2024/10/12 更新

写真a

ヨシダ コウタ
吉田 恒太
YOSHIDA Kohta
所属
脳研究所 基礎神経科学部門 システム脳病態学 特任教授
職名
特任教授
通称等の別名
吉田恒太
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外部リンク

学位

  • 博士号(理学) ( 2011年9月   東京工業大学 )

  • 修士号(理学) ( 2008年3月   東京工業大学 )

  • 学士号(理学) ( 2007年3月   東京工業大学 )

研究キーワード

  • 脳病態

  • 種分化

  • 性染色体

  • 線虫

  • ゲノム

  • 染色体再構成

研究分野

  • ライフサイエンス / 進化生物学

  • ライフサイエンス / 分子生物学

  • ライフサイエンス / 遺伝学

  • ライフサイエンス / ゲノム生物学

経歴(researchmap)

  • 新潟大学 脳研究所   基礎神経科学部門, システム脳病態学分野(進化脳病態)   特任教授

    2024年1月 - 現在

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  • 国立遺伝学研究所   生態遺伝学研究室   特任助教

    2023年4月 - 2023年12月

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    国名:日本国

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  • マックスプランク生物学研究所(テュービンゲン、旧マックスプランク発生生物学研究所、ドイツ)   統合進化生物学部門   シニアスタッフサイエンティスト

    2016年9月 - 2023年3月

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    国名:ドイツ連邦共和国

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  • 国立遺伝学研究所   新分野創造センター・生態遺伝学研究室   日本学術振興会特別研究員(PD)

    2014年4月 - 2016年9月

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  • 国立遺伝学研究所   新分野創造センター・生態遺伝学研究室   特任研究員

    2011年10月 - 2014年3月

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  • 東京工業大学   大学院生命理工学研究科   日本学術振興会特別研究員(DC2)

    2009年4月 - 2011年3月

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経歴

  • 新潟大学   脳研究所 基礎神経科学部門 システム脳病態学   特任教授

    2024年1月 - 現在

学歴

  • 東京工業大学   大学院生命理工学研究科

    2008年4月 - 2011年9月

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    備考: 博士課程修了(理学)

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  • フレッドハッチンソン癌研究センター(アメリカ)   ヒト生物学部門

    2010年10月 - 2010年12月

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    国名: アメリカ合衆国

    備考: 短期留学

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  • 東京工業大学   大学院生命理工学研究科

    2007年4月 - 2008年3月

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    備考: 修士課程修了(理学)

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  • 東京工業大学   生命理工学部   生体システム学科

    2003年4月 - 2007年3月

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所属学協会

  • 日本遺伝学会

    2013年5月 - 現在

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  • 日本進化学会

    2007年6月 - 現在

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論文

  • Genomic reconsideration of fish non-monophyly: why cannot we simply call them all ‘fish’? 査読

    Shigehiro Kuraku, Mana Sato, Kohta Yoshida, Yoshinobu Uno

    Ichthyological Research   2023年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:Springer Science and Business Media LLC  

    Abstract

    Extant ‘fishes’ belong to jawless, cartilaginous, actinopterygian, or sarcopterygian fish lineages. They comprise a non-monophyletic group of vertebrates from which tetrapods are excluded, and they are therefore paraphyletic. Recent advances in whole-genome sequencing have shed light on phylogenetic relationships, divergence times among major fish lineages, and the molecular basis of phenotypic diversity. This review encompasses the diversity of extant fishes and explores the variation in genomic organization and its evolutionary origins. This review begins with evaluating available genomic sequence resources with a focus on literally complete (‘telomere-to-telomere’) sequencing. Next, it discusses among-lineage variations in genomic contents, considering karyotype reports, genome sizes, and whole-genome duplication events. Additionally, we investigate three families of protein-coding genes, visual opsins, aquaporins (Aqps), and Hox genes, as they offer insights into morphological and physiological differences among major fish lineages. Overall, our technical basis of analyzing fish genomes and the knowledge of genomic organization provide valuable insights into our vertebrate-wide understanding of how molecular mechanisms specifying variable phenotypes are encoded in genomic sequence information.

    DOI: 10.1007/s10228-023-00939-9

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    その他リンク: https://link.springer.com/article/10.1007/s10228-023-00939-9/fulltext.html

  • Repositioning of centromere-associated repeats during karyotype evolution in Oryzias fishes. 査読 国際誌

    Satoshi Ansai, Atsushi Toyoda, Kohta Yoshida, Jun Kitano

    Molecular ecology   2023年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    The karyotype, which is the number and shape of chromosomes, is a fundamental characteristic of all eukaryotes. Karyotypic changes play an important role in many aspects of evolutionary processes, including speciation. In organisms with monocentric chromosomes, it was previously thought that chromosome number changes were mainly caused by centric fusions and fissions, whereas chromosome shape changes, that is, changes in arm numbers, were mainly due to pericentric inversions. However, recent genomic and cytogenetic studies have revealed examples of alternative cases, such as tandem fusions and centromere repositioning, found in the karyotypic changes within and between species. Here, we employed comparative genomic approaches to investigate whether centromere repositioning occurred during karyotype evolution in medaka fishes. In the medaka family (Adrianichthyidae), the three phylogenetic groups differed substantially in their karyotypes. The Oryzias latipes species group has larger numbers of chromosome arms than the other groups, with most chromosomes being metacentric. The O. javanicus species group has similar numbers of chromosomes to the O. latipes species group, but smaller arm numbers, with most chromosomes being acrocentric. The O. celebensis species group has fewer chromosomes than the other two groups and several large metacentric chromosomes that were likely formed by chromosomal fusions. By comparing the genome assemblies of O. latipes, O. javanicus, and O. celebensis, we found that repositioning of centromere-associated repeats might be more common than simple pericentric inversion. Our results demonstrated that centromere repositioning may play a more important role in karyotype evolution than previously appreciated.

    DOI: 10.1111/mec.17222

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  • Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives. 査読 国際誌

    Radka Reifová, S Lorena Ament-Velásquez, Yann Bourgeois, Jenn Coughlan, Jonna Kulmuni, Agnieszka P Lipinska, Genta Okude, Laurie Stevison, Kohta Yoshida, Jun Kitano

    Cold Spring Harbor perspectives in biology   2023年9月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.

    DOI: 10.1101/cshperspect.a041607

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  • Do sex-linked male meiotic drivers contribute to intrinsic hybrid incompatibilities? Recent empirical studies from flies and rodents. 査読 国際誌

    Jun Kitano, Kohta Yoshida

    Current opinion in genetics & development   81   102068 - 102068   2023年6月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Intrinsic hybrid incompatibility is one of the important isolating barriers between species. In organisms with sex chromosomes, intrinsic hybrid incompatibility often follows two rules: Haldane's rule and large-X effects. One explanation for these two rules is that sex chromosomes are hotspots for meiotic drivers that can cause intrinsic hybrid incompatibility between geographically isolated populations. Although this hypothesis seems plausible and several empirical data are consistent with it, we are still unsure whether such mechanisms occur in nature, particularly with respect to speciation with gene flow. Here, we review empirical studies that have investigated the roles of meiotic drive in sex-chromosome evolution and speciation and propose future studies necessary for testing this hypothesis.

    DOI: 10.1016/j.gde.2023.102068

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  • Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation 査読

    Kohta Yoshida, Christian Rödelsperger, Waltraud Röseler, Metta Riebesell, Simo Sun, Taisei Kikuchi, Ralf J. Sommer

    Nature Ecology & Evolution   2023年1月

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    担当区分:筆頭著者, 責任著者   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1038/s41559-022-01980-z

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  • The improved genome of the nematode Parapristionchus giblindavisi provides insights into lineage-specific gene family evolution 査読

    Waltraud Röseler, Maximilian Collenberg, Kohta Yoshida, Christa Lanz, Ralf J Sommer, Christian Rödelsperger

    G3 Genes|Genomes|Genetics   2022年9月

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    掲載種別:研究論文(学術雑誌)  

    DOI: 10.1093/g3journal/jkac215

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  • Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology. 査読 国際誌

    Kohta Yoshida, Jun Kitano

    PLOS GENETICS   17 ( 4 )   e1009502   2021年4月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1371/journal.pgen.1009502

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  • Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations. 査読 国際誌

    Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Tomoyuki Kokita, Seiichi Mori, Jun Kitano

    Genome biology and evolution   12 ( 4 )   479 - 492   2020年4月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1093/gbe/evaa065

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  • Functional divergence of a heterochromatin-binding protein during stickleback speciation. 査読 国際誌

    Kohta Yoshida, Asano Ishikawa, Atsushi Toyoda, Shuji Shigenobu, Asao Fujiyama, Jun Kitano

    Molecular ecology   28 ( 6 )   1563 - 1578   2019年3月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    DOI: 10.1111/mec.14841

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  • Two new Species of Pristionchus (Nematoda: Diplogastridae) include the Gonochoristic Sister Species of P. fissidentatus. 査読 国際誌

    Matthias Herrmann, Natsumi Kanzaki, Christian Weiler, Kohta Yoshida, Christian RÖdelsperger, Ralf J Sommer

    Journal of nematology   51   1 - 14   2019年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    The genus Pristionchus (Kreis, 1932) consists of more than 30 soil nematode species that are often found in association with scarab beetles. Three major radiations have resulted in the "maupasi species group" in America, the "pacificus species group" in Asia, and the "lheritieri species group," which contains species from Europe and Asia. Phylogenetic analysis indicates that a group of three species, including the gonochorists P. elegans and P. bucculentus and the hermaphrodite P. fissidentatus, is basal to the above-mentioned radiations. Two novel species are described here: Pristionchus paulseni sp. n. from Taiwan and P. yamagatae sp. n. from Japan by means of morphology, morphometrics and genome-wide transcriptome sequence analysis. Previous phylotranscriptomic analysis of the complete Pristionchus genus recognized P. paulseni sp. n. as the sister species of P. fissidentatus, and thus its importance for macro-evolutionary studies. Specifically, the gonochorist P. paulseni sp. n. and the hermaphrodite P. fissidentatus form a species pair that is the sister group to all other described Pristionchus species. P. paulseni sp. n. has two distinct mouth forms, supporting the notion that the mouth dimorphism is ancestral in the genus Pristionchus. The genus Pristionchus (Kreis, 1932) consists of more than 30 soil nematode species that are often found in association with scarab beetles. Three major radiations have resulted in the “maupasi species group” in America, the “pacificus species group” in Asia, and the “lheritieri species group,” which contains species from Europe and Asia. Phylogenetic analysis indicates that a group of three species, including the gonochorists P. elegans and P. bucculentus and the hermaphrodite P. fissidentatus, is basal to the above-mentioned radiations. Two novel species are described here: Pristionchus paulseni sp. n. from Taiwan and P. yamagatae sp. n. from Japan by means of morphology, morphometrics and genome-wide transcriptome sequence analysis. Previous phylotranscriptomic analysis of the complete Pristionchus genus recognized P. paulseni sp. n. as the sister species of P. fissidentatus, and thus its importance for macro-evolutionary studies. Specifically, the gonochorist P. paulseni sp. n. and the hermaphrodite P. fissidentatus form a species pair that is the sister group to all other described Pristionchus species. P. paulseni sp. n. has two distinct mouth forms, supporting the notion that the mouth dimorphism is ancestral in the genus Pristionchus.

    DOI: 10.21307/jofnem-2019-024

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  • Phylotranscriptomics of Pristionchus Nematodes Reveals Parallel Gene Loss in Six Hermaphroditic Lineages. 査読 国際誌

    Christian Rödelsperger, Waltraud Röseler, Neel Prabh, Kohta Yoshida, Christian Weiler, Matthias Herrmann, Ralf J Sommer

    Current biology : CB   28 ( 19 )   3123 - 3127   2018年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Mutation and recombination are main drivers of phenotypic diversity, but the ability to create new allelic combinations is strongly dependent on the mode of reproduction. While most animals are dioecious (i.e., separated male and female sexes), in a number of evolutionary lineages females have gained the ability to self-fertilize [1, 2], with drastic consequences on effective recombination rate, genetic diversity, and the efficacy of selection [3]. In the genus Caenorhabditis, such hermaphroditic or androdioecious lineages, including C. briggsae and C. tropicalis, display a genome shrinkage relative to their dioecious sister species C. nigoni and C. brenneri, respectively [4, 5]. However, common consequences of reproductive modes on nematode genomes remain unknown, because most taxa contain single or few androdioecious species. One exception is the genus Pristionchus, with seven androdioecious species. Pristionchus worms are found in association with scarab beetles in worldwide samplings, resulting in deep taxon sampling and currently 39 culturable and available species. Here, we use phylotranscriptomics of all 39 Pristionchus species to provide a robust phylogeny based on an alignment of more than 2,000 orthologous clusters, which indicates that the seven androdioecious species represent six independent lineages. We show that gene loss is more prevalent in all hermaphroditic lineages than in dioecious relatives and that the majority of lost genes evolved recently in the Pristionchus genus. Further, we provide evidence that genes with male-biased expression are preferentially lost in hermaphroditic lineages. This supports a contribution of adaptive gene loss to shaping nematode genomes following the evolution of hermaphroditism.

    DOI: 10.1016/j.cub.2018.07.041

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  • The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression. 査読 国際誌

    Mark Ravinet, Kohta Yoshida, Shuji Shigenobu, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

    PLoS genetics   14 ( 5 )   e1007358   2018年5月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

    DOI: 10.1371/journal.pgen.1007358

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  • Samplings of Millipedes in Japan and Scarab Beetles in Hong Kong result in five new Species of Pristionchus (Nematoda: Diplogastridae). 査読 国際誌

    Natsumi Kanzaki, Matthias Herrmann, Kohta Yoshida, Christian Weiler, Christian Rödelsperger, Ralf J Sommer

    Journal of nematology   50 ( 4 )   587 - 610   2018年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    The authors describe five new species of Pristionchus from Japan and Hongkong. Scarab beetle samplings in Hongkong identified P. hongkongensis sp. n. and P. neolucani sp. n., representing the first beetle-associated Pristionchus species from China. Surprisingly, samplings of millipedes in Japan revealed a previously unknown association of Pristionchus nematodes with these arthropods. Specifically, the authors found three previously known Pristionchus species, P. arcanus, P. entomophagus, and P. fukushimae on Japanese millipedes. In addition, the authors found three new Pristionchus species on millipedes, which are described as P. riukiariae sp. n., P. degawai sp. n., and P. laevicollis, sp. n., the latter of which was also found on stag beetles. These species are most closely related to P. maxplancki, P. japonicus, and P. quartusdecimus and belong to the pacificus species-complex. The authors describe all species based on morphology, morphometrics, and genome-wide sequence analysis. Mating experiments indicated that all species are reproductively isolated from each other and in contrast to the species of the "pacificus species-complex sensu stricto" they do not form F1 hybrids. The authors describe five new species of Pristionchus from Japan and Hongkong. Scarab beetle samplings in Hongkong identified P. hongkongensis sp. n. and P. neolucani sp. n., representing the first beetle-associated Pristionchus species from China. Surprisingly, samplings of millipedes in Japan revealed a previously unknown association of Pristionchus nematodes with these arthropods. Specifically, the authors found three previously known Pristionchus species, P. arcanus, P. entomophagus, and P. fukushimae on Japanese millipedes. In addition, the authors found three new Pristionchus species on millipedes, which are described as P. riukiariae sp. n., P. degawai sp. n., and P. laevicollis, sp. n., the latter of which was also found on stag beetles. These species are most closely related to P. maxplancki, P. japonicus, and P. quartusdecimus and belong to the pacificus species-complex. The authors describe all species based on morphology, morphometrics, and genome-wide sequence analysis. Mating experiments indicated that all species are reproductively isolated from each other and in contrast to the species of the “pacificus species-complex sensu stricto” they do not form F1 hybrids.

    DOI: 10.21307/jofnem-2018-044

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  • Two New Species of Pristionchus (Nematoda: Diplogastridae) from Taiwan and the Definition of the pacificus Species-Complex Sensu Stricto. 査読 国際誌

    Kohta Yoshida, Matthias Herrmann, Natsumi Kanzaki, Christian Weiler, Christian Rödelsperger, Ralf J Sommer

    Journal of nematology   50 ( 3 )   355 - 368   2018年

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Pristionchus pacificus Sommer, Carta, Kim, and Sternberg, 1996 is an important model organism in evolutionary biology that aims to integrate developmental biology and evo-devo with population genetics and ecology. Functional studies in P. pacificus are supported by a well-established phylogenetic framework of around 30 species of the genus Pristionchus that have been described in the last decade based on their entomophilic and necromenic association with scarab beetles. Biogeographically, East Asia has emerged as a hotspot of Pristionchus speciation and recent samplings have therefore focused on Islands and mainland settings in East Asia. Here, we describe in a series of three publications the results of our sampling efforts in Taiwan, Japan, and Hongkong in 2016 and 2017. We describe a total of nine new species that cover different phylogenetic species-complexes of the Pristionchus genus. In this first publication, we describe two new species, Pristionchus sikae sp. n. and Pristionchus kurosawai sp. n. that are closely related to P. pacificus . Together with five previously described species they form the " pacificus species-complex sensu stricto" that is characterized by all species forming viable, but sterile F1 hybrids indicating reproductive isolation. P. sikae sp. n. and P. kurosawai sp. n. have a gonochorist mode of reproduction and they are described using morphology, morphometrics, mating experiments, and genome-wide sequence analysis. We discuss the extreme diversification in the pacificus species-complex sensu stricto in East Asia and its potential power to study speciation processes.

    DOI: 10.21307/jofnem-2018-019

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  • Contribution of gene flow to the evolution of recombination suppression in sex chromosomes. 査読 国際誌

    Tomotaka Matsumoto, Kohta Yoshida, Jun Kitano

    Journal of theoretical biology   431   25 - 31   2017年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Polymorphism of alleles that benefit one sex but harm the other (sexually antagonistic alleles) generates selective pressures for reduced recombination between themselves and sex-determination loci. Such polymorphism can be maintained within a population when selection coefficients are sufficiently balanced between males and females. However, if regulatory mutations restrict gene expression only to one sex, these alleles become neutral in the other sex and easily fixed within a population, removing the selective pressures for recombination suppression in sex chromosomes. When there is spatial variation in selection regimes, however, alleles that are deleterious in one sex and neutral in the other can be maintained in other neighboring populations and gene flow may continuously supply deleterious alleles. We hypothesized that this maintenance of genetic variation may promote the establishment of recombination suppression in sex chromosomes even in cases where selection is limited to one sex. Using individual-based simulations, we show that spatial variation in male-limited selection and gene flow can promote the establishment of Y-autosome fusions, a special case of recombination suppression in sex chromosomes. This can be explained by the fact that fused Y-chromosomes that capture alleles that are beneficial for local males have a higher mean fitness compared to unfused Y chromosomes in the presence of deleterious gene flow. We also simulated the case of sex-concordant selection and found that gene flow of alleles that are deleterious in both sexes did not substantially increase the establishment rates of Y-autosome fusions across the parameter space examined. This can be accounted for by the fact that foreign alleles that are deleterious in both sexes can be efficiently removed from the population compared to alleles that are neutral in females. These results indicate that how gene flow affects the establishment rates of Y-autosome fusions depends largely on selection regimes. Spatial variation in sex-specific selection and gene flow should be appreciated as a factor affecting sex chromosome evolution.

    DOI: 10.1016/j.jtbi.2017.08.004

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  • Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes. 査読 国際誌

    Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

    Evolution; international journal of organic evolution   71 ( 3 )   565 - 581   2017年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Differential gene expression can play an important role in phenotypic evolution and divergent adaptation. Although differential gene expression can be caused by both local- and distant-regulatory changes, we know little about their relative contribution to transcriptome evolution in natural populations. Here, we conducted expression quantitative trait loci (eQTL) analysis to investigate the genetic architecture underlying transcriptome divergence between marine and stream ecotypes of threespine sticklebacks (Gasterosteus aculeatus). We identified both local and distant eQTLs, some of which constitute hotspots, regions with a disproportionate number of significant eQTLs relative to the genomic background. The majority of local eQTLs including those in the hotspots caused expression changes consistent with the direction of transcriptomic divergence between ecotypes. Genome scan analysis showed that many local eQTLs overlapped with genomic regions of high differentiation. In contrast, nearly half of the distant eQTLs including those in the hotspots caused opposite expression changes, and few overlapped with regions of high differentiation, indicating that distant eQTLs may act as a constraint of transcriptome evolution. Finally, a comparison between two salinity conditions revealed that nearly half of eQTL hotspots were environment specific, suggesting that analysis of genetic architecture in multiple conditions is essential for predicting response to selection.

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  • Accumulation of Deleterious Mutations on the Neo-Y Chromosome of Japan Sea Stickleback (Gasterosteus nipponicus). 査読 国際誌

    Kohta Yoshida, Takashi Makino, Jun Kitano

    The Journal of heredity   108 ( 1 )   63 - 68   2017年1月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Degeneration of Y chromosomes is a common evolutionary path of XY sex chromosome systems. Recent genomic studies in flies and plants have revealed that even young neo-sex chromosomes with the age of a few million years show signs of Y degeneration, such as the accumulation of nonsense and frameshift mutations. However, it remains unclear whether neo-Y chromosomes also show rapid degeneration in fishes, which often have homomorphic sex chromosomes. Here, we investigated whether a neo-Y chromosome of Japan Sea stickleback (Gasterosteus nipponicus), which was formed by a Y-autosome fusion within the last 2 million years, accumulates deleterious mutations. Our previous genomic analyses did not detect excess nonsense and frameshift mutations on the Japan Sea stickleback neo-Y. In the present study, we found that the nonrecombining region of the neo-Y near the fusion end has accumulated nonsynonymous mutations altering amino acids of evolutionarily highly conserved residues. Enrichment of gene ontology terms related to protein phosphorylation and cellular protein modification process was found in the genes with potentially deleterious mutations on the neo-Y. These results suggest that the neo-Y of the Japan Sea stickleback has already accumulated mutations that may impair protein functions.

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  • Genetic basis for variation in salinity tolerance between stickleback ecotypes. 査読 国際誌

    Makoto Kusakabe, Asano Ishikawa, Mark Ravinet, Kohta Yoshida, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

    Molecular ecology   26 ( 1 )   304 - 319   2017年1月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Adaptation to different salinities can drive and maintain divergence between populations of aquatic organisms. Anadromous and stream ecotypes of threespine stickleback (Gasterosteus aculeatus) are an excellent model to explore the genetic mechanisms underlying osmoregulation divergence. Using a parapatric pair of anadromous and stream stickleback ecotypes, we employed an integrated genomic approach to identify candidate genes important for adaptation to different salinity environments. Quantitative trait loci (QTL) mapping of plasma sodium concentrations under a seawater challenge experiment identified a significant QTL on chromosome 16. To identify candidate genes within this QTL, we first conducted RNA-seq and microarray analysis on gill tissue to find ecotypic differences in gene expression that were associated with plasma Na+ levels. This resulted in the identification of ten candidate genes. Quantitative PCR analysis on gill tissue of additional Japanese stickleback populations revealed that the majority of the candidate genes showed parallel divergence in expression levels. Second, we conducted whole-genome sequencing and found five genes that are predicted to have functionally important amino acid substitutions. Finally, we conducted genome scan analysis and found that eight of these candidate genes were located in genomic islands of high differentiation, suggesting that they may be under divergent selection. The candidate genes included those involved in ATP synthesis and hormonal signalling, whose expression or amino acid changes may underlie the variation in salinity tolerance. Further functional molecular analysis of these genes will reveal the causative genetic and genomic changes underlying divergent adaptation.

    DOI: 10.1111/mec.13875

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  • Whole-genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback. 査読 国際誌

    Kohta Yoshida, Ryutaro Miyagi, Seiichi Mori, Aya Takahashi, Takashi Makino, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

    Ecology and evolution   6 ( 7 )   2190 - 204   2016年4月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Invasive species pose a major threat to biological diversity. Although introduced populations often experience population bottlenecks, some invasive species are thought to be originated from hybridization between multiple populations or species, which can contribute to the maintenance of high genetic diversity. Recent advances in genome sequencing enable us to trace the evolutionary history of invasive species even at whole-genome level and may help to identify the history of past hybridization that may be overlooked by traditional marker-based analysis. Here, we conducted whole-genome sequencing of eight threespine stickleback (Gasterosteus aculeatus) individuals, four from a recently introduced crater lake population and four of the putative source population. We found that both populations have several small genomic regions with high genetic diversity, which resulted from introgression from a closely related species (Gasterosteus nipponicus). The sizes of the regions were too small to be detected with traditional marker-based analysis or even some reduced-representation sequencing methods. Further amplicon sequencing revealed linkage disequilibrium around an introgression site, which suggests the possibility of selective sweep at the introgression site. Thus, interspecies introgression might predate introduction and increase genetic variation in the source population. Whole-genome sequencing of even a small number of individuals can therefore provide higher resolution inference of history of introduced populations.

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  • Genetic Architecture of the Variation in Male-Specific Ossified Processes on the Anal Fins of Japanese Medaka. 査読 国際誌

    Maiko Kawajiri, Shingo Fujimoto, Kohta Yoshida, Kazunori Yamahira, Jun Kitano

    G3 (Bethesda, Md.)   5 ( 12 )   2875 - 84   2015年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Traits involved in reproduction evolve rapidly and show great diversity among closely related species. However, the genetic mechanisms that underlie the diversification of courtship traits are mostly unknown. Japanese medaka fishes (Oryzias latipes) use anal fins to attract females and to grasp females during courtship; the males have longer anal fins with male-specific ossified papillary processes on the fin rays. However, anal fin morphology varies between populations: the southern populations tend to have longer anal fins and more processes than the northern populations. In the present study, we conducted quantitative trait locus (QTL) mapping to investigate the genetic architecture underlying the variation in the number of papillary processes of Japanese medaka fish and compared the QTL with previously identified QTL controlling anal fin length. First, we found that only a few QTL were shared between anal fin length and papillary process number. Second, we found that the numbers of papillary processes on different fin rays often were controlled by different QTL. Finally, we produced another independent cross and found that some QTL were repeatable between the two crosses, whereas others were specific to only one cross. These results suggest that variation in the number of papillary processes is polygenic and controlled by QTL that are distinct from those controlling anal fin length. Thus, different courtship traits in Japanese medaka share a small number of QTL and have the potential for independent evolution.

    DOI: 10.1534/g3.115.021956

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  • A microsatellite-based genetic linkage map and putative sex-determining genomic regions in Lake Victoria cichlids. 査読 国際誌

    Yu Kudo, Masato Nikaido, Azusa Kondo, Hikoyu Suzuki, Kohta Yoshida, Kiyoshi Kikuchi, Norihiro Okada

    Gene   560 ( 2 )   156 - 64   2015年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Cichlid fishes in East Africa have undergone extensive adaptive radiation, which has led to spectacular diversity in their morphology and ecology. To date, genetic linkage maps have been constructed for several tilapias (riverine), Astatotilapia burtoni (Lake Tanganyika), and hybrid lines of Lake Malawi cichlids to facilitate genome-wide comparative analyses. In the present study, we constructed a genetic linkage map of the hybrid line of Lake Victoria cichlids, so that maps of cichlids from all the major areas of East Africa will be available. The genetic linkage map shown here is derived from the F2 progeny of an interspecific cross between Haplochromis chilotes and Haplochromis sauvagei and is based on 184 microsatellite and two single-nucleotide polymorphism (SNP) markers. Most of the microsatellite markers used in the present study were originally designed for other genetic linkage maps, allowing us to directly compare each linkage group (LG) among different cichlid groups. We found 25 LGs, the total length of which was 1133.2cM with an average marker spacing of about 6.09cM. Our subsequent linkage mapping analysis identified two putative sex-determining loci in cichlids. Interestingly, one of these two loci is located on cichlid LG5, on which the female heterogametic ZW locus and several quantitative trait loci (QTLs) related to adaptive evolution have been reported in Lake Malawi cichlids. We also found that V1R1 and V1R2, candidate genes for the fish pheromone receptor, are located very close to the recently detected sex-determining locus on cichlid LG5. The genetic linkage map study presented here may provide a valuable foundation for studying the chromosomal evolution of East African cichlids and the possible role of sex chromosomes in generating their genomic diversity.

    DOI: 10.1016/j.gene.2015.01.057

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  • Ontogenetic stage-specific quantitative trait loci contribute to divergence in developmental trajectories of sexually dimorphic fins between medaka populations. 査読 国際誌

    Maiko Kawajiri, Kohta Yoshida, Shingo Fujimoto, Daniel Frikli Mokodongan, Mark Ravinet, Mark Kirkpatrick, Kazunori Yamahira, Jun Kitano

    Molecular ecology   23 ( 21 )   5258 - 75   2014年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Sexual dimorphism can evolve when males and females differ in phenotypic optima. Genetic constraints can, however, limit the evolution of sexual dimorphism. One possible constraint is derived from alleles expressed in both sexes. Because males and females share most of their genome, shared alleles with different fitness effects between sexes are faced with intralocus sexual conflict. Another potential constraint is derived from genetic correlations between developmental stages. Sexually dimorphic traits are often favoured at adult stages, but selected against as juvenile, so developmental decoupling of traits between ontogenetic stages may be necessary for the evolution of sexual dimorphism in adults. Resolving intralocus conflicts between sexes and ages is therefore a key to the evolution of age-specific expression of sexual dimorphism. We investigated the genetic architecture of divergence in the ontogeny of sexual dimorphism between two populations of the Japanese medaka (Oryzias latipes) that differ in the magnitude of dimorphism in anal and dorsal fin length. Quantitative trait loci (QTL) mapping revealed that few QTL had consistent effects throughout ontogenetic stages and the majority of QTL change the sizes and directions of effects on fin growth rates during ontogeny. We also found that most QTL were sex-specific, suggesting that intralocus sexual conflict is almost resolved. Our results indicate that sex- and age-specific QTL enable the populations to achieve optimal developmental trajectories of sexually dimorphic traits in response to complex natural and sexual selection.

    DOI: 10.1111/mec.12933

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  • Sex chromosome turnover contributes to genomic divergence between incipient stickleback species. 査読 国際誌

    Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Masakado Kawata, Manabu Kume, Seiichi Mori, Catherine L Peichel, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

    PLoS genetics   10 ( 3 )   e1004223   2014年3月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Sex chromosomes turn over rapidly in some taxonomic groups, where closely related species have different sex chromosomes. Although there are many examples of sex chromosome turnover, we know little about the functional roles of sex chromosome turnover in phenotypic diversification and genomic evolution. The sympatric pair of Japanese threespine stickleback (Gasterosteus aculeatus) provides an excellent system to address these questions: the Japan Sea species has a neo-sex chromosome system resulting from a fusion between an ancestral Y chromosome and an autosome, while the sympatric Pacific Ocean species has a simple XY sex chromosome system. Furthermore, previous quantitative trait locus (QTL) mapping demonstrated that the Japan Sea neo-X chromosome contributes to phenotypic divergence and reproductive isolation between these sympatric species. To investigate the genomic basis for the accumulation of genes important for speciation on the neo-X chromosome, we conducted whole genome sequencing of males and females of both the Japan Sea and the Pacific Ocean species. No substantial degeneration has yet occurred on the neo-Y chromosome, but the nucleotide sequence of the neo-X and the neo-Y has started to diverge, particularly at regions near the fusion. The neo-sex chromosomes also harbor an excess of genes with sex-biased expression. Furthermore, genes on the neo-X chromosome showed higher non-synonymous substitution rates than autosomal genes in the Japan Sea lineage. Genomic regions of higher sequence divergence between species, genes with divergent expression between species, and QTL for inter-species phenotypic differences were found not only at the regions near the fusion site, but also at other regions along the neo-X chromosome. Neo-sex chromosomes can therefore accumulate substitutions causing species differences even in the absence of substantial neo-Y degeneration.

    DOI: 10.1371/journal.pgen.1004223

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  • Construction of Chromosome Markers from the Lake Victoria Cichlid Paralabidochromis chilotes and Their Application to Comparative Mapping 査読

    A. Kuroiwa, Y. Terai, N. Kobayashi, K. Yoshida, M. Suzuki, A. Nakanishi, Y. Matsuda, M. Watanabe, N. Okada

    CYTOGENETIC AND GENOME RESEARCH   142 ( 2 )   112 - 120   2014年

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:KARGER  

    Cichlid fishes in the African Great Lakes are known as a spectacular example of adaptive radiation in vertebrates. Four linkage maps have been constructed to identify the genes responsible for adaptation and speciation, and the genetic linkages of those genes are assumed to play an important role during adaptive evolution. However, it is difficult to analyze such linkages because the linkage groups of one species do not match well with those of the other species. Chromosome markers are a powerful tool for the direct identification of linkage homology between different species. We used information about the linkage map of the Lake Malawi cichlid (Labeotropheus fuelleborni/Metriaclima zebra) to isolate bacterial artificial chromosome (BAC) clones from the BAC library of Paralabidochromis chilotes, Lake Victoria. We identified 18 of 22 P. chilotes chromosomes by single- and multi-color BAC fluorescence in situ hybridization using 19 BAC clones. Comparative mapping with the chromosome markers of P. chilotes in Astatotilapia burtoni (2n = 40) from Lake Tanganyika revealed the chromosome rearrangements that have occurred in this lineage. These chromosome markers will be useful for delineating the process of genome and chromosome evolution in African species. (C) 2013 S. Karger AG, Basel

    DOI: 10.1159/000356128

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  • Genetic and neural modularity underlie the evolution of schooling behavior in threespine sticklebacks. 査読 国際誌

    Anna K Greenwood, Abigail R Wark, Kohta Yoshida, Catherine L Peichel

    Current biology : CB   23 ( 19 )   1884 - 8   2013年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Although descriptions of striking diversity in animal behavior are plentiful, little is known about the mechanisms by which behaviors change and evolve between groups. To fully understand behavioral evolution, it will be necessary to identify the genetic mechanisms that mediate behavioral change in a natural context. Genetic analysis of behavior can also reveal associations between behavior and morphological or neural phenotypes, providing insight into the proximate mechanisms that control behavior. Relatively few studies to date have successfully identified genes or genomic regions that contribute to behavioral variation among natural populations or species, particularly in vertebrates. Here, we apply genetic approaches to dissect a complex social behavior that has long fascinated biologists, schooling behavior. We performed quantitative trait locus (QTL) analysis of schooling in an F2 intercross between strongly schooling marine and weakly schooling benthic sticklebacks (Gasterosteus aculeatus) and found that distinct genetic modules control different aspects of schooling behavior. Two key components of the behavior, tendency to school and body position when schooling, are uncorrelated in hybrids and map to different genomic regions. Our results further point to a genetic link between one behavioral component, schooling position, and variation in the neurosensory lateral line.

    DOI: 10.1016/j.cub.2013.07.058

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  • RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks. 査読 国際誌

    Jun Kitano, Kohta Yoshida, Yutaka Suzuki

    BMC genomics   14   214 - 214   2013年4月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    BACKGROUND: Non-coding small RNAs, ranging from 20 to 30 nucleotides in length, mediate the regulation of gene expression and play important roles in many biological processes. One class of small RNAs, microRNAs (miRNAs), are highly conserved across taxa and mediate the regulation of the chromatin state and the post-transcriptional regulation of messenger RNA (mRNA). Another class of small RNAs is the Piwi-interacting RNAs, which play important roles in the silencing of transposons and other functional genes. Although the biological functions of the different small RNAs have been elucidated in several laboratory animals, little is known regarding naturally occurring variation in small RNA transcriptomes among closely related species. RESULTS: We employed next-generation sequencing technology to compare the expression profiles of brain small RNAs between sympatric species of the Japanese threespine stickleback (Gasterosteus aculeatus). We identified several small RNAs that were differentially expressed between sympatric Pacific Ocean and Japan Sea sticklebacks. Potential targets of several small RNAs were identified as repetitive sequences. Female-biased miRNA expression from the old X chromosome was also observed, and it was attributed to the degeneration of the Y chromosome. CONCLUSIONS: Our results suggest that expression patterns of small RNA can differ between incipient species and may be a potential mechanism underlying differential mRNA expression and transposon activity.

    DOI: 10.1186/1471-2164-14-214

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  • The contribution of female meiotic drive to the evolution of neo-sex chromosomes. 査読 国際誌

    Kohta Yoshida, Jun Kitano

    Evolution; international journal of organic evolution   66 ( 10 )   3198 - 208   2012年10月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Sex chromosomes undergo rapid turnover in certain taxonomic groups. One of the mechanisms of sex chromosome turnover involves fusions between sex chromosomes and autosomes. Sexual antagonism, heterozygote advantage, and genetic drift have been proposed as the drivers for the fixation of this evolutionary event. However, all empirical patterns of the prevalence of multiple sex chromosome systems across different taxa cannot be simply explained by these three mechanisms. In this study, we propose that female meiotic drive may contribute to the evolution of neo-sex chromosomes. The results of this study showed that in mammals, the XY(1) Y(2) sex chromosome system is more prevalent in species with karyotypes of more biarmed chromosomes, whereas the X(1) X(2) Y sex chromosome system is more prevalent in species with predominantly acrocentric chromosomes. In species where biarmed chromosomes are favored by female meiotic drive, X-autosome fusions (XY(1) Y(2) sex chromosome system) will be also favored by female meiotic drive. In contrast, in species with more acrocentric chromosomes, Y-autosome fusions (X(1) X(2) Y sex chromosome system) will be favored just because of the biased mutation rate toward chromosomal fusions. Further consideration should be given to female meiotic drive as a mechanism in the fixation of neo-sex chromosomes.

    DOI: 10.1111/j.1558-5646.2012.01681.x

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  • B chromosomes have a functional effect on female sex determination in Lake Victoria cichlid fishes. 査読 国際誌

    Kohta Yoshida, Yohey Terai, Shinji Mizoiri, Mitsuto Aibara, Hidenori Nishihara, Masakatsu Watanabe, Asato Kuroiwa, Hirohisa Hirai, Yuriko Hirai, Yoichi Matsuda, Norihiro Okada

    PLoS genetics   7 ( 8 )   e1002203   2011年8月

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    担当区分:筆頭著者   記述言語:英語   掲載種別:研究論文(学術雑誌)  

    The endemic cichlid fishes in Lake Victoria are a model system for speciation through adaptive radiation. Although the evolution of the sex-determination system may also play a role in speciation, little is known about the sex-determination system of Lake Victoria cichlids. To understand the evolution of the sex-determination system in these fish, we performed cytogenetic analysis in 11 cichlid species from Lake Victoria. B chromosomes, which are present in addition to standard chromosomes, were found at a high prevalence rate (85%) in these cichlids. In one species, B chromosomes were female-specific. Cross-breeding using females with and without the B chromosomes demonstrated that the presence of the B chromosomes leads to a female-biased sex ratio in this species. Although B chromosomes were believed to be selfish genetic elements with little effect on phenotype and to lack protein-coding genes, the present study provides evidence that B chromosomes have a functional effect on female sex determination. FISH analysis using a BAC clone containing B chromosome DNA suggested that the B chromosomes are derived from sex chromosomes. Determination of the nucleotide sequences of this clone (104.5 kb) revealed the presence of several protein-coding genes in the B chromosome, suggesting that B chromosomes have the potential to contain functional genes. Because some sex chromosomes in amphibians and arthropods are thought to be derived from B chromosomes, the B chromosomes in Lake Victoria cichlids may represent an evolutionary transition toward the generation of sex chromosomes.

    DOI: 10.1371/journal.pgen.1002203

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  • Heritable differences in schooling behavior among threespine stickleback populations revealed by a novel assay. 査読 国際誌

    Abigail R Wark, Anna K Greenwood, Elspeth M Taylor, Kohta Yoshida, Catherine L Peichel

    PloS one   6 ( 3 )   e18316   2011年3月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)  

    Identifying the proximate and ultimate mechanisms of social behavior remains a major goal of behavioral biology. In particular, the complex social interactions mediating schooling behavior have long fascinated biologists, leading to theoretical and empirical investigations that have focused on schooling as a group-level phenomenon. However, methods to examine the behavior of individual fish within a school are needed in order to investigate the mechanisms that underlie both the performance and the evolution of schooling behavior. We have developed a technique to quantify the schooling behavior of an individual in standardized but easily manipulated social circumstances. Using our model school assay, we show that threespine sticklebacks (Gasterosteus aculeatus) from alternative habitats differ in behavior when tested in identical social circumstances. Not only do marine sticklebacks show increased association with the model school relative to freshwater benthic sticklebacks, they also display a greater degree of parallel swimming with the models. Taken together, these data indicate that marine sticklebacks exhibit a stronger tendency to school than benthic sticklebacks. We demonstrate that these population-level differences in schooling tendency are heritable and are shared by individuals within a population even when they have experienced mixed-population housing conditions. Finally, we begin to explore the stimuli that elicit schooling behavior in these populations. Our data suggest that the difference in schooling tendency between marine and benthic sticklebacks is accompanied by differential preferences for social vs. non-social and moving vs. stationary shelter options. Our study thus provides novel insights into the evolution of schooling behavior, as well as a new experimental approach to investigate the genetic and neural mechanisms that underlie this complex social behavior.

    DOI: 10.1371/journal.pone.0018316

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書籍等出版物

  • 生物の科学 遺伝 Vol. 66 No. 2

    吉田恒太, 岡田典弘( 担当: 共著 ,  範囲: pp153-158「性決定システムの進化:ビクトリア湖産シクリッドにおけるB染色体の性決定における機能獲得」)

    NTS  2012年 

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MISC

  • Gene Flow and Sex Chromosome Evolution

    Tomotaka Matsumoto, Kohta Yoshida, Jun Kitano

    GENES & GENETIC SYSTEMS   91 ( 6 )   357 - 357   2016年12月

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    記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:GENETICS SOC JAPAN  

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  • Hybrid sterility and functional diversification of a chromatin binding protein in threespine sticklebacks

    Kohta Yoshida, Asano Ishikawa, Takashi Makino, Jun Kitano

    GENES & GENETIC SYSTEMS   90 ( 6 )   380 - 380   2015年12月

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    記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:GENETICS SOC JAPAN  

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  • Test of link between evolution of heterochromatin-binding protein and hybrid sterility in threespine sticklebacks

    Kohta Yoshida, Asano Ishikawa, Takashi Makino, Jun Kitano

    GENES & GENETIC SYSTEMS   89 ( 6 )   288 - 288   2014年12月

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    記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:GENETICS SOC JAPAN  

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  • 利己的な遺伝因子と性染色体進化との強い結びつき (特集 性決定メカニズムの多様性と進化)

    吉田 恒太

    生物科学   65 ( 3 )   146 - 154   2014年2月

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    記述言語:日本語   出版者・発行元:日本生物科学者協会 ; 1949-  

    CiNii Article

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  • The neo-sex-chromosome formation drove the evolution of protein-coding sequences and transcriptome in three-spine sticklebacks

    Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Masakado Kawata, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

    GENES & GENETIC SYSTEMS   88 ( 6 )   356 - 356   2013年12月

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    記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:GENETICS SOC JAPAN  

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  • Chromosome evolution of the cichlid fishes from Lake Victoria

    K. Yoshida, A. Kuroiwa, Y. Terai, S. Mizoiri, M. Aibara, N. Kobayashi, Y. Matsuda, N. Okada

    INTEGRATIVE AND COMPARATIVE BIOLOGY   49   E329 - E329   2009年2月

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    記述言語:英語   掲載種別:研究発表ペーパー・要旨(国際会議)   出版者・発行元:OXFORD UNIV PRESS INC  

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講演・口頭発表等

  • Pristionchus属線虫における温度感受性確率的性決定の進化機構

    吉田恒太

    線虫研究の未来を創る会2024  2024年8月 

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    開催年月日: 2024年8月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • 線虫の染色体数の変化にともなう種分化、ゲノム進化、性決定の進化 招待

    吉田恒太

    第26回日本進化学会神奈川大会  2024年8月 

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    開催年月日: 2024年8月

    記述言語:日本語   会議種別:口頭発表(招待・特別)  

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  • Evolution of androdioecy was involved in acquisition of thermosensitive stochastic sex determination in Pristionchus nematodes

    Kohta Yoshida

    EvoWorm 2024  2024年6月 

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    開催年月日: 2024年6月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • 線虫を用いた種分化研究の新しい展開 招待

    吉田恒太

    統合進化科学セミナー  2024年6月 

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    開催年月日: 2024年6月

    記述言語:英語   会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 線虫でせまる種の起源:大規模ゲノム構造進化が引き起こした種分化 招待

    吉田恒太

    北里大学セミナー  2023年11月 

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    開催年月日: 2023年11月

    記述言語:日本語   会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 線虫における染色体融合が 引き起こした組み換え率の進化と種分化

    吉田恒太

    染色体学会第74回年会  2023年10月 

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    開催年月日: 2023年10月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • Evolution of androdioecy was involved in sex chromosome turnover and evolution of sex determination in Pristoncus nematodes

    Kohta Yoshida, Ralf J. Sommer

    The 4th international Pristionchus meeting  2023年9月 

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    開催年月日: 2023年9月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • Chromosome evolution played multiple roles in speciation in nematodes 招待

    Kohta Yoshida

    8th Asia-Pacific Chromosome Colloquium  2023年9月 

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    開催年月日: 2023年9月

    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • Genome-structural evolution during speciation in Pristionchus nematodes 招待

    Kohta Yoshida

    日本遺伝学会 第95回大会  2023年9月 

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    開催年月日: 2023年9月

    記述言語:英語   会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • 多様性研究のための線虫-プリスティオンクス属の種分化遺伝学を例に

    吉田恒太

    日本進化学会第25回沖縄大会  2023年8月 

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    開催年月日: 2023年8月 - 2023年9月

    記述言語:日本語   会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • Evolution of sex determination in Pristionchus nematodes

    Kohta Yoshida

    線虫研究の未来を創る会 2023  2023年8月 

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    開催年月日: 2023年8月

    記述言語:英語   会議種別:ポスター発表  

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  • Chromosome fusions facilitating speciation of the nematodes

    Kohta Yoshida, Ralf J. Sommer

    SMBE 2023  2023年7月 

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    開催年月日: 2023年7月

    記述言語:英語   会議種別:ポスター発表  

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  • 生物多様性の起源にせまる:線虫の種文化遺伝学の確立 招待

    吉田恒太

    新潟脳神経研究会特別例会  2023年7月 

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    開催年月日: 2023年7月

    記述言語:日本語   会議種別:口頭発表(招待・特別)  

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  • Evolutionary link between androdioecy and evolution of sex determination

    Kohta Yoshida

    Tree of Sex v2.0 Kick-off meeting  2023年6月 

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    開催年月日: 2023年6月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • Genome-structural evolution involved in origin of species 招待

    吉田恒太

    第4回生命科学概論  2023年6月 

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    開催年月日: 2023年6月

    記述言語:日本語   会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • Chromosomal fusions repatterned recombination rate and drove speciation in nematodes

    Yoshida K, Sommer R. J

    Gordon Reseach Conference, speciation 2023  2023年1月 

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    開催年月日: 2023年1月 - 2023年2月

    記述言語:英語   会議種別:ポスター発表  

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  • Chromosomal fusions repatterned recombination rate and drove speciation in nematodes

    Yoshida K, Sommer R. J

    Gordon Reseach Seminar, speciation 2023  2023年1月 

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    開催年月日: 2023年1月

    記述言語:英語   会議種別:ポスター発表  

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  • 線虫研究で『種の起源』のゲノム基盤に迫る 招待

    吉田恒太

    第18回細胞生物学研究室セミナー(広島大学)  2022年9月 

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    開催年月日: 2022年9月

    記述言語:日本語   会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • 線虫の種分化を促進したゲノム構造進化 招待

    吉田恒太

    生命科学セミナー(東北大学)  2022年9月 

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    開催年月日: 2022年9月

    記述言語:英語   会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • ‘Experimental Speciation Genetics’ for demonstration of the genomic basis of speciation 招待

    Kohta Yoshida

    Symposium "New Frontiers in Genetics"  2022年9月 

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    開催年月日: 2022年9月

    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • Speciation and evolution of androdioecy affected by rapid chromosomal evolution in Pristionchus nematodes.

    吉田恒太

    線虫研究の未来を創る会  2022年8月 

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    開催年月日: 2022年8月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • Genome-structural evolution facilitating speciation in nematodes 招待

    Kohta Yoshida

    IEB Seminar, University of Edinburgh  2022年6月 

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    開催年月日: 2022年6月

    記述言語:英語   会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • Genome-structural evolution driving speciation in nematodes 招待

    Kohta Yoshida

    The 20th Biological Webinar, National Institute of Genetics  2021年12月 

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    開催年月日: 2021年12月

    記述言語:英語   会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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  • Pristionchus線虫の近縁種でせまる種分化を促進するゲノム構造変化 招待

    吉田恒太

    第44回日本分子生物学会年会  2021年12月 

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    開催年月日: 2021年12月

    記述言語:日本語   会議種別:口頭発表(招待・特別)  

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  • Speciation genetics of Pristionchus nematodes revealed a role of genome-structural evolution in speciation

    吉田恒太

    The 2nd International Prstionchus Meeting  2021年10月 

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    開催年月日: 2021年10月

    記述言語:英語   会議種別:口頭発表(招待・特別)  

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  • Evolution of genome structure facilitating speciation in Pristionchus

    吉田恒太

    線虫研究の未来を創る会 2021  2021年8月 

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    開催年月日: 2021年8月 - 2021年9月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • 系統比較解析で迫る 染色体進化の方向性と機能

    吉田恒太

    日本進化学会第23回東京大会  2021年8月 

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    開催年月日: 2021年8月

    記述言語:日本語   会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • Chromosome-wide translocation repatterned recombination rates and accumulated reproductive isolations during nematode speciation

    Kohta Yoshida, Christian Rödelsperger, Ralf J. Sommer

    The 2nd AsiaEvo Conference  2021年8月 

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    開催年月日: 2021年8月

    記述言語:英語   会議種別:シンポジウム・ワークショップ パネル(公募)  

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  • Recombination rate repatterning and accumulation of reproductive barriers by chromosome-wide translocation during speciation of nematodes

    Kohta Yoshida, Christian Rödelsperger, Ralf J. Sommer

    Evolution 2021  2021年6月 

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    開催年月日: 2021年6月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • Speciation genomics and evolution of reproduction mode in Pristionchus nematodes 招待

    Kohta Yoshida, Christian Rödelsperger, Ralf J. Sommer

    日本進化学会第21回大会  2019年8月 

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    開催年月日: 2019年8月

    記述言語:日本語   会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • Hybrid introgression analysis for identification of genes for hermaphroditism in Pristionchus nematodes

    Kohta Yoshida, Ralf J. Sommer

    SHOW 2018  2018年2月 

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    開催年月日: 2018年2月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • 核型進化の確率モデル

    吉田恒太, 北野潤

    日本遺伝学会第88回大会  2016年9月 

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    開催年月日: 2016年9月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • 核型進化の確率モデル

    吉田恒太, 北野潤

    日本進化学会第18回大会  2016年8月 

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    開催年月日: 2016年8月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • トゲウオ科魚類近縁種間の雑種不稔とクロマチン結合タンパク質の機能的分化

    吉田恒太, 石川麻乃, 牧野能士, 北野潤

    日本遺伝学会第87回大会  2015年9月 

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    開催年月日: 2015年9月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • トゲウオ科魚類近縁種間の雑種不稔とクロマチン結合タンパク質の機能的分化

    吉田恒太, 石川麻乃, 牧野能士, 北野潤

    日本進化学会第17回大会  2015年8月 

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    開催年月日: 2015年8月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • A rapidly evolving heterochromatin-binding protein and hybrid male sterility in the Japanese Threespine Stickleback species pair

    Kohta Yoshida, Asano Ishikawa, Takashi Makino, Jun Kitano

    The 8th International Stickleback Conference  2015年7月 

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    開催年月日: 2015年7月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • トゲウオ科魚類イトヨにおける雑種不稔の原因遺伝子の探索 招待

    吉田恒太

    第47回日本魚類学会年会  2014年11月 

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    開催年月日: 2014年11月

    記述言語:日本語   会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • トゲウオ科魚類イトヨにおける雑種不稔の原因遺伝子の探索 招待

    Kohta Yoshida, Asano Ishikawa, Takashi Makino, Jun Kitano

    日本遺伝学会第86回大会  2014年9月 

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    開催年月日: 2014年9月

    記述言語:日本語   会議種別:口頭発表(招待・特別)  

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  • トゲウオ科魚類の比較ゲノム解析により明らかになった性染色体の転換と種間のゲノム分化との関係 招待

    吉田恒太

    日本進化学会第16回大会  2014年8月 

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    開催年月日: 2014年8月

    記述言語:日本語   会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • トゲウオ科魚類の種分化に貢献した性染色体の進化 招待

    吉田恒太

    FresHU F3 Green Symposia Series #6「性染色体が生まれるとき」  2014年3月 

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    開催年月日: 2014年3月

    記述言語:日本語   会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • トゲウオ科魚類における新しい性染色体領域の出現は遺伝子のアミノ酸配列と発現量の進化を促進した

    吉田恒太, 牧野能士, 山口勝司, 重信秀治, 長谷部光泰, 河田雅圭, 豊田敦, 藤山秋佐夫, 北野潤

    日本遺伝学会第85回大会  2013年9月 

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    開催年月日: 2013年9月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • Sex chromosome turnover in Japanese threespine sticklebacks 招待

    Kohta Yoshida

    International Mini Symposium of Correlative Gene System "Mechanisms and Function of Sex Chromsome Turnover  2013年5月 

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    開催年月日: 2013年5月

    記述言語:英語   会議種別:シンポジウム・ワークショップ パネル(指名)  

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  • 利己的な遺伝因子のメス減数分裂ドライブによる新しい性決定システムの出現

    吉田恒太, 北野潤

    日本進化学会第14回大会  2012年8月 

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    開催年月日: 2012年8月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • Sex chromosome evolution and speciation in the sympatric pair of Japanese threespine sticklebacks

    Kohta Yoshida, Takashi Makino, Katsushi Yamaguchi, Shuji Shigenobu, Mitsuyasu Hasebe, Seiichi Mori, Catherine L Peichel, Masakado Kawata, Atsushi Toyoda, Asao Fujiyama, Jun Kitano

    The 7th International Stickleback Conference  2012年7月 

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    開催年月日: 2012年7月 - 2012年8月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • ヴィクトリア湖産シクリッドのもつB染色体の性決定における機能獲得

    吉田恒太, 寺井洋平, 溝入真治, 相原光人, 渡邉正勝, 西原秀典, 黒岩麻里, 平井啓久, 平井百合子, 松田洋一, 岡田典弘

    第62回染色体学会年会  2011年11月 

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    開催年月日: 2011年11月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • B chromosomes have gained a function in sex determination in Lake Victoria cichlids

    Kohta Yoshida, Yohey Terai, Asato Kuroiwa, Shinji Mizoiri, Mitsuto Aibara, Hidenori Nishihara, Hirohisa Hirai, Yuriko Hirai, Yoichi Matsuda, Norihiro Okada

    SMBE 2011  2011年7月 

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    開催年月日: 2011年7月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • シクリッドの適応放散に貢献したB染色体

    吉田恒太, 黒岩麻里, 寺井洋平, 溝入真治, 相原光人, 平井啓久, 平井百合子, 西原秀典, 小林直樹, 松田洋一, 岡田典弘

    日本進化学会第12回大会  2010年8月 

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    開催年月日: 2010年8月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • Chromosome evolution of the cichlid fishes from Lake Victoria

    Kohta Yoshida, Asato Kuroiwa, Yohey Terai, Shinji Mizoiri, Mitsuto Aibara, Naoki Kobayashi, Yoichi Matsuda, Norihiro Okada

    The 3rd Asian Chromosome Colloquium  2008年12月 

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    開催年月日: 2008年12月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • ヴィクトリア湖産シクリッドにおける染色体の急速な進化

    吉田恒太, 黒岩麻里, 寺井洋平, 溝入真治, 相原光人, 小林直樹, 松田洋平, 岡田典弘

    日本進化学会第10回大会  2008年8月 

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    開催年月日: 2008年8月

    記述言語:日本語   会議種別:口頭発表(一般)  

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  • Karyotype evolution of cichlid fishes in East African Lakes, Evolution

    Kohta Yoshida, Asato Kuroiwa, Naoki Kobayashi, Norihiro Okada

    Evolution 2007  2007年6月 

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    開催年月日: 2007年6月

    記述言語:英語   会議種別:口頭発表(一般)  

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  • Chromosome evolution and speciation in genomics era 招待

    Kohta Yoshida

    IOS (integration of speciation research) online seminar  2023年4月 

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    記述言語:英語   会議種別:公開講演,セミナー,チュートリアル,講習,講義等  

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▶ 全件表示

受賞

  • 研究奨励賞

    2023年9月   日本進化学会   「種分化を促進したゲノム構造進化の解明」

    吉田恒太

     詳細を見る

  • ネクストリーダー賞

    2021年9月   線虫研究の未来を創る会 2021   口頭発表「Evolution of genome structure facilitating speciation in Pristionchus」

    吉田恒太

     詳細を見る

  • BP(ベストペーパー)賞

    2015年9月   日本遺伝学会第87回大会   口頭発表「トゲウオ科魚類近縁種間の雑種不稔とクロマチン結合タンパク質の機能的分化」

    吉田恒太, 石川麻乃, 牧野能士, 北野潤

     詳細を見る

  • BP(ベストペーパー)賞

    2013年9月   日本遺伝学会第85回大会   口頭発表「トゲウオ科魚類における新しい性染色体領域の出現は遺伝子のアミノ酸配列と発現量の進化を促進した」

    吉田恒太, 牧野能士, 山口勝司, 重信秀治, 長谷部光泰, 河田雅圭, 豊田敦, 藤山秋佐夫, 北野潤

     詳細を見る

共同研究・競争的資金等の研究

  • 線虫の染色体操作による実験的種分化遺伝学の確立

    研究課題/領域番号:23K19388

    2023年8月 - 2025年3月

    制度名:科学研究費助成事業

    研究種目:研究活動スタート支援

    提供機関:日本学術振興会

    吉田 恒太

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    配分額:2860000円 ( 直接経費:2200000円 、 間接経費:660000円 )

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  • 生殖システム進化を駆動するゲノム変化の原理解明と操作

    2018年 - 2023年

    制度名:CREST

    研究種目:ゲノムスケールのDNA 設計・合成による細胞制御技術の創出

    提供機関:科学技術振興機構

    吉田恒太

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    担当区分:研究分担者 

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  • トゲウオ科魚類における雑種不稔の原因遺伝子の探索

    研究課題/領域番号:14J06972

    2014年4月 - 2016年9月

    制度名:科学研究費助成事業 特別研究員奨励費

    研究種目:特別研究員奨励費

    提供機関:日本学術振興会

    吉田 恒太

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    配分額:4940000円 ( 直接経費:3800000円 、 間接経費:1140000円 )

    雑種が子孫を残せなくなる雑種不稔は種分化の決定因子である。これまで実験動物を中心にその原因遺伝子の研究が進められてきたが、実際に種分化の過程にある野外生物での研究は乏しい。われわれは野外で同所的に生息しており最近に分化した二種のトゲウオ科魚類イトヨに着目し、その雑種不稔の原因遺伝子の同定を目的に解析を進めてきた。
    先行研究により明らかになっていた原因領域には複数の遺伝子が含まれており、そこから候補を絞り込む必要があった。われわれはこの領域における精巣に発現し、急速に進化しているクロマチン結合ドメインをもった遺伝子を同定した(以下、遺伝子Aとする)。既知の雑種不和合に関わる遺伝子は同様の特徴を有することからこの遺伝子は強い候補だと考えられる。初年度、次年度の研究により、我々はこの遺伝子のタンパク質が二種で全く異なるヒストン結合性をもつことや核内でのタンパク質の局在も二種間で異なることを明らかにしてきた。
    最終年度では遺伝子Aのトランスクリプトーム解析と精巣の表現型への影響の解析、また進化的研究を進めた。複数の時期のイトヨのトランスクリプトーム解析の結果、遺伝子Aは雑種不稔のあらわれはじめる精巣の発生後期において二種間での発現の違いがあらわれることが明らかになった。表現型への影響の解析では、野生型においてCRISPR/Cas9システムを用いた遺伝子Aの遺伝子破壊を行い、精巣における影響を解析した。サンプル数がいまだ少ないものの、いくらかのサンプルにおいて雑種不稔に似た空洞化した精巣を観察した。進化的研究では遺伝子Aのある領域のシンテニーを複数の生物種で調べ、この遺伝子のオーソログが魚類において倍化し、その一方である遺伝子Aが魚類全体で急速に進化していることがわかった。この現象はショウジョウバエでもみられる現象であり、雑種不稔の原因遺伝子の一般的傾向を示している可能性がある。

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  • ゲノム解読による外来種の適応メカニズムの解明

    2014年4月 - 2015年3月

    制度名:中部科学技術センター学術奨励研究助成金

    提供機関:公益財団法人中部科学技術センター

    吉田恒太

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    担当区分:研究代表者 

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  • 性染色体の出現と進化の分子機構の解析

    研究課題/領域番号:09J08867

    2009年 - 2010年

    制度名:科学研究費助成事業 特別研究員奨励費

    研究種目:特別研究員奨励費

    提供機関:日本学術振興会

    吉田 恒太

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    配分額:2000000円 ( 直接経費:2000000円 )

    当該研究の目的は、ヴィクトリア湖産シクリッドにおいて発見された新しい性染色体についてその進化の分子機構を解析することである。前年度において、その染色体はB染色体という特殊な染色体であることがわかった。B染色体は昆虫において性染色体の起源だといわれており、性染色体とB染色体の双方の性質をもった染色体の発見は脊椎動物の性染色体進化の研究において大きな重要性をもっている。当該年度において、この染色体の配列解析を行い、B染色体でははじめてとなる100kb以上の配列の解析に成功した。B染色体はこれまでほとんど遺伝子を含まないと考えられてきたが、今回の配列解析により、このB染色体は形態形成に関わる遺伝子を含む複数の遺伝子を含み、かつそれらは非常に保存されていることがわかった。さらに、この複数の遺伝子はそれぞれがB染色体で重複していることがわかり、B染色体は予想以上にたくさんの遺伝子で占められていることが明らかとなった。性決定遺伝子の候補遺伝子は現在見つかっておらず、さらなる配列の解析が必要である。現時点では、その機構の全貌が明らかになるところまではいかなかったが、本研究により、新しい性染色体ができる一つのメカニズムとして、遺伝子を大量に含むB染色体が性決定の機能を獲得するという全く新しい知見が明らかとなった。この発見は、動物、植物を含む多くの生物種における性染色体の出現の進化機構を明らかにする上で非常に重要であり、今後の性決定の研究に大きな飛躍を与えるものである。

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