In order to obtain high-resolution data and shed light on the origin of this European Mesolithic C1 haplotype, we target-enriched and sequenced the complete mitochondrial genome of one Yuzhnyy Oleni Ostrov C1 individual. The updated phylogeny of C1 haplogroups indicated that the Yuzhnyy Oleni Ostrov haplotype represents a new distinct clade, provisionally coined “C1f”. We show that all three C1 carriers of Yuzhnyy Oleni Ostrov belong to this clade. No haplotype closely related to the C1f sequence could be found in the large current database of ancient and present-day mitochondrial genomes. Hence, we have discovered past human mitochondrial diversity that has not been observed in modern-day populations so far. The lack of positive matches in modern populations may be explained by under-sampling of rare modern C1 carriers or by demographic processes, population extinction or replacement, that may have impacted on populations of Northeast Europe since prehistoric times.

Citation...

Der Sarkissian C, Brotherton P, Balanovsky O, Templeton JEL, Llamas B, 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 9(2): e87612. doi:10.1371/journal.pone.0087612

See also...

Post-Mesolithic population replacements/extinctions in Northeastern Europe


24 comments:

barakobama said...

Here is a great article from Anthropogenesis from 2012.
http://anthropogenesis.kinshipstudies.org/2012/11/yuzhnyi-olenii-ostrov-ancient-mtdna-evidence-for-amerindian-admixture-in-europe/

The C1f may be originally east Asian(excepted) not west Eurasian.
Quote from the Anthropogenesis article

"Craniologically, the Yuzhnyi Olenii Ostrov burial is dominated by Caucasoid morphology (left) but, importantly, there is a small number of skulls that display Mongoloid traits (right)."

The C1e in Iceland and C1f in Karelia I think both are probably from east Asian admixture. Karelia people were mainly typical Mesolithic European(Maybe ANE I don't know) U5(specifically U5a), U4, and U2e with some east Asian C1f mix.

There are very similar results from other Russian hunter gatherers and bronze-iron age Indo Iranians(+near eastern farmer and east Asian mtDNA). The U5 of Mesolithic Russians may have been entirely under U5a or even U5a1. U5b is dominate in all other region of Europe with Mesolithic mtDNA except for Scandinavia(including Gotland) which also had all U5a and from Motola a mix of U5a1 and U5a2. U5b2 was probably the dominate subclade for Mesolithic west and central Europeans.

I wonder how U5 subclades are distributed today. I except a mix of Mesolithic and later U5 forms in most of Europe. Except eastern where I think most is probably U5a1.


Davidski said...

There seems to have been quite a bit of really old and basal mtDNA C in Europe at one stage. Here's another example...

"Phylogeographic network analysis revealed that our samples are located at or near the ancestral node for haplogroup C and that derived lineages branching from the Neolithic samples were present in Bronze Age Kurgans."

http://eurogenes.blogspot.com.au/2011/09/surprising-adna-results-from-neolithic.html

Chad Rohlfsen said...

I wonder if mtdna c came west with ydna q? Following the last mammoths even.

Davidski said...

No idea, but one of the comments under the above linked post is interesting...

"At some later eastern sites, real Asian admixture may be indicated. But in the case of, for example, individuals buried at Xiaohe (about whose C lineages the authors say: "Given the unique genetic haplotypes and the particular archaeological culture, the time of this admixture could be much earlier than the time at which the Xiaohe people were living at the site. This means that the time of their mingling was at least a 1000 years earlier than previously proposed."), it's more likely there was never any "Asian admixture". The C lineages were part of the gene pool of steppe Caucasoids from the beginning, and the low frequency in present-day Europeans is due to drift, selection, or population movements."

barakobama said...

Davidski I think you have to consider the diversity of other C subclades besides C1 in east and west Eurasians, diversity of its sister cade Z in west and east Eurasians, some Mongoloid type skulls in Yuzhnyi Olenii Ostrov burial, and the rarity of any form of mtDNA M in west Eurasians and its popularity in east Eurasians before saying mtDNA C is European or west Eurasian in general.

Thetarim mummies who were dominated by mtDNA C4 also had totally dark(mainly black) hair(not from genes) unlike Andronovo people and other Indo Europeans in that area from the bronze and iron age who were very light haired(not one had dark brown hair). I haven't read anything about their facial features and skull shape but I would bet many were very Mongoloid. That is probably were the mtDNA C4 came from but there were also some R*'s and a M*. I wouldn't be surprised if all of them were descended from the same great great east Asian grandmother and the same great great east European(Indo European) grandfather.

Davidski said...

Well, it wasn't long ago that any European who belonged to Y-haplogroup C was told he was paternally of Mongol or Turkic descent. Now we know there are subclades within this haplogroup that are native to Europe, like C6. So the fact that Y-hg C is overall an East Eurasian marker isn't very important in this case, because some of its subclades split before the formation of the main genome-wide divisions within Eurasia. It might be the same case for mtDNA C, because it's also a very old marker.

Chad Rohlfsen said...

Yeah, okay. C being 60kya like the ydna makes it possible to be both east and west you think? I wonder if the East and West split was at this time. Tinyuan was already, obviously East at 40kya. I wonder if the split was at 60kya in Central/Southern Asia.

Chad Rohlfsen said...

Even if the C1 split is 17-22kya, it would be easy to assume it is East Eurasian, given its spread in NE Asia and America. The split would have to be Lake Baikal or more likely even further East; if it was popular in Beringia, waiting to cross. It makes sense that way at least. How much more West Eurasian can Native Americans become?

Davidski said...

Its present distribution could be a red herring though. C might be a pan-Eurasian lineage, while C1 might represent some sort of West Eurasian-like admixture in East Asia and the Americas, much like Y-hg Q, which was once thought to be a signal of East Eurasian admixture in Central Asia and West Eurasia.

Chad Rohlfsen said...

I'm not sure about mtDNA C. It seems to behave differently than ydna Q. This goes into Siberia apparently after Q, and rapidly replaces the UP mtDNA lines. I am wondering if both yDNA and mtDNA C's are East Eurasian and do a bit of founder effect type of deal. The autosomal East Eurasian DNA could be pushed to a trickle after a few dozen generations. If these exotic women (if they were different) were prized, as well as their daughters it could replace a good chunk of the mtDNA in a region relatively quickly. Who's to say that East and West Eurasians looked that differently at this time? Every Eurasian could've looked the roughly the same 20-30kya. The difference could've been as slight as the different skull shapes present in Native Americans.

Chad Rohlfsen said...

For all we know, an aquiline or more concave noses with a lower bridge and epicanthic eye folds could've been rather typical on average in all of Northern Eurasia. It still shows up in Northern Europeans. More often in those with lower Neolithic ancestry. Even the San people of Africa have this feature. It could be rather old.

Davidski said...

I honestly don't have any strong opinions about the origins of mtDNA C or C1, and until ancient DNA settles these issues I'll be keeping an open mind.

Chad Rohlfsen said...

Sorry for the third post here. I just wonder how much we can tell by skull shapes 5-10kya even. Look at Loschbour and La Brana. There is no way that they look like the same group. They don't even look like the same hominid. My ex-brother in-law and I have pretty much identical head and facial features. The only difference is that he is 3/4 Native American.

We could find remains that look 100% West Eurasian and turn out 50% East Eurasian. I really hope that they do autosomal DNA on these remains. Any word on if they are testing them?

Chad Rohlfsen said...

Yes, I am totally open as well. I just wont be surprised to see them find something East Eurasian in NE Europe at that time. They weren't that far from Mal'ta, and they ended up in Sweden 9kya. Why couldn't East Eurasians be on their heels? I wouldn't be surprised by anything anymore. I sure as hell didn't expect to see Europeans as dark as Papuans or Sri Lankans 7kya. Amazing stuff! I can't wait to finish my Anthropology studies and get out there!

barakobama said...

By looking at modern mtDNA there are many "European" branches of J, T, and K. But ancient mtDNA has proven they came with near eastern farmers even though today are almost completely absent from the near east. The same could probably be said for super European mtDNA H subclades and many other lineages. There could many different explanations for modern diversity of mtDNA and Y DNA.

barakobama said...

Chad, do you really want to argue about pigmentation again? I am totally willing to but it isn't right for this thread.

Chad Rohlfsen said...

Why argue when you don't understand la Brana and loschbour have the ancestral allele on slc24a5. Like 93-100% of ssa, East Asians and native Americans. They don't have the derived allele in Europe now. So there is no 25-40% lightening in the mesolithics. Get over it.

Chad Rohlfsen said...

Until some new, undiscovered allele pops up, you're gonna have to live with it.

barakobama said...

Do you want to argue in this thread?
http://eurogenes.blogspot.com/2012/12/evidence-for-early-migrations-to-europe.html

Chad Rohlfsen said...

There is no other known allele that affects skin color. There is no point arguing it. They did not have the skin lightening alleles. Period!

Diana said...

Hi: My MTDNA is the extremely rare MTDNA C. It was a surprise because I'm from Puerto Rico I would expect if any, the C1b1 or C1b2, but an this is an important but,my ancestors came from north Europe, West Europe, Peninsula Iberia,Italy traces in the Mediterranean,Africa and Asia. I have matches in Russia,Finland, Denmark,Ireland and as you can suppose with Native Americans, due the MTDNA is the mother of the MTDNA C sudclades.

I have noticed that some (scarcely) Puertoricans have MTDNA C with matches and traces in Russia, Finland, Denmark, Ireland.
I have read the Iceland MTDNA Thesis and make me sense that their was traffic from Iceland to America some branches admix in North Europe. I have matches in Canada and East Coast but It could be an admix more recently.

I know my matches because I did the autosomal test and the MTDNA test and my father did the DNA Y test(he is R1B).

Yes, as far I have saw, I think MTDNA C is mostly East Euro Asia MTDNA.

About the Branas(2014) discovery I read in DIANEKES blog that they were dark skin and blue eyes.No fair skin at all at this time.I read about other ancient MTDNA C Bones recently found in Europe, I can't find the source of the information in my files, I can't remember the country.
I don't know if we are very prized, but I know my Female ancestors have a lots of Kids and many daughters and my MTDNA ancestors live 95 to 99 years old with general good health.That could help a lot!

Diana said...

Gedmatch.com match me with the arcaic Brana Man!

Kate said...

Hi, just wanted to say thanks for this article. And to add myself and my mother as footnotes to this discussion. We recently submitted DNA samples to 23andme. She came back as C1 and I came back as C1b. (There is no question that she is my biological mother. Her test results showed no call for SNP i4001046.)

The interesting thing is that she is just about European as it gets (though we have been Americans for many generations). Other than the mtDNA, her tests returned 0% Asian or Native American ancestry. The farthest we've been able to trace back in a maternal line goes to Spain in the late 1700s, and this is solidly backed up by good documentation. Discovering that we have mtDNA associated with east Asia and the Americas has been a real surprise. It's theoretically possible that our earliest known female-line ancestor had some Middle Eastern ancestry. But this is still a long way from eastern Asia or the Americas.

So it seems we are among a small(?) population of Europeans of this mtDNA haplogroup. I honestly cannot think of a better explanation. I will follow developments on this topic with interest.

Adrian Yohanes Purnomo said...

Diana, i'm Adrian from Surabaya - East Java - Indonesia. Actually my maternal cousins (my mothers brothers son) have an mtDNA Hg M8a2'3. This is extremely rare mtDNA Haplogroup in Indonesia, even though for a Northern China Haplogroups. Contrast with my mtDNA Hg B4c, more spesific B4c2 (perhaps a Southern "Mongoloid" DNA) which my mtDNA Haplogroup were more common in Indonesia, Indochina peninsula and Southern China like Hunan, Hainan Island, Taiwan both Native Taiwanese and "Han" Taiwanese, Fujian, Guangdong, Hong Kong and even ini Pacific Islanders.