This is a very good paper that I don't have time right now to write a long post about; I will update this entry with some excerpts and/or additional thoughts when I can.
The gist of it is that the prehistoric Jomon people of Japan belonged to mtDNA haplogroups tying them to southeastern Siberia, but some haplogroups present there today were lacking in them. Then, the Ainu seem to have inherited the Jomon gene pool, but their major lineages tie them to the Okhotsk people. So, it seems that the deepest ancestry of Japan is not peculiar to it, but rather an extension of ancient Siberian variation with different population strata attributed to the Jomon, the Ainu, and (probably) the modern Japanese.
AJPA DOI: 10.1002/ajpa.21561
Mitochondrial DNA analysis of Hokkaido Jomon skeletons: Remnants of archaic maternal lineages at the southwestern edge of former Beringia
Noboru Adachi et al.
To clarify the colonizing process of East/Northeast Asia as well as the peopling of the Americas, identifying the genetic characteristics of Paleolithic Siberians is indispensable. However, no genetic information on the Paleolithic Siberians has hitherto been reported. In the present study, we analyzed ancient DNA recovered from Jomon skeletons excavated from the northernmost island of Japan, Hokkaido, which was connected with southern Siberia in the Paleolithic period. Both the control and coding regions of their mitochondrial DNA (mtDNA) were analyzed in detail, and we confidently assigned 54 mtDNAs to relevant haplogroups. Haplogroups N9b, D4h2, G1b, and M7a were observed in these individuals, with N9b being the predominant one. The fact that all these haplogroups, except M7a, were observed with relatively high frequencies in the southeastern Siberians, but were absent in southeastern Asian populations, implies that most of the Hokkaido Jomon people were direct descendants of Paleolithic Siberians. The coalescence time of N9b (ca. 22,000 years) was before or during the last glacial maximum, implying that the initial trigger for the Jomon migration in Hokkaido was increased glaciations during this period. Interestingly, Hokkaido Jomons lack specific haplogroups that are prevailing in present-day native Siberians, implying that diffusion of these haplogroups in Siberia might have been after the beginning of the Jomon era, about 15,000 years before present.