Reflections on the face of Japan: a multivariate craniofacial and odontometric perspective

Craniofacial variables for modern and prehistoric Japanese were subjected to multivariate analysis to test the relationships of the people of Japan with mainland Asian and Oceanic samples. The modern Japanese are tied to Koreans, Chinese, Southeast Asians, and the Yayoi rice agriculturalists who entered Japan in 300 B.C. Together they make up a Mainland-Asia cluster of related populations. The prehistoric Jomon foragers, the original inhabitants of the Japanese archipelago, are the direct ancestors of the modern Ainu, who made a recognizable contribution to the warrior class--the Samurai--of feudal Japan. Together, they are associated with Polynesians and Micronesians in a Jomon-Pacific cluster of related populations. Jomon-to-Ainu tooth size reduction proceeded at the same rate as that observable in the post-Pleistocene elsewhere in the Old World.     

Dental caries prevalence as evidence for agriculture and subsistence variation during the Yayoi period in prehistoric Japan: biocultural interpretations of an economy in transition

The Yayoi period represents the earliest point of agricultural dependence in Japan, dating from approximately 2500 BP to AD 300. Yayoi period people consumed wet-rice as a primary subsistence base. This article uses dental caries prevalence to interpret the biocultural implications of agriculture among these people by testing the following hypotheses: 1) Yayoi period agriculturalists had greater frequencies of carious teeth than Jomon period foragers, 2) regional variation in carious tooth frequencies will be observed among Yayoi period agriculturalists, while 3) variation in carious tooth frequencies will be observed between male and female agriculturalists. Statistically significant differences in carious teeth were observed between the agriculturalists from Southern Honshu and all other samples. These differences suggest greater reliance on cariogenic plants among farmers from Southern Honshu and are consistent with an agricultural economy. The people of the Yayoi period from Tanegashima Island and Northern Kyushu did not have significantly different carious tooth frequencies compared to Jomon period foragers. This suggests that rice alone was not a more cariogenic dietary substance than those consumed by Jomon period foragers but a cariogenic food nonetheless. Dietary heterogeneity between the prehistoric people of the Yayoi period from Southern Honshu and those from Northern Kyushu and Tanegashima Island is also inferred from these differences. Significantly greater frequencies of carious teeth among older aged Yayoi period females compared with males suggest dietary differences between the sexes.     

Genetic origins of the Japanese: A partial support for the dual structure hypothesis

Based on the morphological characteristics of the skull and teeth, Hanihara ([1991] Japan Review 2:1–33) proposed the “dual structure model” for the formation of modern Japanese populations. We examine this model by dividing it into two independent hypotheses: 1) the Upper Paleolithic population of Japan that gave rise to the Neolithic Jomon people was of southeast Asian origin, and 2) modern Ainu and Ryukyuan (Okinawa) populations are direct descendants of the Jomon people, while Hondo (Main Island)-Japanese are mainly derived from the migrants from the northeast Asian continent after the Aeneolithic Yayoi period. Our aim is to examine the extent to which the model is supported by genetic evidence from modern populations, particularly from Japan and other Asian areas. Based on genetic distance analyses using data from up to 25 “classic” genetic markers, we find first that the three Japanese populations including Ainu and Ryukyuan clearly belong to a northeast Asian cluster group. This negates the first hypothesis of the model. Then, we find that Ainu and Ryukyuans share a group contrasting with Hondo-Japanese and Korean, supporting the second hypothesis of the model. Based on these results, we propose a modified version of the dual structure model which may explain the genetic, morphological, and archaeological evidence concerning the formation of modern Japanese populations. Am J Phys Anthropol 102:437–446, 1997. © 1997 Wiley-Liss, Inc.     

Patterns of systemic stress during the agricultural transition in prehistoric Japan

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. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.     

Variation in limb proportions between Jomon foragers and Yayoi agriculturalists from prehistoric Japan

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.     

Differentials of Yayoi immigration to Japanas derived from dental metrics

A major influx of new people, today termed Yayoi, migrated from the East Asian continent into the Japanese archipelago during the Aeneolithic and Protohistoric periods and interbred with the preexisting Jomon people. This study classifies ancient and more modern Japanese into natives or immigrants using discriminant analysis based on dental measurements in order to reconstruct the initial impact of the immigrants and the temporal and geographical differentials of mixture with the preexisting people. The results suggest that the earliest immigrants diffused into central Japan, including the Kanto region. The proportion of immigrant origin in the protohistoric Kofun was less in eastern Japan (72%) as compared to western Japan (81%-90%). The proportion of the immigrants in the Kanto District decreased during the medieval period (63%) and increased again in the early modern Edo and later modern times (75%), which might indicate that the gene flow still was occurring from west to east even in these times. Assuming the estimated proportions of either group reflect the intermixture ratio, the recent Japanese people may be regarded as hybrid of the native and immigrant groups with the following approximate ratios: 1:3 for the Kanto Japanese, 2:3 for the Ryukyu Islanders and 7:3 for the Hokkaido Ainu. These estimations support the "dual structure model" formed by Hanihara (1991) for explaining the population history of Japan.     

Changes in mandibular morphology from the Jomon to modern periods in Eastern Japan

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 Yayoi 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. Am J Phys Anthropol 104:227–243, 1997. © 1997 Wiley-Liss, Inc.     

Molecular genetic analysis of remains of a 2,000-year-old human population in China-and its relevance for the origin of the modern Japanese population.

We extracted DNA from the human remains excavated from the Yixi site ( approximately 2,000 years before the present) in the Shandong peninsula of China and, through PCR amplification, determined nucleotide sequences of their mitochondrial D-loop regions. Nucleotide diversity of the ancient Yixi people was similar to those of modern populations. Modern humans in Asia and the circum-Pacific region are divided into six radiation groups, on the basis of the phylogenetic network constructed by means of 414 mtDNA types from 1, 298 individuals. We compared the ancient Yixi people with the modern Asian and the circum-Pacific populations, using two indices: frequency distribution of the radiation groups and genetic distances among populations. Both revealed that the closest genetic relatedness is between the ancient Yixi people and the modern Taiwan Han Chinese. The Yixi people show closer genetic affinity with Mongolians, mainland Japanese, and Koreans than with Ainu and Ryukyu Japanese and less genetic resemblance with Jomon people and Yayoi people, their predecessors and contemporaries, respectively, in ancient Japan.     

Y chromosomal DNA variation and the peopling of Japan.

Four loci mapping to the nonrecombining portion of the Y chromosome were genotyped in Japanese populations from Okinawa, the southernmost island of Japan; Shizuoka and Aomori on the main island of Honshu; and a small sample of Taiwanese. The Y Alu polymorphic (YAP) element is present in 42% of the Japanese and absent in the Taiwanese, confirming the irregular distribution of this polymorphism in Asia. Data from the four loci were used to determine genetic distances among populations, construct Y chromosome haplotypes, and estimate the degree of genetic diversity in each population and on different Y chromosome haplotypes. Evolutionary analysis of Y haplotypes suggests that polymorphisms at the YAP (DYS287) and DXYS5Y loci originated a single time, whereas restriction patterns at the DYS1 locus and microsatellite alleles at the DYS19 locus arose more than once. Genetic distance analysis indicated that the Okinawans are differentiated from Japanese living on Honshu. The data support the hypotheses that modern Japanese populations have resulted from distinctive genetic contributions involving the ancient Jomon people and Yayoi immigrants from Korea or mainland China, with Okinawans experiencing the least amount of admixture with the Yayoi. It is suggested that YAP+ chromosomes migrated to Japan with the Jomon people > 10,000 years ago and that a large infusion of YAP- chromosomes entered Japan with the Yayoi migration starting 2,300 years ago. Different degrees of genetic diversity carried by these two ancient chromosomal lineages may be explained by the different life-styles (hunter-gatherer versus agriculturalist). of the migrant groups, the size of the founding populations, and the antiquities of the founding events.     

Maximum likelihood estimate of life expectancy in the prehistoric Jomon: Canine pulp volume reduction suggests a longer life expectancy than previously thought

Recent theoretical progress potentially refutes past claims that paleodemographic estimations are flawed by statistical problems, including age mimicry and sample bias due to differential preservation. The life expectancy at age 15 of the Jomon period prehistoric populace in Japan was initially estimated to have been ～16 years while a more recent analysis suggested 31.5 years. In this study, we provide alternative results based on a new methodology. The material comprises 234 mandibular canines from Jomon period skeletal remains and a reference sample of 363 mandibular canines of recent‐modern Japanese. Dental pulp reduction is used as the age‐indicator, which because of tooth durability is presumed to minimize the effect of differential preservation. Maximum likelihood estimation, which theoretically avoids age mimicry, was applied. Our methods also adjusted for the known pulp volume reduction rate among recent‐modern Japanese to provide a better fit for observations in the Jomon period sample. Without adjustment for the known rate in pulp volume reduction, estimates of Jomon life expectancy at age 15 were dubiously long. However, when the rate was adjusted, the estimate results in a value that falls within the range of modern hunter‐gatherers, with significantly better fit to the observations. The rate‐adjusted result of 32.2 years more likely represents the true life expectancy of the Jomon people at age 15, than the result without adjustment. Considering ～7% rate of antemortem loss of the mandibular canine observed in our Jomon period sample, actual life expectancy at age 15 may have been as high as ～35.3 years.     

中国人和日本人在人种上的关系——颅骨测量性状的统计分析研究

本研究以北亚、东亚、东南亚和大洋洲一大片区域为背景探索日本人的起源和亲缘关系。结果显示日本旧石器时代港川人、绳文时代和现代人与大约同时期的华南居民有最接近的亲缘关系;从绳文时代到现代日本人的时代变化具有与后者(以及华北居民)相同的趋势。     

Mitochondrial DNA analysis of Jomon skeletons from the Funadomari site, Hokkaido, and its implication for the origins of Native American

Ancient DNA recovered from 16 Jomon skeletons excavated from Funadomari site, Hokkaido, Japan was analyzed to elucidate the genealogy of the early settlers of the Japanese archipelago. Both the control and coding regions of their mitochondrial DNA were analyzed in detail, and we could securely assign 14 mtDNAs to relevant haplogroups. Haplogroups D1a, M7a, and N9b were observed in these individuals, and N9b was by far the most predominant. The fact that haplogroups N9b and M7a were observed in Hokkaido Jomons bore out the hypothesis that these haplogroups are the (pre-) Jomon contribution to the modern Japanese mtDNA pool. Moreover, the fact that Hokkaido Jomons shared haplogroup D1 with Native Americans validates the hypothesized genetic affinity of the Jomon people to Native Americans, providing direct evidence for the genetic relationships between these populations. However, probably due to the small sample size or close consanguinity among the members of the site, the frequencies of the haplogroups in Funadomari skeletons were quite different from any modern populations, including Hokkaido Ainu, who have been regarded as the direct descendant of the Hokkaido Jomon people. It appears that the genetic study of ancient populations in northern part of Japan brings important information to the understanding of human migration in northeast Asia and America.     

Inferring the population expansions in peopling of Japan

Background

Extensive studies in different fields have been performed to reconstruct the prehistory of populations in the Japanese archipelago. Estimates the ancestral population dynamics based on Japanese molecular sequences can extend our understanding about the colonization of Japan and the ethnogenesis of modern Japanese.

Methodology/Principal Findings

We applied Bayesian skyline plot (BSP) with a dataset based on 952 Japanese mitochondrial DNA (mtDNA) genomes to depict the female effective population size (N_ef) through time for the total Japanese and each of the major mtDNA haplogroups in Japanese. Our results revealed a rapid N_ef growth since ∼5 thousand years ago had left ∼72% Japanese mtDNA lineages with a salient signature. The BSP for the major mtDNA haplogroups indicated some different demographic history.

Conclusions/Significance

The results suggested that the rapid population expansion acted as a major force in shaping current maternal pool of Japanese. It supported a model for population dynamics in Japan in which the prehistoric population growth initiated in the Middle Jomon Period experienced a smooth and swift transition from Jomon to Yayoi, and then continued through the Yayoi Period. The confounding demographic backgrounds of different mtDNA haplogroups could also have some implications for some related studies in future.     

Dental anthropological indications of agriculture among the Jomon people of central Japan. X. Peopling of the Pacific

The high rate of crown caries (8.6%; 119/1,377 teeth) and other oral pathologies in 101 central Japan Middle to Late Jomon Period (ca. 1000 B.C.) crania indicate a level of carbohydrate consumption consistent with an agriculture hypothesis. Because Jomon dental crown and root morphology shows strong resemblances with past and present Southeast Asians, but not with ancient Chinese or modern Japanese, Jomon agriculture could be of great antiquity in the isolated Japanese islands. These dental data and other assembled facts suggest that ancestral Jomonese might have carried to Japan a cariogenic cultigen such as taro before the end of the Pleistocene from tropical Sundaland by way of the now-submerged east Asian continental shelf.     

Temporal craniometric changes from the Jomon to the Modern period in western Japan

Temporal changes in morphometric features of human cranial remains from the late Jomon period (1500 B.C.–300 B.C.) to the Modern period (1900–1950 A.D.) in western Japan are examined. The results of univariate and multivariate analysis indicate that the Yayoi people (300 B.C.–300 A.D.), characterized by high faces and tall stature, show morphological discontinuity with the earlier Jomon people, who exhibit lower faces and shorter stature. This discontinuity contrasts with the relatively continuous changes among populations after the Yayoi. Comparing these changes with those documented in the Kanto region of eastern Japan indicates there are significant regional differences in the degree and rate of transformation in certain cranial features, especially facial height, between the two regions. Differences in cranial shape between the two regions become apparent during the Yayoi period and these differences tend to diminish thereafter. The most plausible explanation for these observed changes is the introduction of new genes, coinciding with the arrival of new immigrants from the Asian continent in the northern Kyushu-Yamaguchi region at the beginning of the Yayoi period. Further testing of this hypothesis will be necessary before definitive conclusions can be reached regarding the appearance of modern Japanese. © 1993 Wiley-Liss, Inc.     

Deciduous dental morphology of the prehistoric Jomon people of Japan: Comparison of nonmetric characters

Morphological variations of the deciduous dentition are as useful as those of the permanent dentition for determining the biological affinities of human populations. This paper provides material on morphological variations of deciduous teeth of the prehistoric Japanese population from the Late and the Latest Jomon Period (ca. 2000–ca. 300 B.C.). The expression of nonmetric traits of the deciduous teeth in the Jomon sample shows a closer affinity with modern Japanese and Native American samples than with American White, Asiatic Indian, and African samples. However, the frequency of shoveling in deciduous upper incisors in the Jomon sample is lower than those in modern Japanese and Native American samples. The Jomon sample also expresses a much higher frequency of cusp 6 in deciduous lower second molars than seen in modern Japanese, Ainu, and Native American samples. The frequency in the Jomon sample is equal to that in the Australian Aboriginal sample, which shows cusp 6 most frequently among the samples compared. A somewhat low incidence of incisor shoveling in the Jomon sample was also reported in the permanent dentition (Turner [1976] Science 193:911–913, [1979] Am. J. Phys. Anthropol. 51:619–635, [1987] Am. J. Phys. Anthropol. 73:305–321, [1990] Am. J. Phys. Anthropol. 82:295–317; T. Hanihara [1992] Am. J. Phys. Anthropol. 88:163–182, 88:183–196). However, the frequency of cusp 6 in the Jomon sample shows no significant difference from those of Northeast Asian or Native American samples in the permanent dentition (Turner [1987] Am. J. Phys. Anthropol. 73:305–321; T. Hanihara [1992] Am. J. Phys. Anthropol. 88:1–182, 88:183–196). Evidently, some nonmetric traits express an inter-group difference only in the deciduous dentition. © 1995 Wiley-Liss, Inc.     

Metric dental variation of major human populations

Mesiodistal and buccolingual crown diameters of all teeth recorded in 72 major human population groups and seven geographic groups were analyzed. The results obtained are fivefold. First, the largest teeth are found among Australians, followed by Melanesians, Micronesians, sub-Saharan Africans, and Native Americans. Philippine Negritos, Jomon/Ainu, and Western Eurasians have small teeth, while East/Southeast Asians and Polynesians are intermediate in overall tooth size. Second, in terms of odontometric shape factors, world extremes are Europeans, aboriginal New World populations, and to a lesser extent, Australians. Third, East/Southeast Asians share similar dental features with sub-Saharan Africans, and fall in the center of the phenetic space occupied by a wide array of samples. Fourth, the patterning of dental variation among major geographic populations is more or less consistent with those obtained from genetic and craniometric data. Fifth, once differences in population size between sub-Saharan Africa, Europe, South/West Asia, Australia, and Far East, and genetic drift are taken into consideration, the pattern of sub-Saharan African distinctiveness becomes more or less comparable to that based on genetic and craniometric data. As such, worldwide patterning of odontometric variation provides an additional avenue in the ongoing investigation of the origin(s) of anatomically modern humans.     

A genetic analysis of the Sakishima islanders reveals no relationship with Taiwan aborigines but shared ancestry with Ainu and main‐island Japanese

The Sakishima islands are members of the Ryukyu island chain, stretching from the southwestern tip of the Japanese archipelago to Taiwan in the East China Sea. Archaeological data indicate cultural similarities between inhabitants of prehistoric Sakishima and Neolithic Taiwan. Recent studies based on tooth crown traits show remarkably high inter‐island diversity among Ryukyu islanders, suggesting that the Sakishima islanders might have genetic backgrounds distinct from main‐island Okinawa people. To investigate the genetic diversity of the Ryukyu islanders, we analyzed mtDNA, Y chromosome, and autosomal short tandem repeat loci in a sample of main‐island Okinawa people and Sakishima (Miyako and Ishigaki) islanders whose participated in a previous study of tooth crown morphology. Our phylogenetic analysis of maternal (mtDNA) and paternal (Y chromosome) lineages shows that the Sakishima islanders are more closely related to people from the Japanese archipelago than to Taiwan aborigines. Miyako islanders and the Hokkaido Ainu have the first and second highest frequencies (respectively) of the Y‐chromosomal Alu‐insertion polymorphism, which is a presumable Jomon marker. Genetic diversity statistics show no evidence of demographic reduction or of extreme isolation in each island's population. Thus, we conclude that 1) Neolithic expansion from Taiwan did not contribute to the gene pool of modern Sakishima islanders, 2) male‐lineage of the Ryukyu islanders likely shares a common ancestor with the Hokkaido Ainu who are presumably direct descendants of the Jomon people, and 3) frequent reciprocal gene flow among islands has masked the trace of common ancestry in the Ryukyu island chain. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

A morphometric analysis of the Japanese macaque (Macaca fuscata) mandibular cheek teeth from the Torihama Shell-midden, Early Jomon Period, Fukui Prefecture, Japan

We quantitatively examined the differences in the size and proportion of the Japanese macaque (Macaca fuscata) by comparing the Early Jomon specimens from Torihama shell-midden, Fukui Prefecture and modern specimens from Fukui Prefecture. The purpose of this study was to explore the temporal change in the proportion and size of teeth of the Japanese macaques based on the quantified data. The result of measurements of lower premolars and molars demonstrated that sexual dimorphism was evident only among the modern specimens where the females were significantly smaller than males. The size of male Torihama specimens was within the range of the modern population, whereas the size of the female Torihama specimens was significantly larger than the modern female population. The proportional pattern of premolars and molars for male and female Torihama specimens also differed. The results may suggest a possible difference in the degree of size reduction between males and females since the last glacial period.Morphometric analysis of mandibular cheek teeth from Torihama Shell-midden     

A population genetic study on the transition from Jomon people to Yayoi people

In the study on the origin of Japanese, one of main unsolved problems is the transition from the Jomon people to the Yayoi people. The main difficulty in solving this problem has been the lack of suitable skeletal materials belonging to the time between the two periods, i.e. the final Jomon and the early Yayoi Periods. Therefore, we know few details of the transition period. It is important to know who carried out a drastic change of the Yayoi culture during this transitional period, i.e. the native Jomon people or the immigrant people. By introducing population genetic models, we show that a view that the immigrant people had a significant genetic contribution to the origin of Japanese is compatible with results from anthropological and archeological studies. This result implies that the immigrant people were mainly responsible for the drastic cultural change during the transitional period.