Ancient genomes from the initial Jomon period: new insightsinto the genetic history of the Japanese archipelago 

Noboru Adachi1 *, Hideaki Kanzawa-Kiriyama2 , Takashi Nara3 , Tsuneo Kakuda1 , Iwao Nishida4 , Ken-ichi Shinoda2

Received 23 October 2020; accepted 13 December 2020





Here, we report the entire mitogenome and partial nuclear genome of skeletal remains from the initial Jomon period that were excavated from the Higashimyo shell midden site at Saga City, Kyushu Island, Japan.

Moreover, comparison of three nuclear genomes from the initial to final Jomon periods indicated genetic continuity throughout the Jomon period within the Japanese archipelago with no significant evidence of admixture. 



In fact, previous studies using mitochondrial DNA suggested that there are regional differences in the Jomon people (e.g. Adachi et al., 2009, 2011, 2013; KanzawaKiriyama et al., 2013; Takahashi et al., 2019).

We had the opportunity to carry out aDNA analysis of human skeletal remains excavated from the Higashimyo shell midden site in Saga City, Kyushu Island.

In this study, we report the entire mitogenome and partial nuclear genome of the Higashimyo people. This is the first report on the genetic characteristics of the Jomon people of Kyushu Island and the first genome data from the initial Jomon period.

2021-05-27 (1)

 the mitochondrial DNA haplogroup was M7a1a*

This is consistent with the fact that this sample was from the initial Jomon period.

 For most of the Jomon people in Kyushu and Okinawa that we have analyzed, their haplogroup belonged to M7a1.

Figure 4. Principal-component analysis. Approximately 200K SNPs overlapped with the publicly available genomic dataset for modern populations.

The fact that the Higashimyo Jomon people also had this haplogroup shows that M7a1 was dominant in Kyushu during the Jomon period. This is in contrast to the Jomon people of eastern Japan, where N9b was dominant.

As inferred from the ratio of reads mapped to the Y and X chromosomes, the Higashimyo skeleton examined in this study was considered male (Supplementary Table 2).

The Y-chromosome haplogroup was classified into D1b. D1b-specific alleles were observed at all six SNP sites defining this haplogroup. However, no further subdivision of the D1b haplogroup was possible because of data limitations. D1b2-specific alleles were not observed at the two SNP sites defining this subhaplogroup.

The f4 results also revealed that the Higashimyo data shared significantly more alleles with Japanese, Ulchi, and Koreans than with Han Chinese (Z > 3; Supplementary Table 6, Supplementary Table 7).

These signatures are similar to that of the F23 Hokkaido Jomon (Kanzawa-Kiriyama et al., 2019).