Nov 082012
 

Journal of Human Genetics advance online publication 8 November 2012; doi: 10.1038/jhg.2012.114

The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations

Japanese Archipelago Human Population Genetics Consortium: Jinam et al.

The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.

[Rough first take follows, updates to come.]

Death knell of the “Caucasoid hypothesis”:


No obvious affinities between the Ainu and West Eurasians, not even a little tug towards the CEU pole.


Sans YRI this time. Obvious gradient of admixture (more below on those supposed Ainu right in the middle of the regular Japanese cluster).

A “strange drop of oil” still:

Are they Mongolian? If they are, they have none of the characteristics of that race; and if they are not Mongolian, then they are something like a strange drop of oil in the ocean, being surrounded by Mongols, yet not of them. — Royal Navy Captain H.C. St. John’s 1880 impression of the Hokkaido Ainu.


Lonely leaf on a long branch. Ryukyuans come out quite stably as their nearest sisters, but they’re still not all that close.


Northern vs. southern origin debate clearly not going to be solved by a straightforward crumbling out into “Siberians” or “southeast Asians”. The Ainu are a very differentiated kind of East Eurasian unto themselves.

Internal structure and outliers:

Authors suggest five individuals in red circle on PCA graph (which break out as all-purple at k=4 in the admixture chart) were potentially Sakhalin Ainu, some of whom relocated to the study locality following WWII. Component potentially related to Okhotsk Culture (northern maritime complexes pushing south).

As for the (supposed) Ainu inside Mainland Japanese cluster: there were some Mainland Japanese individuals who married Ainu people in Biratori Town when blood collection was conducted. These genetically non-Ainu people might have been included in the ‘Ainu’ samples we used. The well-known practice of adopting wajin infants could perhaps also account for this.

Either way, sounds like these samples could have benefitted from some better curating.

Admixture plot puzzles:


What accounts for those upticks of dark blue, if they’re actually meaningful, at k=4 and k=5 in Dai, Lahu, and Uyghur? Suspicion that something southerly’s afoot > “ASI”-Ainu connection?

Where to go from here:

It should be noted that Omoto conducted a pioneering study on the phylogenetic relationship of the Ainu population considering various degrees of admixture. When a 60% admixture with the Mainland Japanese was assumed for the modern Ainu population, the ancestral Ainu population was clustered with Sahulian (Papuan and Australian). This sort of simulations based on the real data is needed. Seconded.

What ought to be next: admixture analyses with Australian aboriginal and Papuan (wondering about “Australoid” and more specifically “Murrayian” connections), negrito (particularly Andamanese), Tibetan Plateau (Y-hg D … but keeping expectations low given what Wang et al. (2011) found re: Tibetans and non-Ainu Japanese), Indian subcontinental, and New World references. (Does the Amerindian-like component showing up in northern Europeans seem to be present in the Ainu as well?) “Paleoasiatic” Siberians (especially from Kamchatka and thereabouts), not just Turkic, Mongolic, and Tungusic ones, ought to be included too.

Archaic hominid ancestry values vis-à-vis other East Eurasians?

Future sampling: modern DNA from Nivkhs and other Amur-Sakhalin peoples; aDNA from various localities and time depths in Japanese archipelago (especially those Okinawan cave remains) of course, but also Korean peninsula and Russian Far East. Still more ambitiously, Paleoamerican aDNA (one wonders about all those Jomon-like Kennewick types). Just for kicks, Valdivia-era coastal Peru too.

Adaptive stories? EDAR and co. — wondering about basis of Ainu hirsuteness (and interesting combination of wavy yet very coarse hair), non-sinodont tooth patern. (And what’s going on with proportionally tiny teeth?) ABCC11 and wet earwax, apocrine gland development. Pigmentation alleles. Alcohol dehydrogenases.

  7 Responses to “Rockpool of a retreating sea: The Ainu in the genomic context of East Eurasia”

  1. So, the Caucasoid Ainu theory would seem to be the biggest mistake of mid-Century physical anthropology (e.g., Coon’s 1965 bestseller Living Race of Man). If that’s your worst mistake, that’s not too bad.

  2. The romanticism of the “lost white race” hypothesis was enough to earn it the lion’s share of proponents in America if not most of the West at that point, certainly so in the popular imagination, but Coon’s standpoint was far from the only one — other theorists argued for “Australoid” relationships or proposed that the Ainu were some sort of globally unique “racial isolate”. It looks like these perspectives will have aged a little better.

    (You should also recall that you had physical anthropologists insisting Australomelanesians and Asian negritos were true “Negroids”, that they fall out with Sub-Saharan Africans, which genomic data now very clearly show to be false. But again — despite attempts to portray the simplistic three-race framework as the end-all-be-all scheme — there wasn’t unanimity on this point; other people recognized an Australoid great race. That said, I think many even of these anthropologists would have been a little taken aback at how disparate, both from each other and relative to Melanesians and Australian Aborigines, the various negrito groups actually turned out to be.)

  3. So what exactly are CHB and JPT?

  4. So what exactly are CHB and JPT?

    These are population abbreviations from the International HapMap project: CHB = Han Chinese (Beijing); JPT = Japanese (Tokyo); CEU = Utahns of Northern and Western European extraction; YRI = Yoruba (Ibdan, Nigeria).

  5. The lack of a west Eurasian pull in Ainu doesn’t mean that Ainu are not an isolate in a sea of Mongoloids having affinities with west Eurasians. We don’t know the fraction of the Amerindian component in Ainu but we know that west Eurasians have Amerindian genetic affinities. Hence the Ainu -west Eurasian connection may still hold because both are just subsets of an Amerindian admixture.

  6. People are dismissing the idea of Ainu being ancestrally caucasoid.

    But one must remember that the Jomonese, ancestors of the Ainu were mainly mtDNA Nb,
    which has its origin in mtDNA N, likewise the Caucasoid people.

    Also, one must distinguish between the terms Europeans and Caucasoids, because Europeans are caucasoids but not all Caucasoids are Europeans.

    I think the roots of the Ainu lies among the Caucasoid and aboriginal Australian ancestors,
    including probably the ancestors of the Andamanese.

  7. I meant to say Jomon people were mainly mtDNA N9b.
    Wasn’t Cro-Magnon mtDNA N? Therefore positively related to Ainu ancestors.
    I think mtDNA N proves a connection between European and Ainu.

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