A new analysis of two autosomal DNA samples from 3000 years old Jomon (indigenous Japanese) individuals has been released. This timing would be immediately before or at the time of first sustained contact with the mainland rice farming Yaoyi whose admixture with the Jomon grave rise to most of the modern Japanese gene pool.
Methodologically, this study is distinct because it pools the two ancient DNA samples into one composite sample for analysis of relatedness to other populations since the coverage for each of the individuals separately was poor. The discussion of efforts made to determine the validity of this approach in the paper convincingly demonstrate that this is proper for ancestry analysis purposes.
Like previous studies, it shows a greater Jomon affinity to the Japanese, and in particular to the Ainu and Ryukyuan populations than any other. Likewise, it shows Ainu admixture with Siberian populations that is absent in all ancient Jomon DNA samples and in the Japanese populations that have Jomon admixture from further south than the territory inhabited by the Ainu.
But, the study's estimate of the autosomal contribution of the Jomon to the modern mainland Japanese (12%) is on the low end compared to both prior studies (18%-35%) and the frequency of Y-DNA (35%-45%) and mtDNA (about 35%) traces of the Jomon in modern Japanese populations. It isn't obvious why this would be the case. Perhaps bias due to incomplete sample quality that prevents matches to Japanese DNA that would have been possible to make in better preserved samples could be a factor.
The study also suggests that the Jomon have a West Eurasian leaning genetically, relative to modern Asian populations and that this population, as expected, is basal relative to modern Asian populations other than Papuans.