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PCA plots of the individuals for the three populations in the Japanese Archipelago (Ainu, Ryukyuans and the Mainland Japanese) and other Asian populations. (a) Result with the HGDP-CEPH data set (see Supplementary Table S2 for the list of populations). (b) Result with the HGDP-CEPH data set and the PASNP data set (see Supplementary Table S2 for the list of populations).
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The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes and root populations have been proposed. Here, we determ...
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... see whether this was the case, we calculated the allele-sharing distances between the Ainu and the Mainland Japanese individuals, and compared these with the PC1 coordinates of the Ainu indivi- duals. There was a clear positive correlation (r 2 ¼ 0.542) between the allele-sharing distances and the PC1 coordinates (Supplementary Figure S3). The three Ainu individuals within the Mainland Japanese cluster had the smallest allele-sharing distances, and conversely, the Ainu individuals located farthest from the Mainland Japanese on the PC1 axis tend to have greater allele-sharing distances with the Mainland Japanese population. ...
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... now move to analyses combined with individuals belonging to the 16 HGDP-CEPH populations. Figure 3a shows the PCA result. The overall distribution of individuals in this figure indicates an L shape. ...
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... Ryukyuan and the Mainland Japanese populations were located as if they were pulled by the Ainu population, whereas the remaining East Asian populations were closer to northern East Asian populations (Yakut, Mongolian and Oroqen). This clear dichotomy with the L-shaped constellation remains when we further added individuals of the 14-population PASNP data sets (Figure 3b). The Ainu population is located at the one extreme followed by the Ryukyuan, whereas another extreme is now the Uyghur population. ...
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... This fact indicates that the Ainu, and the two other populations in the Japanese Archipelago (Ryukyuan and Mainland Japanese) to a lesser degree, contain genetic components neither found in the other East Eurasians nor West Eurasians. Another notable addition in Figure 3b is the Korean, who are located between the Mainland Japanese and the Han Chinese in the northern part of China. This result is consistent with that of Tian et al. ...
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... result is consistent with that of Tian et al. 50 The result of the frappe analysis for populations corresponding to Figure 3a is shown in Supplementary Figure S6. When k ¼ 2, the dichotomy pattern is quite similar with that of Figure 2, and additional East Eurasian populations showed similar blue/orange frequencies as in the Han Chinese. ...
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... The capital, Tokyo, is located almost at the center of the main island on the Pacific coast (Figure 1), and the other parts of the country are divided into 46 prefectures. It has been suggested that contemporary Japanese people are descendants of a group consisting of a mixture of the indigenous peoples (Ainu, Ryukyuan and mainlanders) who have been present in Japan since the Jomon era over 10,000 years ago, as well as immigrants who arrived between 2000 and several 100 years ago [16]. Recently, a study reported an analysis of SNPs (single-nucleotide polymorphisms) in each of Japan's 47 prefectures (including Tokyo) [17]. ...
... On the other hand, novel genotypes (II to V and IX) were found in the Japanese strains. Genotype II was near to genotype I, genotype III was near to genotype IV, genotype V was near to genotype VI (identical to genotype 3 in the previous report [15]), and genotype IX was near to genotype VIII (identical to genotype 2 in the previous report [16]) (Figure 4). Microorganisms 2024, 12, x FOR PEER REVIEW 8 of 15 To classify C. dubliniensis isolates via genotyping on the DNA sequences from ITS1 to ITS2 of the intervening 5.8S rRNA gene15, 122 strains of C. dubliniensis (93 from healthy subjects and 29 from patient subjects) isolated in this survey ( Table 2) were analyzed via DNA sequencing, multiple alignment and the drawing of the phylogenetical tree via the neighbor joining method using Clustal W software. ...
... On the other hand, novel genotypes (II to V and IX) were found in the Japanese strains. Genotype II was near to genotype I, genotype III was near to genotype IV, genotype V was near to genotype VI (identical to genotype 3 in the previous report [15]), and genotype IX was near to genotype VIII (identical to genotype 2 in the previous report [16]) ( Figure 4). The ITS sequences were classified into nine genotypes (genotypes I to IX), and genotypes 1 to 4 were derived from a previous report [24]. ...
Introduction: Candida dubliniensis was reclassified from the C. albicans genotype D, and reports show its frequent detection in HIV-positive individuals and easy acquisition of antifungal drug resistance. However, the oral carriage rate in healthy people and contribution to candidiasis in Japan is unclear. Methods: We conducted a cross-sectional survey of the C. dubliniensis carriage rate, performed genotyping and tested antifungal drug susceptibility and protease productivity. Specimens from 2432 Japanese subjects in six regions (1902 healthy individuals, 423 with candidiasis individuals, 107 HIV-positive individuals) were cultured using CHROMagarTMCandida, and the species was confirmed via 25S rDNA amplification and ITS sequences analyzed for genotyping. Results: The C. dubliniensis carriage rate in healthy Japanese was low in the central mainland (0–15%) but high in the most northerly and southerly areas (30–40%). The distribution of these frequencies did not differ depending on age or disease (HIV-infection, candidiasis). Genotype I, previously identified in other countries, was most frequent in Japan, but novel genotypes were also observed. Six antifungal drugs showed higher susceptibility against C. albicans, but protease productivity was low. Conclusions: Oral C. dubliniensis has low pathogenicity with distribution properties attributed to geography and not dependent on age or disease status.
... The Japanese male is believed to exist within the larger framework of a dual structure but has retained genetic structural diversity owing to population shifts, genetic flotation, and the influx of different genes. DNA analysis has recently revealed that the Japanese males migrated from the Korean Peninsula and continental East Asia following the Kofun period (3rd century AD) and that the Okhotsk cultural people also migrated to Hokkaido from the north, leading to the three-step migration model theory [20,21]. Future studies should further elucidate the diversity of Japanese males by identifying the Japanese sub-lineages of haplogroup O3 and examining their frequencies in different regions. ...
... The origins and genetic history of the Jomons have been of keen academic interest not just to understand the Jomons themselves, but also to understand the genetic diversity of present-day populations in the Japanese archipelago. For example, the Ainu from the northernmost region of the archipelago are genetically closer to the Ryukyuans from the southernmost region than to the mainland Japanese in the middle, because they inherited higher proportions of their ancestry from the Jomon-related ancestors than the mainland Japanese did [5][6][7][8][9][10][11][12]. Most archaeogenetic studies on the Jomons mainly targeted mitochondrial haplogroups, finding that distinct haplogroups N9b1 and M7a were representative of the northern and southern Jomons, respectively, thus suggesting an internal population differentiation among the Jomons [13][14][15][16]. ...
The Jomon people were prehistoric residents of the Japanese archipelago who occupied the region from ca. 16,500 to 2,300 years before present (BP). While recent accumulation of ancient genomes and genome-wide data of the Jomons has substantially enhanced our understanding of their genetic profiles and contribution to present-day populations, their genetic history in the Jomon-period archipelago, spanning over 14,000 years in time and 2,000 km in distance, remains scarcely investigated. Here we report multiple findings illuminating the Jomon genetic history based on the analysis of the genetic relationship between published ancient genome-wide data of 23 Jomon and Jomon-like individuals. First, the Initial Jomon individual from Shikoku, dated to ca. 9,000 BP, forms a common outgroup to the remaining later Jomon individuals, suggesting a population turnover in western Japan. Second, genetically Jomon-like individuals outside the Jomon archaeological context, found in the Miyako Island in Ryukyu and the Yokjido island in the southern coast of Korea, show the closest genetic affinity with the Late Jomon individual from Shikoku, narrowing down their sources in space and time. This study highlights a dynamic history of the Jomon people in and out of the Japanese archipelago and calls for a large-scale investigation of the ancient Jomon genomes.
... This postulates that the larger one represents the Hondo population, while the smaller one corresponds to the Ryukyu population [15]. The division of the PCA cluster within the Japanese population aligns with findings reported in previous studies [15][16][17]. The same bifurcation into two clusters, This indicates the presence of genetic structure within the Hondo cluster because the biobanks were located in different locations. ...
... For instance, the population genetic analysis identified two clusters representing the ancestry of Ryukyu Islands, comprising Okinawa Prefecture and the islands of Kagoshima Prefecture and the Hondo region (mainland). This supports the idea that the Hondo and Ryukyu populations are genetically differentiated, as suggested by anthropological studies [15][16][17]. We further found that past population sizes differed between Hondo and Ryukyu. ...
The Japanese archipelago is a terminal location for human migration, and the contemporary Japanese people represent a unique population whose genomic diversity has been shaped by multiple migrations from Eurasia. We analyzed the genomic characteristics that define the genetic makeup of the modern Japanese population from a population genetics perspective from the genomic data of 9,287 samples obtained by high-coverage whole-genome sequencing (WGS) by the National Center Biobank Network. The dataset comprised populations from the Ryukyu Islands and other parts of the Japanese archipelago (Hondo). The Hondo population underwent two episodes of population decline during the Jomon period, corresponding to the Late Neolithic, and the Edo period, corresponding to the Early Modern era, while the Ryukyu population experienced a population decline during the shell midden period of the Late Neolithic in this region. Haplotype analysis suggested increased allele frequencies for genes related to alcohol and fatty acid metabolism, which were reported as loci that had experienced positive natural selection. Two genes related to alcohol metabolism were found to be 12,500 years out of phase with the time when they began to increase in the allele frequency; this finding indicates that the genomic diversity of Japanese people has been shaped by events closely related to agriculture and food production.
... We were also able to detect Jomon-derived variants using AMI, even by changing the population history in the simulations. The evolutionary history of the Japanese archipelago population was somewhat controversial, [5][6][7][8][9][10][11]13,40,41 but whatever population history was correct, the present approach using AMI would enable the detection of Jomon-derived SNPs. Moreover, it would also be applicable to other admixed populations whose source populations have diverged relatively recently. ...
Modern Japanese people have two major ancestral populations: indigenous Jomon hunter-gatherers and continental East Asian farmers. To determine the formation process of the current Japanese population, we developed a detection method for variants derived from ancestral populations using a summary statistic, the ancestry marker index (AMI). We applied AMI to modern Japanese population samples and identified 208,648 single nucleotide polymorphisms (SNPs) that were likely derived from the Jomon people (Jomon-derived variants). Analysis of Jomon-derived variants in 10,842 modern Japanese individuals recruited from all over Japan revealed that the admixture proportions of the Jomon people varied between prefectures, probably owing to the prehistoric population size difference. The estimated allele frequencies of genome-wide SNPs in the ancestral populations of the modern Japanese suggested their adaptive phenotypic characteristics to their respective livelihoods. Based on our findings, we propose a formation model for the genotypic and phenotypic gradations of the current Japanese archipelago populations.
... Because CIN2/3 lesions appear as a result of persistent HPV infection, our data suggest that women in western Japan clear persistent HPV52 more efficiently than those in eastern Japan, even though HPV52 infection in CIN1 is more prevalent in the west. This might be due to geographical differences in the genetic background of Japanese people, because recent genome-wide single nucleotide polymorphism (SNP) studies have revealed that there are considerable regional variations in SNP composition of the present-day Japanese population (12,13). The human leukocyte antigen (HLA) haplotype is one such genetic variant that strongly influences the host's susceptibility and response to viral infection. ...
Although geographical differences in the distribution of human papillomavirus genotypes have been observed worldwide, no studies have reported on national differences in the prevalence of human papillomavirus types in Japan. Here, we report a cross-sectional study to explore regional differences in the prevalence of human papillomavirus types among Japanese women with cervical intraepithelial neoplasia or invasive cervical cancer. Using human papillomavirus genotyping data from the nationwide prospective study on human papillomavirus vaccine effectiveness, we compared the frequency of detection of 15 high-risk and two low-risk human papillomavirus types in each disease category between the women who visited hospitals located in eastern Japan and those who visited hospitals located in western Japan. The risk of cervical intraepithelial neoplasia progression was assessed by calculating a prevalence ratio of each human papillomavirus type for cervical intraepithelial neoplasia grade 2/3 versus grade 1. Among the human papillomavirus types studied, human papillomavirus 52 was detected significantly more frequently in western hospitals than in eastern hospitals in cervical intraepithelial neoplasia grade 1 patients, but was less frequent in cervical intraepithelial neoplasia grade 2/3. The prevalence of particular human papillomavirus types was not significantly different between patients in hospitals in eastern Japan and those in hospitals in western Japan for invasive cervical cancer. In both eastern and western hospitals, a higher risk of cervical intraepithelial neoplasia progression was observed in patients infected with human papillomavirus 16, 31 or 58. In contrast, there was a significantly higher prevalence of human papillomavirus 52 infection in women with cervical intraepithelial neoplasia grade 2/3 than in those with cervical intraepithelial neoplasia grade 1 in eastern hospitals (prevalence ratio, 1.93; 95% confidence interval, 1.48–2.58), but not in western hospitals (prevalence ratio, 1.03; 95% confidence interval, 0.83–1.30). Regional differences of human papillomavirus 52 prevalence in cervical intraepithelial neoplasia lesions may exist and emphasize the importance of continuous monitoring of human papillomavirus type prevalence throughout the country in order to accurately assess the efficacy of human papillomavirus vaccines.
... We found 60 cases with HTLV-1-taxA (44%) and 76 cases with HTLV-1-taxB (56%), which was different from the distribution of those in mainland Japan (11% for HTLV-1-taxA and 89% for HTLV-1-taxB) reported by Furukawa et al. (Figure 5) [99]. Residents of Okinawa Prefecture have a historically and genetically distinct background from those of mainland Japan [101,102], a factor that might underlie this difference. ...
Simple Summary
In recent years, many researchers have devoted their efforts to clarifying the genomic aberrations of adult T-cell leukemia/lymphoma (ATLL), and the overview of somatic alterations has become more apparent. Some study groups have also investigated the clinical significance of genetic alterations in ATLL to improve the therapeutic strategy, and have found key alterations related to pathogenesis. In addition, studies employing advanced technology have revealed the evolutionary processes of tumor cells and novel genetic alterations in ATLL. This review aims to provide readers with current clinical and biological knowledge regarding aspects of genetic alterations to help promote research in ATLL.
Abstract
Adult T-cell leukemia/lymphoma (ATLL) is a refractory T-cell neoplasm that develops in human T-cell leukemia virus type-I (HTLV-1) carriers. Large-scale comprehensive genomic analyses have uncovered the landscape of genomic alterations of ATLL and have identified several altered genes related to prognosis. The genetic alterations in ATLL are extremely enriched in the T-cell receptor/nuclear factor-κB pathway, suggesting a pivotal role of deregulation in this pathway in the transformation of HTLV-1-infected cells. Recent studies have revealed the process of transformation of HTLV-1-infected cells by analyzing longitudinal samples from HTLV-1 carriers and patients with overt ATLL, an endeavor that might enable earlier ATLL diagnosis. The latest whole-genome sequencing study discovered 11 novel alterations, including CIC long isoform, which had been overlooked in previous studies employing exome sequencing. Our study group performed the targeted sequencing of ATLL in Okinawa, the southernmost island in Japan and an endemic area of HTLV-1, where the comprehensive genetic alterations had never been analyzed. We found associations of genetic alterations with HTLV-1 strains phylogenetically classified based on the tax gene, an etiological virus factor in ATLL. This review summarizes the genetic alterations in ATLL, with a focus on their clinical significance, geographical heterogeneity, and association with HTLV-1 strains.
... The second migration events from Northeast Asia occurred after~3000 YBP in the Holocene, together with the introduction of rice farming into the Japanese archipelago, which marks the start of the Yayoi period. Recent genome-wide single-nucleotide polymorphisms studies of the current and ancient Japanese [26][27][28][29] support the dual structure model, in which the Yayoi migrants interbred with the indigenous Jomon people [30,31], as a model for the origin of the present-day Japanese. Considering these population histories, our estimated divergence times of the MRCAs of the Japan-specific HPV16/18/58 genomes imply that these variants were introduced into the Japanese archipelago, most probably with the first migration at 40,000-25,000 YBP ( Figure 7). ...
Human papillomavirus (HPV) is a sexually transmitted virus with an approximately 8-kilo base DNA genome, which establishes long-term persistent infection in anogenital tissues. High levels of genetic variations, including viral genotypes and intra-type variants, have been described for HPV genomes, together with geographical differences in the distribution of genotypes and variants. Here, by employing a maximum likelihood method, we performed phylogenetic analyses of the complete genome sequences of HPV16, HPV18 and HPV58 available from GenBank (n = 627, 146 and 157, respectively). We found several characteristic clusters that exclusively contain HPV genomes from Japan: two for HPV16 (sublineages A4 and A5), one for HPV18 (sublineage A1) and two for HPV58 (sublineages A1 and A2). Bayesian phylogenetic analyses of concatenated viral gene sequences showed that divergence of the most recent common ancestor of these Japan-specific clades was estimated to have occurred ~98,000 years before present (YBP) for HPV16 A4, ~39,000 YBP for HPV16 A5, ~38,000 YBP for HPV18 A1, ~26,000 for HPV58 A1 and ~25,000 YBP for HPV58 A2. This estimated timeframe for the divergence of the Japan-specific clades suggests that the introduction of these HPV variants into the Japanese archipelago dates back to at least ~25,000 YBP and provides a scenario of virus co-migration with ancestral Japanese populations from continental Asia during the Upper Paleolithic period.
... Two strains from Hokkaido cluster with the Sg6 Okinawan strains. This is likely related to the evolutionary structure of Japanese people and of the Okinawa people [24]. The native ethnicity remains in Hokkaido (as Ainu ethnicity) and in Okinawa. ...
The East Asian region, including China, Japan and Korea, accounts for half of gastric cancer deaths. However, different areas have contrasting gastric cancer incidences and the population structure of Helicobacter pylori in this ethnically diverse region is yet unknown. We aimed to investigate genomic differences in H. pylori between these areas to identify sequence polymorphisms associated with increased cancer risk. We analysed 381 H . pylori genomes collected from different areas of the three countries using phylogenetic and population genetic tools to characterize population differentiation. The functional consequences of SNPs with a highest fixation index (Fst) between subpopulations were examined by mapping amino acid changes on 3D protein structure, solved or modelled. Overall, 329/381 genomes belonged to the previously identified hspEAsia population indicating that import of bacteria from other regions of the world has been uncommon. Seven subregional clusters were found within hspEAsia, related to subpopulations with various ethnicities, geographies and gastric cancer risks. Subpopulation-specific amino acid changes were found in multidrug exporters ( hefC ), transporters ( frpB-4 ), outer membrane proteins ( hopI ) and several genes involved in host interaction, such as a catalase site, involved in H 2 O 2 entrance, and a flagellin site mimicking host glycosylation. Several of the top hits, including frpB-4 , hefC , alpB / hopB and hofC, have been found to be differentiated within the Americas in previous studies, indicating that a handful of genes may be key to local geographic adaptation. H. pylori within East Asia are not homogeneous but have become differentiated geographically at multiple loci that might have facilitated adaptation to local conditions and hosts. This has important implications for further evaluation of these changes in relation to the varying gastric cancer incidence between geographical areas in this region.
... This hypothesis was originally proposed on the basis of morphological data but has been widely tested and evaluated across disciplines [see a recent review in (6)]. Genetic studies have identified population stratifications within present-day Japanese populations, supporting at least two waves of migrations to the Japanese archipelago (7)(8)(9)(10). Previous ancient DNA studies have also illustrated the genetic affinity of Jomon and Yayoi individuals to Japanese populations today (11)(12)(13)(14)(15). ...
Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.
