The Ainu ethnogenesis through ancient mtDna

Angela

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See: Noboru Adaci et al
Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data
http://onlinelibrary.wiley.com/doi/10.1002/ajpa.23338/abstract

"Our findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan.
Discussion

Our results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual-structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people."

"From a cultural perspective, it is generally agreed that the ethnic identity of the Ainu was established in the 13th century AD. However, the origin of their biological identity remains unclear, which has been a major focus of anthropological discussion. Conventionally, based on the close morphological resemblance between the Jomon people and the Ainu (e.g., Brace & Nagai, 1982; Dodo & Ishida, 1990; Dodo & Kawakubo, 2002; Hanihara, 1991; Turner, 1976, 1990; Yamaguchi, 1963, 1982), it is generally agreed that the indigenous Hokkaido population maintained its genetic and phenetic characteristics throughout the Neolithic Jomon era to the Ainu era (Figure 2) (Dodo & Kawakubo, 2002)."

"Among the haplogroups observed in the Hokkaido Jomon (N9b1, N9b4, N9b*, D4h2, G1b*, M7a2, M7a*; Adachi et al., 2011), haplogroups N9b1, G1b*, and M7a2 are also observed in the Edo Ainu. Above all, haplogroup N9b1, which is the most frequently observed haplogroup in the Hokkaido Jomon people (55.6%, 30 of 54 individuals; Adachi et al., 2011), is also observed at a relatively high frequency (20.2%, 19 of 94 individuals) in the Edo Ainu. These findings indicate the genetic continuity between the Hokkaido Jomon and the Ainu. This possible genetic continuity is corroborated by Y chromosome DNA analysis of the modern Ainu. Y chromosomal DNA haplogroup D1b, which is considered to be a strong candidate for the Jomon paternal lineage, was observed at high frequency in the modern Ainu (Hammer et al., 2006; Tajima et al., 2004)."

"However, there is a crucial difference between the Hokkaido Jomon people and the Ainu. Four haplogroups (N9b4, N9b*, D4h2, M7a*) are missing in the Edo Ainu, whereas they have 19 haplogroups that are not observed in the Hokkaido Jomon. This raises questions about the conventional hypothesis that the Ainu are the direct descendants of the Hokkaido Jomon people."

"the genetic characteristics of the Ainu are based on the Hokkaido Jomon people and the subsequent input of Lower Amur region Siberian genes through the Okhotsk culture people. However, when examining in detail the haplogroups observed in the Ainu examined in the present study, haplogroups M7a1, M7b1a1a1, D4 (except for D4h2), M8a, Z1a, M9a, F1b, N9a, A5a, and A5c are observed neither in the Hokkaido Jomon nor in the Okhotsk culture people. This suggests the presence of populations other than the Hokkaido Jomon and the Okhotsk culture people that contributed to the formation of the Ainu. Mainland Japanese and the native Siberians are considered to be the major candidates for the origin of these haplogroups because of the proximity of their distributions to Hokkaido."
 
their Y-DNA didn't change though, they are all D-M64.1
they were all over Japan till the Yayoi with Y-DNA O arrived some 2-3 ka
 

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