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