April 30, 2011

O2b and other Y-DNA from Korea and surroundings

In another discussion, Terry brought up this recent paper on O2b and Korean patrilineages (with important references to the rest of East Asia) that I believe is worth mentioning:


Much of the paper is tainted by insistence on lineage age speculations (TMRCA) which help nothing, are unscientific and induce confusion. However I do find interesting that they seem to find (figure 3) that SE Asian instances of O2b (O2b* and O2b1) are derived and not ancestral in relation to NE Asian ones. Hence the occasional O2b found in SE Asia (Indonesia, Vietnam, Thailand, etc.) looks like having originated in Korea or nearby. 

On the other hand the haplotype neighbor-joining structures for O3 and C still look like rooted in the South. In relation to NE Asian C (C1 and C3) I find most curious that a single Korean haplotype would seem to hold together C1 and C3, maybe indicating a joint origin within C for these two NE Asian haplogroups.

Overall I get the impression of a South to North colonization in East Asia, which pretty much set the fundamentals of modern population genetics in the whole region. This process was surely followed at a later time by some North to South backflow, which does not need to be "Neolithic" (beginning in South China at least as early as in the North) nor "Han" (in many cases the relevant haplogroups are definitively not found among North Han but Koreans, Japanese, etc.), it may well be, at least partly, related to the extension of blade industries since c. 20 Ka ago, phenomenon that might have got a southwards pointing vector. 

In any case, an important reference for data miners. 

22 comments:

  1. There must be something wrong with their testing on O3-002611. How come they didn't get any O3-002611 among the samples. And in the chart, O3a3-P201 should include M159, M7, P164/M134/M117.

    http://ranhaer.com/thread-15118-1-1.html

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  2. Now that you mention, it is indeed strange.

    I'd say they did not actually test for it and it's under O3a*. What do you think?

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  3. They list O3-002611 in their chart, haplotree and table 2, but 0% of O3-002611 were there among any the samples. Maybe 002611 were included in O3a*, but it's still strange. Dr. Shi Yan (also one of our forum members) has written to the Korean team for the O3-002611 question.

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  4. This is the response from the Korean author:

    "As your comments, the O3a4-002611 seems to be included in O3a* lineage so that the O3a4-002611 marker will be removed in our data."

    http://ranhaer.com/viewthread.php?tid=15118&page=1#pid224525

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  5. Just as I thought. It seems an edition error rather than anything else. Thanks for the info anyhow.

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  6. "I do find interesting that they seem to find (figure 3) that SE Asian instances of O2b (O2b* and O2b1) are derived and not ancestral in relation to NE Asian ones. Hence the occasional O2b found in SE Asia (Indonesia, Vietnam, Thailand, etc.) looks like having originated in Korea or nearby".

    Good to see you've come round on that one.

    "Overall I get the impression of a South to North colonization in East Asia"

    On what grounds?

    "On the other hand the haplotype neighbor-joining structures for O3 and C still look like rooted in the South".

    But hang on:

    "I'd say they did not actually test for it and it's under O3a*".

    So their data on O3 is far from definitive.

    "I find most curious that a single Korean haplotype would seem to hold together C1 and C3, maybe indicating a joint origin within C for these two NE Asian haplogroups".

    That is interesting. Another interesting item is the proportion of 'other' through much of the region. How much is C and how much F or K?

    "This process was surely followed at a later time by some North to South backflow, which does not need to be 'Neolithic' (beginning in South China at least as early as in the North) nor 'Han' (in many cases the relevant haplogroups are definitively not found among North Han but Koreans, Japanese, etc.), it may well be, at least partly, related to the extension of blade industries since c. 20 Ka ago, phenomenon that might have got a southwards pointing vector".

    I hope I've never given the impression that I think the southward movement is totally 'Han'. I'm certainly prepared to accept it's earlier, although I'd hesistate to claim that it's Paleolithic. I don't think the blade industries presence in the south is as old as 20 Ka ago. It seems it's largely post Hoabinhian.

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  7. "How much is C and how much F or K?"

    Silly me. It's in the paper.

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  8. "Good to see you've come round on that one".

    Another 'lucky guess' on my part?

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  9. Recently,they took samples from North Korea. Pyeongan region had 23% haplogroup C2 M217 and 19.5% O2b. What surprised me was that the hamkyeong samples had a total of 16.3% C. It was interesting because the jurchens had taken over and settled their for centuries but despite that, it was similar to south korea. Whats also interesting was that pyeongan had 6.9% c2b sublineage. This clade is marginal like say 1-2% in east asians but is quite frequent in mongolia and significant in manchuria. All the other south korean populations in the table lacked c2b and had lesser frequencies of C2 like 12 to 16%. What i found out was that north koreans have 10-28% haplogtoup C.

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    1. Interesting, thanks. Do we have a source for that (preferably in English)?

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  10. Heretofore published studies regarding Korean Y-DNA have tended to find C-M217 Y-DNA with greater frequency in samples of Koreans in South Korea (Park et al. 2013, "DNA samples from 300 unrelated Korean males were obtained from the National Biobank of Korea," 50/300 = 16.7% C-M217; Xue et al. 2006, "Korean (Korea)," 7/43 = 16.3% C-M217; Kim et al. 2011, "new Korean samples collected from 506 people residing in six major provinces in Korea," 62/506 = 12.3% C-M217) than in samples of Koreans in China (Xue et al. 2006, "Korean (China)," 3/25 = 12.0% C-M217; Zhong et al. 2010, "Korean (Heilongjiang)," 1/11 = 9.1% C-M217; Zhong et al. 2010, "Korean (Jilin)," 2/35 = 5.7% C-M217). As far as I know, the only sample of Koreans from North Korea for which Y-DNA data have been published in an English-language journal is the sample of Zhong et al. 2010, "Korean (Korea)," 5/19 = 26.3% C-M217.

    Koreans have experienced a very turbulent 20th century, and the suggested geographical pattern (high frequency of C-M217 in the center, i.e. North Korea, moderate frequency in the south, i.e. South Korea, and low frequency in the north, i.e. NE China) is difficult to explain. Denser sampling especially in North Korea and neighboring parts of NE China is warranted.

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  11. There is a youtube video for the pyeongan and hamkyeong samples. I think you can find it by typing korean y chromosome or maybe korean haplogroup in youtube. This guy made pie charts for it. The original is from a table comparing japanese and korean samples but its from a korean naver blog. If you scroll down from the video to the comments section the guy whose youtube name is karo saro also mentions a 27.5% c2e frequency for north koreans. Also, the study called extended y chromosome investigation suggests postglacial migrations of modern humans into east asia via the northern route mentions that they got samples of chinas minorities including one population from north korea. In this case they detected 26.3% haplogroup c from north korea. Whats interesting is that the koreans in china had way lesser. 5.7% and 9.1%. So i personally think that the koreans in china are actually a poor example of the variations in northern korea. In the korean naver blog karo saro had another data where they detected lineages of men from north south korea and japan. In this case, north koreans lacked completely O2b. But its probably because the sample size was small.

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  12. http://blog.naver.com/PostView.nhn?blogId=qudro&logNo=220844635502&parentCategoryNo=&categoryNo=13&viewDate=&isShowPopularPosts=false&from=postView
    above is a korean naver blog written in korean but there is a table comparing japanese and north and south korean variations. this is the where they have the pyeongan an hamkyeong samples.

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  13. http://blog.naver.com/PostView.nhn?blogId=qudro&logNo=220843071387&parentCategoryNo=&categoryNo=13&viewDate=&isShowPopularPosts=false&from=postView

    here is a map indicating the mens lineage and the colors are where the men live or where they got the samples. O2b is strangley absent in north korea but as you can see they didnt test that many men.

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    1. Very interesting, TY. Don't you think that O2b is, even in South Korea, rather concentrated towards the SE? That map gives the impression of the West and North of South Korea being low in O2b, so maybe the pattern goes like that and is not that strictly a N/S contrast almost along the modern truce line.

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  14. I think that haplogroup O2b was much more frequent in ancient times than modern. The reason being is that if you take a look at the japanese variation of y dna and ignore the native jomon component youll see that O2b is by far the most common paternal lineage. The reason for the existence of O m175 subclades in japan is due to the yayoi migration. In japan O3 is less frequent than O2b which is the opposite in korea. Further more the japanese have lesser C than koreans. Infact C1 is a jomon lineage. So if you just look at C2 in japan and exclude the jomonese C1, yayoi populations had lesser c frequency than modern koreans. So personally i think the ancient korean y dna was somewhat different from the modern. In the present day O3 is the most common in korea. Unfortunately, y dna studies as of now, for the most part only give us the makeup of paternal lineages in korea. The exact, real population history is not discussed or unknown.

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    1. FYI, see this: http://forwhattheywereweare.blogspot.com/2013/12/ancient-east-asian-y-dna-maps.html

      It's limited to ancient China Y-DNA but it suggests that O2 (in general) was rare in Neolithic China (only one case detected in the south) and that it became a bit more common towards the Metal Ages (or that it was already there but lucky sites were not studied until this period) to the Southeast of China. So my impression is, whether it expanded in the Metal Ages or was already there, it has a tendency to be an Eastern, maybe partly coastal lineage. I feel that there are enough data points in ancient North China to discard it as a "continental" or "steppe" lineage. So if someone told me that O2b expanded northwards via Okinawa, I'd nod and say: sound about correct, plausible, but of course with great uncertainty (not enough ancient data yet).

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    2. I must correct myself: I should have said O2 in general, O2b should have coalesced in Korea itself or somewhere nearby (per the main entry above) but O2 could well have migrated northwards via the coast or have "always" been a coastal lineage in East Asia.

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    3. Perhaps the clearest evidence for a long-term presence of haplogroup O-M268 (so-called O2 or O1b) in East Asia is the occurrence of O-CTS10887 and its subclades O-PF4341, O-F779, and O-F417 among modern Chinese (and Vietnamese, Japanese, the Dai minority in Yunnan, etc.). Members of O-CTS10887 appear in most published studies of Y-DNA variation as O-M268(xPK4, P49) or O-P31(xM95, M176). (Such Y-DNA also has been found in roughly 1.5% of sampled Koreans: e.g. Xue et al. 2006, 1/25 = 4.0% O-P31(xM95, M176) Koreans in China; Xue et al. 2006, 1/43 = 2.3% O-P31(xM95, M176) Koreans in [South] Korea; Kim et al. 2007, 3/216 = 1.4% O-P31(xM95, M176) Koreans tested at hospitals in Seoul and Daejeon; Park et al. 2012, 7/573 = 1.2% O-P31(xM95, M176) Koreans in Seoul; Park et al. 2012, 3/133 = 2.3% O-P31(xM95, M176) Koreans in Daejeon; Park et al. 2013, 5/300 = 1.7% O-P31(xM95, M176) unrelated Korean males obtained from the National Biobank of Korea). YFull provides the following TMRCA estimates:

      O-K18 (time to most recent common ancestor of O-CTS10887 and O-PK4): 22,200 [95% CI 20,000 <-> 24,400] ybp

      O-CTS10887 (time to most recent common ancestor of O-PF4341, O-F779, and O-F417): 15,900 [95% CI 12,900 <-> 19,000] ybp

      O-F417 (time to most recent common ancestor of O-CTS250 from Beijing, Hubei, and the Dai minority of China and O-F417(xCTS250) from Tokyo, Japan): 11,400 [95% CI 8,800 <-> 14,000] ybp

      O-CTS250 (time to most recent common ancestor of O-F2760 from Beijing, China and the Dai minority and O-CTS250(xF2760) from Hubei, China): 4,600 [95% CI 3,200 <-> 6,500] ybp

      So, despite the overall low frequency of O-CTS10887, it seems very likely that it has been diversifying in East Asia since the Paleolithic era. Purported descendants of Later Han chancellor and King of Wei, Cao Cao, also belong to this haplogroup. I have not seen any evidence that could be taken to suggest that O-CTS10887 has a significant presence in any extant population outside of the Sinosphere, so it is unlikely to represent the descendants of any historical immigrants (unless the immigrant population has been obliterated from the source region in the meantime).

      There is an odd case of O-F1252(xF2924), a sort of "pre-O-M111" member of O-M95, in an individual from Ryazan Oblast of Russia. His TMRCA with O-F2924 is estimated to be 10,500 [95% CI 8,100 <-> 13,100] ybp. It is a bit intriguing, but I think the preponderance of evidence indicates that O-M95 has originated in East Asia and propagated primarily southwestward with a Neolithic dispersal of the ancestor of Austroasiatic languages.

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  15. Oops i accidently posted twice

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    1. Happens often with mobile devices, it seems. Be careful, check your options. I deleted the duplicate comments anyhow, but it's a delicate thing to do.

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  16. As for Korean C-M217, the highest resolution analysis available in any published paper seems to be that of So Yeun Kwon, Hwan Young Lee, Eun Young Lee, Woo Ick Yang, and Kyoung-Jin Shin, "Confirmation of Y haplogroup tree topologies with newly suggested Y-SNPs for the C2, O2b and O3a subhaplogroups." Forensic Science International: Genetics 19 (2015) 42–46.

    50/706 = 7.1% C-CTS2657 (YFull TMRCA 7,300 [95% CI 5,900 <-> 8,800] ybp)
    17/706 = 2.4% C-Z8440 (YFull TMRCA 10,500 [95% CI 8,100 <-> 13,000] ybp)
    67/706 = 9.5% C-Z1300 total (YFull TMRCA 10,700 [95% CI 9,100 <-> 12,300] ybp)

    17/706 = 2.4% C-F845 (YFull TMRCA 7,000 [95% CI 5,400 <-> 8,700] ybp)
    84/706 = 11.9% C-Z1338 total (YFull TMRCA 11,400 [95% CI 10,100 <-> 12,900] ybp)

    5/706 = 0.71% C-L1373 (YFull TMRCA 14,700 [95% CI 13,300 <-> 16,000] ybp)
    89/706 = 12.6% C-M217 total (YFull TMRCA 34,200 [95% CI 31,800 <-> 36,600] ybp)

    2/706 = 0.3% C-M130(xM217)
    91/706 = 12.9% C-M130 total

    A comparison with the data of Park et al. 2013 (2/300 = 0.7% C-M407) allows one to conclude that a majority of Korean members of haplogroup C-M130 should belong to C-CTS2657(xM407). YFull currently has two individuals whose Y-DNA falls into that category: ERR1025626 from Pakistan and NA18749 (Han Chinese in Beijing, China). Both those individuals belong to a clade C-CTS4449. An old study has shown that some Korean members of haplogroup C-M130 have Y-STR haplotypes that are very similar to the Y-STR haplotypes of some Burusho members of haplogroup C-M130; I suspect that these may all belong to C-CTS4449, or at least more generally to C-CTS2657(xM407).

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