論文 - 木村　亮介

Factors associated with bone thickness: Comparison of the cranium and humerus.

Goto S, Kataoka K, Isa M, Nakamori K, Yoshida M, Murayama S, Arasaki A, Ishida H, Kimura R

PloS one ( PLoS ONE )  18 ( 3 ) e0283636   2023年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Population admixtures in medaka inferred by multiple arbitrary amplicon sequencing.

Fujimoto S, Yaguchi H, Myosho T, Aoyama H, Sato Y, Kimura R

Scientific reports ( Scientific Reports )  12 ( 1 ) 19989   2022年11月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Haplotype phasing of a bipolar disorder pedigree revealed rare multiple mutations of SPOCD1 gene in the 1p36-35 susceptibility locus.

Takamatsu G, Yanagi K, Koganebuchi K, Yoshida F, Lee JS, Toyama K, Hattori K, Katagiri C, Kondo T, Kunugi H, Kimura R, Kaname T, Matsushita M

Journal of affective disorders ( Journal of Affective Disorders )  310   96 - 105   2022年08月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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BACKGROUND: The etiology of bipolar disorder (BD) is poorly understood. Considering the complexity of BD, pedigree-based sequencing studies focusing on haplotypes at specific loci may be practical to discover high-impact risk variants. This study comprehensively examined the haplotype sequence at 1p36-35 BD and recurrent depressive disorder (RDD) susceptibility loci. METHODS: We surveyed BD families in Okinawa, Japan. We performed linkage analysis and determined the phased sequence of the affected haplotype using whole genome sequencing. We filtered rare missense variants on the haplotype. For validation, we conducted a case-control genetic association study on approximately 3000 Japanese subjects. RESULTS: We identified a three-generation multiplex pedigree with BD and RDD. Strikingly, we identified a significant linkage with mood disorders (logarithm of odds [LOD] = 3.61) at 1p36-35, supported in other ancestry studies. Finally, we determined the entire sequence of the 6.4-Mb haplotype shared by all affected subjects. Moreover, we found a rare triplet of missense variants in the SPOCD1 gene on the haplotype. Notably, despite the rare frequency, one heterozygote with multiple SPOCD1 variants was identified in an independent set of 88 BD type I genotyping samples. LIMITATIONS: The 1p36-35 sequence was obtained from only a single pedigree. The replicate sample was small. Short-read sequencing might miss structural variants. A polygenic risk score was not analyzed. CONCLUSION: The 1p36-35 haplotype sequence may be valuable for future BD variant studies. In particular, SPOCD1 is a promising candidate gene and should be validated.

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RELN rs7341475 Associates with Brain Structure in Japanese Healthy Females.

Yamaguchi R, Matsudaira I, Takeuchi H, Imanishi T, Kimura R, Tomita H, Kawashima R, Taki Y

Neuroscience ( Neuroscience )  494   38 - 50   2022年07月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Although temperament has been regarded as an innate aspect of human personality, its association with proteins involved in embryonic development is unclear. Reelin, encoded by RELN, plays an important role in brain development. Herein, we investigated the association between the RELN rs7341475 (G/A) single nucleotide polymorphism, detected as a female-specific risk factor for schizophrenia, brain structure, and temperament to elucidate the role of RELN in the development of human personality. In this study, 1580 healthy young Japanese adults were genotyped for RELN rs7341475 and completed the Temperament and Character Inventory. Whole-brain analysis of covariance was conducted to investigate differences between genotypes in regional gray matter volume (rGMV) and cortical morphology. Additionally, multiple regression analysis was performed to examine the association of four temperaments with rGMV. Those statistical analyses were performed separately for males and females. Individuals with G/G homozygosity showed significantly greater rGMV in several areas of the brain, particularly the bilateral cingulate and temporal gyrus, as well as a larger value of fractal dimension in the left lateral occipital cortex. Furthermore, of the four temperaments, the novelty seeking was significantly and positively associated with rGMV in the right superior temporal gyrus, partially overlapping with areas where differences between the rs7341475 genotypes were detected. The above findings were detected only in females, but not in males. This is the first study to demonstrate the contribution of RELN rs7341475 to differences in brain structure in Japanese females, which may indicate vulnerability to schizophrenia and variations in human personality.

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Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish.

Montenegro J, Fujimoto S, Ansai S, Nagano AJ, Sato M, Maeda Y, Tanaka R, Masengi KWA, Kimura R, Kitano J, Yamahira K

Molecular ecology ( Molecular Ecology )  31 ( 14 ) 3798 - 3811   2022年07月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called "pelvic-fin brooding," wherein females carry externally fertilized eggs until hatching using their pelvic fins. Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved at least twice in two distant clades of the Adrianichthyidae. We investigated the genetic architecture of the evolution of this unique mode of reproduction. Morphological analyses and laboratory observations revealed that females of pelvic-fin brooders have longer pelvic fins and a deeper abdominal concavity, and that they can carry an egg clutch for longer than non-brooding adrianichthyids, suggesting that these traits play important roles in this reproductive mode. Quantitative trait locus mapping using a cross between a pelvic-fin brooder Oryzias eversi and a non-brooding O. dopingdopingensis reveals different traits involved in pelvic-fin brooding to be controlled by different loci on different chromosomes. Genomic analyses of admixture detected no signatures of introgression between two lineages with pelvic-fin brooders, indicating that introgression is unlikely to be responsible for repeated evolution of pelvic-fin brooding. These findings suggest that multiple independent mutations may have contributed to the convergent evolution of this novel mode of reproduction.

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An Empirical Investigation on the Sexual Selection Hypothesis of Human Phenotypic Diversity: A Test in Okinawa and Mainland Japan

Nojo S, Kimura R, Ihara Y

Letters on Evolutionary Behavioral Science   13 ( 1 ) 21 - 27   2022年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Analysis of human clinical and environmental Leptospira to elucidate the eco-epidemiology of leptospirosis in Yaeyama, subtropical Japan.

Sato Y, Hermawan I, Kakita T, Okano S, Imai H, Nagai H, Kimura R, Yamashiro T, Kajita T, Toma C

PLoS neglected tropical diseases ( PLoS Neglected Tropical Diseases )  16 ( 3 ) e0010234   2022年03月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Triangulation supports agricultural spread of the Transeurasian languages.

Robbeets M, Bouckaert R, Conte M, Savelyev A, Li T, An DI, Shinoda KI, Cui Y, Kawashima T, Kim G, Uchiyama J, Dolińska J, Oskolskaya S, Yamano KY, Seguchi N, Tomita H, Takamiya H, Kanzawa-Kiriyama H, Oota H, Ishida H, Kimura R, Sato T, Kim JH, Deng B, Bjørn R, Rhee S, Ahn KD, Gruntov I, Mazo O, Bentley JR, Fernandes R, Roberts P, Bausch IR, Gilaizeau L, Yoneda M, Kugai M, Bianco RA, Zhang F, Himmel M, Hudson MJ, Ning C

Nature ( Nature )  599 ( 7886 ) 616 - 621   2021年11月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The origin and early dispersal of speakers of Transeurasian languages—that is, Japanese, Korean, Tungusic, Mongolic and Turkic—is among the most disputed issues of Eurasian population history1–3. A key problem is the relationship between linguistic dispersals, agricultural expansions and population movements4,5. Here we address this question by ‘triangulating’ genetics, archaeology and linguistics in a unified perspective. We report wide-ranging datasets from these disciplines, including a comprehensive Transeurasian agropastoral and basic vocabulary; an archaeological database of 255 Neolithic–Bronze Age sites from Northeast Asia; and a collection of ancient genomes from Korea, the Ryukyu islands and early cereal farmers in Japan, complementing previously published genomes from East Asia. Challenging the traditional ‘pastoralist hypothesis’6–8, we show that the common ancestry and primary dispersals of Transeurasian languages can be traced back to the first farmers moving across Northeast Asia from the Early Neolithic onwards, but that this shared heritage has been masked by extensive cultural interaction since the Bronze Age. As well as marking considerable progress in the three individual disciplines, by combining their converging evidence we show that the early spread of Transeurasian speakers was driven by agriculture.

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Polygenic risk score for bipolar disorder associates with divergent thinking and brain structures in the prefrontal cortex.

Takeuchi H, Kimura R, Tomita H, Taki Y, Kikuchi Y, Ono C, Yu Z, Matsudaira I, Nouchi R, Yokoyama R, Kotozaki Y, Nakagawa S, Hanawa S, Iizuka K, Sekiguchi A, Araki T, Miyauchi CM, Ikeda S, Sakaki K, Dos S Kawata KH, Nozawa T, Yokota S, Magistro D, Imanishi T, Kawashima R

Human brain mapping ( Human Brain Mapping )    2021年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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It has been hypothesized that a higher genetic risk of bipolar disorder (BD) is associated with greater creativity. Given the clinical importance of bipolar disorder and the importance of creativity to human society and cultural development, it is essential to reveal their associations and the neural basis of the genetic risk of bipolar disorder to gain insight into its etiology. However, despite the previous demonstration of the associations of polygenic risk score (PRS) of BD and creative jobs, the associations of BD-PRS and creativity measured by the divergent thinking (CMDT) and regional gray matter volume (rGMV) as well as regional white matter volume (rWMV) have not been investigated. Using psychological analyses and whole-brain voxel-by-voxel analyses, we examined these potential associations in 1558 young, typically developing adult students. After adjusting for confounding variables and multiple comparisons, a greater BD-PRS was associated with a greater total CMDT fluency score, and a significant relationship was found in fluency subscores. A greater BD-PRS was also associated with lower total mood disturbance. Neuroimaging analyses revealed that the BD-PRS was associated with greater rGMV in the right inferior frontal gyrus, which is a consistently affected area in BD, as well as a greater rWMV in the left middle frontal gyrus, which has been suggested to play a central role in the increased creativity associated with the risk of BD with creativity. These findings suggest a relationship between the genetic risk of BD and CMDT and prefrontal cortical structures among young educated individuals.

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Admixture with indigenous people helps local adaptation: admixture-enabled selection in Polynesians.

Isshiki M, Naka I, Kimura R, Nishida N, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R, Ohashi J

BMC ecology and evolution ( BMC Ecology and Evolution )  21 ( 1 ) 179   2021年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Background Homo sapiens have experienced admixture many times in the last few thousand years. To examine how admixture affects local adaptation, we investigated genomes of modern Polynesians, who are shaped through admixture between Austronesian-speaking people from Southeast Asia (Asian-related ancestors) and indigenous people in Near Oceania (Papuan-related ancestors). Methods In this study local ancestry was estimated across the genome in Polynesians (23 Tongan subjects) to find the candidate regions of admixture-enabled selection contributed by Papuan-related ancestors. Results The mean proportion of Papuan-related ancestry across the Polynesian genome was estimated as 24.6% (SD = 8.63%), and two genomic regions, the extended major histocompatibility complex (xMHC) region on chromosome 6 and the ATP-binding cassette transporter sub-family C member 11 (ABCC11) gene on chromosome 16, showed proportions of Papuan-related ancestry more than 5 SD greater than the mean (> 67.8%). The coalescent simulation under the assumption of selective neutrality suggested that such signals of Papuan-related ancestry enrichment were caused by positive selection after admixture (false discovery rate = 0.045). The ABCC11 harbors a nonsynonymous SNP, rs17822931, which affects apocrine secretory cell function. The approximate Bayesian computation indicated that, in Polynesian ancestors, a strong positive selection (s = 0.0217) acted on the ancestral allele of rs17822931 derived from Papuan-related ancestors. Conclusions Our results suggest that admixture with Papuan-related ancestors contributed to the rapid local adaptation of Polynesian ancestors. Considering frequent admixture events in human evolution history, the acceleration of local adaptation through admixture should be a common event in humans.

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Species divergence and repeated ancient hybridization in a Sulawesian lake system.

Mandagi IF, Kakioka R, Montenegro J, Kobayashi H, Masengi KWA, Inomata N, Nagano AJ, Toyoda A, Ansai S, Matsunami M, Kimura R, Kitano J, Kusumi J, Yamahira K

Journal of evolutionary biology ( Journal of Evolutionary Biology )    2021年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes; of these, one lake is inhabited by two species. Morphological and population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that these two sympatric species are phylogenetically sister to but substantially reproductively isolated from each other. Analyses of admixture and comparison of demographic models revealed that the two sympatric species experienced several substantial introgressions from outgroup populations that probably occurred soon after they had secondary contact with each other in the lake. However, the ratio of migrants from the outgroups was estimated to be different between the two species, which is consistent with the hypothesis that these introgressions aided their divergence or prevented them from forming a hybrid swarm. Repeated lake fragmentations and fusions may have promoted diversification of this freshwater fish species complex that is endemic to this ancient lake system.

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Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan.

Sato T, Adachi N, Kimura R, Hosomichi K, Yoneda M, Oota H, Tajima A, Toyoda A, Kanzawa-Kiriyama H, Matsumae H, Koganebuchi K, Shimizu KK, Shinoda KI, Hanihara T, Weber A, Kato H, Ishida H

Genome biology and evolution ( Genome biology and evolution )  13 ( 9 )   2021年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Recent studies on paleogenomics have reported some Paleolithic and Neolithic genomes that have provided new insights into the human population history in East and Northeast Asia. However, there remain some cases where more recent migration events need to be examined to elucidate the detailed formation process of local populations. Although the area around northern Japan is one of the regions archaeologically suggested to have been affected by migration waves after the Neolithic period, the genetic source of these migrations are still unclear. Thus, genomic data from such past migrant populations would be highly informative to clarify the detailed formation process of local populations in this region. Here, we report the genome sequence of a 900-year-old adult female (NAT002) belonging to the prehistoric Okhotsk people, who have been considered to be the past migrants to northern Japan after the Neolithic period. We found a close relationship between NAT002 and modern Lower Amur populations and past admixture events between the Amur, Jomon, and Kamchatka ancestries. The admixture dating suggested migration of Amur-related ancestry at approximately 1,600 BP, which is compatible with the archaeological evidence regarding the settlement of the Okhotsk people. Our results also imply migration of Kamchatka-related ancestry at approximately 2,000 BP. In addition, human leukocyte antigen (HLA) typing detected the HLA-B*40 allele, which is reported to increase the risk of arthritis, suggesting the genetic vulnerability of NAT002 to hyperostosis, which was observed around her chest clavicle.

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Mesozoic origin and 'out-of-India' radiation of ricefishes (Adrianichthyidae).

Yamahira K, Ansai S, Kakioka R, Yaguchi H, Kon T, Montenegro J, Kobayashi H, Fujimoto S, Kimura R, Takehana Y, Setiamarga DHE, Takami Y, Tanaka R, Maeda K, Tran HD, Koizumi N, Morioka S, Bounsong V, Watanabe K, Musikasinthorn P, Tun S, Yun LKC, Masengi KWA, Anoop VK, Raghavan R, Kitano J

Biology letters ( Biology Letters )  17 ( 8 ) 20210212   2021年08月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The Indian subcontinent has an origin geologically different from Eurasia, but many terrestrial animal and plant species on it have congeneric or sister species in other parts of Asia, especially in the Southeast. This faunal and floral similarity between India and Southeast Asia is explained by either of the two biogeographic scenarios, 'into-India' or 'out-of-India'. Phylogenies based on complete mitochondrial genomes and five nuclear genes were undertaken for ricefishes (Adrianichthyidae) to examine which of these two biogeographic scenarios fits better. We found that Oryzias setnai, the only adrianichthyid distributed in and endemic to the Western Ghats, a mountain range running parallel to the western coast of the Indian subcontinent, is sister to all other adrianichthyids from eastern India and Southeast-East Asia. Divergence time estimates and ancestral area reconstructions reveal that this western Indian species diverged in the late Mesozoic during the northward drift of the Indian subcontinent. These findings indicate that adrianichthyids dispersed eastward 'out-of-India' after the collision of the Indian subcontinent with Eurasia, and subsequently diversified in Southeast-East Asia. A review of geographic distributions of 'out-of-India' taxa reveals that they may have largely fuelled or modified the biodiversity of Eurasia.

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Fine-Scale Genetic Structure and Demographic History in the Miyako Islands of the Ryukyu Archipelago.

Matsunami M, Koganebuchi K, Imamura M, Ishida H, Kimura R, Maeda S

Molecular biology and evolution ( Molecular Biology and Evolution )  38 ( 5 ) 2045 - 2056   2021年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The Ryukyu Archipelago is located in the southwest of the Japanese islands and is composed of dozens of islands, grouped into the Miyako Islands, Yaeyama Islands, and Okinawa Islands. Based on the results of principal component analysis (PCA) on genome-wide single nucleotide polymorphisms (SNPs), genetic differentiation was observed among the island groups of the Ryukyu Archipelago. However, a detailed population structure analysis of the Ryukyu Archipelago has not yet been completed. We obtained genomic DNA samples from 1,240 individuals living in the Miyako Islands, and we genotyped 665,326 SNPs to infer population history within the Miyako Islands, including Miyakojima, Irabu and Ikema islands. The haplotype-based analysis showed that populations in the Miyako Islands were divided into three subpopulations located on Miyakojima northeast, Miyakojima southwest, and Irabu/Ikema. The results of haplotype sharing and the D statistics analyses showed that the Irabu/Ikema subpopulation received gene flows different from those of the Miyakojima subpopulations, which may be related with the historically attested immigration during the Gusuku period (900 - 500 BP). A coalescent-based demographic inference suggests that the Irabu/Ikema population firstly split away from the ancestral Ryukyu population about 41 generations ago, followed by a split of the Miyako southwest population from the ancestral Ryukyu population (about 16 generations ago), and the differentiation of the ancestral Ryukyu population into two populations (Miyako northeast and Okinawajima populations) about 7 generations ago. Such genetic information is useful for explaining the population history of modern Miyako people and must be taken into account when performing disease association studies.

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The human EDAR 370V/A polymorphism affects tooth root morphology potentially through the modification of a reaction-diffusion system.

Kataoka K, Fujita H, Isa M, Gotoh S, Arasaki A, Ishida H, Kimura R

Scientific reports ( Scientific Reports )  11 ( 1 ) 5143   2021年03月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Morphological variations in human teeth have long been recognized and, in particular, the spatial and temporal distribution of two patterns of dental features in Asia, i.e., Sinodonty and Sundadonty, have contributed to our understanding of the human migration history. However, the molecular mechanisms underlying such dental variations have not yet been completely elucidated. Recent studies have clarified that a nonsynonymous variant in the ectodysplasin A receptor gene (EDAR 370V/A; rs3827760) contributes to crown traits related to Sinodonty. In this study, we examined the association between the EDAR polymorphism and tooth root traits by using computed tomography images and identified that the effects of the EDAR variant on the number and shape of roots differed depending on the tooth type. In addition, to better understand tooth root morphogenesis, a computational analysis for patterns of tooth roots was performed, assuming a reaction-diffusion system. The computational study suggested that the complicated effects of the EDAR polymorphism could be explained when it is considered that EDAR modifies the syntheses of multiple related molecules working in the reaction-diffusion dynamics. In this study, we shed light on the molecular mechanisms of tooth root morphogenesis, which are less understood in comparison to those of tooth crown morphogenesis.

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Population genetic structure and evolution of Batesian mimicry in <i>Papilio polytes</i> from the Ryukyu Islands, Japan, analyzed by genotyping-by-sequencing.

Sato Y, Tsurui-Sato K, Katoh M, Kimura R, Tatsuta H, Tsuji K

Ecology and evolution ( Ecology and Evolution )  11 ( 2 ) 872 - 886   2021年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Batesian mimicry is a striking example of Darwinian evolution, in which a mimetic species resembles toxic or unpalatable model species, thereby receiving protection from predators. In some species exhibiting Batesian mimicry, nonmimetic individuals coexist as polymorphism in the same population despite the benefits of mimicry. In a previous study, we proposed that the abundance of mimics is limited by that of the models, leading to polymorphic Batesian mimicry in the swallowtail butterfly, Papilio polytes, on the Ryukyu Islands in Japan. We found that their mimic ratios (MRs), which varied among the Islands, were explained by the model abundance of each habitat, rather than isolation by distance or phylogenetic constraint based on the mitochondrial DNA (mtDNA) analysis. In the present study, this possibility was reexamined based on hundreds of nuclear single nucleotide polymorphisms (SNPs) of 93 P. polytes individuals from five Islands of the Ryukyus. We found that the population genetic and phylogenetic structures of P. polytes largely corresponded to the geographic arrangement of the habitat Islands, and the genetic distances among island populations show significant correlation with the geographic distances, which was not evident by the mtDNA-based analysis. A partial Mantel test controlling for the present SNP-based genetic distances revealed that the MRs of P. polytes were strongly correlated with the model abundance of each island, implying that negative frequency-dependent selection interacting with model species shaped and maintained the mimetic polymorphism. Taken together, our results support the possibility that predation pressure, not isolation by distance or other neutral factors, is a major driving force of evolution of the Batesian mimicry in P. polytes from the Ryukyus.

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個体間・集団間のゲノムの「違い」を理解する

木村 亮介

日本遺伝カウンセリング学会誌   42   199 - 206   2021年

掲載種別: 研究論文（学術雑誌）

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Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations.

Gakuhari T, Nakagome S, Rasmussen S, Allentoft ME, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R, Mizushima S, Kondo O, Shigehara N, Yoneda M, Kimura R, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Tsurumoto T, Wakebe T, Shitara H, Hanihara T, Willerslev E, Sikora M, Oota H

Communications biology ( Communications Biology )  3 ( 1 ) 437 - 437   2020年08月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is  characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

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Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka.

Gamage CD, Sato Y, Kimura R, Yamashiro T, Toma C

PLoS neglected tropical diseases ( PLoS Neglected Tropical Diseases )  14 ( 7 ) e0008437 - 22   2020年07月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Author summary Leptospirosis is a widespread bacterial zoonosis with increasing importance due to its vast range of reservoir hosts. Early symptoms are shared by other infectious diseases common in tropical and sub-tropical regions, where the real burden and risk factors need to be known. In Sri Lanka, leptospirosis is mostly an occupational disease associated with freshwater or animal exposure in agriculture communities. Thus, there is a need for understanding the epidemiology of leptospirosis in agrarian regions of the country for developing better prevention and intervention strategies. In this study, we applied an environmental DNA metabarcoding methodology to understand the environmental microbiome, potential reservoir animals and theLeptospiraspecies circulating in two different agro-ecological regions of Sri Lanka: Kandy (wet region mid-country region 2) and Girandurukotte (intermediate region low-country region 2). It is known that pathogenicLeptospiraare excreted through the urine of reservoir animals in the environment, where they can persist in humid conditions. Congruently, this study showed a higher detection of pathogenicLeptospirain the environment of Kandy where the environmental microbiome showed a higher diversity than Girandurukotte. Potential animal reservoirs were also detected in samples positive for pathogenicLeptospira, suggesting that environmental DNA metabarcoding can provide important information for management and intervention strategies to control leptospirosis.Background Leptospirosis is one of the most significant zoonoses across the world not only because of its impact on human and animal health but also because of the economic and social impact on agrarian communities. Leptospirosis is endemic in Sri Lanka where paddy farming activities, the use of draught animals in agriculture, and peridomestic animals in urban and rural areas play important roles in maintaining the infection cycle of pathogenicLeptospira, especially concerning animals as a potential reservoir. In this study, an environmental DNA (eDNA) metabarcoding methodology was applied in two different agro-ecological regions of Sri Lanka to understand the eco-epidemiology of leptospirosis. Methodology/Principal findings Irrigation water samples were collected in Kandy District (wet zone mid-country region 2) and Girandurukotte, Badulla District (intermediate zone low-country region 2); and analysed for the presence of pathogenicLeptospira, associated microbiome and the potential reservoir animals. Briefly, we generated PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. The analysis of eDNA showed different environmental microbiomes in both regions and a higher diversity ofLeptospiraspecies circulating in Kandy than in Girandurukotte. Moreover, the number of sequence reads of pathogenicLeptospiraspecies associated with clinical cases such asL.interroganswas higher in Kandy than in Girandurukotte. Kandy also showed more animal species associated with pathogenic bacterial species than Girandurukotte. Finally, several pathogenic bacterial species includingArcobacter cryaerophilus, responsible for abortion in animals, was shown to be associated with pathogenicLeptospira. Conclusions/Significance Leptospirosis has been considered to be endemic in wet regions, consistently, leptospiral sequences were detected strongly in Kandy. The greatLeptospiraspecies diversity in Kandy observed in this study shows that the etiological agents of leptospirosis in Sri Lanka might be underestimated. Furthermore, our eDNA metabarcoding can be used to discriminate bacterial and animal species diversity in different regions and to explore environmental microbiomes to identify other associated bacterial pathogens in the environment.

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琉球列島における全ゲノム配列データを用いたヒト集団史の推定

小金渕 佳江, 松波 雅俊, 今村 美菜子, 河合 洋介, 徳永 勝士, 前田 士郎, 石田 肇, 木村 亮介

Anthropological Science(Japanese Series) ( (一社)日本人類学会 )  128 ( 1 ) 52 - 53   2020年06月

掲載種別: 研究論文（その他学術会議資料等）

Admixture and natural selection shaped genomes of an Austronesian-speaking population in the Solomon Islands.

Isshiki M, Naka I, Watanabe Y, Nishida N, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Eddie R, Ohtsuka R, Ohashi J

Scientific reports ( Scientific Reports )  10 ( 1 ) 6872   2020年04月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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ゲノムで解き明かされるヒトの遺伝適応：ヒトは如何にして厳しい環境や病原体を克服したのか？

木村 亮介

日本マススクリーニング学会誌   30   237 - 245   2020年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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琉球諸語研究における方言系統地理学の可能性

狩俣 繁久, 木村 亮介

フィールドと文献から見る日琉諸語の系統と歴史   -   2020年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Evidence for sympatric speciation in a Wallacean ancient lake.

Sutra N, Kusumi J, Montenegro J, Kobayashi H, Fujimoto S, Masengi KWA, Nagano AJ, Toyoda A, Matsunami M, Kimura R, Yamahira K

Evolution; international journal of organic evolution ( Evolution )  73 ( 9 ) 1898 - 1915   2019年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Sympatric speciation has been demonstrated in few empirical case studies, despite intense searches, because of difficulties in testing the criteria for this mode of speciation. Here, we report a possible case of sympatric speciation in ricefishes of the genus Oryzias on Sulawesi, an island of Wallacea. Three species of Oryzias are known to be endemic to Lake Poso, an ancient tectonic lake in central Sulawesi. Phylogenetic analyses using RAD-seq-derived single nucleotide polymorphisms (SNPs) revealed that these species are monophyletic. We also found that the three species are morphologically distinguishable and clearly separated by population-structure analyses based on the SNPs, suggesting that they are reproductively isolated from each other. A mitochondrial DNA chronogram suggested that their speciation events occurred after formation of the tectonic lake, and existence of a historical allopatric phase was not supported by coalescent-based demographic inference. Demographic inference also suggested introgressive hybridization from an outgroup population. However, differential admixture among the sympatric species was not supported by any statistical tests. These results all concur with criteria necessary to demonstrate sympatric speciation. Ricefishes in this Wallacean lake provide a promising new model system for the study of sympatric speciation.

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Study on existence of the fisheries resources abundance by using environmental deoxyribonucleic acid (e-DNA) approach at fishing grounds in the Sulawesi Sea, Indonesia

Masengi K, Mandagi IF, Manu L, Silooy F, Labaro IL , Masengi AWR, Sebua N, Masengi EIKG, Pinontoan B, Hutabarat Y, Hukom F, Iwata M, Abe Y, Sato Y, Kimura R, Yamahira K

IOP Conference Series: Materials Science and Engineering ( IOP Conference Series: Materials Science and Engineering )  567 ( 1 )   2019年08月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Biomedical and genetic characteristics of the Ryukyuans: demographic history, diseases and physical and physiological traits.

Koganebuchi K, Kimura R

Annals of human biology ( Annals of Human Biology )  46 ( 4 ) 354 - 366   2019年06月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Context: The Ryukyu Islands stretch across a southwestern area of the Japanese Archipelago. Because of their unique geographical and historical backgrounds, Ryukyuans have their own genetic and phenotypic characteristics, which have been disclosed in previous anthropological and biomedical studies. Objective: The history, peopling and biomedical and genetic characteristics of Ryukyuans are reviewed and future research directions are discussed. Conclusion: Morphological and genetic studies have suggested the complex demographic history of Ryukyuans and their relationships with other Asian populations. Knowledge of population formation processes is important to understand the distribution of pathogens. In viral infectious diseases, some strains that may be associated with disease symptoms are specific to Ryukyuans. Dramatic changes in diet have played an important role among Ryukyuans in terms of increases in lifestyle-related diseases and mortality risks. To achieve a better understanding of pathogenic disease factors, further integration of findings regarding the genetic and biomedical characteristics of the Ryukyuans is needed.

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Evidence for frequency-dependent selection maintaining polymorphism in the Batesian mimic <i>Papilio polytes</i> in multiple islands in the Ryukyus, Japan.

Tsurui-Sato K, Sato Y, Kato E, Katoh M, Kimura R, Tatsuta H, Tsuji K

Ecology and evolution ( Ecology and Evolution )  9 ( 10 ) 5991 - 6002   2019年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Batesian mimicry is a well-studied adaptation for predation avoidance, in which a mimetic species resembles an unpalatable model species. Batesian mimicry can be under positive selection because of the protection gained against predators, due to resemblance to unpalatable model species. However, in some mimetic species, nonmimetic individuals are present in populations, despite the benefits of mimicry. The mechanism for evolution of such mimetic polymorphism remains an open question. Here, we address the hypothesis that the abundance of mimics is limited by that of the models, leading to mimetic polymorphism. In addition, other forces such as the effects of common ancestry and/or isolation by distance may explain this phenomenon. To investigate this question, we focused on the butterfly, Papilio polytes, that exhibits mimetic polymorphism on multiple islands of the Ryukyus, Japan, and performed field surveys and genetic analysis. We found that the mimic ratio of P. polytes was strongly correlated with the model abundance observed on each of the five islands, suggesting negative frequency-dependent selection is driving the evolution of polymorphism in P. polytes populations. Molecular phylogenetic analysis indicated that the southern island populations are the major source of genetic diversity, and the middle and northern island populations arose by relatively recent migration. This view was also supported by mismatch distribution and Tajima's D analyses, suggesting a recent population expansion on the middle and northern islands, and stable population persistence on the southern islands. The frequency of the mimetic forms within P. polytes populations is thus explained by variations in the model abundance rather than by population structure. Thus, we propose that predation pressure, rather than neutral forces, have shaped the Batesian mimicry polymorphism in P. polytes observed in the Ryukyus.

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Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan.

Sato Y, Mizuyama M, Sato M, Minamoto T, Kimura R, Toma C

Scientific reports ( Scientific Reports )  9 ( 1 ) 6575   2019年04月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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東アジアにおけるヒトの遺伝適応の痕跡を求めて

木村 亮介

日本生理人類学会誌 ( 日本生理人類学会 )  24 ( 2 ) 87 - 91   2019年

掲載種別: 研究論文（学術雑誌）

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Modern humans dispersed into East Asia approximately 40K years ago and genetically adapted to unprecedentedenvironmental conditions. Signatures of local genetic adaptations, which are engraved in our genome, can bedetected using population genomics approaches. Human genome variation data have enabled a comprehensive searchfor genetic variants showing such signatures as well as for those associated with phenotypic variation. Although ourknowledge about local genetic adaptations has increased due to recent research efforts, little is known about whatselective pressures acted on the selected variants.

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Association of an intronic SNP of the EFEMP1 gene with height in Tongans

Isshiki M.

Meta Gene ( Meta Gene )  17   172 - 176   2018年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Growth hormone receptor gene is related to root length and tooth length in human teeth.

Hikita Y, Yamaguchi T, Tomita D, Adel M, Nakawaki T, Katayama K, Maki K, Kimura R

The Angle orthodontist   88 ( 5 ) 575 - 581   2018年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Association between the FGFR1 rs13317 single nucleotide polymorphism and orbitale-nasion depth based on cephalometric images.

Adel M, Yamaguchi T, Tomita D, Kim YI, Takahashi M, Nakawaki T, Hikita Y, Haga S, Nadim M, Kawaguchi A, Isa M, El-Kenany W, El-Kadi AA, Park SB, Ishida H, Maki K, Kimura R

Journal of human genetics ( Journal of Human Genetics )  63 ( 8 ) 901 - 909   2018年08月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The fibroblast growth factor receptor 1 (FGFR1) gene plays an important role in craniofacial morphogenesis. In our previous study, an association between FGFR1 single nucleotide polymorphisms (SNPs) and craniofacial morphology was demonstrated in Japanese and Korean subjects. The present study aimed to evaluate the relationship between a common FGFR1 SNP (rs13317) with craniofacial morphology, increasing the number of measurements and examining Egyptian subjects (n = 191) in addition to the Japanese (n = 211) and Korean (n = 226) subjects. Genotyping for rs13317 was performed using the TaqMan assay, and its associations with 81 craniofacial measurements derived from lateral and posteroanterior cephalograms were analyzed by multiple regression analysis controlling sex and facial size. The results from each of the populations were then statistically combined. In the Egyptian subjects, rs13317 was significantly associated with the nasion-orbitale depth (P = 0.00040), and a suggestive association was also observed in the Japanese (P = 0.037) and Korean subjects (P = 0.045). The combined analysis revealed that only the nasion-orbitale depth showed a significant association (P = 0.000062) and that several measurements showed a suggestive association. Our results strongly indicate that rs13317 is associated with a smaller depth between the nasion and orbitale, representing a relative protrusion of the cheekbones and retrusion of the nasal root. A similar characteristic is also observed in individuals with Pfeiffer syndrome, which is caused by a dysfunctional FGFR1 mutation.

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Relationship between tooth length and three-dimensional mandibular morphology.

Hikita Y, Yamaguchi T, Tomita D, Adel M, Nakawaki T, Katayama K, Maki K, Kimura R

The Angle orthodontist ( Angle Orthodontist )  88 ( 4 ) 403 - 409   2018年07月 [ 査読有り ]

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Association study of CREBRF missense variant (rs373863828:G &gt; A; p.Arg457Gln) with levels of serum lipid profile in the Pacific populations.

Ohashi J, Naka I, Furusawa T, Kimura R, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R

Annals of human biology ( Annals of Human Biology )  45 ( 3 ) 215 - 219   2018年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Spatial relationships of the bronchial arteries to the left recurrent laryngeal nerve in the sub-aortic arch area.

Hayasaka K, Ishida H, Kimura R, Nishimaki T

Surgery today ( Surgery Today )  48 ( 3 ) 346 - 351   2018年03月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Purpose: To safely perform lymphadenectomy in the sub-aortic arch area during esophagectomy for esophageal cancer, we investigated the spatial relationships between the bronchial arteries (BAs) and the left recurrent laryngeal nerve (LRLN). Methods: For this macro-anatomical study, 72 cadavers were used. Results: Of the 195 dissected BAs, 15 (7.7%) arteries ran dorsally across the LRLN. Such a running pattern of the BA was found in 15 (20.8%) of the 72 cadavers. Fourteen (93.3%) of the 15 arteries ran anteriorly along the left side of the esophagus, and 13 (86.7%) passed further to the lateral side of the left main bronchus to reach the ventral surface of the tracheobronchus we named this running pattern “Type III”. Of the 51 arteries with the Type III pattern, 25.5% ran across the dorsal side of the LRLN. Conclusion: Approximately 20% of the cadavers had BAs running dorsally to the LRLN in the sub-aortic arch area. Most of these arteries had the Type III pattern. One-quarter of the BAs with the Type III pattern showed this running pattern. Care must be practiced to safely perform lymphadenectomy for esophageal cancer in patients with Type III BAs.

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Interferon regulatory factor 6 variants affect nasolabial morphology in East Asian populations.

Tomita D, Yamaguchi T, Nakawaki T, Hikita Y, Adel M, Kim YI, Haga S, Takahashi M, Kawaguchi A, Isa M, Park SB, Ishida H, Maki K, Kimura R

Archives of oral biology ( Archives of Oral Biology )  85   142 - 147   2018年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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OBJECTIVE: The interferon regulatory factor 6 gene (IRF6) is one of the most conspicuous genes among a large number of candidate risk genes for non-syndromic cleft lip with or without cleft palate, which is considered to be a multifactorial defect. Variants of IRF6 are also suggested to affect normal craniofacial variations, especially in the area of the nose and the upper lip. In the present study, we used lateral cephalograms to establish the relationship between IRF6 and sagittal nasolabial morphology in healthy East Asian subjects. DESIGN: Genomic DNA was extracted from 215 Japanese and 226 Korean individuals, and genotyped for five IRF6 single nucleotide polymorphisms (SNPs): rs17389541, rs642961, rs2013162, rs2235371, and rs7802. These SNPs were tested by multiple regression analyses for their association with craniofacial measurements obtained from lateral cephalometrics. RESULTS: We detected a significant association between the derived variants, rs2013162 and rs2235371 and the distances between a facial bone plane indicated by distance from Nasion and Point A (NA plane) to soft tissue landmarks; the Subalare (NA-Sbal) and the Subnasale (NA-Sn) in the sagittal plane. CONCLUSION: Our results indicate that IRF6 variants play an important role in the normal range of variation in nasolabial soft-tissue morphology.

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Mitochondrial DNA variations in Austronesian-speaking populations living in the New Georgia Islands, the Western Province of the Solomon Islands.

Issiki M, Naka I, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Ohtsuka R, Ohashi J

Journal of human genetics ( Journal of Human Genetics )  63 ( 1 ) 101 - 104   2018年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Computed tomography examinations of the surface and internal morphologies of the upper face in Ryukyu Islanders and mainland Japanese population

ITO TSUYOSHI, KIMURA RYOSUKE, RYUKODEN AZUSA, TSUCHIYA NANAE, MURAYAMA SADAYUKI, ISHIDA HAJIME

Ａｎｔｈｒｏｐｏｌｏｇｉｃａｌ　Ｓｃｉｅｎｃｅ ( 日本人類学会 )  126 ( 3 ) 123 - 133   2018年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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<p>Using computed tomography, we examined the surface and internal morphologies of the upper face of people living on the Ryukyu Islands and mainland Japanese, focusing on the nasal root protrusion and eyeball position. The results showed that the nasal root protrusion on the surface was influenced by a combination of changes in both hard and soft tissues, such as skeletal nasal protrusion, eyeball recession, and skin thickness. The eyeball position became more posterior as the orbital cavity height and depth increased. Compared with people originating from mainland Japan, Ryukyu Islanders had a more prominent nasal root at both surface and skeletal levels, and a lower orbital rim relative to its internal height. However, a significant difference in the eyeball position and skin thickness was not detected. Therefore, the skeletal nasal root protrusion, not soft tissue configuration, is likely to account for the difference in the surface nasal root protrusion between the two populations. These findings will contribute to a better understanding of the association between hard and soft tissue configurations and the diversification of human facial features at the individual and population levels.</p>

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ゲノム情報から人類集団間交配を考える

木村 亮介

生物科学   70   140 - 144   2018年

掲載種別: 研究論文（学術雑誌）

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A missense variant, rs373863828-A (p.Arg457Gln), of CREBRF and body mass index in Oceanic populations.

Naka I, Furusawa T, Kimura R, Natsuhara K, Yamauchi T, Nakazawa M, Ataka Y, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R, Ohashi J

Journal of human genetics ( Journal of Human Genetics )  62 ( 9 ) 847 - 849   2017年09月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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It has been suggested that a 'thrifty' genotype hypothesis can account for high prevalence of obesity in the island populations of Oceania. A recent genome-wide association study revealed that a missense variant, rs373863828-A (p.Arg457Gln), of the CREBRF gene (encoding CREB3 regulatory factor) was associated with an excessive increase in body mass index (BMI) in Samoans. In the present study, the association of rs373863828-A with an increase in BMI was examined in four Austronesian (AN)-speaking populations in Oceania. We found that rs373863828-A was frequently observed (frequency of 0.15) in Tongans (Polynesians), and was strongly associated with higher BMI (P=6.1 x 10(-4)). A single copy of the rs373863828-A allele increased BMI by 3.09 kg m(-2) after adjustment of age and sex. No significant association was detected in the other three AN-speaking populations (Melanesians and Micronesians) living in Solomon Islands. This was probably due to the low allele frequency (0.02-0.06) of rs373863828-A as well as small sample size. The rs373863828-A allele was not found in both AN-speaking and non-AN-speaking Melanesians living in Papua New Guinea. Our results suggest that rs373863828-A of CREBRF, a promising thrifty variant, arose in recent ancestors of AN-speaking Polynesians.

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A new anatomical classification of the bronchial arteries based on the spatial relationships to the esophagus and the tracheobronchus.

Hayasaka K, Ishida H, Kimura R, Nishimaki T

Surgery today ( Surgery Today )  47 ( 7 ) 883 - 890   2017年07月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Purpose To reveal the patterns of the mediastinal course of the bronchial arteries (BAs). Methods The BAs were dissected to determine the positional relationships of their mediastinal courses with the tracheobronchus and the esophagus in 72 adult cadavers. Results The mediastinal courses of the 227 BAs found in this study were classified into 4 types. There were 61 and 163 BAs passing the right side (Type I) and the left side (Type II reaching dorsal surface (n = 98), or Type III reaching ventral surface (n = 65) of the tracheobronchus) of the esophagus, respectively. Three BAs originated from the subclavian artery (Type IV). All Type I BAs were right BAs, whereas 91.8% of the Type II BAs were left BAs. However, 43.1 and 56.9% of the Type III BAs were the right and left BAs, respectively. Conclusion The classification of the mediastinal course of the BAs determined by the spatial relationships to the tracheobronchus and the esophagus may be clinically useful, because each category of this classification can be determined during esophagectomy and indicates whether the BA is a right or left BA.

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Characterising private and shared signatures of positive selection in 37 Asian populations.

Liu X, Lu D, Saw WY, Shaw PJ, Wangkumhang P, Ngamphiw C, Fucharoen S, Lert-Itthiporn W, Chin-Inmanu K, Chau TN, Anders K, Kasturiratne A, de Silva HJ, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Takeuchi F, Yamamoto K, Yokota M, Mamatyusupu D, Yang W, Chung YJ, Jin L, Hoh BP, Wickremasinghe AR, Ong RH, Khor CC, Dunstan SJ, Simmons C, Tongsima S, Suriyaphol P, Kato N, Xu S, Teo YY

European journal of human genetics : EJHG ( European Journal of Human Genetics )  25 ( 4 ) 499 - 508   2017年04月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.

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Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands.

Nakagome S, Chinen H, Iraha A, Hokama A, Takeyama Y, Sakisaka S, Matsui T, Kidd JR, Kidd KK, Said HS, Suda W, Morita H, Hattori M, Hanihara T, Kimura R, Ishida H, Fujita J, Kinjo F, Mano S, Oota H

Human genetics ( Human Genetics )  136 ( 4 ) 387 - 397   2017年04月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Growth hormone receptor gene variant and three-dimensional mandibular morphology.

Nakawaki T, Yamaguchi T, Isa M, Kawaguchi A, Tomita D, Hikita Y, Suzuki-Tomoyasu Y, Adel M, Ishida H, Maki K, Kimura R

The Angle orthodontist ( Angle Orthodontist )  87 ( 1 ) 68 - 73   2017年01月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Objective: To examine the relationship between three-dimensional mandibular morphology and growth hormone receptor (GHR) gene variants in a healthy Japanese population. Materials and Methods: The subjects, who were unrelated Japanese orthodontic patients, consisted of 64 men and 114 women. Using the Taqman genotyping assay, GHR gene rs6184 and rs6180 variants were detected in genomic DNA extracted from saliva. Mandibular volume and length were measured from cone-beam computed tomography images that were analyzed using Analyze image-processing software. The relationship between GHR gene variants and three-dimensional mandibular morphology was statistically examined. Results: Statistical significance for the relationship between the distance between the left and right coronoid processes and rs6180 was noted (P &lt; .05). Conclusion: Our results indicate that the GHR variant rs6180 is associated with the distance between the left and right coronoid process in the Japanese subjects.

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The fine-scale genetic structure and evolution of the Japanese population.

Takeuchi F, Katsuya T, Kimura R, Nabika T, Isomura M, Ohkubo T, Tabara Y, Yamamoto K, Yokota M, Liu X, Saw WY, Mamatyusupu D, Yang W, Xu S, Japanese Genome Variation Consortium., Teo YY, Kato N

PloS one ( PLoS ONE )  12 ( 11 ) e0185487   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The contemporary Japanese populations largely consist of three genetically distinct groups Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.

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Polymorphisms associated with a tropical climate and root crop diet induce susceptibility to metabolic and cardiovascular diseases in Solomon Islands.

Furusawa T, Naka I, Yamauchi T, Natsuhara K, Eddie R, Kimura R, Nakazawa M, Ishida T, Ohtsuka R, Ohashi J

PloS one ( PLoS ONE )  12 ( 3 ) e0172676   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The people of the Solomon Islands represent an Austronesian (AN)-speaking population's adaptation to a humid tropical environment and subsistence of tuberous crops. Genome-wide association studies (GWASs) of other populations (e.g. the Human Genome Diversity Project [HGDP]) have suggested the existence of genotypes adaptive to ecoregion, diet, and subsistence, and that those genotypes are also associated with metabolic and cardiovascular diseases. Recently, the incidence of non-communicable diseases has been increasing in the Solomon Islands. In the present study, we explored the association of genotypes adaptive to a tropical environment and tuberous crop diet with metabolic and cardiovascular conditions in rural and urban AN-speaking Melanesian and Micronesian populations of the Solomon Islands. A total of 561 participants were genotyped for single nucleotide polymorphisms (SNPs) potentially associated with a tropical environment (rs174570 and rs2237892) and a tuberous crop diet (rs162036, rs185819, and rs2722425). The results showed that the allele frequencies of the Solomon Islands populations adopted patterns similar to those in populations from other hot, tropical areas with a tuberous crop diet in previous studies. Furthermore, rs162036, rs185819, rs2237892, and rs2722425 were all strongly associated with one or more metabolic and cardiovascular conditions. The derived allele of rs2722425 (i.e. rs2722425-G) was significantly associated with an elevated LDL level (P = 0.000264) even after the significance level was adjusted for multiple testing (i.e., alpha = 0.0005). Our results suggest that the inhabitants of the Solomon Islands exhibit the effects of the tropical environment and tuberous crop diet on their allele frequencies, and that their susceptibility to metabolic and cardiovascular diseases is therefore considered to be associated with their environment and diet.

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Contribution of FGFR1 Variants to Craniofacial Variations in East Asians.

Adel M, Yamaguchi T, Tomita D, Nakawaki T, Kim YI, Hikita Y, Haga S, Takahashi M, Nadim MA, Kawaguchi A, Isa M, El-Kenany WH, El-Kadi AA, Park SB, Ishida H, Maki K, Kimura R

PloS one ( PLoS ONE )  12 ( 1 ) e0170645   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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FGFR1 plays an important role in the development of the nervous system as well as the regulation of the skeletal development and bone homeostasis. Mutations in FGFR1 genes affect skull development, specifically suture and synchondrosis, resulting in craniosynostosis and facial abnormalities. We examined subjects with normal skull morphology for genetic polymorphisms that might be associated with normal craniofacial variations. Genomic DNA was obtained from 216 Japanese and 227 Korean subjects. Four FGFR1 SNPs, namely, rs881301, rs6996321, rs4647905, and rs13317, were genotyped. These SNPs were tested for association with craniofacial measurements obtained from lateral and posteroanterior cephalometries, in which principle component analysis was performed to compress the data of the craniofacial measurements. We observed that SNPs rs13317 and rs6996321 were correlated with the overall head size and midfacial development, indicating that FGFR1 SNPs played crucial roles in the normal variation of human craniofacial morphology. Subjects with the derived alleles of SNPs rs13317 and rs6996321 had a small face and a facial pattern associated with a retruded midface and relatively wide-set eyes. These facial features were similar to but were milder than those of individuals with Pfeiffer syndrome, which is caused by a dysfunctional mutation in FGFR1.

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Comprehensive genetic exploration of selective tooth agenesis of mandibular incisors by exome sequencing.

Yamaguchi T, Hosomichi K, Yano K, Kim YI, Nakaoka H, Kimura R, Otsuka H, Nonaka N, Haga S, Takahashi M, Shirota T, Kikkawa Y, Yamada A, Kamijo R, Park SB, Nakamura M, Maki K, Inoue I

Human genome variation ( Human Genome Variation )  4   17005 - 17005   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Tooth agenesis is described as the absence of one or more teeth. It is caused by a failure in tooth development and is one of the most common human developmental anomalies. We herein report genomic analyses of selective mandibular incisor agenesis (SMIA) using exome sequencing. Two Japanese families with SMIA were subjected to exome sequencing, and family with sequence similarity 65 member A (FAM65), nuclear factor of activated T-cells 3 (NFATC3) and cadherin-related 23 gene (CDH23) were detected. In the follow-up study, 51 Japanese and 32 Korean sporadic patients with SMIA were subjected to exome analyses, and 18 reported variants in PAX9, AXIN2, EDA, EDAR, WNT10A, BMP2 and GREM2 and 27 variants of FAM65, NFATC3 and CDH23 were found in 38 patients. Our comprehensive genetic study of SMIA will pave the way for a full understanding of the genetic etiology of SMIA and provide targets for treatment.

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An ancestral haplotype of the human PERIOD2 gene associates with reduced sensitivity to light-induced melatonin suppression.

Akiyama T, Katsumura T, Nakagome S, Lee SI, Joh K, Soejima H, Fujimoto K, Kimura R, Ishida H, Hanihara T, Yasukouchi A, Satta Y, Higuchi S, Oota H

PloS one ( PUBLIC LIBRARY SCIENCE )  12 ( 6 ) e0178373   2017年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Humans show various responses to the environmental stimulus in individual levels as "physiological variations." However, it has been unclear if these are caused by genetic variations. In this study, we examined the association between the physiological variation of response to light-stimulus and genetic polymorphisms. We collected physiological data from 43 subjects, including light-induced melatonin suppression, and performed haplotype analyses on the clock genes, PER2 and PER3, exhibiting geographical differentiation of allele frequencies. Among the haplotypes of PER3, no significant difference in light sensitivity was found. However, three common haplotypes of PER2 accounted for more than 96% of the chromosomes in subjects, and 1 of those 3 had a significantly low-sensitive response to light-stimulus (P &lt; 0.05). The homozygote of the low-sensitive PER2 haplotype showed significantly lower percentages of melatonin suppression (P 0.05), and the heterozygotes of the haplotypes varied their ratios, indicating that the physiological variation for light-sensitivity is evidently related to the PER2 polymorphism. Compared with global haplotype frequencies, the haplotype with a low-sensitive response was more frequent in Africans than in non-Africans, and came to the root in the phylogenetic tree, suggesting that the low light-sensitive haplotype is the ancestral type, whereas the other haplotypes with high sensitivity to light are the derived types. Hence, we speculate that the high light-sensitive haplotypes have spread throughout the world after the Out-of-Africa migration of modern humans.

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Whole-body patterns of the range of joint motion in young adults: masculine type and feminine type.

Moromizato K, Kimura R, Fukase H, Yamaguchi K, Ishida H

Journal of physiological anthropology ( Journal of Physiological Anthropology )  35 ( 1 ) 23   2016年10月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Degenerative changes in the appendicular joints of ancient human populations from the Japan Islands

Suzuki S.

Quaternary International ( Quaternary International )  405   147 - 159   2016年06月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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An Okhotsk adult female human skeleton (11th/12th century AD) with possible SAPHO syndrome from Hamanaka 2 site, Rebun Island, northern Japan

OKAMOTO Yuka, ISHIDA Hajime, KIMURA Ryosuke, SATO Takehiro, TSUCHIYA Nanae, MURAYAMA Sadayuki, FUKASE Hitoshi, NAGAOKA Tomohito, ADACHI Noboru, YONEDA Minoru, WEBER Andrzej, KATO Hirofumi

Ａｎｔｈｒｏｐｏｌｏｇｉｃａｌ　Ｓｃｉｅｎｃｅ ( 日本人類学会 )  124 ( 2 ) 107 - 115   2016年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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<p>We present the oldest human skeletal case yet identified with possible SAPHO syndrome (synovitis, acne, pustulosis, hyperostosis, osteitis), a chronic disease involving the skin, bone, and joints. A human skeleton with a severe pathological condition was recovered from a shell mound of the prehistoric Okhotsk culture at the Hamanaka 2 site, Rebun Island, Hokkaido, Japan in 2013. Morphological and <i>Amelogenin</i> gene analyses determined the sex as female, and the age at time of death was estimated to be in the forties using analysis of the auricular surface of the ilium. The stable isotope ratios of this individual (NAT002) and other Hamanaka 2 samples indicated a heavy dependence on marine mammals and fish for dietary protein intake. Radiocarbon age on collagen from the bone of NAT002 was 1689 ± 20 BP, or 1060–1155 (68.2%) calAD. Macroscopic and computed tomography (CT) findings indicated diffuse hyperostosis in the axial and appendicular skeleton, including the mandible, vertebrae, clavicles, sternum, scapulae, humeri, radii, ulnae, and ilium, caused by osteitis and synovitis. The bilateral clavicles were most affected, in which CT imaging revealed irregular cortical thickening, termed 'grotesque periostitis.' The case was diagnosed as most likely having SAPHO syndrome, although dermatological findings could not be detected. Although SAPHO syndrome is a fairly new concept in autoimmune diseases, this case suggests the syndrome originated much earlier in human history.</p>

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A comparative study of craniofacial measurements between Ryukyuan and mainland Japanese females using lateral cephalometric images

YAMAUCHI Tadashi, KIMURA Ryosuke, KAWAGUCHI Akira, SATO Takehiro, YAMAGUCHI Kyoko, TOMA Takashi, MIYAMOTO Kiyoto, FUKASE Hitoshi, YAMAGUCHI Tetsutaro, ISHIDA Hajime

Ａｎｔｈｒｏｐｏｌｏｇｉｃａｌ　Ｓｃｉｅｎｃｅ ( 日本人類学会 )  124 ( 1 ) 45 - 62   2016年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Using lateral cephalometric images, we compared the skeletal and soft tissue configurations of Ryukyuan and mainland Japanese females. We collected lateral cephalometric images of 30 females each from Okinawa Island and mainland Japan. Sixty landmarks were plotted on each image. Then, based on the coordinates of the landmarks, 68 distances and 34 angles were calculated according to orthodontic and anthropometric methods. We confirmed that the Ryukyuans have a smaller height in the upper and midfacial region than the mainland Japanese. Moreover, our findings indicate that, compared with the mainland Japanese females, the Ryukyuan females clearly have the following features: (1) a shallower mandibular notch, (2) an anterior-inclined symphysis of mandible, and (3) a smaller depth from upper lip to incisors. We also found that an anterior-inclined mandibular corpus and incisors are associated with a smaller distance between the surfaces of the upper lip and teeth and with a more protruded lip shape.

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Mapping the genetic diversity of HLA haplotypes in the Japanese populations.

Saw WY, Liu X, Khor CC, Takeuchi F, Katsuya T, Kimura R, Nabika T, Ohkubo T, Tabara Y, Yamamoto K, Yokota M, Japanese Genome Variation Consortium., Teo YY, Kato N

Scientific reports ( Scientific Reports )  5   17855   2015年12月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

　概要を見る

Japan has often been viewed as an Asian country that possesses a genetically homogenous community. The basis for partitioning the country into prefectures has largely been geographical, although cultural and linguistic differences still exist between some of the districts/prefectures, especially between Okinawa and the mainland prefectures. The Major Histocompatibility Complex (MHC) region has consistently emerged as the most polymorphic region in the human genome, harbouring numerous biologically important variants; nevertheless the presence of population-specific long haplotypes hinders the imputation of SNPs and classical HLA alleles. Here, we examined the extent of genetic variation at the MHC between eight Japanese populations sampled from Okinawa, and six other prefectures located in or close to the mainland of Japan, specifically focusing at the haplotypes observed within each population, and what the impact of any variation has on imputation. Our results indicated that Okinawa was genetically farther to the mainland Japanese than were Gujarati Indians from Tamil Indians, while the mainland Japanese from six prefectures were more homogeneous than between northern and southern Han Chinese. The distribution of haplotypes across Japan was similar, although imputation was most accurate for Okinawa and several mainland prefectures when population-specific panels were used as reference.

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Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data.

Nakagome S, Sato T, Ishida H, Hanihara T, Yamaguchi T, Kimura R, Mano S, Oota H, Asian DNA Repository Consortium.

Molecular biology and evolution ( Molecular Biology and Evolution )  32 ( 6 ) 1533 - 43   2015年06月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-gatherers known as Jomon, who are assumed to have originated in southeast Asia and lived in the Japanese archipelago greater than 10,000 years ago, admixed with an agricultural people known as Yayoi, whom were migrants from the East Asian continent 2,000-3,000 years ago. Meanwhile, some anthropologists propose that rather, morphological differences between the Jomon and Yayoi people can be explained by microevolution following the lifestyle change. To resolve this controversy, we compared three demographic models by approximate Bayesian computation using genome-wide single nucleotide polymorphism (gwSNP) data from the Ainu people who are thought to be direct descendants of indigenous Jomon. If we assume Chinese people sampled in Beijing from HapMap have the same ancestry as Yayoi, then the hybridization model is predicted to be between 29 and 63 times more likely than the replacement and transformation models, respectively. Furthermore, our data provide strong support for a model in which the Jomon lineages had population structure diversified in local areas before the admixture event. Initial divergence between the Jomon and Yayoi ancestries was dated to late Pleistocene, followed by the divergence of Jomon lineages at early Holocene. These results suggest gwSNP data provides a detailed picture of the complex hybridization model for Japanese population history.

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Common polymorphisms in WNT10A affect tooth morphology as well as hair shape.

Kimura R, Watanabe C, Kawaguchi A, Kim YI, Park SB, Maki K, Ishida H, Yamaguchi T

Human molecular genetics ( Human Molecular Genetics )  24 ( 9 ) 2673 - 80   2015年05月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Hair and teeth are appendages of ectodermal origin, and there are common molecular backgrounds involved in their formation. To date, it has been revealed that a non-synonymous polymorphismin EDAR has effects on the morphological variation in both hair and teeth. Previous association studies have confirmed that single-nucleotide polymorphisms (SNPs) in/near THADA, FRAS1, WNT10A, NAF1 and FGFR2 are associated with hair morphology. In this study, we thus examined whether these SNPs are also associated with dental characteristics. We measured metric dental traits including crown size and also evaluated non-metric dental traits using plaster casts obtained from subjects (272 Japanese and 226 Koreans). DNA samples were prepared from the subjects and genotyped for the hair morphology-associated SNPs. We observed a significant association of crown size with an SNP in WNT10A (rs7349332), but not with SNPs in other genes. Therefore, we further examined four SNPs within and around WNT10A, among which rs10177996 had the strongest association with dental traits. World distribution of the derived allele in rs10177996, which is associated with larger teeth, showed that Eurasians have a higher allele frequency than Africans. Together with previous studies on hair morphology, this study demonstrated that common variations in WNT10A have pleiotropic effects on the morphology of ectodermal appendages.

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D-12-19 3次元顔面形態の局所的統計解析(D-12.パターン認識・メディア理解A(パターンメディアの認識・理解・生成),一般セッション)

中津 美冴, 韓 先花, 木村 亮介, 陳 延偉

電子情報通信学会総合大会講演論文集 ( 一般社団法人電子情報通信学会 )  2015 ( 2 )   2015年02月 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Common polymorphisms in WNT10A affect tooth morphology as well as hair shape.

Kimura R, Watanabe C, Kawaguchi A, Kim YI, Park SB, Maki K, Ishida H, Yamaguchi T

Hum Mol Genet ( その他の出版社 )  24   2673 - 2680   2015年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Model-Based Verification of Hypotheses on the Origin of Modern Japanese Revisited by Bayesian Inference Based on Genome-Wide SNP Data.

Nakagome S, Sato T, Ishida H, Hanihara T, Yamaguchi T, Kimura R, Mano S, Oota H, Consortium ADR

Molecular Biology and Evolution ( その他の出版社 )  32   1533 - 1543   2015年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

ゲノム情報から古代人の姿を探る

木村 亮介

細胞工学   34   1172 - 1176   2015年

掲載種別: 研究論文（学術雑誌）

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  CiNii Research

Genome-Wide SNP Analysis Reveals Population Structure and Demographic History of the Ryukyu Islanders in the Southern Part of the Japanese Archipelago.

Sato T, Nakagome S, Watanabe C, Yamaguchi K, Kawaguchi A, Koganebuchi K, Haneji K, Yamaguchi T, Hanihara T, Yamamoto K, Ishida H, Mano S, Kimura R, Oota H

Molecular Biology and Evolution ( その他の出版社 )  31   2929 - 2940   2014年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Comparative analysis of facial morphology between Okinawa Islanders and mainland Japanese using three-dimensional images.

Miyazato E, Yamaguchi K, Fukase H, Ishida H, Kimura R

American Journal of Human Biology ( その他の出版社 )  26   538 - 548   2014年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Human genetic research, race, ethnicity and the labeling of populations: recommendations based on an interdisciplinary workshop in Japan.

Takezawa Y, Kato K, Oota H, Caulfield T, Fujimoto A, Honda S, Kamatani N, Kawamura S, Kawashima K, Kimura R, Matsumae H, Saito A, Savage PE, Seguchi N, Shimizu K, Terao S, Yamaguchi-Kabata Y, Yasukouchi A, Yoneda M, Tokunaga K

BMC Medical Ethics ( その他の出版社 )  15   33   2014年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Genome-wide association study of degenerative bony changes of the temporomandibular joint.

Yamaguchi T, Nakaoka H, Yamamoto K, Fujikawa T, Kim YI, Yano K, Haga S, Katayama K, Shibusawa T, Park S, Maki K, Kimura R, Inoue I

Oral Diseases ( その他の出版社 )  20   409 - 415   2014年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

The role of polymorphisms associated with early tooth eruption in dental and occlusal traits in East Asian populations.

Yamaguchi T, Kawaguchi A, Kim YI, Naga S, Katayama K, Ishida H, Park SB, Maki K, Kimura R

Korean Journal of Orthodontics ( その他の出版社 )  44   96 - 102   2014年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers.

Said HS, Suda W, Nakagome S, Chinen H, Oshima K, Kim S, Kimura R, Iraha A, Ishida H, Fujita J, Mano S, Morita H, Dohi T, Oota H, Hattori M

DNA Research ( その他の出版社 )  21   15 - 25   2014年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Interpretations of practical population genetics analyses of genome-wide SNP data on human demography in Dynamics of Learning in Neanderthals and Modern Humans Volume 2: Cognitive and Physical Perspectives (eds. Akazawa, T., Ogihara, N., Tanabe, H.C., Terashima, H.)

Kimura R

その他の掲載誌 ( Springer )    105 - 117   2014年 [ 査読有り ]

掲載種別: 研究論文（その他学術会議資料等）

Association of ADRB2 polymorphism with triglyceride levels in Tongans.

Naka I, Ohashi J, Kimura R, Inaoka T, Matsumura Y

Lipids in Health and Disease ( その他の出版社 )  12   110   2013年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Evaluation of the allele-sharing approach, known as the IBS method, in kinship analysis.

Tamura T, Osawa M, Kimura R, Inaoka Y, Tanaka S, Satoh F, Sato I

Journal of Forensic and Legal Medicine ( その他の出版社 )  20   112 - 116   2013年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

A functional SNP upstream of the beta-2 adrenergic receptor gene (ADRB2) is associated with obesity in Oceanic populations.

Naka I, Hikami K, Nakayama K, Koga M, Nishida N, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ataka Y, Ishida T, Inaoka T, Iwamoto S, Matsumura Y, Ohtsuka R, Tsuchiya N, Ohashi J

International Journal of Obesity ( その他の出版社 )  37   1204 - 1210   2013年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Metric characteristics of human limb bones in Asian and Japanese populations.

Kudaka M, Fukase H, Kimura R, Hanihara T, Matsumura H, Saso A, Fukumine T, Ishida H

Anthropological Science ( その他の出版社 )  121   49 - 62   2013年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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A genome-wide association study of third molar agenesis in Japanese and Korean populations.

Haga S, Nakaoka H, Yamaguchi T, Yamamoto K, Kim YI, Samoto H, Ohno T, Katayama K, Ishida H, Park SB, Kimura R, Maki K, Inoue I

Journal of Human Genetics ( その他の出版社 )  58   799 - 803   2013年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Hypertension-susceptibility gene prevalence in the Pacific Islands and associations with hypertension in Melanesia.

Furusawa T, Naka I, Yamauchi T, Natsuhara K, Eddie R, Kimura R, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ataka Y, Ohtsuka R, Ohashi J

Journal of Human Genetics ( その他の出版社 )  58   142 - 149   2013年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Association of melanocortin 1 receptor gene (MC1R) polymorphisms with skin reflectance and freckles in Japanese.

Yamaguchi K, Watanabe C, Kawaguchi A, Sato T, Naka I, Shindo M, Moromizato K, Aoki K, Ishida H, Kimura R

Journal of Human Genetics ( その他の出版社 )  57   700 - 708   2012年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Effects of an Asian-specific nonsynonymous EDAR variant on multiple dental traits.

Park JH, Yamaguchi T, Watanabe C, Kawaguchi A, Haneji K, Takeda M, Kim YI, Tomoyasu Y, Watanabe M, Oota H, Hanihara T, Ishida H, Maki K, Park SB, Kimura R

Journal of Human Genetics ( その他の出版社 )  57   508 - 514   2012年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

DRD4 VNTR polymorphism in Oceanic populations.

Naka I, Ohashi J, Kimura R, Furusawa T, Yamauchi T, Nakazawa M, Natsuhara K, Ataka Y, Nishida N, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R

Anthropological Science ( その他の出版社 )  120   151 - 155   2012年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Association of common PAX9 variants with permanent tooth size variation in non-syndromic East Asian populations.

Lee WC, Yamaguchi T, Watanabe C, Kawaguchi A, Takeda M, Kim YI, Haga S, Tomoyasu Y, Ishida H, Maki K, Park SB, Kimura R

Journal of Human Genetics ( その他の出版社 )  57   654 - 659   2012年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations.

Jinam T, Nishida N, Hirai M, Kawamura S, Oota H, Umetsu K, Kimura R, Ohashi J, Tajima A, Yamamoto T, Tanabe H, Mano S, Suto Y, Kaname T, Naritomi K, Yanagi K, Niikawa N, Omoto K, Tokunaga K, Saitou N, Japanese Archipelago H

Journal of Human Genetics ( その他の出版社 )  57   787 - 795   2012年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Advanced CT images reveal nonmetric cranial variations in living humans.

Saitou N, Kimura R, Fukase H, Yogi A, Murayama S, Ishida H

Anthropological Science ( その他の出版社 )  119   231 - 237   2011年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans.

Myles S, Lea RA, Ohashi J, Chambers GK, Weiss JG, Hardouin E, Engelken J, Macartney-Coxson DP, Eccles DA, Naka I, Kimura R, Inaoka T, Matsumura Y, Stoneking M

BMC Medical Genetics ( その他の出版社 )  12   10   2011年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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The serum leptin level and body mass index in Melanesian and Micronesian Solomon Islanders: focus on genetic factors and urbanization.

Furusawa T, Naka I, Yamauchi T, Natsuhara K, Kimura R, Nakazawa M, Ishida T, Nishida N, Eddie R, Ohtsuka R, Ohashi J

American Journal of Human Biology ( その他の出版社 )  23   435 - 444   2011年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

The Q223R polymorphism in LEPR is associated with obesity in Pacific Islanders.

Furusawa T, Naka I, Yamauchi T, Natsuhara K, Kimura R, Nakazawa M, Ishida T, Inaoka T, Matsumura Y, Ataka Y, Nishida N, Tsuchiya N, Ohtsuka R, Ohashi J

Human Genetics ( その他の出版社 )  127   287 - 294   2010年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Epstein-Barr virus strains defined by the latent membrane protein 1 sequence characterize Thai ethnic groups.

Saechan V, Settheetham-Ishida W, Kimura R, Tiwawech D, Mitarnun W, Ishida T

Journal of General Virology ( その他の出版社 )  91   2054 - 2061   2010年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Mapping human genetic diversity in Asia.

Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, Calacal GC, Chaurasia A, Chen CH, Chen JM, Chen YT, Chu JY, Cutiongco-de la Paz EMC, De Ungria MCA, Delfin FC, Edo J, Fuchareon S, Ghang H, Gojobori T, Han JS, Ho SF, Hoh BP, Huang W, Inoko H, Jha P, Jinam TA, Jin L, Jung J, Kangwanpong D, Kampuansai J, Kennedy GC, Khurana P, Kim HL, Kim K, Kim S, Kim WY, Kimm K, Kimura R, Koike T, Kulawonganunchai S, Kumar V, Lai PS, Lee JY, Lee S, Liu ET, Majumder PP, Mandapati KK, Marzuki S, Mitchell W, Mukerji M, Naritomi K, Ngamphiw C, Niikawa N, Nishida N, Oh B, Oh S, Ohashi J, Oka A, Ong R, Padilla CD, Palittapongarnpim P, Perdigon HB, Phipps ME, Png E, Sakaki Y, Salvador JM, Sandraling Y, Scaria V, Seielstad M, Sidek MR, Sinha A, Srikummool M, Sudoyo H, Sugano S, Suryadi H, Suzuki Y, Tabbada KA, Tan A, Tokunaga K, Tongsima S, Villamor LP, Wang E, Wang Y, Wang HF, Wu JY, Xiao HS, Xu SH, Yang JO, Shugart YY, Yoo HS, Yuan WT, Zhao GP, Zilfalil BA, Consortium HPAS, Indian Genome Variation C

Science ( その他の出版社 )  326   1541 - 1545   2009年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

SNP association and sequence analysis of the NOS1AP gene in SIDS.

Osawa M, Kimura R, Hasegawa I, Mukasa N, Satoh F

Legal Medicine ( その他の出版社 )  11 ( Suppl 1 ) S307-308   2009年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

A common variation in EDAR Is a genetic determinant of shovel-shaped incisors.

Kimura R, Yamaguchi T, Takeda M, Kondo O, Toma T, Haneji K, Hanihara T, Matsukusa H, Kawamura S, Maki K, Osawa M, Ishida H, Oota H

American Journal of Human Genetics ( その他の出版社 )  85   528 - 535   2009年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Stature estimation formulae from radiographically determined limb bone length in a modern Japanese population.

Hasegawa I, Uenishi K, Fukunaga T, Kimura R, Osawa M

Legal Medicine ( その他の出版社 )  11   260 - 266   2009年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

FGFR2 is associated with hair thickness in Asian populations.

Fujimoto A, Nishida N, Kimura R, Miyagawa T, Yuliwulandari R, Batubara L, Mustofa MS, Samakkarn U, Settheetham-Ishida W, Ishida T, Morishita Y, Tsunoda T, Tokunaga K, Ohashi J

Journal of Human Genetics ( その他の出版社 )  54   461 - 465   2009年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness.

Fujimoto A, Kimura R, Ohashi J, Omi K, Yuliwulandari R, Batubara L, Mustofa MS, Samakkarn U, Settheetham-Ishida W, Ishida T, Morishita Y, Furusawa T, Nakazawa M, Ohtsuka R, Tokunaga K

Human Molecular Genetics ( その他の出版社 )  17   835 - 843   2008年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

A functional single-nucleotide polymorphism in the CR1 promoter region contributes to protection against cerebral malaria.

Teeranaipong P, Ohashi J, Patarapotikul J, Kimura R, Nuchnoi P, Hananantachai H, Naka I, Putaporntip C, Jongwutiwes S, Tokunaga K

Journal of Infectious Diseases ( その他の出版社 )  198   1880 - 1891   2008年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Significant association between TIM1 promoter polymorphisms and protection against cerebral malaria in thailand.

Nuchnoi P, Ohashi J, Kimura R, Hananantachai H, Naka I, Krudsood S, Looareesuwan S, Tokunaga K, Patarapotikul J

Annals of Human Genetics ( その他の出版社 )  72   327 - 336   2008年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Appropriate data cleaning methods for genome-wide association study.

Miyagawa T, Nishida N, Ohashi J, Kimura R, Fujimoto A, Kawashima M, Koike A, Sasaki T, Tanii H, Otowa T, Momose Y, Nakahara Y, Gotoh J, Okazaki Y, Tsuji S, Tokunaga K

Journal of Human Genetics ( その他の出版社 )  53   886 - 893   2008年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Variant between CPT1B and CHKB associated with susceptibility to narcolepsy.

Miyagawa T, Kawashima M, Nishida N, Ohashi J, Kimura R, Fujimoto A, Shimada M, Morishita S, Shigeta T, Lin L, Hong SC, Faraco J, Shin YK, Jeong JH, Okazaki Y, Tsuji S, Honda M, Honda Y, Mignot E, Tokunaga K

Nature Genetics ( その他の出版社 )  40   1324 - 1328   2008年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Gene flow and natural selection in Oceanic human populations inferred from genome-wide SNP typing.

Kimura R, Ohashi J, Matsumura Y, Nakazawa M, Inaoka T, Ohtsuka R, Osawa M, Tokunaga K

Molecular Biology and Evolution ( その他の出版社 )  25   1750 - 1761   2008年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

A replication study confirmed the EDAR gene to be a major contributor to population differentiation regarding head hair thickness in Asia.

Fujimoto A, Ohashi J, Nishida N, Miyagawa T, Morishita Y, Tsunoda T, Kimura R, Tokunaga K

Human Genetics ( その他の出版社 )  124   179 - 185   2008年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

A practical genome scan for population-specific strong selective sweeps that have reached fixation.

Kimura R, Fujimoto A, Tokunaga K, Ohashi J

PLoS One ( その他の出版社 )  2   e286   2007年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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FTO polymorphisms in oceanic populations.

Ohashi J, Naka I, Kimura R, Natsuhara K, Yamauchi T, Furusawa T, Nakazawa M, Ataka Y, Patarapotikul J, Nuchnoi P, Tokunaga K, Ishida T, Inaoka T, Matsumura Y, Ohtsuka R

Journal of Human Genetics ( その他の出版社 )  52   1031 - 1035   2007年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Coexistence of five G6PD variants indicates ethnic complexity of Phuket islanders, Southern Thailand.

Ninokata A, Kimura R, Samakkarn U, Settheetham-Ishida W, Ishida T

Journal of Human Genetics ( その他の出版社 )  51   424 - 428   2006年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Polymorphisms in the ABO blood group gene in three populations in the New Georgia group of the Solomon Islands.

Ohashi J, Naka I, Kimura R, Tokunaga K, Yamauchi T, Natsuhara K, Furusawa T, Yamamoto R, Nakazawa M, Ishida T, Ohtsuka R

Journal of Human Genetics ( その他の出版社 )  51   407 - 411   2006年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

HLA-DRB1 polymorphism on Ha'ano island of the Kingdom of Tonga.

Ohashi J, Naka I, Kimura R, Tokunaga K, Nakazawa M, Ataka Y, Ohtsuka R, Inaoka T, Matsumura Y

Anthropological Science ( その他の出版社 )  114   193 - 198   2006年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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Anthropometry of 5-19-year-old Tongan children with special interest in the high prevalence of obesity among adolescent girls.

Fukuyama S, Inaoka T, Matsumura Y, Yamauchi T, Natsuhara K, Kimura R, Ohtsuka R

Annals of Human Biology ( その他の出版社 )  32   714 - 723   2005年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Allele-specific transcript quantification detects haplotypic variation in the levels of the SDF-1 transcripts.

Kimura R, Nishioka T, Soemantri A, Ishida T

Human Molecular Genetics ( その他の出版社 )  14   1579 - 1585   2005年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Cis-acting effect of the IL1B C-31T polymorphism on IL-1 beta mRNA expression.

Kimura R, Nishioka T, Soemantri A, Ishida T

Genes and Immunity ( その他の出版社 )  5   572 - 575   2004年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

The SDF1-G801A polymorphism is not associated with SDF1 gene expression in Epstein-Barr virus-transformed lymphoblastoid cells.

Kimura R, Nishioka T, Ishida T

Genes and Immunity ( その他の出版社 )  4   356 - 361   2003年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

Anthropological implication of the SDF1-3 ' A allele distribution in Southeast Asia and Melanesia.

Kimura R, Soemantri A, Settheetham-Ishida W, Ohtsuka R, Inaoka T, Pookajorn S, Tiwawech D, Duanchang P, Ishida T

Journal of Human Genetics ( その他の出版社 )  47   117 - 121   2002年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

The human SDF1 gene polymorphism is located on a mutational hot spot that was identified by the hominoid genome study.

Kimura R, Ishida T

Human Biology ( その他の出版社 )  73   891 - 896   2001年 [ 査読有り ]

掲載種別: 研究論文（学術雑誌）

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