Gene Expression

Korean genetic relationships

There’s a new paper, The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers:

Methodology and Results
We analyzed mitochondrial DNA…sequence variation in the hypervariable segments I and II…and haplogroup-specific mutations in coding regions in 445 individuals from seven east Asian populations…In addition, published mtDNA haplogroup data…mtDNA HVS-I sequences…Y chromosome haplogroup data…and Y chromosome STR da…were analyzed to elucidate the genetic structure of East Asian populations. All the mtDNA profiles studied here were classified into subsets of haplogroups common in East Asia, with just two exceptions. In general, the Korean mtDNA profiles revealed similarities to other northeastern Asian populations through analysis of individual haplogroup distributions, genetic distances between populations or an analysis of molecular variance, although a minor southern contribution was also suggested. Reanalysis of Y-chromosomal data confirmed both the overall similarity to other northeastern populations, and also a larger paternal contribution from southeastern populations.

Conclusion
The present work provides evidence that peopling of Korea can be seen as a complex process, interpreted as an early northern Asian settlement with at least one subsequent male-biased southern-to-northern migration, possibly associated with the spread of rice agriculture.

Last month I posted on the genetic map of East Asia. That paper surveyed hundreds of thousands of variant loci in the autosomal genome, and mapped the variation in the populations on a 2-dimensional chart. Like the genetic maps of Europe there wasn’t too much of a surprise. So what value-add is there in this sort of study which examines uniparental lineages, that is, genes inherited only through the maternal (mtDNA) and paternal (Y) lineages? Here’s the table to look at:

i-edd77d4ec2b2fd60e2b980d860e4186d-journal.pone.0004210.t005.jpg

As you can see, the female lineages are biased toward northern East Asian lineages, while the male lineages are biased toward southern East Asian lineages. Uniparental lineages which exhibit sex-based asymmetries gives us some information in terms of long term demographic process. Yesterday I blogged a paper about Iceland which confirms that Icelanders are a mix of British, Irish and Norse, with the Norse component predominant in the Y lineages and the British & Irish in the mtDNA lineages. Biases in the origin of male and female lineages are extremely common in the New World. The authors make the case that the Y lineages might be evidence of the spread of agriculture from Southeast Asia. I immediately assumed that before even getting to their speculation as no other social-historical phenomenon comes to mind. From Wikipedia:

Mainstream archaeological evidence derived from palaeoethnobotanical investigations indicate that dry-land rice was introduced to Korea and Japan some time between 3500 and 1200 BC. The cultivation of rice in Korea and Japan during that time occurred on a small-scale, fields were impermanent plots, and evidence shows that in some cases domesticated and wild grains were planted together. The technological, subsistence, and social impact of rice and grain cultivation is not evident in archaeological data until after 1500 BC. For example, intensive wet-paddy rice agriculture was introduced into Korea shortly before or during the Middle Mumun Pottery Period (c. 850-550 BC) and reached Japan by the Final Jōmon or Initial Yayoi circa 300 BC.

It’s the intensive period that I suspect might have left a south-north genetic overlay in the Y. Here’s a close up of a section of the SNP substructure paper with populations labeled:

i-ad1e083b55dd6a2caa1c34c32ba5d075-koreans.jpg

The chart is pretty straightforward, though I would note most Chinese Americans have origins in South China, especially Fujian and the area around Canton. Taiwanese are mostly Fujianese by origin. Remember this chart is based on patterns of variation within the autosomal genome, and displays the two biggest components of variation which can be extracted out as independent dimensions. The horizontal axis is somewhat suggestive to me, I have to wonder if the South Chinese, Koreans and Japanese are further to the left because they have all been subject to the expansion of rice farmers 2-3,000 years ago. Remember that the original Han Chinese culture in the Yellow River basin was based around millet dry farming, the addition of rice agriculture into the Han culture toolkit was an adoption from the indigenous peoples south of the Yangtze, many of whom were Sinicized and likely are the ancestors (at least in part) of the Chinese dialect groups. The Japanese themselves are a compound, likely of the ancient Jomon peoples with Siberian affinities, and the later Yayoi rice farmers who arrived ~2,000 years ago, and began in the southwestern islands and slowly moved east and then north (the Yayoi are the cultural ancestors of the modern Japanese, though a substantial proportion of Jomon ancestry seems likely).

Finally, one last comment about the idea that this was a male mediated migration. One doesn’t need to imagine a male-biased migrant population. It could be that the original rice farmers who brought the lifestyle attained a relatively high status among the indigenous peoples whom they settled. In this case one could imagine that the male newcomers could leverage their status into reproductive output to a far greater extent than the females of their group.

Comments

  1. #1 Martin R
    January 17, 2009

    one could imagine that the male newcomers could leverage their status into reproductive output to a far greater extent than the females of their group.

    Please explain. If group A attains higher status than group B, then how would that benefit the men of A more than the women from a reproductive perspective? Do you envision a situation where, as soon as a group A woman becomes pregnant, her husband sneaks off and impregnates a low-status group B woman? You’re thinking about the greater time investment in a child by its mother?

  2. #2 razib
    January 17, 2009

    If group A attains higher status than group B, then how would that benefit the men of A more than the women from a reproductive perspective?

    rich men can have dozens of children if they can afford it. rich women can not have dozens of children. “dozens” is an extreme case, but illustrates the points that the marginal potential reproductive returns toward more resources for a male is much higher than a female. male reproductive potential is ‘scalable,’ female reproduction is not.

    and yes, the man could sneak off. but i’m actually thinking both polygyny and serial monogamy.

  3. #3 Barry S.
    January 17, 2009

    This brought to mind a classic Korean proverb that can be literally translated as “South Man, North Woman” and is taken to mean that the most beautiful women on the Korean peninsula are found in the North (present-day North Korea) and that the most capable, impressive, best men are in the Southern part of Korea. (In the context of the explanation of the proverb, the women are always described as beautiful, whereas the men are described in Korean words that could be translated as charismatic, strong, impressive, assertive, etc. but not necessarily as physically handsome or attractive.) The proverb is taken to indicate where to find the ideal mates for each respective sex in Korea.

    Also the Southern regions of the Korean peninsula traditionally have been and still are the agricultural centers of Korea. As you go North it becomes very mountainous rendering large scale agriculture difficult.

  4. #4 bioIgnoramus
    January 17, 2009

    Did Korea and Japan have agriculture before the arrival of rice cultivation?

    Is there agreement on where rice cultivation started? South China? Further south?

    Anyway, interesting stuff.

  5. #5 razib
    January 17, 2009

    Did Korea and Japan have agriculture before the arrival of rice cultivation?

    yes, but not “intensive” forms. the jomon are sometimes characterized as pre-agricultural, but i don’t think that’s totally true. but when i say not intensive, i think it might have been even less intensive than contemporary slash & burn farmers.

    Is there agreement on where rice cultivation started? South China? Further south?

    the strain in japan and korea is from south china.

  6. #6 bioIgnoramus
    January 17, 2009

    Thanks, R.

  7. #7 AG
    January 17, 2009

    Look at genetic map, no wonder northern Hans call their country as zhong guo (central country). Middle kindom is kind of less accurate interpretation.

    China is equivalent to a central european country to europe. Hm, Is Germany or Poland central?

  8. #8 Huxley
    January 18, 2009

    “China is equivalent to a central european country to europe. Hm, Is Germany or Poland central?”

    I would say Germany. It touches eastern, western, northern, and (if you include ethnically and historically German Austria) southern Europe. A Chinese born friend of mine said that Canton/Guangdong had a similar place in China as Bavaria in Germany. He meant that they both maintained a certain amount of fierce cultural independence and proud distinctiveness from the rest of the country. I suppose you could compare further and say that both Beijing and Berlin are largely political cities while Shanghai and Frankfurt are largely commercial/financial cities on the border between the northern and southern parts of the countries. Likewise there is a slight genetic difference between northern and southern Germans (Nordic vs. Alpine sub-races) and northern versus southern Han Chinese. In both cases the northerners are paler and taller.

  9. #9 mongobanjum
    January 19, 2009

    The study using 200K SNPs that the blogger posted was proven to be quite inaccurate.

    http://img356.imageshack.us/img356/2914/41133325sm7.png

    A new study using 650K SNPs (more than 3 times the significance of the previous study) placed Japanese much closer to the CHB cluster than previously noticed.

    Also, quite interestingly, the Japanese were less “northern” than the Naxi, an ethnic group of SE Asia (Yunnan). The “northern” admixture among Japanese was comparable to the CHB, and the overall distances were closer to CHB than to northern groups.

    The Yakut and Cambodian clusters still proved to be isolated populations using 650K SNPs.

    Interestingly, the Korean cluster occupied a position among the Tungusic northern populations, and overall distances to CHB were more distant than CHB to JPT.

    The Vietnamese cluster occupied a position mid-way between the Cambodian and CHB cluster, though closer to the macro-southeast Asian cluster (particularly to the Dai ethnic group).

  10. #10 razib
    January 19, 2009

    you should post the link to the paper itself so that people can judge which is more accurate. saying something was “proven quite inaccurate” based on a follow up paper makes you sound like you have an 8 year old’s understanding of science ;-) (or english is your second language).

  11. #11 mongobanjum
    January 19, 2009

    ok, here is the study (26 pages)- this really is a huge and important study. Even Dienke’s anthropology blog mentioned this as the most important study out of all studies that used SNP genotyping.

    http://hagsc.org/myerslab/papers/LiAbsher-SOM-HGDP.pdf

  12. #12 razib
    January 19, 2009

    that’s an older paper FYI. yes, it is an important paper. but it isn’t “3 X’s as significant”.

  13. #13 mongobanjum
    January 19, 2009

    What I meant as in “3 times as significant” is that it used far more SNPs (more than 3 times) than the other study. If you can suggest another terminology, it would be appreciated.

    Older paper, but still done in end of 2008, the same period as done on the paper using 200K SNPs. And the paper is 26 pages long, much much longer than the paper dealing with 200K SNPs.

    Also, forgot to mention that there are 10,000,000 SNPs in the human genome, and 650K SNPs is still quite a small number, but unarguably a better guide to population genetics than the 200K SNP paper.

  14. #14 razib
    January 19, 2009

    What I meant as in “3 times as significant” is that it used far more SNPs (more than 3 times) than the other study. If you can suggest another terminology, it would be appreciated.

    your clarification is what you should have used initially. “significant” has a particular connotation in science.

    And the paper is 26 pages long, much much longer than the paper dealing with 200K SNPs.

    look, you make yourself sound stupid citing page count. honestly. myer et al deal was a worldwide survey, the plos one paper was just focusing on asians. naturally there’d be a page length difference ;-)

    for distinguishing between populations i don’t think 200 vs. 600 K makes that much of a difference. or they shouldn’t. that’s why i don’t put as much weight on the multiplicative difference as you do. i am agnostic as to which paper to go with. i don’t think anything is definitive right now. you should just chill and stop waving the myer et al paper around as “proof.”

  15. #15 mongobanjum
    January 19, 2009

    200K vs 650K has proved to make quite a difference, especially in that paper.

  16. #16 mongobanjum
    January 19, 2009

    I forgot to also mention that the study using 200K SNPs, it seems almost oblivious to me that CHB should be closer (FST distances) to the Mongols and Tungusic people than the Koreans. Obviously, the validity of the study is not normal as Koreans are much closer to Mongols and Tungusic people, genetically, than CHB should be, since Koreans have about 15-20% of the C3-M217(xC3c), and have a shared maternal ancestry with the northern populations (Mongols and Tungusic people). The C3c subclade is a secondary expansion that is rather recent (about 1000 years old).

    Also the phenotype resemblances between the Koreans and Mongols and Tungusic people is another factor that is not valid with the results in the study that used 200K SNPs. Any person with at least half a brain would notice that Koreans resemble Mongolians and Tungusic people far more than northern Han Chinese does.

    After one has seem many Japanese people, Japanese people on the other hand, with respect to phenotype, do not resemble Mongols and Tungusic people at all, rather, they resemble the southern Chinese and some ethnic groups of SE Asia. Japanese also lack the distinctly northern C3-M217, which is frequent on the neighbouring northeast Asian mainland.

  17. #17 deadpost
    January 19, 2009

    Interesting with the Southern men and Northern women in terms of reproductive success, but I’m just curious– Aren’t Southern mongoloids considered to be more “pedomorphic” than Northerners or vice-versa? Would the more pedomorphic tribe when meeting a new more robust tribe have ever lost out their females the style it happens today (see interracial dating and east Asians today)? Well, considering Ainu vs. Yayoi, perhaps not? What accounts for this? Less female choice in older times vs. new.?

  18. #18 Aung Zeya
    February 18, 2009

    The 650K SNP paper has been doing the rounds on the web as some sort of definitive proof of the place of Koreans within E Asian populations despite the study not including Koreans . I can’t help noticing the .png file has a speculative Korean cluster DIY’ed onto it :)

  19. #19 Alex
    February 26, 2009

    mongobanjum, LOL man. You make yourself look stupid.

    There is definitely a casually observed phenomenon which has Koreans and Manchu resmebling each other, admitted even by the Manchu who are the most virulent anti-Koreanists. Manchu’s language is Tungusic(originally) but their genetics has been found to differ significantly from other Tungusic peoples.
    Also phenotypical resemblance does not necessarily translate into genetic affinity. But most of time with the right time depth(of genetic markers) this can be seen. We will see if this can be captured with the refinement of genetic markers.

    This new paper is inherently flawed because it is based on the flawed Kim W’s data that seem to have problem with typing SRY465(I personally talked to underhill). Chris Tyler-Smith was probably just put in there. He probably does not even know that he was listed as a co-author. I know this because I worked in this field.

    SRY465T has not been so far detected outside Korea/Manchuria/Japan except some sporadic presence among Vietnamese, Mongols etc.
    To class it as “southern lineage” is comical at best.
    Korea also has a regional variation and it appears that the south-western region on which W Kim is based has a higher percentage of M122C. Anyway I will do the talking with my paper.

    And aung zeya, you are being hysterical and makes yourself look even stupider than mongobanjum. That figure is included in the original paper. Are you chinese?

  20. #20 mongobanjum
    February 28, 2009

    I got this PCA chart from decodeme genetics, which uses more than/approximately 1 million SNP in their analysis
    http://img413.imageshack.us/img413/8438/73797387ys1.png
    I wouldn’t be surprised if at least one Korean sample was added, he/she would fit into the empty space around the lone “Mongola” point, which is closest to “Northern Han”(aka CHB) and “Japanese”(aka JPT- Tokyo). AFAIK they used the HGDP sample, which was also used entirely in Myers et al(2008).

    It appears that with more and more SNP tested, the “Japanese” are inclined more towards the southern populations (being almost identical to northern Han in terms of the north-south migrations axis using >1000K SNP) and the Tu are more inclined towards northern populations. It also comes without any doubt that the samples within each cluster are separated more clearly, while it has little effect in separating clusters from other clusters (look at JPT and CHB, and also Naxi and Yi). In fact, it sometimes has the opposite effect, bringing some clusters closer together.

    To say studies using different numbers of SNP (particularly a higher multiple difference) should not differ significantly is definitely flawed.