Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan

Abstract

We investigated mitochondrial DNA haplogroups of four Jomon individuals from the Sanganji shell mound in Fukushima, Tohoku district, Japan. Partial nucleotide sequences of the coding and control region of mitochondrial DNA were determined. The success rate of sequencing increased when we analyzed short DNA sequences. We identified haplogroups from all four samples that were analyzed; haplogroup frequencies were 50% (n = 2) for N9b and 50% (n = 2) for M7a2. Haplogroup N9b has been previously observed in high frequencies in the other Tohoku Jomon, Hokkaido Jomon, Okhotsk, and Ainu peoples, whereas its frequency was reported to be low in the Kanto Jomon and the modern mainland Japanese. Sub-haplogroup M7a2 has previously been reported in the Hokkaido Jomon, Okhotsk, and modern Udegey (southern Siberia) peoples, but not in the Kanto Jomon, Ainu, or Ryukyuan peoples. Principal component analysis and phylogenetic network analysis revealed that, based on haplogroup frequencies, the Tohoku Jomon was genetically closer to the Hokkaido Jomon and Udegey people, than to the Kanto Jomon or mainland modern Japanese. The available evidence suggests genetic differences between the Tohoku and Kanto regions in the Jomon period, and greater genetic similarity between the Tohoku Jomon and the other investigated ancient (Hokkaido Jomon, Okhotsk) and modern (Siberian, Udegey in particular) populations. At the same time, the Tohoku and Hokkaido Jomon seem to differ in sub-haplotype representations, suggesting complexity in Jomon population structure and history.

Human genetic diversity in the Japanese Archipelago: dual structure and beyond

“…Early studies of ancient DNA tended to focus on mtDNA, mainly due to larger copy numbers of the molecule that remained in the ancient samples compared to the nuclear genome. mtDNA extracted from Jomon samples shows enrichment for haplogroups N9b and M7a (Adachi et al, 2011;Kanzawa-Kiriyama et al, 2013). These two haplogroups are rarely found in other populations except in the Japanese Archipelago, which further supports the idea of Jomon ancestry in modern Japanese.…”

Jomon genome sheds light on East Asian population history

“…The libraries were sequenced to average coverages of 1.85-fold for autosomal genome and 146-fold for mitochondrial genome, with low estimated contamination rate of 0.5% (95% CI: 0.01-2.2%, Fig.S3 ) [19] . We found IK002 to be assigned to mitochondrial haplogroup N9b1, which is rare among present-day Japaneses people (< 2.0%) , but typically found in previous studies of Jomon mtDNA [20,21] .…”

An assessment of postcranial indices, ratios, and body mass versus eco‐geographical variables of prehistoric Jomon, Yayoi agriculturalists, and Kumejima Islanders of Japan

“…With restricted migration and little gene flow (Relethford‐Blangero analysis), genetic drift and hunter‐gatherer type Indian Knoll nutritional stress may have been the culprits maintaining the mismatch morphology in Jomon. We must also note that haplogroup N9b has a high frequency in the mtDNA of Jomon, which others have interpreted as long‐term isolation of Jomon from continental populations (Adachi et al, ; Kanzawa‐Kiriyama et al, ). Our Relethford‐Blangero analysis using the regional samples Kanto, Tokai, and Chugoku showed evidence of restricted migration.…”

“…Based on the studies of mitochondrial DNA (mtDNA) sequences and haplotype groups of Jomon researchers (Adachi et al, ; Adachi, Sawada, Yoneda, Kobayashi & Hoh, ; Horai et al, ; Kanzawa‐Kiriyama, Saso, Suwa, & Saitou, ; Shinoda & Kanai, ), haplogroup N9b has a high frequency in the mtDNA of Jomon and a low frequency in modern Eurasians. This suggests genetic drift or long‐term isolation of Jomon from continental populations, although mtDNA—maternal inheritance—cannot tell the whole story.…”