Archaeological evidence indicates that dogs appeared in Japan at least 9300 years ago, during the Jomon period. The Jomon period dogs (Jomon dogs) retained the morphological characteristics of ancient domestic dogs throughout the Jomon period, possibly due to their geographical isolation from continental dogs. Therefore, we expect them to retain the genetic characteristics of ancient domestic dogs. To explore this possibility, we determined the mitochondrial genomes of five Jomon dogs, including one of the oldest dogs in Japan (7400-7200 cal BP), and seven late-8th-century Japanese dogs (Suwada dogs). We analyzed these sequences with 719 mitochondrial genomes of ancient and modern canids. The dog mitochondrial DNA (mtDNA) sequences have been grouped into six clades (haplogroups A-F), and clade A comprises six sub-clades (sub-haplogroups A1-A6). Classification of the Jomon dogs' mtDNA haplotypes revealed that these dogs belong to a nested A2/A3 sub-haplogroup not shared by other modern or ancient samples. The mtDNA sequences of Jomon dogs form a monophyletic clade which is sister to the A3 sub-clade in the phylogenetic trees. Network analysis showed that the Jomon dogs' mtDNA sub-clade diverged close to the base of the A2 and A3 haplotype network, which was centered by an ancient dog from South China. The Jomon dog mtDNAs diverged from A3 (~11500 years ago) soon after the A2 and A3 divergence (~12800 years ago), indicating early divergence of the Jomon dogs' sub-clade. These results suggest that the Jomon dogs were possibly introduced into the Japanese archipelago 11500-9300 years ago. The mtDNAs of late-8th-century dogs were more diverse and were different haplogroups than that of Jomon dogs, suggesting that other haplogroups likely replaced the haplogroup of Jomon dogs through the introduction of dogs that accompanied the migration of people into Japan in later periods.

Telomere length has recently gained popularity as a biomarker of aging-related diseases. Dried blood spot (DBS) samples are commonly used to measure telomere length for human biology research, but studies assessing intra- and inter-assay variations are scarce. The objective of the present study was to analyze and elucidate the extent of intra- and inter-assay variation of DBS telomere length measurement. The DBS telomere length of a male subject was determined by quantitative polymerase chain reaction (qPCR) using four different protocols with two different container types (96-well plates and 8-well tubes) and two different primer sets (tel1b–tel2b and tel1–tel2). The measurement of telomere length with 8-well tubes and the tel1–tel2 primer set demonstrated the lowest intra-assay coefficient of variation (CV) (6.0%) and gave an inter-assay CV of 5.0%. The protocol for 96-well plates typically resulted in high intra-assay CVs (>27%). Assessment of intra-assay variation is essential when DBS telomere length is measured by qPCR.

Recent fossil records have suggested that human erect bipedal locomotion started in Africa probably more than 6 million years ago. However, debate continues regarding how locomotion was acquired by our prehuman ancestors. Fossils and the genetic traits of recent humans and animals cannot answer this question directly. Therefore, the present paper reviews acquisition models of human bipedalism and explanations regarding how humans acquired bipedalism based on a comparative kinesiology of contemporary mammal species. Nonhuman primates are adequate models of human bipedal acquisition because of not only the phylogenetically close relationship with humans, but also the trend toward hindlimb dominance and orthograde positional behavior in daily life. Although dissimilar to the erect bipedalism seen in humans, nonhuman primates adopt bipedal positional behavior in the wild. All nonhuman primates use the arboreal environment, but some groups of species utilize the ground predominantly. Compared with relatively terrestrial nonhuman primates, relatively arboreal primates show more similarities with humans in their bipedal locomotion. Comparisons among primate species and between nonhuman primates and nonprimate mammals indicate that human-like bipedal characteristics are strongly related to arboreal life. Our prehuman ancestors likely started and adapted to bipedal locomotion while living in trees; this process is referred to as the generalized arboreal activity model. When humans began terrestrial locomotion, they likely performed proficient bipedalism from the first step. The generalized arboreal activity model presented here does not contradict the fossil records.

This paper examines periodontal disease as well as other oral health indicators of the Jomon population in order to understand variations in their lifestyle and their response to dietary diversity. The oral conditions of three Jomon populations in Late Jomon period are evaluated using two periodontal indicators, namely the distance measured between the cement–enamel junction to the alveolar crest (CEJ-AC distance), and the degree of inflammation of the alveolar septum. The incidence of affected individuals with moderate to severe periodontal disease ranges from 31.8% to 38.6% based on the evaluation of the CEJ-AC distance, and from 38.4% to 66.0 % based on the interdental septum morphology, respectively. Comparisons of the inter-site difference (which includes that between coastal and inland populations) and sex differences were conducted with a combined dataset of the periodontal and oral health indicators (caries, antemortem tooth loss, wear, and chipping). The results indicated that inter-site and inter-sex differences are smaller in the cases with periodontal disease than in those with caries and antemortem tooth loss. In particular, almost no difference was found in the periodontal conditions between the coastal and inland sites. Although previous studies have indicated the effect of occlusal wear on the CEJ-AC distance, the results of the multivariate analysis show that the inflammation of the interdental septum is more relevant than the occlusal wear. In addition, the sex difference was significant compared to the inter-site difference, and each sex difference within a site showed a common trend. Detected inter-site and sex differences are discussed and assumed to be associated with bioarchaeological background.

The reconstruction of everyday diets in villages is important for understanding the diversity of diets and commerce networks of food items in premodern Japan. However, premodern diets in villages have not been well studied compared with those in cities. In this study, stable isotope analyses were performed on 23 adult human skeletons excavated from Sendaiji, a mountainous woodland village of underground Christians in Osaka in premodern Japan. No significant isotopic differences was found between individuals identified as Buddhists and those identified as Christians or between females and males. The total mean carbon, nitrogen, and sulfur isotope ratios were -21.1 0.4, 11.6 1.0, and 8.9 1.3, respectively. The carbon isotope ratios in Sendaiji were the lowest among the studied premodern populations probably because these individuals consumed woodland foods that are affected by the canopy effect. No significant correlation between sulfur and nitrogen isotope ratios was apparent, suggesting that there was little contribution from marine foods or marine fertilizers to the diet of individuals in premodern Sendaiji. The relatively high nitrogen isotope ratios in Sendaiji were possibly because of the denitrification in paddy rice fields, ammonium uptake by paddy rice, use of animal fertilizers, and/ or consumption of freshwater fish. To our knowledge, this is the first detailed bioarchaeological study of the premodern diet in a mountainous village in western Japan.

Animal vocalizations range from tonal sounds to irregular atonal sounds and are generated from non-linear oscillations of the vocal folds as well as from turbulent noise in the glottis. Comprehensive study on bioacoustic signals indicates the existence of a diversity of non-linear phenomena, such as limit cycles, subharmonics, biphonation, chaos, and bifurcations in animal vocalizations, which may provide keys to understanding animal communications. In this paper, we review the concept of nonlinear dynamics and its methodology as applicable to bioacoustics. Acoustical analysis of recorded sounds, simulation of a biomechanical model of the voice production system, and physical experiment of the vocal tract and vocal folds are presented to demonstrate non-linear features inherent in animal vocalizations. We focus on source–filter interaction as one of the main regulators of the non-linear property that can lead either to efficient vocalization or to voice instability in animal sounds. A combination of different approaches is suggested to be of great use for extracting the essential features of non-linear dynamics in animal vocalizations.

Considering the geographical setting of the Japanese archipelago at the periphery of the Asian continent, regional variation in Jomon phenotypes can be interpreted as an outcome of population history. In this paper, we focused on regional variation in the Jomon craniofacial morphology and assumed that the observed regional differences were a reflection of the formation process of the Jomon population, which is a mixture of intrinsic expansion of an initial population with extrinsic influence of hypothetical gene flow. Compiled craniometric data from archeological site reports indicate that Jomon skulls, especially in the neurocranium, exhibit a discernible level of northeast-to-southwest geographical cline across the Japanese archipelago, placing the Hokkaido and Okinawa samples at both extreme ends. A quantitative genetic approach using an R-matrix method indicates that the cranial parts of the neurocranium and mandible exhibit a proportionately larger regional variation, the former of which confirms a trend of geographical cline and reveals the respective region presumably having different population histories with their respective local backgrounds. The following scenarios can be hypothesized with caution: (a) the formation of Jomon population seemed to proceed in eastern or central Japan, not western Japan (Okinawa or Kyushu regions); (b) the Kyushu Jomon could have a small-sized and isolated population history; and (c) the population history of Hokkaido Jomon could have been deeply rooted and/or affected by long-term extrinsic gene flows.

This paper presents the first radiological investigation of a collection of Sicilian mummies held in a crypt beneath the Mother Church of Piraino, Italy. The chamber contains 26 preserved bodies of religious dignitaries, either conserved vertically in special wall niches or horizontally on wooden shelves. The majority of bodies are clothed, and transportation outside of the crypt was not feasible. Therefore assessment of the remains via paleoradiological methods appeared to be the most convenient approach to investigate this precious ethno-anthropological heritage. Radiological examination of 23 of these mummies yielded information relating to their funerary treatment and some of the pathological alterations associated with the remains. These included osteoarthritis, diffuse idiopathic skeletal hyperostosis, and neoplasms, as well as any trauma present. These analyses provided insights into mortuary behavior and the osteobiographies of these clerical figures.

In the eastern Pampa–Patagonia transition, hunter-gatherer groups experienced a series of changes in social organization (e.g. subsistence, mobility, and demography) during the Late Holocene (c. 3000–250 years BP), mainly in the last c. 1000 years. In this context, some biological aspects, including health, might have also been modified. The aim of this paper is to present a review and synthesis of a recent pathological analysis of hunter-gatherer skeletons from the lower basin of the Colorado River (Argentina) during the Late Holocene. The sample includes 94 individuals from six archaeological sites. Bone and dental pathologies (e.g. osteoarthrosis, systemic stress, bone infections, trauma, caries, periodontal disease, antemortem tooth loss, and dental calculus) were considered. The results show low frequencies in most of the bone and oral pathologies. Trauma, infectious, and systemic stress processes did not show large variation among samples from the Late Holocene. However, increasing prevalence of dento-alveolar lesion and osteoarthrosis were observed in samples from the final moments of this period (c. 1000–250 years BP). These results are discussed taking into account the archaeological model proposed for the eastern Pampa–Patagonia transition, which suggests social transformations and reorganizations during the last 1000 years.

A complete deciduous dentition was excavated from the Mesolithic site of Damdama (8800– 8600 BC) in the Gangetic Plain of north India. The site yielded remains of 47 individuals, including one child specimen 3.0–3.5 years of age, in association with an aceramic, microlithic technology and a seminomadic foraging pattern. Because sub-adult dental remains from Mesolithic contexts are very rare in South Asia, this specimen yields critical insight into deciduous dental attributes, including: (i) tooth crown size and temporal trends in dental reduction; (ii) non-metric dental morphology and biological affinity; and (iii) dental pathology, physiological stress, and diet. Standardized methods were employed in each component of the analysis, and most comparative samples were analyzed by the author, reducing the potential for inter-observer variance in data collection.