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Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603–1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history.

Objectives: 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 Edo people for the taxonomic identification of food species. Materials and Methods: 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 was also carried out to investigate dietary diversity. Results: 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. Discussion: Most of the plant taxonomic groups are present in Japan and include 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 starch analysis and stable isotope analysis.

We investigated mitochondrial DNA haplogroups of four Jomon individuals from the San- ganji 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 ana- lyzed; 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.

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., 論文

The Late Pleistocene human fossils recovered from the Minatogawa fissure in Okinawa Island are important in understanding the population history of the Japan archipelago. Based on high-resolution laser scanning, we conducted a three-dimensional (3-D) topographic evaluation of the glabellar and superciliary regions of the Minatogawa and Jomon crania. We aimed to address the question of whether the glabellar morphology of the Minatogawa crania can be seen as a possible ancestral condition of the Jomon people, or whether it more likely represents a distinct morphological pattern. In addition to comparative descriptions and evaluations of the visualized topography, we conducted principal components and cluster analyses using a data set of approximately 240 points located within a confined glabellofrontal area. Results indicate that the male Minatogawa I exhibits a distinct rhomboid to ovoid glabellosuperciliary prominence, in the form of an undifferentiated swollen structure that encompasses both glabellar and superciliary arch regions. Unlike the Jomon condition, this leads to a lack of concave inferolateral contour of the prominence and the virtually complete obliteration of bilateral superciliary expression. The Minatogawa II and IV female crania also exhibit the same morphological pattern at weaker levels. On the other hand, absolute glabellar projection of Minatogawa I is not as great as the developed Jomon examples. This indicates that it is the pattern that is distinctive of Minatogawa, rather than glabellar prominence itself.

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.

Radiocarbon ages were determined for 25 samples of human skeletal remains previously assigned or attributable to the Yayoi period (tentatively considered ca. 500 BC to 300 AD) of the Kanto district, Japan. Suzuki (1969) and others, predominantly on cranial morphology, recognized that the Kanto Yayoi series contains three morphological groups: the native Jomon, transitional, and Kofun types. Morphological variation of the Kanto Yayoi people was considered to be chronologically based and formed the basis of Suzuki’s transformation hypothesis of the origin of the Japanese, which assumed limited influence, in eastern Japan, from continental immigrants. The 14C dates of the present study, determined for fragmentary postcranial elements of the same general assemblage, showed that these ‘Yayoi’ series, in part, contain skeletal remains of different ages, including those attributable to the Jomon and Kofun periods. All specimens from the Sano site that were examined were found to most likely derive from the Jomon period, while the dated Ourayama and Iwatsubo remains are best interpreted to be of Yayoi age. The Awajinsha and Bishamon samples were found to be of mixed chronological compositions. The implications of these results are discussed.

Vertebral assimilation was observed in an adult male Ainu skeleton from the Tokoro Chashi site of the early modern period in Tokoro, Hokkaido, Japan. The vertebral bodies and right zygapophyseal joint between the 12th thoracic and 1st lumbar vertebrae were completely united by osseous tissue, with anterior wedge shape and 42% loss of anterior vertebral body height. Differential diagnosis suggested that this was a healed state of pyogenic spondylitis.

The Nabe-kaburi 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 Nabe-kaburi 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 Mycobacterium leprae (M. leprae) DNA in archaeological human skeletal remains from Nabe-kaburi burials. The paleopathological data from three Nabe-kaburi 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 M. leprae-specific DNA using a combination of whole genome amplification, PCR analysis and DNA sequencing. M. leprae 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 Nabe-kaburi burials were performed for people affected by leprosy. Demonstration of the presence of M. leprae DNA, combined with archeological and anthropological examinations, will aid in solving the mystery of why Nabe-kaburi burials were performed in medieval Japan.