Ainu Origins

Razib has flagged a December 2012 study on autosomal DNA in Ainu and other Japanese populations.  The full study is pay per view, but the abstract is as follows:

57 Journal of Human Genetics 787-795 (December 2012)

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

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.

The Yayoi people arrived in Japan from Korea immediately following the Jomon period in Japan around 900 BCE to 800 BCE.  They brought with them the core of what would become the modern Japanese language, cavalry warriors, and the rice farming method of food production used on the mainland.  The precise Korean culture on the then balkanized Korean penninsula that was ancestral to the Yayoi is disputed, but linguistically there were not a Tibeto-Burman people although they were a people who had experienced considerable Chinese cultural influence.

The culture created by the fusion of the Yayoi superstrate and the Jomon substrate upon the arrival of the Yayoi in Japan did not include all of Japan's main Honshu Island until about 1000 CE or later. 

The genetic evidence shows that while the Jomon language and much of its culture was wiped out on Honshu, that a very substantial proportion of the genetic ancestry of the modern Japanese people is Jomon in comparison to other historically or archaeologically attested encounters between hunter-gatherer populations and farmers.  The Jomon had pottery long before they were farmers, contrary to the experience in the Fertile Crescent where there was a long pre-Pottery Neolithic period, and in most other places.

The Ainu and Ryukuan ethnic minorities in Japan are widely believed to have significantly more indigineous Japanese (i.e. Jomon) ancestry and less Yayoi ancestry than the majority ethnicity in Japan. This autosomal genetic study appears to confirm this conclusion.

But, the genetics of the Ainu come with a twist. The Ainu appear to have another ancestral component not present in the also Jomon derived Ryukuan people. The obvious guess in the absence of the closed access paper, based on uniparental data available about the Ainu, would be that this other component is some now existing or now extinct or moribund Northeast Asian Paleo-Siberian popuation.

The Jomon are also very notable for being the apparent source of Y-DNA haplogroup D, a paternal lineage that is virtually absent in mainland East Asia and Southeast Asia, which is absent outside Tibet and the Andaman Islands except for trace to moderate frequencies similar to the Tibetan rather than to Japanese populations in North Asia.  Y-DNA haplogroup D is more closely related to Y-DNA haplogroup E, which is the predominant Y-DNA haplogroup in modern Africa, than to any of the other Eurasian Y-DNA haplogroups.  This suggests that the members of this migration wave may have been part of a migration wave distinct from that of the main Out of Africa migration that was ancestral to most of the rest of Eurasia.

There are two possible "two wave" scenarios.  In one, the people of the Y-DNA haplogroup D came first and were brought to extinction by a later wave of migration in the remainder of East Eurasia, Australia, Melanesia and Oceania who arrived in Australia and Papua New Guinea not later than 45,000 years ago.  In the other scenario, the people of Y-DNA haplogroup D were a secondary wave of out of Africa migration to Asia that was left with the territory that the first wave populations didn't occupy, didn't want, or couldn't defend, not later than about 30,000 years ago when Japan and Tibet were first populated, which is still well before the last glacial maximum ca. 20,000 years ago.

In the latter scenario, which I think is more likely, the Y-DNA haplogroup D people could have migrated either via a coastal maritime "Southern route" along the Southern coast of mainland Asia, or via a "Northern route" travelling to Tibet and Japan via Central Asia and/or Siberia and then migrating from Tibet to the parts of South Asia and Andaman Islands where Y-DNA haplogroup D is now found from Tibet.  I am increasingly coming around to the Northern route, rather than the maritime coastal Southern route as the more plausible of the two possibilities.  Other routes, such as a migration first to South India, then to Tibet, and from Tibet onto Japan are possible, but not necessarily persuasive since the archaeological evidence points to Tibet being populated from the direction of China, rather than India.

However, there is strong circumstantial evidence to suggest that the original Y-DNA haplogroup D people overwhelmingly had mtDNA haplogroup M.  Neither Y-DNA haplogroup D nor mtDNA haplogroup M (or its descendants) are associated with any West Eurasian populations.  So, if this D/M population did migrate via a Northern route, it is not easy to explain why they left no West Eurasian relic populations.