What can variation in stature reveal about environmental differences between prehistoric Jomon foragers? Understanding the impact of systemic stress on developmental stability

This study documents and interprets systemic stress during the agricultural transition in prehistoric Japan using linear enamel hypoplasia (LEH) defects and cribra orbitalia (CO) lesions. Middle to Final Jomon cultures (5000-2300 BP) from Honshu Island represent the foraging samples, while Yayoi cultures (2500-1700 BP) represent the early agricultural samples. Jomon foragers from eastern Japan had broad-based, intensive economies. Jomon foragers from western Japan had a greater focus on seasonally available, nutritionally poor resources, while Yayoi people were descendents of migrants from the East Asian continent and introduced wet rice economies to Japan. This study tests the hypotheses that wet rice economies will be associated with a lower prevalence of teeth/individuals affected by LEH defects in western Japan, while few differences in the prevalence of teeth/individuals with LEH defects will be observed between eastern Jomon people and Yayoi farmers. It is further predicted that similar CO prevalence will be observed between Jomon and Yayoi people given environmental similarities. Significantly greater frequencies of teeth affected by LEH defects are observed among western Jomon compared to Yayoi people. The prevalence of teeth with LEH defects is slightly elevated among eastern Jomon foragers compared to Yayoi agriculturalists. Significant differences in CO prevalence are not observed. Systemic stress prevalence in western Japan likely declined following wet-rice agriculture because this crop provided a predictable, renewable resource base. Systemic stress prevalence was similar between eastern Jomon and Yayoi people because both groups practiced intensive subsistence strategies. Similar CO prevalence reflects infectious diseases associated with living conditions.

Current archaeological evidence indicates that greater dietary reliance on marine resources is recorded among the eastern Jomon, while plant dependence prevailed in western/inland Japan. The hypothesis that the dietary choices of the western/inland Jomon will be associated with greater systemic stress is tested by comparing carious tooth and enamel hypoplasia frequencies between the eastern and western/inland Jomon. Demographic collapse coincides with climate change during the Middle to Late Jomon period, suggesting dwindling resource availability. It is hypothesized that this change was associated with greater systemic stress and/or dietary change among the Middle to Late Jomon. This hypothesis is tested by comparing enamel hypoplasia and carious tooth frequencies between Middle to Late and Late to Final Jomon foragers. Enamel hypoplasia was significantly more prevalent among the western/inland Jomon. Such findings are consistent with archaeological studies that argue for greater plant consumption and stresses associated with seasonal resource depletion among the western/inland Jomon. Approximately equivalent enamel hypoplasia frequencies between Middle to Late and Late to Final Jomon foragers argues against a demographic collapse in association with diminished nutritional returns. Significant differences in carious tooth frequencies are, however, observed between Middle to Late and Late to Final Jomon foragers. These results suggest a subsistence shift during the Middle to Late Jomon period, perhaps in response to a changed climate. The overall patterns of stress documented by this study indicate wide-spread environmentally directed biological variation among the prehistoric Jomon.

This study focuses on Japanese Sus and their relationships with humans during the Jomon period. Since pig (Sus scrofa f. domestica) is the only domestic ungulate species of which the wild progenitor (Sus scrofa) naturally inhabits Japan, the relationship of Sus and humans, including possible local domestication in the Japanese archipelago, is one of the major issues in archaeozoological studies in Japan. There are two subspecies of wild boar in Japan, Ryukyu wild boar (S. scrofa riukiuanus) and Japanese wild boar (S. scrofa leucomystax). Today the former subspecies inhabits the Amami-Ohshima, Tokunoshima, Okinawa, Ishigaki, and Iriomote islands of the Ryukyu archipelago and the latter the main islands of the Japanese archipelago (Honshu, Shikoku, and Kyushu, but not Hokkaido). Our study deals with the latter subspecies, the Japanese wild boar. The primary aim is to examine and compile data on the regional and temporal variation of the size of the Japanese wild boar during the Jomon period, and of kill-off patterns. This, we think, is necessary for discussing whether or not a domestication process was underway during the Jomon period. Information on the variation within the wild boar population during the Jomon period also helps to evaluate the domestic or wild status of Sus remains from the later Yayoi Period (c.2700–1700 BP). The Jomon period lasted about 10,000 years, from 13000 to 2500 cal. BP, and, based on pottery types and styles, is divided into six phases: Incipient, Earliest, Early, Middle, Late, and Final. The subsistence economy during the Jomon period was primarily based on hunting and gathering, but it has been argued that some form of incipient plant cultivation was already practiced at least from the Early Jomon period, possibly even from the Incipient Jomon period on (e.g. Matsumoto 1979; Kasahara 1981; Umemoto & Moriwaki 1983; Habu 2001). Also, an increasing degree of sedentism is observed in central and eastern Japan from the Middle Jomon period on. Pottery was used from the beginning of the Jomon period. Jomon culture is also characterized by exquisite wood craftsmanship, as represented by lacquer ware found at some waterlogged sites.

Variation in limb proportions between prehistoric Jomon and Yayoi people of Japan are explored by this study. Jomon people were the descendents of Pleistocene nomads who migrated to the Japanese Islands around 30,000 yBP. Phenotypic and genotypic evidence indicates that Yayoi people were recent migrants to Japan from continental Northeast Asia who likely interbred with Jomon foragers. Limb proportions of Jomon and Yayoi people were compared using RMA regression and "Quick-Test" calculations to investigate relative variability between these two groups. Cluster and principal components analyses were performed on size-standardized limb lengths and used to compare Jomon and Yayoi people with other groups from various climatic zones. Elongated distal relative to proximal limb lengths were observed among Jomon compared to Yayoi people. Jomon limb proportions were similar to human groups from temperate/tropical climates at lower latitudes, while Yayoi limb proportions more closely resemble groups from colder climates at higher latitudes. Limb proportional similarities with groups from warmer environments among Jomon foragers likely reflect morphological changes following Pleistocene colonization of the Japanese Islands. Cold-derived limb proportions among the Yayoi people likely indicate retention of these traits following comparatively recent migrations to the Japanese Islands. Changes in limb proportions experienced by Jomon foragers and retention of cold-derived limb proportions among Yayoi people conform to previous findings that report changes in these proportions following long-standing evolution in a specific environment.

Aromatic rice (Oryza sativa L.) cultivated in Japan is regionally differentiated by geographical distribution and characteristics. We aimed to characterize the lineage of Japanese aromatic rice using DNA markers. Based on analyses with nuclear SSR markers, we found that Japanese aromatic rice cultivars belong, with one exception, to japonica but showed some differences from authentic japonica and were divided into two clades that were distributed in western and eastern Japan, respectively. Further analyses with organelle markers showed that most of the cultivars in eastern Japan had cytoplasm characterized by tropical japonica, whereas most of those in western Japan had cytoplasm characterized by temperate japonica. We postulate that the ancestor of the cultivars in eastern Japan differs from those of the cultivars in western Japan, and that the two groups may have been separately introduced from Taiwan into Japan. The cytoplasm of aromatic rice cultivars in western Japan may have originated from tropical japonica and been substituted into the cytoplasm of temperate japonica through hybridization between tropical japonica as a male parent and temperate japonica as a female parent.

The onset, dispersal and crop preferences of early agriculture in the Japanese archipelago as derived from seed impressions in pottery

We describe the oldest evidence of gout from skeletal remains found in Asia. A middle-aged male skeleton excavated from the shell mound at Ohta in Onomichi-city, Hiroshima prefecture, Western Japan (the middle Jomon period: 4500-3500 BP), showed erosive arthritis in the forefoot. The characteristic feature of the erosions observed in the present skeleton is a periosteal bone apposition at the outer aspect of the involved cortex and a “punched-out” configuration as seen in radiographs. In addition to thesepaleopathological indings, a pauciarticular nature, involvement of the forefoot, male gender and a lack of perilesional osteopenia provided further support for the diagnosis of tophaceous gout. Because gout is associated with good nutrition, the presence of some well-nourished society in Jomon period should be considered.

The Japanese Archipelago hosts a rich butterfly fauna, and elucidating the genetic structures of multiple species is necessary to clarify their formation processes. This study aimed to reveal the genetic structure and distribution formation process of Parnassius citrinarius, which is widely distributed across the Japanese Archipelago from Hokkaido to Shikoku, through phylogeographic analysis based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence. Thirty haplotypes were revealed from 311 individuals from 47 sites, indicating significant differences in the genetic structures between the eastern and western parts of the Japanese Archipelago. In Eastern Japan, multiple genetic clusters were found, with some sites harboring two clusters. The divergence times among populations in Eastern Japan were relatively recent, and no genetic differentiation was observed between regions, including between Hokkaido and Honshu, which are separated by a narrow strait. In contrast, in Western Japan, including Shikoku, unique genetic clusters were observed in each region. The phylogenetic relationships among populations were regionally clustered, and the divergence times were relatively ancient. The distribution and genetic structure of P. citrinarius in the Japanese Archipelago have been significantly influenced by temperature fluctuations and the presence of geographical barriers during the Pleistocene glacial-interglacial cycles, including the potential formation of refugia in Western Japan.

Patterns in dental enamel hypoplasia by sex and age at death in two archaeological populations

To clarify the environmental distribution of Vibrio vulnificus, sea water, sea mud, and oysters were examined at 13 sites, i.e. 4 sites in the Tokyo Bay (eastern Japan) and 9 sites (5 sites for oysters) in Tokushima Prefecture (western Japan). 1. V. vulnificus was isolated from 80 (54.8%) of the 146 samples of sea water examined. It was isolated from 19 (41.3%) of the 46 samples from western Japan and 61 (61.0%) of the 100 samples from eastern Japan. 2. It was isolated from 40 (40.8%) of the 98 samples of sea mud obtained in eastern Japan. 3. It was isolated from 655 (30.3%) of the 2,165 samples of oysters. They were 30 (9.7%) of 309 samples from western Japan and 625 (33.7%) of 1,856 samples from eastern Japan. 4. The density of V. vulnificus was 0.3-1.1 x 10(6) MPN/L in seawater, 0.3-1.1 x 10(5) MPN/100 g in sea mud, and 0.3-1.1 x 10(7) MPN/100 g in oysters. 5. Seasonally, V. vulnificus was isolated from 44 (6.2%) of the 713 samples in spring, 450 (72.6%) of the 620 samples in summer, 264 (51.8%) of the 510 samples in fall, and 17 (3.0%) of the 56 samples in winter. Thus, the isolation rates of V. vulnificus from sea water and oysters tended to be higher in eastern Japan than in western Japan and to be highest in summer, then, in fall.

This study evaluates two hypotheses that address how Late/Final Jomon period people responded to early-life stress using linear enamel hypoplasia (LEH) and incremental microstructures of enamel. The first hypothesis predicts that Jomon people who experienced early-life stressors had greater physiological competence in responding to future stress events (predictive adaptive response). The second hypothesis predicts that Jomon people traded-off in future growth and maintenance when early investment in growth and survival was required (plasticity/constraint). High resolution tooth impressions were collected from intact, anterior teeth and studied under an engineer's measuring microscope. LEH were identified based on accentuated perikymata and depressions in the enamel surface profile. Age of formation for each LEH was estimated by summing counts of perikymata and constants associated with crown initiation and cuspal enamel formation times. The relationship between age-at-first-defect formation, number of LEH, periodicity between LEH, and mortality was evaluated using multiple regression and hazards analysis. A significant, positive relationship was found between age-at-death relative to age-at-first-defect formation and a significant, negative relationship was found between number of LEH relative to age-at-first-defect formation. Individuals with earlier forming defects were at a significantly greater risk of forming defects at later stages of development and dying at younger ages. These results suggest that Late/Final Jomon period foragers responded to early-life stressors in a manner consistent with the plasticity/constraint hypothesis of human life history. Late/Final Jomon period individuals were able to survive early-life stressors, but this investment weakened responses to future stress events and exacerbated mortality schedules.

Third molar (M3) agenesis has become prevalent since the terminal Pleistocene in humans. Population-level studies suggest that M3 agenesis is related to genetic factors and to environmental stresses such as malnutrition and infectious diseases. In addition, the fact that there are populations, such as the Jomon people, that have a high frequency of enamel hypoplasia (EH), an indicator of stress, but a low M3 agenesis rate, suggests that there are population differences in how the effects of environmental stress on M3 agenesis are manifested. In this study, I used EH to investigate the effects of environmental stress on M3 agenesis in three populations with different genetic bases: recent Japanese (1868–1926), Jomon people, and Islamic Mesopotamians. The results showed the effects of environmental stress on M3 agenesis in recent Japanese and Islamic Mesopotamians, but not in Jomon people. Furthermore, it was shown that M3 agenesis of recent Japanese and Islamic Mesopotamians are similarly susceptible to environmental stress. Thus, the results showed that the extent to which environmental stress affects M3 formation varies among populations. Since M3 agenesis was observed even in Jomon people, whose M3s are not thought to have been affected by environmental stress, it is reasonable to assume that M3 agenesis can be congenital or caused by environmental stress, and each cause of agenesis occurred independently in human populations.

The Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500–2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.

Starting 16000 years ago, the Neolithic lifestyle known as the Jomon culture spread across the Japanese archipelago. Although extensively studied by archaeology and physical anthropology, little is known about the genetic characteristics of the Jomon people. 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. This is the first genome analysis of the initial Jomon people of Kyushu Island. These results provide important data for understanding the temporal transition and regional differences of the Jomon people. The mitochondrial DNA and Y-chromosome haplogroups were similar to those found in the previously reported later Jomon people. 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. This indicates that the genetic differentiation found among the Jomon people was promoted by the progression of regionalization throughout the Jomon period. Further accumulation of high-quality Jomon genome data spanning a wide range of regions and ages will clarify both intimate regional and temporal differences of the Jomon people and details of their admixture history with rice farmers, as suggested by Jomon mitochondrial genome data. The results obtained from this study provide important information for further analysis.

Metric characteristics of the mandibles of modern and various historical populations from the Kanto region (east-central Japan) were compared with those of their possible ancestral populations, i.e., the Jomon population from Kanto and the Yayoi population from northern Kyushu and Yamaguchi (western Japan). The Jomon people were aboriginal Holocene inhabitants of Japan, while the Yoyoi skeletal series are considered to largely represent immigrants from the Asian continent. Compared to the presumed ancestral morphology, the mandibles of the modern and pre-modern peoples of Kanto showed a marked narrowing, as well as reduction in the regions of major masticatory muscle attachments. The main cause of this underdevelopment is likely to be a diminished chewing stress, resulting in insufficient stimulation for proper growth of the jaw bone. In contrast, symphyseal height increased compared to the earlier Kanto populations. This may be a reflection of the existence of significant Yayoi genetic contribution in the formation of the modern and pre-modern Kanto populations. On the other hand, the mandibles of the protohistoric to medieval populations of the Kanto region are morphologically closer to Jomon. Therefore, they seem to have been genealogically continuous from the native Jomon people with some degree of gene flow stemming from the immigrants.