Current Affiliation Organization 【 display / non-display 】

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• Genetic and morphological variations in humans

Published Papers 【 display / non-display 】

Published Papers 【 display / non-display 】

• 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 [ Peer Review Accepted ]

  Type of publication: Research paper (scientific journal)

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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   2022.11 [ Peer Review Accepted ]

  Type of publication: Research paper (scientific journal)

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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   2022.08 [ Peer Review Accepted ]

  Type of publication: Research paper (scientific journal)

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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   2022.07 [ Peer Review Accepted ]

  Type of publication: Research paper (scientific journal)

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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   2022.07 [ Peer Review Accepted ]

  Type of publication: Research paper (scientific journal)

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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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Other Papers 【 display / non-display 】

Other Papers 【 display / non-display 】

• 琉球列島人の集団ゲノム解析

  松波雅俊, 今村美菜子, 小金渕佳江, 木村亮介, 堀越桃子, 寺尾知可史, 鎌谷洋一郎, 石田肇, 前田士郎

  日本進化学会大会プログラム・講演要旨集(Web)   21st   105 (WEB ONLY)   2019.08

   

  J-GLOBAL

• SEARCH FOR SIGNATURES OF HUMAN GENETIC ADAPTATIONS IN EAST ASIA

  KIMURA Ryosuke

  Japanese Journal of Physiological Anthropology ( Japan Society of Physiological Anthropology )  24 ( 2 ) 87 - 91   2019  [Refereed]

   

  DOI

• Just-completed sympatric speciation in an ancient lake

  NOBU Sutra, MOKODONGAN Daniel Frikli, NAGANO Atsushi J, MATSUNAMI Masatoshi, KIMURA Ryosuke, YAMAHIRA Kazunori

  日本生態学会大会講演要旨(Web)   65th   ROMBUNNO.P2‐126 (WEB ONLY)   2018

   

  J-GLOBAL

• Highly-structured freshwater fish populations within a single river system

  MANDAGI Ixchel Feibie, MANDAGI Ixchel Feibie, LAWELLE Sjamsu Alam, MASENGI Kawilarang, Warouw Alex, MOKODONGAN Daniel Frikli, NAGANO Atsushi J, MATSUNAMI Masatoshi, KIMURA Ryosuke, YAMAHIRA Kazunori

  日本生態学会大会講演要旨(Web)   65th   ROMBUNNO.P2‐125 (WEB ONLY)   2018

   

  J-GLOBAL

• 口唇裂をもたらすIRF6遺伝子多型は東アジア健常集団における口唇鼻形態と関連する

  冨田 大介, 山口 徹太郎, 中脇 貴俊, 疋田 悠, Adel Mohamed, 芳賀 秀郷, 高橋 正皓, 木村 亮介, 槇 宏太郎

  東京矯正歯科学会雑誌 ( 東京矯正歯科学会 )  27 ( 2 ) 142 - 142   2017.12

   

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Grant-in-Aid for Scientific Research 【 display / non-display 】

Grant-in-Aid for Scientific Research 【 display / non-display 】

• Grant-in-Aid for Scientific Research(B)

  Project Year: 2021.04  -  2024.03 

  Direct: 13,400,000 (YEN)  Overheads: 17,420,000 (YEN)  Total: 4,020,000 (YEN)

• Genetic adaptation of human skin traits to the environment in the Asia-Pacific region

  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

  Project Year: 2020.04  -  2022.03 

  Direct: 8,300,000 (YEN)  Overheads: 10,790,000 (YEN)  Total: 2,490,000 (YEN)

• Transitions of human populations in the region around Lake Baikal: Inference from ancient genomes

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

  Project Year: 2018.10  -  2021.03 

  Investigator(s): Kimura Ryosuke 

  Direct: 13,800,000 (YEN)  Overheads: 17,940,000 (YEN)  Total: 4,140,000 (YEN)

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  The region around Lake Baikal in Siberia is an important area to understand the formation of Northeast Asian human populations. In this study, we applied next-generation sequencing to ancient bone and tooth specimens that were excavated from archaeological sites dated from Neolithic to Medieval periods in the Republic of Buryatia. As results, we found that Early Neolithic individuals in Buryatia had a similar genetic background with individuals of the same periods in the Cis-Baikal region. From the Late Neolithic to Iron Age, Buryatia individuals overlapped with the Early Neolithic individuals while Cis-Baikal individuals genetically shifted toward Western Eurasians. In addition, individuals of the Medieval period had a variety of origins: One was suggested to have originated from East Asia but another from Central Asia. The present study contributes to reveal the history of the peopling of Buryatia.

• A feasibility study on genome analysis of ancient humans in the Lake Baikal area

  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

  Project Year: 2017.04  -  2019.03 

  Direct: 4,000,000 (YEN)  Overheads: 5,200,000 (YEN)  Total: 1,200,000 (YEN)

• Grant-in-Aid for Scientific Research(C)

  Project Year: 2014  -  2016 

  Direct: 1,100,000 (YEN)  Overheads: 330,000 (YEN)  Total: 1,430,000 (YEN)

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