A new open access study of Japanese autosomal genetics reaffirms that conclusion and suggests a Northest Asian affinity of a Jomon component.
Our results showed that the genetic contributions of Jomon, the Paleolithic contingent in Japanese, are 54.3∼62.3% in Ryukyuans and 23.1∼39.5% in mainland Japanese, respectively.
Dienekes' rightly notes, however the possibility that some of the putatively Jomon genetic contributions may actually be a component of the Yayoi, who may have been an admixed population with Altaic (e.g. Turkish and Mongolian) and East Asian (e.g. Han Chinese) components.
Some background material in the paper is helpful in framing the issues, although less well fleshed out than one might hope if one was hoping for a really compelling multidisciplinary case for a particular hypothesis, and also a bit less open minded concerning more complex possibilities that the evidence suggests than one might hope.
In the ‘continuity’ model, modern Japanese are considered as direct decedents of Jomon, the inhabitants of Japan in Paleolithic time, while their morphology showed secular changes. In the ‘admixture’ model, Jomon admixed with the Yayoi, more recent continental immigrants, which is consistent with the rapid changes in morphology and culture which took place synchronically about 2,500 years before present (BP). In the ‘replacement’ model, Paleolithic Jomon was completely replaced by the continental immigrants (Yayoi) after their arrival. To date, the ‘admixture’ model is seemingly better supported by the increasing lines of evidence of multiple genetic components found in modern Japanese.
The upper Paleolithic populations, i.e. Jomon, reached Japan 30,000 years ago from somewhere in Asia when the present Japanese Islands were connected to the continent. The separation of Japanese archipelago from the continent led to a long period (∼13,000 – 2,300 years B.P) of isolation and independent evolution of Jomon. The patterns of intraregional craniofacial diversity in Japan suggest little effect on the genetic structure of the Jomon from long-term gene flow stemming from an outside source during the isolation. The isolation was ended by large-scale influxes of immigrants, known as Yayoi, carrying rice farming technology and metal tools via the Korean Peninsula. The immigration began around 2,300 years B.P. and continued for the subsequent 1,000 years. Based on linguistic studies, it is suggested that the immigrants were likely from Northern China, but not a branch of proto-Korean.
Genetic studies on Y-chromosome and mitochondrial haplogroups disclosed more details about origins of modern Japanese. In Japanese, about 51.8% of paternal lineages belong to haplogroup O6, and mostly the subgroups O3 and O2b, both of which were frequently observed in mainland populations of East Asia, such as Han Chinese and Korean. Another Y haplogroup, D2, making up 35% of the Japanese male lineages, could only be found in Japan. The haplogroups D1, D3, and D*, the closest relatives of D2, are scattered around very specific regions of Asia, such as the Andaman Islands, Indonesia, Southwest China, and Tibet. In addition, C1 is the other haplogroup unique to Japan. It was therefore speculated that haplogroups D2 and O may represent Jomon and Yayoi migrants, respectively. However, no mitochondrial haplotypes, except M7a, that shows significant difference in distribution between modern Japanese and mainlanders5. Interestingly, a recent study of genome-wide SNPs showed that 7,003 Japanese individuals could be assigned to two differentiated clusters, Hondo and Ryukyu, further supporting the notion that modern Japanese may be descendent of the admixture of two different components.
The linguistic reference made really doesn't fairly represent the linguistic evidence about the origins of the Japanese language (probably the strongest contender is that the Japanese is a descendant of a language of the Korean penninsula that died out in Korea when the Korean consolidated politically into a kingdom that spoke a different Korean language).
Japanese and Korean linguistic affinities, to the extent that they are not true linguistic isolates, are more Altaic than Sino-Tibetan (i.e. Chinese), even though Japanese has heavy lexical borrowings from Chinese and even though Japan shows a substantial East Asian genetic contribution. This is suggestive of a Yayoi population with an Altaic pastoralist horse riding warrior superstrate and a large East Asian rice farmer foot soldier substrate.
The paper also fails to address just how divergent D2 is from the other Y-DNA D haplogroups or how "bushy" it is, suggesting a long period of independent divergence from the other Y-DNA D haplogroups which overlap each other more completely. It is also a bit odd that mtDNA evidence, which is available for Japan, isn't discussed at all. Likewise, likely overall scenarios on the human settlement of Asia drawn from uniparental data and paleoclimate studies is not discussed.
It is disappointing to see a paper on Jomon genetic contributions that doesn't reference what little is known about Ainu genetics or even acknowledge its relevance. And, an absence of a fuller exploration of the settlement history of the Ryukyuans, which is mostly within or immediately prior to the historically documented era, or of the historically documented history of the settlement of Japan's main island, Hondo, on which Yayoi settlement was mostly restricted to the Southern part of the island until about 1000 C.E., is also regrettable (likewise, an absence of a sample from modern Hokkaidō limits the usefulness of the analysis).
The failure to consider those points matters because there are population models that deserve attention that don't receive analysis in this paper.
The Ainu are the closest living descendants of the Jomon and persisted longest in Northern Japan, where they were also most succeptible to subsequent influence from and admixture with Paleosiberians. Ainu genetic studies, limited as they are, suggest an original Ainu population that admixes gradually with Northeast Asian trading partners of Paleosiberian stock.
It also isn't obvious, however, that the Jomon were monolithic. This is a subject of considerable debate in the world of linguistics. It is possible that Southern Japan and Northern Japan may have had distinct indigeneous populations prior to the arrival of the Yayoi.