Ainu/Ryukyuan paper

The paper I had mentioned earlier is online (and open access!) at the Journal of Human Genetics. From the paper:

The SNP genotype data determined in this study are available upon requests to corresponding authors, under the conditions of collaboration with us and with an appropriate approval of human genomic DNA research ethics committee of institutions to which researchers involved in the data analyses belong.

I guess that means that I won't be able to use this data, but hopefully it will be made available to academic researchers who can use it for different analyses than those presented in this paper, some of which I have suggested here.

For example, in my review of MULTIMIX, I noted that populations that have 100% of one component in ADMIXTURE analysis (which has the same model as frappe used here) are not necessarily unadmixed. So, for example, the frappe analysis shown at the top left shows some Ainu individuals fully on the "blue" Ainu cluster, and others having evidence of admixture. But, are the "100% Ainu" really unadmixed? Using either the aforementioned MULTIMIX or ALDER, it may be possible to show if even they have some admixture. And, using the methodology introduced in a recent Mexican admixture study it may be possible to create "virtual" unadmixed Ainu genomes.

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*: Timothy Jinam1,18, Nao Nishida2,19, Momoki Hirai3,19, Shoji Kawamura3,19, Hiroki Oota4,19, Kazuo Umetsu5,19, Ryosuke Kimura6,19, Jun Ohashi7,19, Atsushi Tajima8,19, Toshimichi Yamamoto9,19, Hideyuki Tanabe10,19, Shuhei Mano11,19, Yumiko Suto12,19, Tadashi Kaname13, Kenji Naritomi13, Kumiko Yanagi13, Norio Niikawa14, Keiichi Omoto15,19, Katsushi Tokunaga2,19 and Naruya Saitou1,16,17,19

Abstract

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.

Link