A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan

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

Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan.

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

Metric characteristics of human limb bones in Asian and Japanese populations

Twelve metric variables of the humerus, radius, femur, and tibia were investigated in 11 male samples from northeastern and eastern Asian populations. Variations among regions and correlations between latitude and respective measurements and indices were calculated and a principal component analysis was conducted to elucidate human limb bone characteristics. Significant correlation and marginally significant correlation were found for the maximum subtrochanteric diameter (r = 0.662, P = 0.027) and the platymeric index (r = −0.583, P = 0.060) with latitude, respectively, suggesting that the femur of northern Asians had a wide and flat subtrochanteric shape. The second principal component of the principal component analysis shows that the northeastern samples with comparatively long shaft length and thin and flat shaft diameters were discriminated from the southern samples; the second principal component was significantly correlated with latitude (r = −0.743, P = 0.009). The estimated Fst value of 0.432–0.336 shows that the variation in limb bone measurements across regions is rather large, at approximately two or three times the low levels of interregional variation (0.078–0.180) in analyses of cranial and dental data. Limb bone morphology has been repeatedly proposed to be more strongly influenced by environmental and nutritional factors than cranial and dental traits, but this study is the first to confirm it on the basis of statistical analysis

Paleopathological Evidence and Detection of <i>Mycobacterium leprae</i> DNA from Archaeological Skeletal Remains of <i>Nabe-kaburi</i> (Head-Covered with Iron Pots) Burials in Japan

<div><p>The <i>Nabe-kaburi</i> is a unique burial method, the purpose of which is shrouded in mystery. The burials were performed during the 15^th to 18^th centuries in eastern Japan, and involved covering the heads of the deceased with iron pots or mortars. The identification of leprosy-specific osteological lesions among some of the excavated remains has led to the suggestion that <i>Nabe-kaburi</i> burials were a reflection of the social stigma against certain infectious diseases, such as leprosy, tuberculosis or syphilis. However, molecular evidence for the presence of disease has been lacking. The goal of this study was to detect <i>Mycobacterium leprae</i> (<i>M. leprae</i>) DNA in archaeological human skeletal remains from <i>Nabe-kaburi</i> burials. The paleopathological data from three <i>Nabe-kaburi</i> burials were re-evaluated before small samples were taken from affected and control areas. DNA was extracted and used as a template to target the <i>M. leprae</i>-specific DNA using a combination of whole genome amplification, PCR analysis and DNA sequencing. <i>M. leprae</i> DNA fragments were detected in the two sets of skeletal remains that had also shown paleopathological evidence of leprosy. These findings provide definitive evidence that some of the <i>Nabe-kaburi</i> burials were performed for people affected by leprosy. Demonstration of the presence of <i>M. leprae</i> DNA, combined with archeological and anthropological examinations, will aid in solving the mystery of why <i>Nabe-kaburi</i> burials were performed in medieval Japan.</p></div

Location of the <i>Tawara-ga-yatsu</i> and the <i>Usukubo</i> sites in Japan.

<p>Shaded area denotes the <i>Kanto</i> area. Inset illustrates the locations in relation to Tokyo.</p

Chronological and geographical distribution of <i>Nabe-kaburi</i> burials in Japan.

a<p>Shaded area in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088356#pone-0088356-g001" target="_blank">Figure 1</a>.</p