Tuesday, February 16, 2016

Asia Has Five mtDNA Gene Pools



I have added over 2,000 mtDNA samples from Asia and 1,000 from Europe to my mtDNA database in the last few days. Thanks to HaploGrep I've been able to analysis the data more than twice as fast.

With the new data from Asia, I've learned that there are at least Five mtDNA gene pools in Asia. I've also found geographic diversity in East Asian mtDNA and origins of Western mtDNA in Asia.

In the next few weeks I will 1: Research the mtDNA and genome-wide relationship between ancient and modern Siberians, 2: Do more thorough work on European mtDNA with 1,000s of new samples, 3: Collect 1,000s of mtDNA samples from Africa, and 4: Collect many 1,000s of Mito-genomes from Ian Logan which I can now do very quickly thanks to HaploGrep. So, there's a lot to look forward to on this blog if you're interested in mtDNA.

This spreadsheet shows the five mtDNA gene Pools of Asia and regional haplogroups of East Asian mtDNA.

Regional Asian mtDNA

In total there are at least six mtDNA gene pools in Eurasia. Below is a link to a map of the six mtDNA gene pools of Eurasia along with the list of haplogroups in each gene pool.

Eurasian mtDNA Gene Pools

Here are mtDNA Haplogroup frequencies in Asia: Asia mtDNA Frequencies. I included frequencies of South Asian-specfic haplogroups in South Asians and the frequencies of West Eurasian haplogroups in Asia.

Geographic Diversity in East Asian mtDNA

The East Asian mtDNA gene pool is the geographically the largest in the world. Obviously they can't all have the exact same mtDNA. So, I gathered the frequencies of R9 and C subclades in this spreadsheet to find differences: C, R9. East Asia.

There are noticeable differences in subclade frequencies. The biggest is between Siberia and other East Asians. Siberians have a very high frequency of C4a1, C4a2'3'4, and C5 and all three are near non-existent in other East Asians. Tibet/Nepal also have a decent amount of those C subclades, probably because they live near Siberia.

There's also regional-trends in the frequencies of R9 subclades. The most popular R9 subclade in NorthEast and SouthEast Asia is F1a, in Siberia F1b, and in Tibet/Nepal F1c1a. As with C, Tibet/Nepal have a connection with Siberia because of a high frequency of F1b. There's also a high frequency of F4b, R9c1, and F3b in Taiwan and R9b1a in Burma, which are near non existent in other East Asians.

All other East Asian haplogroups can't easily find haplogroups with low-coverage testing, like H in West Eurasia. So, it was hard to find differences in subclade frequencies in other haplogroups, but I did find some. I wrote those differences down here: Regional Asian mtDNA

M7 has consistent strong presence in NorthEast Asia, a weaker presence in SouthEast Asia, and is pretty much unheard of in all other East Asians. M8a consistently pops up in Siberia and NorthEast Asia, and rarely anywhere else. M9a is absent in SouthEast Asia and consistently pops up in other East Asians. E is non-existent in all East Asians except Tawian where it is pretty popular. I also found many D-subclades that are exclusive to certain countries or regions.

NorthEast Asians(Japan, Korea, China) are fairly similar. Tawian and Siberia are differnt from NorthEast Asia in many ways. There are Palaeilthic-splits in mtDNA and more recent links that they have with NorthEast Asia. Nepal and Tibet have a significant amount of South Asian mtDNA, connections with Siberia, and their own unique bottle-neck lineages. Despite Tibet being in the country of China, it's important to remember they aren't Chinese at all, they were just conquered by Chinese.

Origins of Western mtDNA in Siberia and South Asia

West Eurasian mtDNA in Asia peaks in West Siberia and South Asia at about 30%. Every where else in Asia West Eurasian mtDNA is pretty much non-existent. South Asia and Siberia received their Western mtDNA from very differnt sources. Siberian's Western mtDNA is almost entirely from Eastern Europe and South Asian Western mtDNA has unknown sources.

Siberian's Western mtDNA specifically looks like it comes from Pre-Historic Russia(U4, U5a, U2e, T1a, J1b1a1). They probably have a mixture of Mesolithic Russian and Bronze age Andronovo mtDNA(J1b1a1, T1a, J1c, I, H2a1, H6). The composite of Siberian Western mtDNA, is very similar to Catacomb and Andronovo, especially because of their strangely high frequencies of U4.

Siberians also have a string of typical West Asian subclades of U; U7, U1, and U3. It is strange that they don't have a lot non-U West Asian haplogroups. Maybe there were Ancient West Asians who were mostly U7, U1, and U3 like there were ancient Europeans who were mostly U5, U4, and U2e. I doubt it, but it's possible.

South Asian Western mtDNA is dominated by U2(xU2e) and U7. The U2(xU2e) subclades are rarely found outside of South Asia, so have probably been in South Asia for 10,000s of years and not recent arrivals from West Eurasia. The sources of South Asia's U2 is likely a population closely related to Paleolithic North Eurasians, like Ma'lta boy and Kostinki man. The high amount of U7, like in some Siberians, is very strange. U7 is popular in neighbors of South Asia, like Iranians, but it isn't nearly as popular compared to other Western lineages as U7 is in South Asia. Maybe South Asia's U7 and U2 are from the same source.

Non U7 and U2 South Asian Western mtDNA is a mixture of West Asian-specific and European-specific. West Asian-specific mtDNA in my South Asian data besides U7 is includes HV and R0a. Both are more typical of SouthWest Asia than Iran, but still fairly popular in Iran. It's hard to explain the consistent presence of U5a, U4, and J1b1a1, all typical of Bronze age East Europe, in South Asia if all their Western mtDNA is from neighbors in West Asia.

24 comments:

  1. Very interesting, but not surprising. The boundaries are all geographical. I have always assumed quite a a-DNA separation as people from each region actually look different but it's nice to see the difference shows up in the mt-DNA as well.

    Interesting to see that the edge of the Iranian Plateau is a boundary. It links up with the southern edge of the Tibetan Plateau. East and West Eurasia are separated by the Atai/Pamir chain. The other main boundary is Wallace's Line in SE Asia. But interestingly there is a boundary between New Guinea and Australia. Such a boundary has always been obvious to me but it tends to disprove the idea that humans on the two land masses were simply separated by rising sea level. It suggests the 'land bridge' between the two was never actually dry land during the spread of modern humans. Lastly the Andaman Islands stand on their own. There is nothing at all to indicate they are remnant of the first 'great southern coastal migration'.

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  2. The general outline may be correct but don't you think that there may be other micro-regions we should not ignore just because they are small: Andaman and Wallacea at the very least, possibly also the following aboriginal isolated pops.: Ainu, Filipino Negritos and Orang Asli, all them remnants of the early settlement of Asia. Finally Siberia is a complicated mix in autosomal DNA but maybe it may be seen in plain blue using only mtDNA as reference.

    The borders between regions should be fuzzy and overlapping. Not sure what you call West Eurasian mtDNA in India, I'm guessing that U2, U7 and W but these can also be seen (at least U7 and W) as South Asian mtDNA in West Eurasia. It's part of the fuzzy quasi-boundary: it's old stuff that just ignores it, just like happens with Y-DNA (R1a, L, T, J2, etc. - H even!)

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    1. Maju, finally i already know about my Parent's Uniparental Haplogroups.
      My Paternal Grandfather's, My Father's, Me and My Brother's have Y DNA Haplogroup O-CTS11856 (FTDNA: Big Y) / O-CTS5492 (Geno 2.0). Maybe Y DNA Haplogroup O-M122 +M134 +M117 +M133.
      My Paternal Grandmother's, My Father's Sister and His mtDNA belong to Haplogroup M* from FTDNA mtDNA Plus+ (HVR1 + HVR2). A Malaysian Man share a similar Maternal Haplogroup with My Father's side. He have an mtDNA Hg M7c1c3 and a rare Y DNA Hg NO-F549 from The Geno 2.0 results. He have exacly same of mtDNA Mutations with My Father's Sister. The results are:
      HVR1: 16223T, 16295T, 16362C, 16519C.
      HVR2: 73G, 146C, 199C, 263G, 309.1C, 309.2C, 315.1C, 489C, 522-, 523-.
      My Maternal Grandmother's, My Mother, Me and My Brother are belongs to mtDNA Haplogroup B4c (FTDNA mtFull Sequence) or B4c2 (Geno 2.0).
      My Maternal Grandfather's and Her Brothers Y Chromosome DNA are belongs to The Y DNA Hg O-CTS4960 (perhaps Y Hg O-M122 +M134 +M117) from The Geno 2.0 NG DNA Test. Similar with My Y DNA Hg O-CTS5492 or O-CTS11856, both of these Paternal Haplogroups have Positive Mutations: +M175 +M122 +M325 +P201 +P164 +M134 and +M117 (+M133 for me).
      So, what's your conclutions with these My Uniparental Haplogroups?
      + My FTDNA Family Finder Autosomal DNA is still Pending, i wait my Family Finder DNA Test Result until now.

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  3. I agree that micro-regions exist within the main ones. But the variation within each macro-region tends to be more clinal than that between the macro-regions, as in the example given for eastern Asia. We also know South Asia consists of ASI and ANI, basically clinal from northwest to southeast. This presumably indicates geographic boundaries are less definite within each macro-region. Most of the isolated aboriginal groups you mention have received extensive admixture from their neighbours, although a paper a few years ago demonstrated that the cline in Wallacea is particularly steep. And the Andaman Islands are actually given their own macro-region.

    I agree that Siberia is a complicated mix in autosomal DNA, but it is not homogeneous using mt-DNA either, as the post points out. But overall it is part of East Asia (as is America), and as such is distinct from the other macro-regions.

    The borders are indeed fuzzy and overlapping, the most obvious one being the northern boundary between East Asia and West Eurasia. That boundary in fact is clinal once more. In fact that appears to be the most porous boundary between the macro-regions and has probably always been the site of movement in both directions. Far more so that is any other boundary, even that between West Eurasia and South Asia.

    We are also well aware of the fact that Y-DNA is much more mobile than it mt-DNA. It is no surprise therefore that Y-DNA crosses all the boundaries much more readily that does mt-DNA.

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    1. Terryt, that mean a Human Maternal Haplogroups and Human Autosomal DNA have more represent about "pure" Ethnic groups, Human "Race", or something like these.....

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  4. I would quibble with the label Oceania for what are basically Papuans, particularly when places like New Zealand are not included in the areas so labeled. I would also think that the line between that region and Southeast Asia ought to be an island or two to the west of what as shown at the Wallace line rather than Papua New Guinea. Indeed, if you drilled down in more detail, I strongly suspect that you could find more than one mtDNA cluster within Papua New Guinea by distinguishing between biogeographic zones like the Papuan highlands v. coastal areas.

    It is very easy to do an mtDNA inventory for the Americas, which are, obviously, derivative of populations that once inhabited Northern Asia. The color coding seems to imply that the Americans are being included in East Asia, but the list presented when you click on the relevant part of the map is both overinclusive (it includes lots of mtDNA hgs not found in the Americas) and underinclusive (it excludes hgs like X that are found in the Americas). Indeed, for that matter, it is very easy to distinguish between the mtDNA hgs found in South America, in North America, and in circumpolar areas of the Americas.

    One common way to present this kind of data would be to have a detailed mtDNA phylogenic tree and then to color code the nodes according to geography.

    Is this analysis utilizing a cutoff of some sort (frequencies of less than X% excluded, unless an mtDNA hg is found only in the region in question). If there is a firm rule that is being used, it should be stated.

    It would also be neat to add archaic mtDNA clusters.

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  5. I would quibble with the label Oceania for what are basically Papuans, particularly when places like New Zealand are not included in the areas so labeled. I would also think that the line between that region and Southeast Asia ought to be an island or two to the west of what as shown at the Wallace line rather than Papua New Guinea. Indeed, if you drilled down in more detail, I strongly suspect that you could find more than one mtDNA cluster within Papua New Guinea by distinguishing between biogeographic zones like the Papuan highlands v. coastal areas.

    It is very easy to do an mtDNA inventory for the Americas, which are, obviously, derivative of populations that once inhabited Northern Asia. The color coding seems to imply that the Americans are being included in East Asia, but the list presented when you click on the relevant part of the map is both overinclusive (it includes lots of mtDNA hgs not found in the Americas) and underinclusive (it excludes hgs like X that are found in the Americas). Indeed, for that matter, it is very easy to distinguish between the mtDNA hgs found in South America, in North America, and in circumpolar areas of the Americas.

    One common way to present this kind of data would be to have a detailed mtDNA phylogenic tree and then to color code the nodes according to geography.

    Is this analysis utilizing a cutoff of some sort (frequencies of less than X% excluded, unless an mtDNA hg is found only in the region in question). If there is a firm rule that is being used, it should be stated.

    It would also be neat to add archaic mtDNA clusters.

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  6. "I would quibble with the label Oceania for what are basically Papuans, particularly when places like New Zealand are not included in the areas so labelled".

    I agree. There were at least three quite different movements from SE Asia across Wallace's Line. Each one managing to move further out into Oceania than the previous ones.

    "I would also think that the line between that region and Southeast Asia ought to be an island or two to the west of what as shown at the Wallace line rather than Papua New Guinea".

    I am very sure the boundary is Wallace's Line. The triangle of islands formed by Sumba, Timor and Alor/Flores appear to be much more 'Papuan' than 'East Asia' although that is in the process of changing. The group is immediately east of the Line from Bali, although I think Sulawesi is going to prove very interesting in the future.

    "I strongly suspect that you could find more than one mtDNA cluster within Papua New Guinea by distinguishing between biogeographic zones like the Papuan highlands v. coastal areas".

    There is definitely a strip of mt-DNA B along the northern coastline. This almost certainly came in with the Austronesian expansion.

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  7. Yes..I am from Malaysia and my mtDNA is from haplogroup M7c1c3. My rare YDNA haplogroup is haplogroup NO-F549 (or K2a). I still keep looking for research on my rare YDNA haplogroup. Hope one day I can know more about my ancestor. Thanks Adrian Yohanes Purnomo.

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  8. Interesting that you are K2a, or NO. Makes sense as all the other K2s are SE Asian, specifically island SE Asian. I am certain that K2 originated in that region but K2a must have spread north as I'm also sure the O haplotypes spread south from somewhere between the mid Yangtze and Yellow Rivers.

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    1. Terryt, can you explain about an Asian Y DNA Haplogroups O2b / O1b1-M176 and O3 / O2-M122. All of these O's have a Southern Origin. In fact, The Y DNA Hg O1b1-M176 which is more abundant for Korean, Japanese Yayoi and Manchuria, share a common ancestors with Southeast Asian and Southern Chinese Y DNA Hg 02 / O1-P31. Emperor Cao Cao is the best example for His Y DNA Hg O2* / O1-P31. Mostly "Han" Chinese Deep Paternal ancestors Y DNA Hg O2-M122 +M325 +P201 +P164 +M134 (Beta Male) +M117 (Alpha Male). But, i saw on internet when "Han" Chinese Paternal Deep ancestors: O2-JST1126 (Omega Male) and the most common "Han" Chinese Y DNA Haplogroup O-M134 and M117 which these Y DNA are strongly associated with The Huaxia People from The Central Plain around Yangtze and Yellow Rivers who became an ancestor of the "Han" Chinese Male, have a common Paternal ancestors Y DNA Hg O2-P201 (Austronesian) and Y DNA Hg O2-P164 (Micronesian). Maybe these Y DNA Hg O2-M134 and O2-M117 mutation appear in the Yellow - Yangtze Rivers area, but i can't deny when these O's M134 and M117 were the descendants from Southern China and Micronesia Y DNA Hg O2-P164. I don't know about The "Han" Chinese Y DNA Hg O2-JST1126 but this Haplogroup also share a common ancestors with anothers O's subrances, The Y Chromosome DNA Haplogroup O2*-M122.

      To be honest, i saw a lot of Chinese, Southeast Asians (Vietnamese, Indonesia, Filipina, etc.....and Northeast Asians (Japanese, Korean, Mongolian and The Kazakhstan) netizen don't like to have connection with the "Han" Chinese Y DNA Hg O2-JST1126 and Y DNA Hg O2-M134, O2-M117. They proud with their Paternal DNA Haplogroup: Y Hg O1a-M119 + O1b1a-M95 for Southeast Asian. Japanese and Korean Y Hg O1b2-M176 and the Y Hg C2-M217 + N*-M231 and Q-M242 for an Altaic People.
      Basically, the Y DNA Hg O2-M122, M325, JST1126, M134, M117 and M133, frankly, less desirable for an Eastern Eurasians people, However.

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  9. I see the whole O group phylogeny has been updated. I'll check it through and see what the old groups have been renamed as and get back to you.

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  10. I see you are actually using the older nomenclature but I couldn't follow some of your groupings. And you do seem a bit confused.

    "but i can't deny when these O's M134 and M117 were the descendants from Southern China and Micronesia Y DNA Hg O2-P164".

    O-P164 is O3a2c, not O2, and strongly associated with Sino-Tibetan speakers and not at all with Micronesians as far as I'm aware. M134 (O3a2c1) and M117 (O3a2c1a) do both O3 in the old nomenclature, separate branches from O2. descend from O3a2c but none are particularly 'southern'. Have you seen this paper:

    https://www.researchgate.net/publication/6180520_Y_chromosomes_of_Prehistoric_People_along_the_Yangtze_River

    Places all three O haplotypes in the Yangtze region before the Han expansion.

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    1. Terryt,
      Thanks for an article from researchgate.net who gived for me. Luckily, China have some Geneticists / Scientists like Dr Felix Li Jin, Li Hui, etc. I hope i can meet them someday, somewhere.
      Ok, i will learn more about The Y Chromosome Haplogroup O and the connection about 3 Chinese Neolithic Supergrandfathers: Y Hg O-JST002611, O-M134 and O-M117. I think i must take a second "opinion" to Mrs Roberta Estes, an FTDNA Corespondent, Dr Miguel Vilar and 'hopefully' Dr Spencer Wells from The Genographic Project.
      Terryt, frankly from your feedback, you make me look stupid. Basically i just confirm about the connections of an East Asian Y DNA Hg C and D, compare to another Asians Y DNA Hg NO, N, O and Q carrier (an F's and K's descendants) so do with an East Asians Mitochondrial DNA and an Autosomal / Nuclear DNA. I have difficulty to communicate to the another persons via "Cyberworld" and the Social Media like Facebook, Instagram, etc. I don't want to make a misperception which it can make be worse.

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  11. Dear Terryt

    Can I find more information about my YDNA haplogroup NO F549? Which tribes most frequently belong this haplogroup? How many people did you discover in your database same with mine?

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  12. Dear Terryt

    Can I find more information about my YDNA haplogroup NO F549? Which tribes most frequently belong this haplogroup? How many people did you discover in your database same with mine?

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  13. "Terryt, frankly from your feedback, you make me look stupid".

    I certainly did not intend that. You can safely assume you know much more about aspects of the subject than I do. Where my interest lies is in Polynesian origins. From that I have been able to unpick the various movements across Wallace's Line.

    "I see the whole O group phylogeny has been updated"

    The main adjustment has been to connect the old O1 and O2 into a single branch, now called O1a1 and O1a2 respectively. O3 is now called O2.

    "can you explain about an Asian Y DNA Haplogroups O2b / O1b1-M176 and O3 / O2-M122. All of these O's have a Southern Origin. In fact"

    I am sure the O haplotypes have a more northern origin. I'll try to explain, but using the old nomenclature so it's easier to follow. We know that the Mongoloid phenotype is intrusive into SE Asia to at least as far north as northern Vietnam, and probably southern China. That intrusion is from no more than some 10,000 years ago and the only possible connection is with the O haplotypes. We also know that some sort of K2a made it far to the northwest by 45,000 years ago (Ust-Ishm) and west to Oase by 37-42,000 years ago. And N is part of the NO clade and it is primarily a northern haplotype. That provides plenty of room in the north for NO's origin. We can also be very sure that O1a (along with mt-DNA B4a1a) was responsible for carrying the Austronesian languages from Taiwan to the Philippines as recently as some 5000 years ago. That fits the date 3300 BC. for the presence of O1 at the mouth of the Yangtze at Liangzhu. The Austro-Asiatic languages were apparently slightly earlier arrivals in SE Asia but presumably arrived in the south as a result of the Chinese Neolithic expansion. They are closely associated with O2 although the haplotype spread much further than did the languages. The Neolithic started in the middle Yangtze and Yellow Rivers and so it is safe to assume the common ancestor of O1 and O2 had departed from that region. We also know that O2b is simply the northern version of O2a and presumably their common ancestor lived somewhere near where the haplotypes meet or even overlap.

    "Basically i just confirm about the connections of an East Asian Y DNA Hg C and D, compare to another Asians Y DNA Hg NO, N, O and Q carrier (an F's and K's descendants)"

    I think people are easily led astray if they try to combine all the haplotypes into a single migration. Each has its own individual history. For example C is split into two branches but I suspect the split between C1a and C1b happened very soon after the split between C1 and C2. C2 is the northern branch and C1 is fundamentally southern with the exception of C1a. I see that Y-DNA C's phylogeny has also been updated. Here it is:

    http://isogg.org/tree/ISOGG_HapgrpC.html

    Note the link includes the distribution of various branches.

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  14. "Can I find more information about my YDNA haplogroup NO F549?"

    Try the person listed as contact for haplogroup K

    http://isogg.org/tree/ISOGG_HapgrpK.html

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  15. By the way Adrian haplogroups K and C are earlier into SE Asia than are the Os. Even though NO is a member of K2a it is quite possible (in fact I believe probable) that K2a had moved north considerably before NO formed. In fact the expansion of O may have obliterated earlier K2 haplogroups on the mainland. There is a very steep cline between 'Papuan' and 'East Asian' phenotypes just east of Wallace's Line just as there has been very little movement of Y-DNA across the line. Just O1a associated with the Austronesian expansion and O2a associated with the Austronesian expansion which I suspect was associated with the Late Hoabinhian. There has also been a much more recent crossing of the line by O3 haplotypes.

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    1. I want the Anthropologist Geneticists and the Scientists especially a Chinese Geneticist like Prof Jin Li and Dr Li Hui to explain more detail about the conclusions for this topic even to an Amateur and Social Public. I "need" an Autosomal DNA, not just from both Y DNA and an Mitochondrial DNA for Human Deep Ancestors. It's better for me to follow the Scientist, not from this forum, etc.

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  16. hi admin, can you provide some haplogorup frequncies for haplogroup z3a/z3a1a and f1d/f1d1. since these haplogroup frequncies are found in higher number in my curent study but I was unable to determine its origin in terms of higer frequncies. Thanks

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  17. From Miss Roberta Estes website - DNA Explained - she found a German man who he have: 100% European from his Autosomal DNA which this DNA responsible for him and our Physical Appearance. His Maternal mtDNA was belongs to Haplogroup I (L3 - N - I) / Western Eurasian type. But his Paternal line Y Chromosome was belongs to Haplogroup C2c-P35.1.

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