The Jomon period of the Japanese Archipelago, characterized by cord-marked ‘jomon' potteries, has yielded abundant human skeletal remains. However, the genetic origins of the Jomon people and their relationships with modern populations have not been clarified. We determined a total of 115 million base pair nuclear genome sequences from two Jomon individuals (male and female each) from the Sanganji Shell Mound (dated 3000 years before present) with the Jomon-characteristic mitochondrial DNA haplogroup N9b, and compared these nuclear genome sequences with those of worldwide populations. We found that the Jomon population lineage is best considered to have diverged before diversification of present-day East Eurasian populations, with no evidence of gene flow events between the Jomon and other continental populations. This suggests that the Sanganji Jomon people descended from an early phase of population dispersals in East Asia. We also estimated that the modern mainland Japanese inherited <20% of Jomon peoples' genomes. Our findings, based on the first analysis of Jomon nuclear genome sequence data, firmly demonstrate that the modern mainland Japanese resulted from genetic admixture of the indigenous Jomon people and later migrants.

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.

An increasing number of studies determine endocranial capacity (ECC) digitally using serial computed tomographic (CT) scan data. However, the multiple causes of errors inherent in such measurements and the resulting degree of accuracy have not yet been fully examined. In the present study, five observers estimated the ECCs of two modern human crania by segmentation of CT data (voxel size 0.380 mm) and by means of the conventional millet seed method. The ECC estimations were much more consistent in the CT-based (technical error, TEM = 1.4 cc) than the millet seed (TEM = 11.8 cc) methods. The estimated capacities also tended to be larger in the latter, suggesting possible systematic bias. Next, the causes and degree of error in the CT-based method were examined. Error due to size calibration of the CT images was no more than 3 cc (± 1.5 cc) per 1000 cc. Errors involved in delineating the endocranial cavity were evaluated as follows. First, we adopted a segmentation routine in which a single global threshold value was applied to most of the volume, and then supplemented locally by more appropriate values in the regions where the global value was insufficient. We then estimated the potential error introduced by choosing a global threshold value. We found this to be within 5 cc (per 1000 cc). This error range increased to 7.5 cc (per 1000 cc), when using a lower resolution data set (slice thickness 1.14 mm). Another source of interobserver error involves the blocking of foramina and canals, which we estimated to be less than 2 cc (per 1000 cc). Adding these various effects, our investigations indicate that ECC estimations based on high-resolution CT data are accurate to within ± 5 cc per 1000 cc. Finally, we reevaluated the ECC of the Minatogawa 1 skull to be 1335 cc (with a probable range of 1327-1343 ± 5 cc), considerably smaller than the originally reported value of 1390 cc obtained by the millet seed method.

Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th-19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.