New aDNA data from Ainu of Edo period calls for review of dual structure population theory

Excerpted from Adachi et al.,’s 2017 paper:
Ethnic deprivation of the Ainu inferred from ancient mtDNA

Nowadays, among the theories explaining the population history of the Japanese, the dual-structure model proposed by Hanihara (1991) is the most widely accepted. This model assumes that the first occupants of the Japanese archipelago came from somewhere in Southeast Asia and they gave rise to the Jomon people. Thereafter, the second wave of migration from Northeast Asia took place in and after the Aeneolithic Yayoi age. These two populations gradually mixed with each other and brought the Japanese people into existence. In this model, the Ainu are considered to be descended from the Jomon peo- ple, with little admixture with other populations.
However, the results of our study suggest that the later admixture of Ainu with other populations than Jomon people was more consider- able than it was proposed until today.
First, our results showed that the genetic influence of the Okhotsk culture people on the Ainu is significant. The proportion of Okhotsk- type haplogroups in the Edo Ainu was 35.1%, which is as high as that of the Jomon-type haplogroups (30.9%). This suggests that the Okhotsk culture people were one of the main genetic contributors to the formation of the Ainu.
Moreover, intriguingly, a genetic contribution of the mainland Jap- anese to the Edo Ainu is evident (28.1%), which is almost as consider- able as those of the Jomon and the Okhotsk culture people. As referred to above, conventionally, the genetic influence of the mainland Japanese on the Ainu is considered to have been limited until the Meiji government started sending settlers to Hokkaido as a national policy in 1869. However, our findings cast doubt on this accepted notion.
In addition, Siberian-type haplogroups are observed in the Edo Ainu. Although their frequency is low (7.3%), as described earlier, the existence of these haplogroups may hint at the continuity of the genetic relationship between the Ainu and native Siberians even after the Okhotsk culture disappeared from Hokkaido. However, the number of Okhotsk people who were genetically analyzed is still small (n 5 37; Sato et al., 2009), so it is possible that these haplogroups will be identi- fied in the Okhotsk people in further study.
4.2 | Regional differences of the Ainu
By classifying the mtDNA haplogroups into four types as described ear- lier, regional differences of the Ainu people were highlighted. Judging from the data shown in Table 2, the high frequencies of Jomon-type haplogroups in northeastern/central Hokkaido (44.2%) and the high frequencies of mainland Japanese-type haplogroups in southwestern Hokkaido (37.3%) might be plausible reasons for these regional differences.
This result is consistent with the result of a morphological analysis by Ossenberg et al. (2006). They described that, among the Ainu in Hokkaido, individuals in southeastern Hokkaido (this area is contained within our category of “northeastern/central Hokkaido”) are the closest to the Jomon people, whereas the individuals in western Hokkaido (this area is included within our category of “southwestern Hokkaido”) are the closest to mainland Japanese. This result is considered reasona-ble, given the geographical proximity of southwestern Hokkaido to the main island of Japan.
However, surprisingly, there were no regional differences in the frequencies of the Okhotsk-type haplogroups (35.3% in southwestern Hokkaido and 34.9% in northeastern/central Hokkaido). This indicates that the genetic influence of the Okhotsk culture people diffused rap- idly in the fledgling Ainu.
As described earlier, Segawa (2007) stated that the invasion of the Satsumon culture people into the areas inhabited by the Okhotsk cul- ture people and the subsequent decline of Okhotsk culture occurred rapidly. The Okhotsk culture people were considered to have been assimilated rapidly into the Satsumon culture during this process, and became part of the basis of the Ainu.
In the current study, we clarified that the Ainu were established from the Hokkaido Jomon people and subsequently underwent considerable admixture with adjacent populations. The present study strongly rec- ommends review of the widely accepted dual-structure model regard- ing the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people. However, the causes of the regional differences in the genetic influence of the Okhotsk culture people on the Ainu remain unresolved by mtDNA analysis. Nuclear genome analysis using next-generation sequencing is expected to be helpful to resolve this issue.

Noboru Adachi
Northeastern/ Southwestern Central
Total Hokkaido Hokkaido type (n594) (n551) (n543)
Hokkaido Jomon
N9b1 20.2 (n519) 13.7 (n57) 27.9 (n512)
M7a2 2.1 (n52) 2.0 (n51) 2.3 (n51)
G1b* 8.5 (n58) 3.9 (n52) 14.0 (n56)
Total 30.9 (n529) 19.6 (n510) 44.2 (n519)
Okhotsk type
Y1 31.9 (n530) 29.4 (n515) 34.9 (n515)
C5a2b 3.2 (n53) 5.9 (n53) 0
Total 35.1 (n533) 35.3 (n518) 34.9 (n515)
Mainland Japanese type
D4 (exc. D4o1) 11.7 (n511) 17.6 (n59) 4.7 (n52)
M7b1a1a1 3.2 (n53) 5.9 (n53) 0
F1b1a 2.1 (n52) 3.9 (n52) 0
N9a 1.1 (n51) 2.0 (n51) 0
M7a1a7 2.1 (n52) 2.0 (n51) 2.3 (n51)
A5a 1.1 (n51) 2.0 (n51) 0
A5c 6.4 (n56) 3.9 (n52) 9.3 (n54)
Total 27.7 (n526) 37.3 (n519) 16.3 (n57)
Siberian type
D4o1 2.1 (n52) 3.9 (n52) 0
G1b1 1.1 (n51) 0 2.3 (n51)
Z1a 1.1 (n51) 2.0 (n51) 0
M8a 1.1 (n51) 0 2.3 (n51)
M9a 1.1 (n51) 2.0 (n51) 0
Total 6.4 (n56) 7.8 (n54) 4.7 (n52)