HLA class II alleles in Ainu living in Hidaka district,Hokkaido, northern Japan

The Ainu people are considered to be the descendants of preagricultural native populations of northern Japan, while the majority of the population of contemporary Japan (Wajin) is descended mainly from postneolithic migrants. Polymorphisms of the HLA-DRB1, DRB3, and DQB1 alleles were investigated in DNA samples of 50 Ainu living in Hidaka district, Hokkaido. Unique features of the Ainu in this study were high incidences of DRB1*1401, DRB1*1406, and a newly described allele, DRB1*1106 (20%, 17%, and 5%, respectively). On the other hand, several common alleles in Wajin (DRB1*1502, 1302, 0803, and 1501) were found at relatively low frequencies (1–2%) in Ainu. Previously DRB1*1406 was described as a characteristic allele of some Native American or northeast Asian ethnic groups, and DRB1*1106 had been found in only two Singapore Chinese and one Korean. Principal component analysis of various populations based on HLA class II allele frequencies places the Ainu population midway between other east Asian populations, including Wajin, and Native Americans. These observations may support the hypothesis that the Ainu people are the descendants of some Upper Paleolithic populations of northeast Asia from which Native Americans are also descended. © 1996 Wiley-Liss, Inc.     

Deep History of East Asian Populations Revealed Through Genetic Analysis of the Ainu

Despite recent advances in population genomics, much remains to be elucidated with regard to East Asian population history. The Ainu, a hunter–gatherer population of northern Japan and Sakhalin island of Russia, are thought to be key to elucidating the prehistory of Japan and the peopling of East Asia. Here, we study the genetic relationship of the Ainu with other East Asian and Siberian populations outside the Japanese archipelago using genome-wide genotyping data. We find that the Ainu represent a deep branch of East Asian diversity more basal than all present-day East Asian farmers. However, we did not find a genetic connection between the Ainu and populations of the Tibetan plateau, rejecting their long-held hypothetical connection based on Y chromosome data. Unlike all other East Asian populations investigated, the Ainu have a closer genetic relationship with northeast Siberians than with central Siberians, suggesting ancient connections among populations around the Sea of Okhotsk. We also detect a recent genetic contribution of the Ainu to nearby populations, but no evidence for reciprocal recent gene flow is observed. Whole genome sequencing of contemporary and ancient Ainu individuals will be helpful to understand the details of the deep history of East Asians.     

Evolution of the Ainu Language in Space and Time

Languages evolve over space and time. Illuminating the evolutionary history of language is important because it provides a unique opportunity to shed light on the population history of the speakers. Spatial and temporal aspects of language evolution are particularly crucial for understanding demographic history, as they allow us to identify when and where the languages originated, as well as how they spread across the globe. Here we apply Bayesian phylogeographic methods to reconstruct spatiotemporal evolution of the Ainu language: an endangered language spoken by an indigenous group that once thrived in northern Japan. The conventional dual-structure model has long argued that modern Ainu are direct descendants of a single, Pleistocene human lineage from Southeast Asia, namely the Jomon people. In contrast, recent evidence from archaeological, anthropological and genetic evidence suggest that the Ainu are an outcome of significant genetic and cultural contributions from Siberian hunter-gatherers, the Okhotsk, who migrated into northern Hokkaido around 900–1600 years ago. Estimating from 19 Ainu language varieties preserved five decades ago, our analysis shows that they are descendants of a common ancestor who spread from northern Hokkaido around 1300 years ago. In addition to several lines of emerging evidence, our phylogeographic analysis strongly supports the hypothesis that recent expansion of the Okhotsk to northern Hokkaido had a profound impact on the origins of the Ainu people and their culture, and hence calls for a refinement to the dual-structure model.     

Mitochondrial DNA polymorphism among five Asian populations

Mitochondrial DNA (mtDNA) polymorphisms were detected using 13 restriction enzymes on the total DNA obtained from blood samples of five Asian populations: Japanese and Ainu of northern Japan, Korean, Negrito (Aeta) of the Philippines, and Vedda of Sri Lanka. Of a total of 28 restriction-enzyme morphs detected, eight had not been reported previously. By combining the morphs, we were able to classify mtDNAs of 243 individuals into 20 mtDNA types. Phylogenetic analyses using maximum parsimony and genetic distance methods both showed that the Japanese, Ainu, and Korean populations were closely related to each other. Aeta was found to show a relatively close relationship to these three populations, confirming the conclusion from previous studies of blood markers. In contrast, Vedda was quite different from the other four populations.     

Japanese tooth size: past and present

Mesial-distal and buccal-lingual crown measurements were made on male and female samples of recent Japanese teeth from three locations, Fukuoka, Kyoto, and Tokyo, and for Hokkaido Ainu and Koreans. Similar data were collected for prehistoric Middle-to-Late Jomon Japanese and from Yayoi specimens representing the first agriculturalists to appear in Japan. From a tooth-by-tooth comparison of cross-sectional areas, it was shown that the modern Japanese samples did not differ from one part of Japan to another. Korean tooth size also is not significantly different from Japanese, while Ainu have the smallest teeth recorded in Asia. The Yayoi who brought rice to Japan about 300 B.C. came in with teeth that were the same size as Chinese Neolithic teeth. They encountered a resident Jomon population whose teeth were 10% smaller. From tooth size measures alone, it is most economical to suggest that, if the rates of reduction observed elsewhere in the world applied in Japan, the recent Ainu would best be regarded as the direct descendants of the Jomon, while the modern Japanese are the results of in situ reduction from the incoming Yayoi. Other aspects of craniofacial morphology suggest that some Jomon was incorporated by the Yayoi. The modern Japanese, then, while predominantly derived from the Yayoi, would include a Jomon component.     

HLA genes and haplotypes in Ryukyuans suggest recent gene flow to the Okinawa Islands.

Polymorphism of HLA genes was investigated in a population sample of Ryukyuans living on the main island of Okinawa (n = 197), in the southwestern islands of Japan. Serological typing was applied to class I loci (HLA-A, -B, and -C) and to HLA-DRB1; nucleotide sequence-level typing was performed using PCR microtiter plate hybridization and PCR single-strand conformation polymorphism methods. Ryukyuans showed a higher frequency of DRB1*0405 and lower frequencies of DRB1*1502 and DRB1*1302 compared with Hondo Japanese living on main islands. Principal components and phylogenetic analyses of 12 East Asian populations, including Ryukyuans, were performed based on the allele frequencies of HLA-A, -B, and -DRB1. In the principal components analysis 3 Japanese populations (Ryukyuans, Hondo Japanese, and Ainu) formed a cluster and showed the highest affinity to 2 Korean populations. In the phylogenetic tree Ryukyuans and Ainu were neighbors, but the genetic distance between them was larger than the distances between Ryukyuans and Hondo Japanese and between Ryukyuans and Korean populations. The geographic cline of the predominant haplotype in Ryukyuans, A*24-B*54-DRB1*0405, suggests that an ancestral population possessing A*24-B*54-DRB1*0405 moved into the Okinawa Islands after the divergence of Ryukyuans from the Ainu. Such a recent gene flow, probably from South China to the Okinawa Islands, is considered the major cause of difference in genetic characteristics between Ryukyuans and the Ainu.     

Craniometric variation of the Ainu: an assessment of differential gene flow from northeast Asia into northern Japan, Hokkaido

In and after the latest Neolithic period in Japan (approximately B.P. 2,300 years), there were two distinct waves of migration from eastern Asia. One is well known as successive episodes in which indigenous inhabitants of main-island Japan were intruded on by new arrivals with advanced technology, and of a different genetic stock. Another migration of people and culture, identified as the Okhotsk culture, reached the northeastern part of Hokkaido. As opposed to main-island Japan, the morphological continuity from the Neolithic to recent inhabitants in Hokkaido (Ainu) is notable, so that the evidence of admixture easily could have escaped notice. In this study, the effects of gene flow from an outside source on the pattern of among-group variation of Hokkaido Ainu are examined by means of two models. One is the R-matrix model comparing observed and expected craniometric variation for estimating differential external gene flow into a region. The other is a simple simulation model that estimates admixture in a population with two parental populations. The two approaches give similar results. The results suggest the possibility of admixture between the migrants from Northeast Asia, the Okhotsk culture people, and the indigenous inhabitants in Hokkaido during the 5th to 12th centuries A.D., at least in northeastern Hokkaido. Such gene flow may have a certain degree of effect on the genetic structure of recent Ainu. The findings further suggest morphological heterogeneity in Northeast Asia during the Holocene that has relevance for understanding the morphological heterogeneity seen through time in the New World.     

Allozyme variation and behavioural dimorphism among populations of Littorina brevicula (Philippi) from Japan

In Amakusa (Japan), an apparently homogeneous population of Littorina brevicula, divides into two groups during the reproductive season (winter). Some snails migrate to the lower intertidal zone, while the rest remain in the upper zone. This migration behaviour might be controlled genetically and the behavioural dimorphism may be maintained by assortative mating. To evaluate this hypothesis, we studied genetic variation at four polymorphic enzyme loci (Pgm, Aldh, Ipp, Gpt) in both groups, as well as in seven other samples from the coast of Japan and Vostok Bay (Russian coast of the Sea of Japan). There were no significant allele frequency differences between the two behavioural groups of snails with differing migration patterns (2 = 8.411, df = 12, p > 0.5). The samples from Japan belong to a panmictic population. Yet, a significant heterogeneity was found between the sample from Vostok Bay and the samples from Japan, indicating a reduced gene flow between these regions. Generally, observed genotype frequencies showed good fits to Hardy-Weinberg equilibrium expectations at three of the four loci investigated.     

Expression of adenovirus type 12 early region 1 in KB cells transformed by recombinants containing the gene.

The adenovirus type 12 (Ad12) early region 1 (E1) gene was introduced into KB cells by using a dominant selection vector, pSV2-gpt, and over 80 Gpt+ KB cell clones were established. Three types of recombinant DNAs (gAE1A, gARC, and gABA) were constructed. They contained the AccI-H, EcoRI-C, and BamHI-A fragments, respectively, of Ad12 DNA in pSV2-gpt. Five of 50 (10%) gABA-transformed cell clones, 12 of 18 (67%) gAE1A-transformed cell clones, and 10 of 18 (56%) gARC-transformed cell clones complemented the growth of Ad5 dl312 (deletion in E1A) and were designated as Gpt+ Ad+ cell clones. In these cell clones at their early passages, recombinant genome sequences were detected in cellular DNA and were expressed. T antigen g (the E1A gene product) was detected by immunofluorescence. The Gpt+ Ad+ cell clones supported the growth of Ad5 deletion mutants in parallel with the expression of Ad12 E1A or E1A plus E1B genes. After infection of Gpt+ Ad+ cell clones with Ad5 dl312, the early genes of dl312 were efficiently transcribed, indicating the expression of the pre-early function of the Ad12 E1A gene. Two clones each from gAE1A-,gARC-, and gABA-transformed cells were subcultured for a long period to determine the stability of the transfecting DNAs. Subculture in a nonselective medium resulted in cells which lost the transfecting DNAs. Subculture in a selective medium resulted in the selection of cells which maintained the gpt gene expression but lost the Ad12 gene expression. These results indicate that the transfecting DNA is present in an unstable state in KB cells.     

Distribution of GPT types in Norway.

GPT phenotype determinations were performed in 4,148 unrelated Norwegians. The frequencies of the two common alleles were Gpt1 = 0.537 and Gpt2 = 0.461. A total of 13 individuals showed the phenotypic expression of 3 rare GPT alleles, Gpt3, Gpt6, and Gpt7. No heterogeneity in phenotype distribution was found, neither in the two sexes nor regionally in Norway. 97 foreigners involved in paternity cases in Norway showed a phenotype distribution not differing from that of Norwegians. In two small additional samples of Ethiopians and Easter Islanders, Gpt1 frequencies were 0.737 and 0.531, respectively. There were significant differences in phenotype distribution between NOrwegians and all African populations tested, some of the Asiatic population, Lapps and a few other populations.     

Pseudomonas aeruginosa plasmids as suicide vectors in Escherichia coli: resolution of genomic cointegrates through short regions of homology.

Pseudomonas aeruginosa plasmids which cannot replicate in Escherichia coli have been used to introduce specific modifications into the E. coli chromosome by homologous recombination ('gene targeting'). The E. coli gene (gpt) encoding guanine-xanthine phosphoribosyltransferase (Gpt) was used for initial targeting studies owing to the availability of a powerful positive selection for loss of the Gpt+ phenotype (6-thioguanine resistance or 6TGR or Gpt-). P. aeruginosa plasmids containing selectable markers flanked by gpt sequences were introduced as supercoiled DNA into an E. coli strain which contained a normal gpt locus. Primary cointegration of such plasmids into the E. coli genome results in a gene duplication event which maintains Gpt function; a secondary recombinational event which resolves the cointegrate either reverses the primary event or results in replacement of the original gpt copy with the modified version. A 316-bp region of homology was sufficient for cointegrate formation, and resolution of the cointegrates through a shorter (92 bp) homologous flank was selectable through loss of Gpt function. The frequency of cointegrate resolution under these conditions was significantly above the spontaneous gpt mutational loss rate.     

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.     

Men,women and “Japanese” as outsiders: A case study of postcards with Ainu images

The depiction of the Ainu in photography, as created and circulated in Japan starting from the Meiji era, provides us with a case study to investigate how gender and ethnic differences are related to the construction of self/other relations in modern Japan. I consider the imaginary relations between Japanese viewers and Ainu images ranging from paintings to photographs and, in doing so, make use of metaphorical meanings and imaginary mythical structures for the analogy of contentious ethnic relations from the age of mechanical reproduction, as Walter Benjamin suggested. I will examine the different images of Ainu men and women interwoven with an imaginary Japaneseness regarding the cultural meanings of insider and outsider within the process of colonization in Hokkaido during the Meiji era. Likewise, with the notion of stranger‐king political transformation emphasized by Marshall Sahlins in his Fijian studies, this article serves as a challenge to discern the construction of Japaneseness in terms of mythical motifs and stranger‐king political transformations from a visual perspective.     

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.     

Phenotypic distributions of red cell glutamate-pyruvate transaminase (E.C.2.6.1.2) isoenzymes in British and New York populations.

1444 persons of British nationality living in London, and 294 Caucasians, 258 Negroes, 310 Hispanic persons, and 151 Chinese persons living in New York were tested for glutamate-pyruvate transaminase phenotype. The Gpt1 frequency in the British population was found to be 0.5277, the Gpt2 frequency was 0.4716, and two GPT 3-2 persons were found. The Gpt1 frequencies in the New York population were: 0.4834 in Chinese; 0.5226 in Hispanic persons; 0.8101 in Negroes; and 0.5306 in Caucasians. Two Caucasians possessed the GPT 3-2 phenotype.     

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.     

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.     

Regional differences in craniofacial diversity and the population history of Jomon Japan

The people associated with the Jomon culture, the Neolithic inhabitants of Japan, are one of the key groups in the population history of East Asia, because they retain many archaic characters that may be traced back to Eurasian Upper Palaeolithic hunter–gatherers. In this study, the regional diversity of the Jomon skeletal series was estimated by applying the R‐matrix method to 34 craniofacial measurements. The patterns of intraregional variation indicate little effect on the genetic structure of the Jomon from long‐term gene flow stemming from an outside source. The regional diversities were further estimated by pooling all individuals into regional aggregates, and by computing the mean variance within local groups in each region. Although the pattern of phenotypic variation differs depending on the unit of analysis, the gradient of the diversity retains its identity. The Hokkaido region, the northernmost part of the Japanese archipelago, has the highest variance, followed by the regions of eastern Japan, while the southwestern regions have the lowest variance. These findings suggest that the Jomon ancestors of the northern part of Japan might have expanded southward to Honshu Island. Global analyses including samples from Eurasia, Africa, and Australia dating roughly to the same chronological periods as those of the Jomon samples, indicate that the Jomon cranial series share part of their ancestral gene pool with early northeastern Asians. The present findings support the archeologically suggested population growth and expansion in the northern half of the Eurasian continent during the late Pleistocene and early Holocene periods. Am J Phys Anthropol, 2009. © 2008 Wiley‐Liss, Inc.     

Genetic variation and differentiation in the Japanese five-lined skink,Eumeces latiscutatus (Reptilia: Squamata)

The genetic variation in Eumeces latiscutatus from the main islands of Japan and the northern Ryukyus was investigated and compared with that of its close relatives (E. okadae and E. marginatus) using allozyme data. All three samples from the northern Tokara Island Group, currently identified as E. latiscutatus, were shown to belong to E. marginatus and not to E. latiscutatus. The non-monophyly of the northern Tokara samples and the great genetic differences within these samples may have resulted from colonization from more than one source population by northeastward overseas dispersal. The samples from the Izu Peninsula were genetically much closer to E. okadae than the other conspecific ones. This indicates that the samples from the Izu Peninsula and the other samples of E. latiscutatus should be treated as distinct species, and that E. latiscutatus from the Izu Peninsula and E. okadae from the Izu Island Group may be treated as conspecific. Samples from western Japan were genetically well differentiated from those of eastern Japan. Within the western group, the samples from the Osumi Island Group was genetically distinct from those from the other regions, by possessing unique alleles. Our phenograms also reveal a distant affinity between samples from the Danjo Island Group and the main islands of Japan. This may be the result of long geographic isolation of the Osumi and Danjo Island Groups from Kyushu. By contrast, samples from Sapporo and Aomori were poorly differentiated genetically in spite of the long separation of these two localities by the Tsugaru Strait. This suggests that overseas dispersal of E. latiscutatus occurred across this strait after its formation.