Korean genetics: between China and Japan with some unique personality

New paper on Korean genetics:

Jonshung Jung, Hoyoung Kang et al. Gene Flow between the Korean Peninsula and Its Neighboring Countries. PLoS ONE 2010. Open access.

The most relevant results are probably in these graphs that follow:

Figure 3: Genetic Structure

Legend and details for the various samples can be seen in figure 2. Notice please that CB (Cambodian) is mistakenly placed in Northern Asia, when it should be in Southern Asia (i.e. SE Asia) along with Vietnamese (VN) and Vietnamese-Koreans (VC probably though elsewhere tagged as VK).

Notice also that there are two K=5 in the global cluster analysis (C), one of them marked as RH, what means "recombination hotspot", which is a technical albeit interesting matter they deal with in extent in the supplementary materials. The conclusion seems to be that these recombination hotspots can induce distortions in the cluster analysis and that should be dealt with in order to prevent confusing results.

Anyhow the most valid run for the global dataset is surely K=4, showing four neatly distinct clusters: Africans, Europeans (or West Eurasians), Amerindians and East Asians. The minor "admixture" apparent levels among Amerindians and some East Asians (Mongolians, Cambodians) may or not mean admixture. In my opinion, based on comparison with other different studies, I think it does not but rather indicates a lesser degree of affinity with the main cluster and therefore some small degree of affinity with other Eurasians. Careful sampling strategies, such as the one done by Hui Li last year may be needed to discern what exactly means, if anything at all.

Most probably the "European affinity" apparent in these two cases just means some Central Eurasian (or Siberian) affinity of Mongols, as shown in Hui Li's paper, as well as in Amerindians, and some South Asian affinity of Cambodians as detected for neighboring Thais in the recent paper by Jinchuang Xing.

When comparing East Asians alone (B), three clusters are apparent (K=3): a "Mongolian" one (blue), a SE Asian one (green), more intense in Cambodians than Vietnamese, and the middle East Asian one including Chinese, Korean and Japanese (and largely Vietnamese too). K=4 seems to indicate a diffuse (low level) Japanese-Korean affinity but this is better seen in the middle East Asian comparison.

In panel A (with only Chinese, Koreans and Japanese), we can see three clusters again (K=3): Chinese (green), Japanese (red) and Korean (blue). However most Koreans are not clearly differentiated from their neighbors, specially Chinese, and only the insular population of Jeju shows a much stronger Korean-specific homogeneity (though still with some Japanese influence).

Figure 4: MDS and NJ Tree of Korean, Chinese and Japanese


MDS stands for multidimensional scaling, a way of visually presenting statistical data in two or more dimensions, somewhat similar to PCA. NJ stands for neighbor-joining, a method used to build affinity trees in genetics that you are probably familiar with.

According to the legend, in the MDS plot (A) the 1st (horizontal) dimension includes 90% of the variance, while the 2nd (vertical) dimension only 1%! It could perfectly be a linear plot with most East Asians clustering to the left and a small odd group to the right. This "odd group" is mostly made of SE Koreans, plus three Japanese Koreans (from Kobe) and one Kobe Japanese.

However this must be an error of the legend and the vertical axis is without doubt the 1st dimension. Notice the scale, which is of 1/1000 order of magnitude in the horizontal axis and only 1/10 in the vertical one. Notice also how a China-Korea-Japan, with some eccentricity for Korea, is fully consistent with all other data provided.

The NJ tree indicates an apparent first divergence in three branches:

1. A Japanese-only branch (most Japanese fall here)
2. A mostly Korean branch, including also one Japanese and three Chinese
3. The major branch including most Koreans and Chinese, as well as two Japanese. This one, in turn splits in:

3a. Including the two remnant Japanese and all the rest being Koreans.
3b. A large branch including only Koreans and Chinese. It divides in two:

3b1. Almost only Koreans (only one Chinese here I think), with high incidence of SW Koreans.
3b2. Many Koreans too (with high incidence of SE Koreans) plus most Chinese, concentrated in a particular sub-branch (bottom of graph).

Caution must be placed to Korean-centric readings in any case because Koreans are clearly oversampled, what is surely distorting the tree structure to at least some extent. However if this structure could find confirmation in further more balanced studies, it might well support a colonization process along the coast, which is pretty much mainstream these days.

Koreans anyhow mostly cluster with Chinese here too, which is consistent with the STRUCTURE analysis, showing some SW-SE (West-East?) internal polarity in the peninsula.

Notice that no sampling was undertaken, without doubt because of the political circumstances, in the northern half of the peninsula. Notice also that both Chinese samples are from the North (Beijing and Manchuria).

New paper on Y-DNA haplogroup C

Natsuya points me to this new paper on the distribution and likely spread of Y-DNA haplogroup C, with special focus on East Asia and subhaplogroup C3.

Hua Zhong et al. Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. Journal of Human Genetics 2010. Pay per view (but you can read it freely at ZohoViewer).

CONCLUSIONS
We demonstrated the phylogeographic distribution of one of the most ancient non-African Y-chromosome lineages, from which we inferred the prehistoric migration and expansion of the Hg C lineage. We propose that Hg C was derived from the African exodus and gradually colonized South Asia, Southeast Asia, Oceania and East Asia by a single Paleolithic migration from Africa to Asia and Oceania, which occurred more than 40KYA. The prehistoric northward migration of Hg C in mainland East Asia likely followed the coastline and is consistent with the northward migration of other East Asian Y-chromosome haplogroups.

Nothing too new as you can see, however the the data detail and the neighbor-joining trees of haplotypes for C3 and C5 are of some interest, suggesting that C3 probably coalesced a Mid-East Asia (China and surroundings) rather than SE or NE Asia.

C6 was not located anywhere, suggesting that it's just a very minor clade. In contrast South Asian specific C5 was detected among 2.5% of Indians and 1.5% of Southern Pakistanis, reminiscent of a back-migration from SE Asia by the same "coastal route" that was used to reach SE Asia at an earlier moment.

It's interesting also the still rather high amount of undefined C* found in various areas: 4.6% in Philippines, 5.6% in East Indonesia, 5.9% in Micronesia, 5.6% in Australian Aborigines, 9.1% among the Mulau of Guangxi, 6.9 among the Shui of Guizhou, 7.6 among the Yao of Guangxi, 7.7 among the Tujia of Hubei, 8.2 among the Hui of Ningxia and 6.7 among the Hezhe of Heilojiang. It is also potentially interesting the 0.5% in India because it might have greater densities in some of its very diverse populations (but it's treated as a single homogenous sample in this paper).

East Asian autosomal genetics, second round

I already commented on the HUGO paper (paywall, but full PDF here) before as a "working note". Recent discussion at another blog has got me working again on it.

I ended up with this map reflecting as well as possible the geographical distribution of the various components:


Names (arbitrary but descriptive) are my creation, as are the arrows illustrating possible gene flows. Question marks indicate where there's lack of data. Continuous lines indicate "pure" areas, dotted lines indicate greater or thinner presence of each component.

I suspect that the blue component represents the Neolithic stock, spreading first autonomously and then also (but more limitedly) in admixture with other components. If so, the other major components may have receded before it or may have just absorbed each other in mutual interactions.


Observations

The expansion of the Peninsular component to Indonesia did not carry the Neolithic component. So either is pre-Neolithic of was made by non-mixed Austroasiatic peoples after getting the "neolithic package" from further north without getting the genes.

The expansion of the Neolithic component to sub-Hymalayan South Asia did not carry other Eastern components, so it happened before or, in any case, in a separate way to admixture with other East Asian groups.

The South Maritime (Austronesian) expansion happened also independently from any genetic input, other than admixture with native Austronesians and Melanesians (West and East of Wallace Line respectively)

North and South Maritime populations did not interact, not even in the mainland, excepting Han expansion. This is quite curious and might explain the physiognomic differences between northern and southern "Mongoloids" much better than old hypothesis of admixture with Negritos/Melanesians.

Several distinct aboriginal groups seem to have receded before Austroasiatic and Austronesian expansion without significantly penetrating the settlers' genetic pools. These are mostly Negritos (Malay and Filipino) but also the Proto-Malay and the Mentawai. The Hmong, even if a larger ethnicity, can be argued to have suffered a similar destiny, absorbing a lot of Neolithic component and impacting other groups only minimally. In this they are similar to Austroasiatics, though in ISEA, the overlaying component is Austronesian, not Continental (and they have been absorbed linguistically).


Reconstructing the past

A plausible reconstruction of pre-Neolithic/Early Neolithic distribution could be this map:

Colors as above. I ignored the Mlabri and Proto-Malay. Please don't be too nit-picky with the necessary/convenient simplifications, thanks.

I understand that some quite reasonable ethnic interpretations can be made:

Sino-Tibetan: Neolithic Blue with various mixtures. Northern Neolithic may soon have evolved into a Blue-Yellow mix speaking proto-Sinitic.

Tai-Kadai (Kradai): Neolithic Blue with South Maritime Green (Southern Neolithic genesis).

Austroasiatic: Red, often with Neolithic Blue. Must have existed in Sundaland prior to Austronesian expansion and prior or simultaneous to Neolithic (Blue) expansion. Did they arrive there as Neolithic settlers, Epipaleolithic maybe, or were there "all the time"?

Austronesian: Bright Green, often in admixture. Must be original from the Taiwan-Philippines-SE China area.

Hmong-Mien: Along with their ethnic component (Light Blue), they display Neolithic Blue with minor Bright Green, suggesting that they adopted Neolithic before Tai-Kadai genesis. They have absorbed some Tai-Kadai blood but their genesis seems older than that (peripheral South Neolithic genesis).

Melanesian, Filipino Negrito and Malaysian Negrito are three different stocks.

New paper on Chinese autosomal microsatellites

I'll comment more tomorrow maybe but here is the link anyhow.

Hongbin Lin et al., Genetic Relationships of Ethnic Minorities in Southwest China Revealed by Microsatellite Markers. PLoS ONE 2010. Open access.

Something that seems pretty obvious is that Guandong Chinese (Han) cluster apart from Northern Chinese (Han) and together with SE populations (Tai-Kadai and Mon-Khmer). However there is no absolute divide and depending on the method of analysis used populations cluster somewhat differently.

The most divergent groups are Tajiks (no surprise here) and the Drung a small Tibeto-Burman nation from Yunnan.



Update (Oct 17 2012): 

I never really got to review this paper properly but at the very least I must include here fig. 3:

... and fig. 4:

... which illustrate how Southern Han from Guangdong cluster with other SE Asians (specially Daic peoples) and not Northern Han (nor Tibeto-Burman, nor Mongol). Even more clearly than some other Southern ethnicities.

Macro-haplogroup N in East Asia, Chen 2009

A reader has been so kind to send me a copy of this Chinese paper, which I have hanged at ZohoViewer:

Chen Zhiyong, Migration and Diversification of Mitochondrial Haplogroup N in EastAsians. Communication on Contemporary Anthropology 2009.

The paper is in Chinese (and can't find any English version) but has loads of nice and informative graphs and maps with legend in both languages about macro-haplogroup N and some of its derivatives, specially A and N9 (incl. Y).

As the saying goes: an image is worth more than a thousand words... specially if these are in a language you can't understand. Still, if any of you can read some Chinese and give some feedback, I'm of course interested.

Most importantly the paper seems to confirm a SE Asian origin for macro-haplogroup N. Specifically it suggests a SE Asia as probable origin:

Fig.2 A simplified Median-joining Network of haplogroup N based on mitochondrial HVS-1 Keys for the colors: Red for the Tonkin Bay area, Green for South China, Orange for North China, and Blue for Southeast Asia.

Fig. 4 The frequency distributions of unclassified N [top] and N*(16223) [bottom]

Another relevant finding is that haplogroup A seems to be also original (like nearly everything) from South China/SE Asia:

Fig.10 Diffusion of the mitochondrial proto-A haplogroup. Blue clines stand for the total frequency, and red clines stand for the mutation rate within the population.

Notice that "proto-A" seems to mean A* rather than some pre-A standing between the N and A nodes. That's what I gather from the phylogenetic context in other figures but if anyone can clarify further, I'll be thankful.

Finally as the genetics of SE Asia and in particular Island SE Asia have been recently matter of lengthy discussions in this blog, I think that this map on ISEA N9 (N9a and Y2) may be interesting:

Fig.28 Distributions of the mitochondrial haplogroups Y2 and N9a in Southeast Asia. Blue stands for Y2, and red for N9a6.

But anyhow, take a look at the paper even if you can't speak Chinese because there are a lot of maps and phylogenetic graphs, all of them of interest.

One thing they have in common though: the spread of all lineages seems to begin in South China/SE Asia.

East Asian autosomal DNA (working note)

This is a highly simplified (approximate, tentative, very rough) geographical interpretation of the HUGO consortium autosomal DNA clustering (paywall but someone hang it HERE - look at the details and not just this poor map, a mere working note, before assuming too many things, please), which produces five major components for East Asians and Melanesians at K=14. The rest are minority components (represented as circles) or South/West Asian ones (not shown here).

Continuous lines show the approximate areas with 50% or more of that component, dotted lines the areas (also approximate) with 20% or more.



Only three of the main components appear as majoritary in some populations: the yellow component, which reaches its highest frequency among Ryukyuans, the light green component which can be described as "Austronesian" but that is also important among Tai-Kadai and Southern Han and the dark green component, which is highest among Boungaville Melanesians and then in Eastern Lesser Sunda (Alor) and could be described as "Melanesian".

The red component is highest among Austroasiatic speakers, as well as Malaysian Malays, including Sea Dayaks (but not Proto-Malays nor Orang Asli), Javanese and Sundanese. The blue component is widespread among continental East Asian peoples (and Hymalayas) but shows no area nor ethnicity where is most concetrated.

Minor components (big dots) correspond to the Hmong-Mien (cyan, which share the blue and light green components too), the Mlabri (light purple, a tiny Austroasiatic hunter-gatherer group), Orang-Asli Negritos (dark red), Proto-Malay (purple-blue), Land Dayaks (grey here but white in the paper) and Filipino Negritos (dark purple).

Related posts:
- East Asians originated in SE Asia
- Indonesian Y-DNA is mostly Paleolithic
- Genetics of the Mlabri, Austroasiatic hunter-gatherers in Thailand

See also the supplementary materials: even more details!

Genetics of the Mlabri, Austroasiatic hunter-gatherers in Thailand

Shuhua Xu et al., Genetic evidence supports linguistic affinity of Mlabri -- a hunter-gatherer group in Thailand. BMC Genetics, 2010. Open access.

Abstract (provisional)

Background

The Mlabri are a group of nomadic hunter-gatherers inhabiting the rural highlands of Thailand. Little is known about the origins of the Mlabri and linguistic evidence suggests that the present-day Mlabri language most likely arose from Tin, a Khmuic language in Austro-Asiatic language family. This study aims to examine whether the genetic affinity of the Mlabri is consistent with this linguistic relationship, and to further explore the origins of this enigmatic population.

Results

We conducted a genome-wide analysis of genetic variation using more than fifty thousand single nucleotide polymorphisms (SNPs) typed in thirteen population samples from Thailand, including the Mlabri, Htin and neighboring populations of the Northern Highlands, speaking Austro-Asiatic, Tai-Kadai and Hmong-Mien languages. The Mlabri population showed higher LD and lower haplotype diversity when compared with its neighboring populations. Both model-free and Bayesian model-based clustering analyses indicated a close genetic relationship between the Mlabri and the Htin, a group speaking a Tin language.

Conclusion

Our results strongly suggested that the Mlabri share more recent common ancestry with the Htin. We thus provided, to our knowledge, the first genetic evidence that supports the linguistic affinity of Mlabri, and this association between linguistic and genetic classifications could reflect the same past population processes.

While finding out about the Mlabri, an ethnicity I had never before heard of, and confirming that hunter-gatherers of Austroasiatic language do not just exist nowadays in Malaysia, is interesting in itself, what most has provoked my attention is the genetic comparison between various South East Asian ethnicities and the HapMap North Chinese and Japanese samples.

It seems that the paper has come right in time to illustrate the ongoing debate elsewhere on this blog, on whether there is any specific marker to Northern Han (or even Han in general) and other major East Asian populations such as Koreans and Japanese.

What I am realizing is that there is nothing really specific and that these northern populations almost invariably cluster with some of their southern neighbors, which are much more diverse. This really surprises me a bit because I would have expected that the Neolithic of the Yellow River, surely at the origin of the Chinese ethnicity (Han, Hui) would have been created by a somewhat distinct group that we should be able to identify by some genetic marker or set of markers, even if they spread southwards as the Chinese empire did.

Not at all. It seems that such specificity is almost invisible and that the Han (as well as genetically similar Korean and Japanese peoples) are very much unspecific in terms of genetic markers that could be easy to spot. They rather seem like melting pots of lineages which are traced to likely origins in the South of East Asia.

And, as I say this study comes very handy to illustrate this pattern within autosomal DNA as well, with Chinese and Japanese clustering with Hmong-Mien specially and then with Tai-Kadai peoples.

The neighbor-joining (NJ) tree:

The Htin and Mlabri are of course Austroasiatic, even if color-coded differently. JPT stands from Japanese from Tokyo and CHB as Chinese from Beijing (they are standard HapMap samples). The Karen are Tibeto-Burman speakers.

The maximum likelihood (ML) tree:

Careful here because the color-coding is not linguistic. As said before the Karen are Tibeto-Burman speakers and not Austroasiatic as would seem from their clustering and red color. CEU are Caucasoids of European ancestry from Utah and YRI are Yoruba from Nigeria (again standard HapMap samples for comparison). Cursive text is mine.

In this ML tree is maybe where the clustering is more apparent: the whole East Asia is first divided between the Mon and all the rest. They are neighbors of the Karen and linguistically most related to other Austroasiatics but they clearly cluster apart from all.

Then they branch into other Austroasiatics plus Karen (TB) and Tai-Kadai, Hmong-Mien and northern ethnicities. And this last group branches out into Tai (a branch of Tai-Kadai) and an amalgam of other Tai-Kadai (Yao), Hmong-Mien (Hmong) and the northern ethnicities. And only at this stage a North-South divide becomes apparent.

East Asian alcohol intolerance gene mapped

Yi Peng et al. The ADH1B Arg47His polymorphism in East Asian populations and expansion of rice domestication in history. BMC Evolutionary Biology, 2010. Open access.

The authors have mapped the allele for alcohol intolerance within the gene among Chinese populations, both Han and non-Han (cf. table 1 for frequencies). There are sharp differences among ethnicities with Tibeto-Burman and Austroasiatic nations showing low levels of the allele.

The highest densities of the allele are in the province of Zhejiang, just south of Shanghai, where nearly everybody is alcohol intolerant. The authors have estimated possible ages for the origin and spread of this allele and conclude that it originated and spread with rice agriculture. However I am not fully convinced, as happens with all molecular clock estimates. Whatever the case it does seem reasonable to accept that the seemingly oldest variants of the allele are in Central/South Western China.


Above: map of the alcohol intolerance allele included in the study (notice that the Chinese border is pretty much fictitious, including all claims the PRC may have) with clines of frequency and symbols for different estimated ages.

Notice that if the claim of Neolithic origin and spread of this allele is correct it would frontally clash with the notion that the Mongoloid morphotype spread within this same period. Personally I am pretty much skeptic of both claims. However I can imagine that this allele may have spread along some South to North demic expansion like the one associated to Y-DNA haplogroup O maybe.

East Asians originated in SE Asia.

Just found at Dienekes what seems to be the definitive evidence for a south to north colonization of East Asia. This was quite obvious to me but will be hard to swallow for those who are used to other classical (but seemingly erroneous) interpretation.

The press release emphasizes this fact:

The scientists also reported a clear increase in genetic diversity from northern to southern latitudes. Their findings also suggest that there was one major inflow of human migration into Asia arising from Southeast Asia, rather than multiple inflows from both southern and northern routes as previously proposed. This indicates that Southeast Asia was the major geographic source of East Asian and North Asian populations.

The HUGO Pan-Asian SNP Consortium, Mapping Human Genetic Diversity in Asia. Science, 2009. (Paywall but supplementary material is free).

From the supplemental material I picked this max. likelihood tree, where the Eastern Eurasian divergence node seems quite apparent:

click to expand

Notice that the Papuan sample is negligible: only 5 individuals!

Also discussed at BBC.

Dog origin anywhere in Eurasia

It was claimed some years ago (Savolainen et al., 2002) that dog domestication had happened apparently in East Asia, reasoning based on the genetic diversity of the animals sampled in that region. But now new research by Adam Boyko and colleagues challenges this after having sampled numerous dogs through Africa, while in honeymoon, Boyko has found that the diversity there is comparable to that found in East Asia.

But the study does not challenge the fundamental notion that the domestic dog descends from the Eurasian grey wolf (Canis lupus), so Africa cannot be the place where it was first domesticated. Where then? The question remains unanswered by the moment and East Asia could still be the place but the evidence is inconclusive.

The highest diversity found in Africa and East Asia so far doesn't seem to correspond to anything but the fact that village dogs, in contrast to purebreeds and mixes from these breeds, are intrinsecally much more diverse genetically. It is rural disinterest for dog breeding what has preserved that higher diversity, not any aboriginal pervivence.

It may be worth remembering here too that the oldest dogs found in the archaeological record belong to the Aurignacian culture of Europe, specifically in modern Belgium. It is also interesting to mention in this regard that this dog is apparently not the direct ancestor of modern dogs, at least matrilineally. (Note: I found another media article claiming that there are dog remains from Britain from before 100,000 BP, what would make the domestication a Neanderthal achievement - I cannot confirm this claim though).

Source: BBC.
.

From Archaeonews: oldest Taiwan hearth, Starcevo Neolithic 1000 years older

From Stone Pages' Archaeonews we get some brief entries of significance this week:

1. Oldest Taiwan hearth is 20,000 years old. The Baisandong hearth is the oldest sign of human presence in the island, pushing the known arrival of humans back by 5000 years.

2. Dig at Vinkovci (Croatia) re-dates the Neolithic Starcevo culture as 1,000 years older. The new datation is from c. 6000 BCE (or 8000 years ago).
.

Ainu finally recognized as indigenous people by Japan

After centuries of disrespect, land robbery and forced assimilation the descendants of the ancient Jomon people (the first known to work pottery anywhere, in spite of being hunter-gatherers) will be finally been acknowledged a status as indigenous group today by the Japanese Parliament.

The Ainu, descendants of the epipaleolithic Jomon culture dwelt once in all or nearly all Japan but were displaced by the agriculturalist Yayoi invaders beginning c. 500 BCE, who migrated probably from coastal China (Jiangsu province). In the following centuries they were displaced further and further northwards until the rather unhospitable island of Honsu became their last refuge.

An Ainu elder from the times of B&W photography

Japan has a centralist nationalist tradition and had so far declined to accept the existence of the Ainu as a separate ethnicity. They even called them "former aborigines", suggesting that assimilaton was the only way to go. Japan has also another ethnic minority in the south: the Ryukyuans, whose language is akin to Japanese (Japonic family) but different.

The new legal recognition comes as response of growing Ainu activism and ethnic pride in the last decades. It is so far only of symbolic value but should be the basic legal frame that may allow the administration to develope further measures in the future. Time will say but is at least a step forward.