November 07, 2012

Major new Ainu genetic study forthcoming

Genetic kinship found between Ainu and native Okinawans (The Asahi Shimbun):
The researchers examined and compared the DNA of 36 Ainu, 35 native Okinawans, and 243 people living in Honshu and elsewhere in Japan. They also studied the DNA of ethnic Han Chinese living in Beijing. The Ainu DNA was from stored samples that had been collected about 30 years ago.

The analysis found that the DNA of the Ainu bore closest similarity to people who had lived for generations in Okinawa. There was increasing dissimilarity with--in this order--those from Honshu, South Koreans and Chinese.
Meanwhile, the researchers found that the DNA of people living in Honshu showed similarities with that of South Koreans and Chinese.

The findings were to be published Nov. 1 in the Journal of Human Genetics.
I don't see the paper on the journal site yet. Loh et al. (2012) were able to infer that admixture in the Japanese occurred 45 +/- 6 generations ago, and involved at least 41 +/- 3% Yayoi ancestry. Another recent paper (He et al. 2012) estimated 23.1∼39.5% "Paleolithic" ancestry in mainland Japanese. But both studies lacked an Ainu genetic sample, which will apparently now become available (and I hope publicly so).

It will now be possible both to do a 2-reference text of admixture with software like ALDER for the Japanese, but also, and perhaps more importantly, to do a 1-ref test of admixture for the Ainu themselves! It is important to remember that the Ainu are not unmodified descendants of the Jomon, and their own ancestry is likely to be complex.

And, there will now be a second population of Y-haplogroup D descendants (the Ainu) to complement the Andamanese islanders genotyped by Reich et al. (2009). It is not clear to me whether there will be any autosomal signal left to link these peoples together, but the issue can now be investigated.

Finally, there is the whole issue of the relationship of the Ainu with West Eurasians; while research has not been supportive of that notion, it may still be useful to see whether the hirsuteness of the Ainu and other phenotypic similarities with Europeans have the same genetic aetiology or not. A link of a different kind that might be useful to investigate is the East Eurasian/Amerindian-like gene flow into Europe which seems to be more pronounced for Amerindians: will the signal also be present for the Ainu, and how strong will it be? And, of course there is that whole other issue of levels of affinity to Eurasian archaic hominins...

It is great that the last few gaps in our sampling of world genetic variation are being filled. Time and again we have discovered that at the "edges of variation" we often find the most interesting nuggets of information about our prehistoric past (e.g., Sardinians re: prehistoric Europe, Australo-Melanesians re: Denisovan admixture, Amerindians re: North Eurasian admixture in Europe, Khoe-San re: earliest divergences in the human family). The Ainu are likely to offer us new insight not only about their own origins, and those of the Japanese, but also about events taking place much further from the isles of Japan.

11 comments:

bfde8a60-7627-11e1-94ed-000bcdcb471e said...

Hmm..admixture age of 1300 years seems a bit recent. Yayoi cultures started several hundred years earlier.

Ezr said...

"Hmm..admixture age of 1300 years seems a bit recent. Yayoi cultures started several hundred years earlier."

---That they "started" doesn't mean they got to the northernmost areas early.

The Ainu are probably descended from a very small subset of the pre-Yayoi population, one that was isolated in Hokkaido until recently, then expanded to northern Honshu when it was abandoned due to climate change and then receded back to their Hokkaido refugium when Japanese expansionism began -

Witness the obvious and transparent Ainu etymologies of many northern Honshu places, suggesting shallow linguistic separation across the strait (not to mention the lack of linguistic diversity of Hokkaido and Sakhalin Ainu itself).

When you look at it from that angle and look at the history of northern Honshu, 1300 years becomes too early, rather than too recent.

pconroy said...

@1,

But if Yayoi farmers settle among Jomon hunter-gatherers, they would probably remain a distinct ethnicity for some time - maybe centuries - before they started admixing with them

Slumbery said...

bfde8a60-7627-11e1-94ed-000bcdcb471e:

Admixture does not happen overnight after the populations met, so this is not strange.

I also can't wait for more details.

Jim said...

"Yayoi cultures started several hundred years earlier."

Yes, but that does not mean the admixture did.

Onur said...

The non-Yayoi genetic element in the Ainu must be a good representative of the genetics of the pre-Yayoi population of the entirety of what is now Japan, as the fact that the two geographically most remote and at the same time the least Yayoi-admixed populations of Japan, the Ainu and Okinawans, show the greatest genetic similarity to each other strongly indicates that the pre-Yayoi population of what is now Japan was genetically quite homogeneous. Hence the non-Yayoi genetic element in the Ainu must be well representative of the genetics of the pre-Yayoi inhabitants of the entirety of what is now Japan. Any conjecture about the earliness of the ALDER-based inferred date of the Jomon-Yayoi admixture in the general Japanese population does not make any sense. The ALDER-based inferred date is too late for that admixture in a historical and archaeological sense. That must be because of the continuous and complex nature of the Jomon-Yayoi admixture process and the simplistic nature of the dating methods rather than the lateness of the Jomon-Yayoi admixture process.

Andrew Oh-Willeke said...

The very high percentage of Jomon ancestry in the Japanese is pretty remarkable (and consistently fairly high across different methodologies for estimating it compared to other similar first farmer admixture cases), given that the Jomon are usually conceptualized as being a hunting-gathering population that encountered the rice farming Yaoyi with mounted horsemen, although their culture was more sedentary (it had one of the earliest pottery making cultures) than most which was made possible by its fishing means of subsistence similarly to the Native Americans of the American Northwest and also similar to the Pitted Ware/Comb Ceramic Uralic peoples of far Northern Europe who were among the last Europeans to convert to farming and herding.

Northern Honshu was not under Yaoyi control until ca. 1000 CE and was probably part of the same population culturally, genetically and linguistically as the Ainu until then, which is many centuries after the rest of the island had been fully assimiliated and I understand that there is some discernable genetic trace of this distinction in contemporary populations in Northern Honshu.

But, 1300 years still sounds to young for a representative sample of Japanese people as a whole, which the the moderate deviation in Northern Honshu which would make up only a small part of the total sample shouldn't modify much.

One complicating factor may have been that representing the genetic source of the Japanese as a single Jomon-Yayoi admixture event may be a poor fit to history. Subsequent to first contact the was sustained and continued moderate levels of migration into Japan from the Chinese Empire that continued until perhaps 1,300 years ago (mostly in the form of high prestige body type women, skilled farmers, literate technocrats, and servants). ALDER may be flagging the end of that several century period of gradual demographically significant migration (not that different in character from 19th and 20th century immigration to the U.S. and Europe) rather than its beginning.

This migration also made a very material contribution to the Japanese language lexically, although it does not appear to have altered the core grammatical structure of the Japanese language very much.

terryt said...

"The analysis found that the DNA of the Ainu bore closest similarity to people who had lived for generations in Okinawa. There was increasing dissimilarity with--in this order--those from Honshu, South Koreans and Chinese.
Meanwhile, the researchers found that the DNA of people living in Honshu showed similarities with that of South Koreans and Chinese".

Is there anything at all surprising in that? I have always assumed that what Onur has said is correct, 'the non-Yayoi genetic element in the Ainu must be well representative of the genetics of the pre-Yayoi inhabitants of the entirety of what is now Japan'.

"Finally, there is the whole issue of the relationship of the Ainu with West Eurasians; while research has not been supportive of that notion, it may still be useful to see whether the hirsuteness of the Ainu and other phenotypic similarities with Europeans have the same genetic aetiology or not".

I suspect that the Australian Aborigines will prove to be closer to the Ainu than will West Eurasians. Mind you, I fully accept the possibility that all three will be related.

Justin said...

Excellent write-up by Dienekes.

I'm interested in whether this genetic study can confirm that the Ainu and Okinawans have genetic affinities with Melanesians, Papuans and other Australoid populations.

If not, I hope ADMIXTURE runs can be done comparing the genotypes of the Jomonese populations of Japan with other populations.

The interesting thing is that the Ainu and Okinawans have mostly wet earwax and Sundadont dental pattern. Continental Northeast Asians (particularly Northern Han Chinese, Koreans and Tungusic peoples) have dry earwax and Sinodont dental pattern.

It's also worthy to note that the Ainu are not the true descendants of the Jomon because there is evidence of inter-marrying of Ainu with Nivkhs and other nearby populations.

It is more likely that the Okinawans are better representatives of the Jomon population.

terryt said...

"One complicating factor may have been that representing the genetic source of the Japanese as a single Jomon-Yayoi admixture event may be a poor fit to history".

Yes. The idea that just two populations have entered Japan is extremely unlikely. Japanese haplogroups are quite diverse, probably indicating diverse source populations. Y-DNA C1, C3, D2, O2b and O3 probably each came in independently. And Japan has a very diverse selection of mt-DNA.

Pat and Sawa Savage '07 said...

Publication was delayed because of server problems due to Hurricane Sandy, but it's up online now open access here: http://www.nature.com/jhg/journal/vaop/ncurrent/pdf/jhg2012114a.pdf

It's important to note that, although the Ainu are *closest* to the Ryukyu, they're still very different from them and from everyone else. Also, the most likely candidates for Siberian admixture (Nivkh, Koryak, etc.) were not analyzed. Still, quite powerful support for the Ainu-Ryukyuan dual origin hypothesis, although I personally think that the "dual structure" hypothesis, although useful, is a little too simplified with regard to the Ainu.