魚類多様性の進化ダイナミクス: 網羅的大規模分子系統樹からのアプローチ

2008 Fiscal Year Annual Research Report

• Project/Area Number: 19207007
• Research Institution: The University of Tokyo
• Principal Investigator: 西田 睦 The University of Tokyo, 海洋研究所, 教授 (90136896)
• Co-Investigator(Kenkyū-buntansha): 馬渕 浩司 東京大学, 海洋研究所, 助教 (50401295)
• Keywords: 進化 / 魚類 / ミトコンドリア / 多様性 / 分子系統 / メダカ / トゲウオ / シクリッド

Research Abstract

平成20年度は、昨年度に引き続き、スズキ類(Percomorpha)魚類のミトコンドリア(ミト)ゲノム全長塩基配列のデータ収集を行ったが、平行して行ったスズキ類の特定の一部を対象とした系統解析において、魚類学上重要な成果をいくつか得ることができた。代表的な成果としては、実験モデル生物として近年重要性がさらに増している2種類の魚類、メダカとトゲウオの系統的位置に関する成果が挙げられる。メダカを含むメダカ亜目は、ダツ類に近いという説とカダヤシ類に近いという説があったが、これまでの短い部分塩基配列に基づく解析では統計的に信頼のおける結果が得られていなかった。今回、ミトゲノム全長塩基配列に基づく解析を行ったところ、メダカ亜目は、カダヤシ類より、サンマやトビウオを含むダツ類により近いことが高い信頼性を持って提示された。更に、これらのスズキ類内部における系統的位置に注目すると、メダカやサンマ、トビウオ、カダヤシを含むトウゴロウイワシ系は、適応放散のモデル生物として注目されているシクリッド類とかなり近縁であることが判明した。一方、トゲウオの系統的位置に関しても新たな知見が得られた。これまでトゲウオ科の中で最も初期に分化したのは、これと姉妹群関係にあるクダヤガラ類と類似した細長い体型を持つS, spinachia であると考えられていたが、ミトゲノム全長配列と11個の核遺伝子に基づいた解析を行ったところS, spinachia は、トゲウオ科の中で最も派生的な種として位置づけられた。この結果は、トゲウオ科魚類の進化的柔軟性を示しており、今後トゲウオ類のゲノム進化を検証する上で非常に興味深い知見であるといえる。

Research Products

• [Journal Article] Evolution of multiple phosphodiesterase isoforms in stickleback invoIved in cAMP signal transduction pathway. (2009)
  • Author(s): Sato, Y. , Y. Hashiguchi, and M. Nishida.
  • Journal Title: BMC Systems Biology 3 Pages: 23
  • Peer Reviewed
• [Journal Article] Different hatching strategisc in embryos of two species, pacific herring Clupea pallasii and Japanese anchovy Engraulis japonicus, that belong tu the same order Clupeiformes, and their environmental adaptation. (2009)
  • Author(s): Kawaguchi, M. , H. Fujita, N. Yoshizaki, J. Hiroi, H. Okouchi, Y. Nagakura, T. Noda, S. Watanabe, S. Katayama, S. Iwamuro, M. Nishida, I. Iuchi, and S. Yasumasu.
  • Journal Title: Journal of Experimental Zoology, Part B: Molecular and Developmental Evolution 312B Pages: 95-107
  • Peer Reviewed
• [Journal Article] Explosive speciation of Takifugu: another use of fugu as a model system for evolutionary biology. (2009)
  • Author(s): Yamanoue, Y. , M. Miya, K. Matsuura, S. Miyazawa, N. Tsukamoto, H. Doi, H. Takahashi, K. Mabuchi, M. Nishida, and H. Sakai.
  • Journal Title: Molecular Biology and Evolution 26 Pages: 623-629
  • Peer Reviewed
• [Journal Article] Unique patterns of pelvic fin evolution: a case study of balistoid fishes (Pisces: Tetraodontiformes) based on whole mitochondrial genome sequences. (2009)
  • Author(s): Yamanoue, Y. , M. Miya, K. Matsuura, H. Sakai, M. Katoh, and M. Nishida.
  • Journal Title: Molecular Phylogenetics and Evolution 50 Pages: 179-189
  • Peer Reviewed
• [Journal Article] Stickleback phylogenies resoIved: Evidence from mitochondrial genomes and 11 nuclear genes. (2009)
  • Author(s): Kawahara, R. , M. Miya, K. Mabuchi, T. J. Near, and M. Nishida.
  • Journal Title: Molecular Phylogenetics and Evolution 50 Pages: 401-404
  • Peer Reviewed
• [Journal Article] Deep-Sea mystery solved: astonishing larval transformations and extreme sexual dimorphism unite three fish families. (2009)
  • Author(s): Jolmson, G. D. , J. R. Paxton, T. T. Sutton, T. P. Satoh, T. Sado, M. Nishida, and M. Miya.
  • Journal Title: Biology Letters 5 Pages: 235-239
  • Peer Reviewed
• [Journal Article] Hatching enzyme of the ovoviviparous black rockfish Sebasts shflegelii-enovironmental adaptation of the hatching enzyme and evolutionary aspects of formation of the pseudogene. (2008)
  • Author(s): Kawaguchi, M. , M. Nakagawa, T. Noda, N. Yoshizaki, J. Hiroi, M. Nishida, I. Iuchi, and S. Yasumasu
  • Journal Title: FEBS Journal 275 Pages: 2884-2898
  • Peer Reviewed
• [Journal Article] Evolutionary patterns and selective pressures of odorant/pheromone receptor gene families in teleost fishes. (2008)
  • Author(s): Hashiguchi, Yasuyuk, Yoshimi Furuta, and Mutsumi Nishida.
  • Journal Title: PloS ONE 3 Pages: e4083
  • Peer Reviewed
• [Journal Article] Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, Silversides, and their relatives) : The first evidence based on whole mitogenome sequences. (2008)
  • Author(s): Setiamarga, I)avin, H. E. , Masaki Miya, Yusuke Yamanoue, Kohji Mabuchi, Takashi P. Satoh, Jun G Inoue, Mutsumi Nishida.
  • Journal Title: Molecular Phylogenetics and Evolution 49 Pages: 598-605
  • Peer Reviewed
• [Journal Article] Isolation and characterization of 15microsatellite loci for the Japanese gudgeon Sarcocheilichthys variegatus. (2008)
  • Author(s): Fujita, S. , T. Komiya, H. Takeshima, K. Watanabe, and M. Nishida.
  • Journal Title: Molecular Ecology Resources 8 Pages: 1335-1337
  • Peer Reviewed
• [Journal Article] Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences. (2008)
  • Author(s): Azuma, Y. , Y. Kumazawa, M. Miya, K. Mabuchi, and M. Nishida.
  • Journal Title: BMC Evolutionary Biology 8 Pages: 215
  • Peer Reviewed
• [Journal Article] A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification? (2008)
  • Author(s): Yamanoue, Y. , M. Miya, K. Matsuura, M. Katoh, H. Sakai, and M. Nishida.
  • Journal Title: BMC Evolutionary Biology 8 Pages: 212
  • Peer Reviewed
• [Journal Article] The phylogenetic position of an undescribed paedomorphic clupeiform: Mitogenomic evidence. (2008)
  • Author(s): Lavoue, S. , M. Miya, A. Kawaguchi, T. Yoshino and M. Nishida.
  • Journal Title: Ichthyolqgical Research 55 Pages: 328-334
  • Peer Reviewed
• [Journal Article] Heterotypy in N-terminal region of Growth/Differentiation Factor5 (GDF5) mature protein during evolution of teleosts. (2008)
  • Author(s): Fujimura, K. , Y. Terai, N. Ishiguro, M. Miya, M. Nishida, and N. Okada.
  • Journal Title: Molecular Biology and Evolution 25 Pages: 797-800
  • Peer Reviewed
• [Journal Article] Monophyly, phylogenetic position and inter-familial relationships of the Alepocephaliformes (Teleostei) based on whole mitogenome sequences. (2008)
  • Author(s): Lavoue, S. , M. Miya, J. Y. Poulsen, P. R. Moller, and M. Nishida.
  • Journal Title: Molecular Phylogenetics and Evolution 47 Pages: 1111-1121
  • Peer Reviewed
• [Journal Article] Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives) : a new pespective based on whole mitogerlme sequences from 75 higher teleosts. (2008)
  • Author(s): Kawahara, R. , M. Miya, K. Mabuchi, S. Lavoue, J. G. Inoue, T. P. Satoh, A. Kawaguchi, and M. Nishida.
  • Journal Title: Molecular Phylogenetics and Evolution 46 Pages: 224-236
  • Peer Reviewed
• [Journal Article] Isolation and characterisation of 39 microsatellite loci in the endangered Japanese loach Leptobotia curta. (2008)
  • Author(s): Watanabe, K. , H. Takeshima, A. Iwata, T. Abe, K. Uehara, R. Kakioka, D. Kihira, and M. Nishida.
  • Journal Title: Molecular Ecology Notes 8 Pages: 145-148
  • Peer Reviewed
• [Journal Article] Isolation and characterization of microsatellite loci in the cichlid fish in Lake Victoria, Haplochlomis chilotes. (2008)
  • Author(s): Maeda, K. , H. Takeshima, S. Mizoiri, N. Okada, M. Nishida, and H. Tachida.
  • Journal Title: Molecular Ecology Notes 8 Pages: 428-430
• [Journal Article] Mitochondrial DNA analysis reveals cryptic large-scale invasion of non-native genotypes of common carp Cyprinus caprio in Japan. (2008)
  • Author(s): Mabuchi, K. , H. Senou, and M. Nishida.
  • Journal Title: Molecular Ecology 17 Pages: 796-806
  • Peer Reviewed
• [Journal Article] Population structure of two closely related pelagic cichlids in Lake Victoria, Haplochromis pyrrhocephalus and H. laparogramma.
  • Author(s): Maeda, K. , M. Takeda, K. Kamiya, M. Aibara, S. I. Mzighani, M. Nishida, S. Mizoiri, T. Sato, Y. Terai, N. Okada, and H. Tachida.
  • Journal Title: Gene (in press)
  • Peer Reviewed
• [Journal Article] Screening the V2R-type putative odorant receptor gene repertoire in Bitterling Tanakia Lanceolata.
  • Author(s): Hashiguchi, Y. and M. Nishida.
  • Journal Title: Gene (in press)
  • Peer Reviewed
• [Journal Article] Electric charge divergence in proteins: insights into the evolution of their three-dimensional properties
  • Author(s): Sato, Y. and M. Nishida.
  • Journal Title: Gene (in press)
  • Peer Reviewed
• [Journal Article] Isolation and characterization of 13 microsatellite loci in the nine-spined stickleback (Pungitius pungitius) and cross-species amplification in 5 stickleback species (family Gasterosteidae).
  • Author(s): Meguro, Y. , H. Takahashi, H. Takeshima, M. Nishida, and A. Goto.
  • Journal Title: Conservation Genetics Resources (in press)
  • Peer Reviewed
• [Journal Article] Genetic population structure of a reef goby, Bathygobius cocosensis, in the northwestern Pacific.
  • Author(s): Mukai, T. , S. Nakamura, and M. Nishida.
  • Journal Title: Ichthyological Research (in press)
  • Peer Reviewed
• [Journal Article] The historical bigeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha).
  • Author(s): Inoue, J. G. , Y. Kumazawa, M. Miya, and M. Nishida.
  • Journal Title: Molecular Phylogenetics and Evolution (in press)
  • Peer Reviewed
• [Journal Article] Reconstructing thr phylogenetic relationships of the earth's most diverseclade of freshwater fishes-Order Cypriniformes (Actinopterygii: Ostariophysi): A case ctudy using multiple nuclear loci and the mitochondrial genome.
  • Author(s): Mayden, R. L. , Wei-Jen Chen, H. L. Bart, M. H. Doosey, A. M. S. , K. L. Tang, R. M. Wood, M. K. Agnew, L. Yang, M. V. Hirt, M. D. Clements, K. Saitoh, T. Sado, M. Miya, and M. Nishida.
  • Journal Title: Molecular Phylogenetics and Evolution (in press)
• [Journal Article] Molecular approaches to the study of biological invasions: applicability to ecosystem management. (In Japanese with English abstract)
  • Author(s): Nishikawa, Y. , R. Yonekura, K. Iwasaki, M. Nishida, K. Kawamura, and H. Kawai.
  • Journal Title: Japanese Journal of Ecology (in press)
• [Presentation] トラフグ・インスリン様成長因子1のイントロン配列および各種成長関連遺伝子の仔魚期における発現量と成長との関連. (2009)
  • Author(s): 古川聡史・黒須洋平・木下滋晴・金子元・武島弘彦・西田睦・渡部終五
  • Organizer: 日本水産学会春季大会
  • Place of Presentation: 東京
  • Year and Date: 20090300
• [Presentation] Microsatellite and mitochondrial DNA analyses for genetic diversity between two closely related Takifugu pufferfish, torafugu T. rubripes and karasu T. chinensis. (2009)
  • Author(s): R. , Md. Shaheed, S. Furukawa, T. Mochizuki, H. Doi, M. Nishida, and S. watabe
  • Organizer: 日本水産学会春季大会
  • Place of Presentation: 東京
  • Year and Date: 20090300
• [Presentation] 共生褐虫藻から探るムカデミノウミウシと褐虫藻の共生関係の進化. (2008)
  • Author(s): 依籐実樹子・川原玲香・馬渕浩司・渡邉俊樹・西田睦
  • Organizer: 日本サンゴ礁学会大会
  • Place of Presentation: 静岡
  • Year and Date: 20081100
• [Presentation] サンゴ白化現象早期診断のためのストレスバイオマーカー遺伝子の探索. (2008)
  • Author(s): 伊藤吉彦・湯山育子・渡邉俊樹・西田睦
  • Organizer: 日本サンゴ礁学会大会
  • Place of Presentation: 静岡
  • Year and Date: 20081100
• [Presentation] Zooplankton community genomics-beyond barcoding of marine animals. (2008)
  • Author(s): Machida, R. J. , Y. Hashiguchi, M. Nishida, and S. Nishida
  • Organizer: 50th Anniversary Symposium of SCOR (Science Committee on Ocean Research)
  • Place of Presentation: Woods Hole, MA, USA
  • Year and Date: 20081000
• [Presentation] Significance of intensive and extensive genetic analysis of species and their natural populations. (2008)
  • Author(s): Nishida, Mutsumi.
  • Organizer: Fifth World Fisheries Congress
  • Place of Presentation: Yokohama
  • Year and Date: 20081000
• [Presentation] The structural integration of insulin-like growth factor-1 and 2 genes and their regulatory regions in torafugu pufferfish Takifugu rubripes inmlicated for fast growth. (2008)
  • Author(s): Furukawa, S. , H. Takeshima, M. Nishida, and S. Watabe.
  • Organizer: Fifth World Fisheries Congress
  • Place of Presentation: Yokohama
  • Year and Date: 20081000
• [Presentation] 孵化酵素LCA魚種特異的卵膜分解. (2008)
  • Author(s): 川口眞理・清水昭男・廣井準也・井内一郎・安増茂樹・西田睦
  • Organizer: 東京大学生命科学ネットワークシンポジウム2008
  • Place of Presentation: 東京
  • Year and Date: 20080900
• [Presentation] 魚類の進化を探る: その多様性への多面的アプローチ (2008)
  • Author(s): 西田 睦
  • Organizer: 日本動物学会大会
  • Place of Presentation: 福岡
  • Year and Date: 20080900
• [Presentation] ニシン目に属する2魚種ニシンとカタクチイワシにおける異なる環境に適応した孵化戦略 (2008)
  • Author(s): 川口眞理・藤田英明・吉崎範夫・廣井準也・岩室祥一・井内一郎・安増茂樹・西田睦
  • Organizer: 日本動物学会大会
  • Place of Presentation: 福岡
  • Year and Date: 20080900
• [Presentation] アユの適応遺伝子探索におけるHiCEP法の有効性の検証. (2008)
  • Author(s): 武島弘彦・東陽一郎・井口恵一朗・西田睦
  • Organizer: 日本魚類学会年会
  • Place of Presentation: 松山
  • Year and Date: 20080900
• [Presentation] AFLP分析によって明らかになったトラフグ属魚類の自然種間交雑. (2008)
  • Author(s): 善家裕太朗・高橋洋・酒井治己・土井啓行・松浦啓一・西田睦
  • Organizer: 日本魚類学会年会
  • Place of Presentation: 松山
  • Year and Date: 20080900
• [Presentation] 琵琶湖におけるコイの日本在来mtDNAハプロタイプの分布. (2008)
  • Author(s): 馬渕浩司・瀬能宏・武島弘彦・中井克樹・西田睦
  • Organizer: 日本魚類学会年会
  • Place of Presentation: 松山
  • Year and Date: 20080900
• [Presentation] イトヨ自然集団における嗅覚受容体遺伝子ファミリーの適応進化. (2008)
  • Author(s): 橋口康之・西田睦
  • Organizer: 日本魚類学会年会
  • Place of Presentation: 松山
  • Year and Date: 20080900
• [Presentation] ミトコンドリアゲノムと11の核遺伝子配列から明らかになったトゲウオ亜目魚類の系統関係. (2008)
  • Author(s): 川原玲香・宮正樹・馬渕浩司・西田睦
  • Organizer: 日本魚類学会年会
  • Place of Presentation: 松山
  • Year and Date: 20080900
• [Presentation] 幼形進化的シラスウオ属魚類の起源: ミトコシドリアゲノム全長配列による分子系統解析. (2008)
  • Author(s): 昆健志・宮正樹・R. Lukas・中谷将典・佐藤崇・吉野哲夫・西田睦
  • Organizer: 日本魚類学会年会
  • Place of Presentation: 松山
  • Year and Date: 20080900
• [Presentation] ミトコンドリアゲノム全塩基配列に基づくトウゴロウイウシ系魚類の分子系統. (2008)
  • Author(s): D. H. E. SETIAMARGA・宮正樹・山野上祐介・馬渕浩司・佐藤崇・井上潤・西田睦
  • Organizer: 日本魚類学会年会
  • Place of Presentation: 松山
  • Year and Date: 20080900
• [Presentation] ダルマガレイ科魚類におけるミトコンドリアゲノムの進化. (2008)
  • Author(s): 佐藤崇・宮正樹・西田睦
  • Organizer: 日本魚類学会年会
  • Place of Presentation: 松山
  • Year and Date: 20080900
• [Presentation] Mitogenomic evidence reveals large genetic divergence between two populations of Pantodon buchholzi. (2008)
  • Author(s): Lavoue, S. , M. Miya, and M. Nishida.
  • Organizer: Fourth International Conference of the Pan African Fish and Fisheries Association
  • Place of Presentation: Ethiopia
  • Year and Date: 20080900
• [Presentation] 祖先配列の最尤推定に基づくPGIおよびALDタンパク質電荷の進化解析 (2008)
  • Author(s): 佐藤行人・西田睦
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京
  • Year and Date: 20080800
• [Presentation] イトヨ嗅覚受容体遺伝子群における適応進化の網羅的検索 (2008)
  • Author(s): 橋口康之・西田睦
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京
  • Year and Date: 20080800
• [Presentation] 養鶏進化に隠された多様性: サンゴ礁性シラスウオ属魚類に発見された多くの隠蔽種 (2008)
  • Author(s): 昆健志・吉野哲夫・向井貴彦・西田睦
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京
  • Year and Date: 20080800
• [Presentation] 卵膜タンパク質と孵化酵素の"分子共進化"?: 孵化酵素LCEの魚種特異的卵膜分解. (2008)
  • Author(s): 川口眞理・清水昭男・廣井準也・井内一郎・安増茂樹・西田睦
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京
  • Year and Date: 20080800
• [Presentation] 魚類特異的ゲノム倍化に由来する多数の重複適伝子の"sub-neofunctionalization"による存続. (2008)
  • Author(s): 佐藤行人・橋口康之・西田睦
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京
  • Year and Date: 20080800
• [Presentation] 硬骨魚類の分岐年代推定におけるシクリッド系統地理の有効性. (2008)
  • Author(s): 東陽一郎・熊澤慶伯・宮正樹・馬渕浩司・西田睦
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京
  • Year and Date: 20080800
• [Presentation] 「ありふれた魚」に隠されていた大きな集団分化: 東アジアのフナの分子系統地理. (2008)
  • Author(s): 高田未来美・立原一憲・昆健志・山本軍次・西田睦
  • Organizer: 日本進化学会第10回大会
  • Place of Presentation: 東京
  • Year and Date: 20080800
• [Presentation] Mitogenomic evaluation of historical biogeography of cichlids toward reliable dating of teleostean divergences. (2008)
  • Author(s): Azuma, Y. , Y. Kumazawa, M. Miya, K. Mabuchi, and M. Nishida
  • Organizer: Society for Molecular Biology and Evolution
  • Place of Presentation: Barcelona, Spain
  • Year and Date: 20080600
• [Book] 生物系統地理学-種の起源をさぐる (2008)
  • Author(s): ジョン・C・エイビス著, 西田睦 ・武藤文人(監訳)
  • Total Pages: 303
  • Publisher: 東京大学出版会