Development of fish diversity studies by next-generation mitogenome sequencing: From Sanger method to massively parallel method

• Project/Area Number: 23370041
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biodiversity/Systematics
• Research Institution: University of the Ryukyus (2013); The University of Tokyo (2011-2012)
• Principal Investigator: NISHIDA Mutsumi 琉球大学, その他部局等, 理事 (90136896)
• Co-Investigator(Kenkyū-buntansha): TAKESHIMA Hirohiko 東京大学, 農学生命科学研究科, 助教 (50573086) ; MIYA Masaki 千葉県立中央博物館, 研究員 (30250137)
• Project Period (FY): 2011-04-01 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000); Fiscal Year 2013: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000); Fiscal Year 2012: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000); Fiscal Year 2011: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
• Keywords: 進化 / 集団・種多様性 / 遺伝的多様性

Research Abstract

Whole mitochondrial genome (mitogenome) sequences are extremely useful for resolving phylogenies of animals including fishes. This study aims to establish efficient procedures to obtain mitogenome data from many samples including degraded ones by using "next-generation" massively parallel sequencing technologies. For samples in good condition, long-PCR amplification/purification and parallel tagged sequencing successfully provided mitogenome data from many samples simultaneously, suggesting that this is a rather easier method for such samples. For degraded samples, many segments from mitogenome were successfully captured by using the capture-on-beads method with double indexing. Thus, we conclude that efficient procedures have been established to have large mitogenome data from many samples including degraded ones by using next-generation sequencing technologies.

Research Products

• [Journal Article] Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei) (2014)
  • Author(s): Ha Yeun Song, K. Mabuchi, T. P. Satoh, J. A. Moore, Y. Yamanoue, M. Miya, M. Nishida
  • Journal Title: Gene Volume: 542 Issue: 2 Pages: 146-155
  • DOI: 10.1016/j.gene.2014.03.040
  • Peer Reviewed
• [Journal Article] Variation in morphological characteristics of Japanese fluvial sculpin related to different environmental conditions in a single river system in eastern Japan. (2014)
  • Author(s): Natsumeda, T., T. Tsuruta, H. Takeshima, S. Awata, K. Iguchi
  • Journal Title: Ecology of Freshwater Fish Volume: 23 Issue: 2 Pages: 114-120
  • DOI: 10.1111/eff.12045
  • Peer Reviewed
• [Journal Article] Phylogeny of the Elopomorpha (Teleostei): Evidence from six nuclear and mitochondrial markers. (2014)
  • Author(s): Chen, J.-N., Lopez, J.A., Lavoue, S., Miya, M., Chen, W.-J.
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 70 Pages: 152-161
  • DOI: 10.1016/j.ympev.2013.09.002
  • Peer Reviewed
• [Journal Article] Molecular identification of species and ploidy of Carassius fishes in Lake Biwa, using mtDNA and microsatellite multiplex PCRs (2014)
  • Author(s): T. Mishina, M. Takada, H. Takeshima, M. Nakano, R. Tabata, M. Nishida, K. Watanabe
  • Journal Title: Ichthyological Research Volume: 61 Issue: 2 Pages: 169-175
  • DOI: 10.1007/s10228-014-0388-9
  • NAID: 40020049201
  • Peer Reviewed
• [Journal Article] Isolation and characterization of microsatellite loci in the Asian horn snail Batillaria attramentaria (Mollusca, Gastropod). (2014)
  • Author(s): Itoh, H., S. Kamimura, H. Takeshima, S. Kojima
  • Journal Title: Molecular Ecology Resources Volume: in press
  • Peer Reviewed
• [Journal Article] Mitogenomic evidence for an Indo-West Pacific origin of the Clupeoidei (Teleostei: Clupeiformes) (2013)
  • Author(s): Lavoué, S., Miya, M., Musikasinthorn, P., Chen, W.J. & Nishida, M.
  • Journal Title: PLoS ONE Volume: 8 Issue: 2 Pages: e56485-e56485
  • DOI: 10.1371/journal.pone.0056485
  • Peer Reviewed
• [Journal Article] Evolutionary origin of the Scombridae (tunas and mackerels) : members of a Paleogene adaptive radiation with 14 other pelagic fish families (2013)
  • Author(s): Miya, M., Friedman, M., Satoh, T.P., Takeshima, H., Sado, T., Iwasaki, W., Yamanoue, Y., Nakatani, M., Mabuchi, K., Inoue, J.G., Poulsen, J.Y., Fukunaga, T., Sato, Y. and Nishida, M
  • Journal Title: PLOS ONE Volume: 8 Issue: 9 Pages: e73535-e73535
  • DOI: 10.1371/journal.pone.0073535
  • Peer Reviewed
• [Journal Article] MitoFish and MitoAnnotator : a mitochondrial genome database of fish with an accurate and automatic annotation pipeline (2013)
  • Author(s): Iwasaki, W., Fukunaga T., Isagozawa R., Yamada K., Maeda Y., Satoh T.P., Sado T., Mabuchi K., Takeshima H., Miya, M. and Nishida M
  • Journal Title: Molecular Biology and Evolution Volume: 30 Issue: 11 Pages: 2531-2540
  • DOI: 10.1093/molbev/mst141
  • Peer Reviewed
• [Journal Article] Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei) (2013)
  • Author(s): Poulsen, J.Y., Byrkjedal I., Willassen E., Rees D., Takeshima H., Satoh T.P., Shinohara G., Nishida M. & Miya M.
  • Journal Title: BMC Evolutionary Biology Volume: 13 Issue: 1 Pages: 111-111
  • DOI: 10.1186/1471-2148-13-111
  • Peer Reviewed
• [Journal Article] Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis. (2013)
  • Author(s): Imoto, J. M., K. Saitoh, T. Sasaki, T. Yonezawa, J. Adachi, Y. P. Kartavtsev, M. Miya, M. Nishida, N. Hanzawa
  • Journal Title: Gene Volume: 514 Issue: 2 Pages: 112-124
  • DOI: 10.1016/j.gene.2012.10.019
  • Peer Reviewed
• [Journal Article] Sub-functionalization of duplicated genes in the evolution of nine-spined stickleback hatching enzyme (2013)
  • Author(s): Mari Kawaguchi
  • Journal Title: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Volume: 320 Issue: 3 Pages: 140-150
  • DOI: 10.1002/jez.b.22490
  • Peer Reviewed
• [Journal Article] Adaptive evolution of fish hatching enzyme: one amino acid substitution results in differential salt dependency of the enzyme. (2013)
  • Author(s): Kawaguchi, M., S. Yasumasu, A. Shimizu, N. Kudo, K. Sano, I. Iuchi, M. Nishida
  • Journal Title: The Journal of Experimental Biology Volume: 216 Pages: 1609-1615
  • DOI: 10.1242/jeb.069716
  • Peer Reviewed
• [Journal Article] Molecular co-evolution of a protease and its substrate elucidated by analysis of the activity of predicted ancestral hatching enzyme. (2013)
  • Author(s): Kawaguchi, M., K. Inoue, I. Iuchi, M. Nishida, S. Yasumasu
  • Journal Title: BMC Evolutionary Biology Volume: 13 Issue: 1 Pages: 231-231
  • DOI: 10.1186/1471-2148-13-231
  • Peer Reviewed
• [Journal Article] Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae). (2013)
  • Author(s): Tang, K.L., Agnew, M.K., Hirt, M.V., Lumbantobing, D.N., Raley, M.E., Sado, T., Teoh, V.-H., Yang, L., Bart, H.L., Harris, P.M., He, S., Miya, M., Saitoh, K., Simons, A.M., Wood, R.M., Mayden, R.L.
  • Journal Title: Zootaxa Volume: 3681 Pages: 101-135
  • Peer Reviewed
• [Journal Article] Molecular phylogenetic relationship of Tetraodon pufferfish based on mitochondrial DNA analysis. (2013)
  • Author(s): Igarashi Y, Doi H, Yamanoue Y, Kinoshita S, Ishibashi T, Ushio H, Asakawa S, Nishida M, Watabe S.
  • Journal Title: Fisheries Science Volume: 79 Issue: 2 Pages: 243-250
  • DOI: 10.1007/s12562-013-0598-5
  • Peer Reviewed
• [Journal Article] Pike and salmon as sister taxa: Detailed intraclade resolution and divergence time estimation of Esociformes + Salmoniformes based on whole mitochondrial genome sequences. (2013)
  • Author(s): Campbell, M.A., Lopez, J.A., Sado, T., Miya, M.
  • Journal Title: Gene Volume: 530 Issue: 1 Pages: 57-65
  • DOI: 10.1016/j.gene.2013.07.068
  • Peer Reviewed
• [Journal Article] Remarkable consistency of exon-intron structure of hatching enzyme genes and molecular phylogenetic relationships of teleostean fishes (2012)
  • Author(s): Mari Kawaguchi, Sebastien Lavoue, Junya Hiroi, Hirofumi Hayano, Ichiro Iuchi, Shigeki Yasumasu, Mutsumi Nishida
  • Journal Title: Environmental Biology of Fishes Volume: (in press) Issue: 3 Pages: 567-576
  • DOI: 10.1007/s10641-011-9920-1
  • Peer Reviewed
• [Journal Article] Comparable ages for the independent origins of electrogenesis in African and South American weakly electric fishes (2012)
  • Author(s): Lavoue, S., Miya, M., Arnegard, M.E., Sullivan, J.P., Hopkins, C.D. & Nishida, M
  • Journal Title: PloS One Volume: 7 Issue: 5 Pages: e36287-e36287
  • DOI: 10.1371/journal.pone.0036287
  • Peer Reviewed
• [Journal Article] A molecular timescale for the evolution of the African freshwater fish family Kneriidae (Teleostei: Gonorynchiformes) (2012)
  • Author(s): Lavoué, S., Miya, M., Moritz, T. & Nishida, M.
  • Journal Title: Ichthyological Research Volume: 52 Issue: 2 Pages: 104-112
  • DOI: 10.1007/s10228-011-0258-7
  • NAID: 10030628297
  • Peer Reviewed
• [Journal Article] Preface: Micro-and macroevolution of fishes. (2012)
  • Author(s): M. Nishida and K. Maekawa
  • Journal Title: Environmental Biology of Fishes Volume: 94 Issue: 3 Pages: 503-504
  • DOI: 10.1007/s10641-012-0008-3
  • Peer Reviewed
• [Journal Article] A set of SNPs near or within STR regions useful for discriminating native Lake Biwa and introduced "Eurasian" strains of common carp (2012)
  • Author(s): Mabuchi, K., H. Song, H. Takeshima, and M. Nishida
  • Journal Title: Conservation Genetics Resources Volume: (in press) Issue: 3 Pages: 649-652
  • DOI: 10.1007/s12686-012-9613-x
  • Peer Reviewed
• [Journal Article] Hidden Diversity in a Reef-Dwelling Sea Slug, Pteraeolidia ianthina (Nudibranchia, Aeolidina), in the Northwestern Pacific. (2012)
  • Author(s): M. Yorifuji, H. Takeshima, K. Mabuchi, M. Nishida
  • Journal Title: Zoological Science Volume: 29 Issue: 6 Pages: 359-367
  • DOI: 10.2108/zsj.29.359
  • NAID: 40019296425
  • Peer Reviewed
• [Journal Article] Differential gene expression in juvenile polyps of the coral Acropora tenuis exposed to thermal and chemical stresses (2012)
  • Author(s): Yuyama I, Ito Y, Watanabe T, Hidaka M, Suzuki Y, Nishida M
  • Journal Title: J. Exp. Mar. Biol. Ecol Volume: 430-431 Pages: 17-24
  • DOI: 10.1016/j.jembe.2012.06.020
  • Peer Reviewed
• [Journal Article] Body plan convergence and diversity shaped by mass extinction in the evolution of skates and rays (Chondrichthyes : Batoidea) (2012)
  • Author(s): Aschliman, N.C., Nishida, M., Miya, M., Inoue, J.G., Rosana, K.M., Naylor, G.J.P.
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 63 Issue: 1 Pages: 28-42
  • DOI: 10.1016/j.ympev.2011.12.012
  • Peer Reviewed
• [Journal Article] Cryptic species of the gobioid paedomorphic genus Schindleria from Palau, western Pacific Ocean (2011)
  • Author(s): Kon, T., T.Yoshino, M.Nishida
  • Journal Title: Ichthyological Research Volume: 58 Issue: 1 Pages: 62-66
  • DOI: 10.1007/s10228-010-0178-y
  • NAID: 10028174054
  • Peer Reviewed
• [Journal Article] Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence (2011)
  • Author(s): Lavoue, S., M.Miya, M.E.Arnegard, P.B.McIntyre, V.Mamonekene, M.Nishida
  • Journal Title: Proceedings of the Royal Society B : Biological Sciences Volume: 278 Issue: 1708 Pages: 1003-1008
  • DOI: 10.1098/rspb.2010.1639
  • Peer Reviewed
• [Journal Article] Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes(Actinopterygii : Ostariophysi) (2011)
  • Author(s): Saitoh K, Sado T, Doosey MH, Bart HL, Inoue JG, Nishida M, Mayden RL and Miya M
  • Journal Title: Zoological Journal of the Linnean Society Volume: 161 Issue: 3 Pages: 633-662
  • DOI: 10.1111/j.1096-3642.2010.00651.x
  • Peer Reviewed
• [Journal Article] Multiple invasions into freshwater by pufferfishes(Teleostei : Tetraodontidae): a mitogenomic perspective (2011)
  • Author(s): Yamanoue, Y., M. Miya, H. Doi, K. Mabuchi, H. Sakai, and M. Nishida
  • Journal Title: PLoS ONE Volume: 6 Issue: 2 Pages: e17410-e17410
  • DOI: 10.1371/journal.pone.0017410
  • Peer Reviewed
• [Journal Article] Correlation of accumulated mRNA levels of growth hormone, growth hormone receptor I and insulin-like growth factor I with the larval body size of F2 offspring derived from a fast-growing strain and wild fish of torafugu Takifugu rubripes (2011)
  • Author(s): Kaneko, G., S.Furukawa, Y.Kurosu, T.Yamada, H.Takeshima, M.Nishida, T.Mitsuboshi, T.Otaka, K.hirasu, T.Koda, Y.Takemasa, S.Aki, T.Mochizuki, H.Fukushima, Y.Fukuda, S.Kinoshita, S.Asakawa, S.Watabe
  • Journal Title: Journal of Fish Biology Volume: 79 Pages: 854-874
  • Peer Reviewed
• [Journal Article] Evolutionary history of Otophysi(Teleostei), a major clade of the modern freshwater fishes : Pangaean origin and Mesozoic radiation (2011)
  • Author(s): Nakatani M, Miya M, Mabuchi K, Saitoh K and Nishida M
  • Journal Title: BMC Evolutionary Biology Volume: 11 Issue: 1 Pages: 177-177
  • DOI: 10.1186/1471-2148-11-177
  • Peer Reviewed
• [Journal Article] Low genetic differentiation between two geographically separated populations of demersal gadiform fishes in the Southern Hemisphere (2011)
  • Author(s): Takeshima, H., A.Hatanaka, S.Yamada, Y.Yamazaki, I.Kimura, M.Nishida
  • Journal Title: Genes and Genetic Systems Volume: 86 Pages: 339-349
  • NAID: 10030209981
  • Peer Reviewed
• [Journal Article] Remarkable consistency of exon-intron structure of hatching enzyme genes and molecular phylogenetic relationships of teleostean fishes
  • Author(s): Kawaguchi, M., S.Lavoue, J.Hiroi, H.Hayano, I.Iuchi, S.Yasumasu, M.Nishida
  • Journal Title: Environmental Biology of Fishes Volume: (in press)
  • Peer Reviewed
• [Journal Article] A molecular timescale for the evolution of the African freshwater fish family Kneriidae (Gonorynchiformes)
  • Author(s): Lavoue, S., M.Miya, T.Moritz, M.Nishida
  • Journal Title: Ichthyological Research Volume: (in press)
  • Peer Reviewed
• [Journal Article] Hidden diversity in a reef-dwelling sea slug, Pteraeolidia ianthina (Nudibranchia, Aeolidida), in the northwestern Pacific
  • Author(s): Yorifuji, M., H.Takeshima, K.Mabuchi, M.Nishida
  • Journal Title: Zoological Science Volume: (in press)
  • Peer Reviewed
• [Presentation] 次世代シーケンシングによるアユの集団ミトコンドリアゲノミクスへのアプローチ (2013)
  • Author(s): 武島弘彦, ら
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 神戸ポートアイランド, 兵庫県
  • Year and Date: 2013-12-03
• [Presentation] 高性能自動アノテーションパイプラインMitoAnnotatorの実装による魚類ミトコンドリアゲノムデータベースMitoFishの充実 (2013)
  • Author(s): 西田睦, ら
  • Organizer: 2013年度日本魚類学会年会
  • Place of Presentation: 宮崎観光ホテル, 宮崎県
  • Year and Date: 2013-10-05
• [Presentation] Molecular phylogenetic approach to diversity of fishes (2013)
  • Author(s): Nishida, M
  • Organizer: Gordon Research Conference "Marine Molecular Ecology"
  • Place of Presentation: The HongKong University of Science and Technology, HongKong
  • Year and Date: 2013-08-13
• [Presentation] Phylogenetics and diversification of Percomorpha-An introduction to the symposium. (2013)
  • Author(s): Miya, M. and T.J. Near.
  • Organizer: The 9th Indo-Pacific Fish Conference
  • Place of Presentation: Okinawa Convention Center, Okinawa, Japan
• [Presentation] Paleogene adaptive radiation of tunas and their pelagic relatives revealed by bioinformatic and mitogenomic analyses. (2013)
  • Author(s): Miya, M., M. Freedman, T.P. Satoh, H. Takeshima, T. Sado, Y. Yamanoue, K. Mabuchi & M. Nishida.
  • Organizer: The 9th Indo-Pacific Fish Conference
  • Place of Presentation: Okinawa Convention Center, Okinawa, Japan
• [Presentation] Molecular systematics and historical biogeography of the perch-ike fishes (Teleostei: Perciformes). (2013)
  • Author(s): Chen W.-J., S.H. Liu, R. Ruiz-Carus, S. Lavoue, M. Miya, H.-K. Mok & R.L. Mayden.
  • Organizer: The 9th Indo-Pacific Fish Conference
  • Place of Presentation: Okinawa Convention Center, Okinawa, Japan
• [Presentation] Mitochondrial phylogenomics to resolve cypriniform tree of life: Higher-level and detailed relationships inferred from over 500 sequences. (2013)
  • Author(s): Saitoh K, T. Sado, M. Nishida, R.L. Mayden, M. Miya
  • Organizer: The 9th Indo-Pacific Fish Conference
  • Place of Presentation: Okinawa Convention Center, Okinawa, Japan
• [Presentation] Phylogeny of the lefteye flounders (family Bothidae): a mitogenomic perspective. (2013)
  • Author(s): Satoh T.P., M. Miya, M. Nishida.
  • Organizer: The 9th Indo-Pacific Fish Conference
  • Place of Presentation: Okinawa Convention Center, Okinawa, Japan
• [Presentation] Dates and rates of major pelagic deep-sea fish radiations. (2013)
  • Author(s): Poulsen J.Y., M. Miya, A. Kawaguchi, T.P. Satoh, S.W. Knudsen, E. Willassen, I. Byrkjedal, M. Friedman.
  • Organizer: The 9th Indo-Pacific Fish Conference
  • Place of Presentation: Okinawa Convention Center, Okinawa, Japan
• [Presentation] Mitogenomic phylogeny of acanthuroid fishes (Actinopterygii: Perciformes) and evolutionary origins of distinct larvae. (2013)
  • Author(s): Yamanoue Y., M. Miya, K. Mabuchi, M. Nishida
  • Organizer: The 9th Indo-Pacific Fish Conference
  • Place of Presentation: Okinawa Convention Center, Okinawa, Japan
• [Presentation] A ‘living-fossil’ eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau. (2013)
  • Author(s): Johnson G.D., H. Ida, J.Sakaue, T. Sado, T. Asahida, M. Miya
  • Organizer: Symposium on Systematics and Diversity of Fishes.
  • Place of Presentation: National Museum of Nature and Science, Tokyo, Japan
• [Presentation] Evolution of the paedomorphic gobioid fishes revealed by whole mitogenome sequences with supermatrix analysis. (2013)
  • Author(s): Kon, T., M. Miya, T. Sado, L. Ruber, T.P. Satoh, T. Yoshino, M. Nishida
  • Organizer: Symposium on Systematics and Diversity of Fishes.
  • Place of Presentation: National Museum of Nature and Science, Tokyo, Japan
• [Presentation] Molecular phylogenetic approach to diversity of fishes. (2013)
  • Author(s): Nishida M.
  • Organizer: Gordon Research Conference "Marine Molecular Ecology"
  • Place of Presentation: The HongKong University of Science and Technology, HongKong.
  • Invited
• [Presentation] 琵琶湖固有魚類のミトコンドリアゲノムの多試料塩基配列の同時決定と適応進化解析 (2013)
  • Author(s): 田畑諒一・武島弘彦・平瀬祥太朗・西田睦・渡辺勝敏
  • Organizer: NGS現場の会 第三回研究会
  • Place of Presentation: 神戸国際会議場
• [Presentation] 次世代シーケンサーによる魚類ミトコンドリアゲノミクス：Parallel Tag Sequencingのプロトコル確立 (2013)
  • Author(s): 平瀬祥太朗・武島弘彦・西田睦・岩崎渉
  • Organizer: NGS現場の会 第三回研究会
  • Place of Presentation: 神戸国際会議場
• [Presentation] 高性能自動アノテーションパイプラインMitoAnnotatorの実装による魚類ミトコンドリアゲノムデータベースMitoFishの充実． (2013)
  • Author(s): 西田 睦・福永 津嵩・砂子澤 遼太・山田 浩一郎・佐藤 崇・佐土 哲也・宮 正樹・武島 弘彦・馬渕 浩司・前田 泰伸・岩崎 渉
  • Organizer: 2013年度日本魚類学会年会
  • Place of Presentation: 宮崎観光ホテル、宮崎県
• [Presentation] ハゼ亜目魚類の多様化プロセス：ミトゲノム全長配列とSupermatrix法による網羅的系統解析 (2013)
  • Author(s): 昆 健志・佐土 哲也・L. Ruber ・佐藤 崇・吉野哲夫・西田 睦・宮 正樹
  • Organizer: 2013年度日本魚類学会年会
  • Place of Presentation: 宮崎観光ホテル、宮崎県
• [Presentation] 次世代シーケンシングによる魚類の大量ミトコンドリアゲノム分析法の確立 (2013)
  • Author(s): 武島弘彦・平瀬祥太朗・岩崎渉・田畑諒一・渡辺勝敏・西田睦
  • Organizer: 2013年度日本魚類学会年会
  • Place of Presentation: 宮崎観光ホテル、宮崎県
• [Presentation] 琵琶湖における多倍数性フナ類の遺伝的構造 (2013)
  • Author(s): 三品達平・田畑諒一・中野光議・高田未来美・武島弘彦・西田睦・渡辺勝敏
  • Organizer: 2013年度日本魚類学会年会
  • Place of Presentation: 宮崎観光ホテル、宮崎県
• [Presentation] 琵琶湖固有魚類の起源と進化：ミトコンドリアゲノムにおける適応進化の可能性 (2013)
  • Author(s): 田畑諒一・武島弘彦・平瀬祥太朗・西田睦・柿岡諒・小宮竹史・渡辺勝敏
  • Organizer: 2013年度日本魚類学会年会
  • Place of Presentation: 宮崎観光ホテル、宮崎県
• [Presentation] 日本在来コイのレフュージアとしての琵琶湖 (2013)
  • Author(s): 馬渕浩司・ソン ハヨン・武島弘彦・中井克樹・瀬能宏・西田睦
  • Organizer: 2013年度日本魚類学会年会
  • Place of Presentation: 宮崎観光ホテル、宮崎県
• [Presentation] 南シナ海沿岸魚類の多様性形成史に関する比較系統地理学的研究（予報） (2013)
  • Author(s): 武藤望生・高木映・本村浩之・緒方悠香・S. Pornpatimakorn ・R. Babaran ・佐藤崇・武島弘彦・武藤文人・石川智士
  • Organizer: 2013年度日本魚類学会年会
  • Place of Presentation: 宮崎観光ホテル、宮崎県
• [Presentation] MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. (2013)
  • Author(s): Iwasaki, W., T. Fukunaga, R. Isagozawa, K. Yamada, Y. Maeda, T.P. Satoh, T. Sado, K. Mabuchi, H. Takeshima, M. Miya, M. Nishida
  • Organizer: 日本バイオインフォマティクス学会2013年年会
  • Place of Presentation: タワーホール船堀、東京都
• [Presentation] 次世代シーケンシングによるアユの集団ミトコンドリアゲノミクスへのアプローチ (2013)
  • Author(s): 武島弘彦・平瀬祥太朗・岩崎渉・井口恵一朗・西田睦
  • Organizer: 第36回日本分子生物学会年会
  • Place of Presentation: 神戸ポートアイランド、兵庫県
• [Presentation] 東日本大震災が三陸アユの遺伝的集団構造に与えた影響 (2012)
  • Author(s): 武島弘彦・山野目健・淀太我・関野静雄・畑正好・大竹二雄・西田睦
  • Organizer: 平成24年度日本水産学会春季大会
  • Place of Presentation: 東京海洋大学(品川キャンパス),東京都
  • Year and Date: 2012-03-27
• [Presentation] 津波に被災したアユ地域個体群の動態予想 (2012)
  • Author(s): 井口恵一朗・山野目健・淀太我・関野静雄・武島弘彦・畑正好・大竹二雄・西田睦
  • Organizer: 平成24年度日本水産学会春季大会
  • Place of Presentation: 東京海洋大学(品川キャンパス),東京都
  • Year and Date: 2012-03-27
• [Presentation] ムカデミノウミウシに潜む遺伝的多様性 (2012)
  • Author(s): 依藤 実樹子・武島弘彦・馬渕浩司・西田 睦
  • Organizer: 日本貝類学会2012年度大会
  • Place of Presentation: 東京家政学院， 東京
• [Presentation] Phylogenetic analysis of syngnathoid fishes based on whole mitochondrial genome sequences:Limits and intrarelationships of the "Syngnathoidei". (2012)
  • Author(s): H. Song, K. Mabuchi, T. P. Satoh, M. Miya, M. Nishida
  • Organizer: Fish Barcode of Life World Conference
  • Place of Presentation: 麗水（Yeosu), Korea
• [Presentation] Fish mitochondrial phylogenomics and DNA barcoding. (2012)
  • Author(s): M. Nishida and M. Miya
  • Organizer: Fish Barcode of Life World Conference
  • Place of Presentation: 麗水（Yeosu), Korea
  • Invited
• [Presentation] Lake Biwa as a refuge of native Japanese common carp (2012)
  • Author(s): K. Mabuchi, H. Song, H. Takeshima, K. Nakai, H. Senou and M. Nishida
  • Organizer: 2012 ASLO Aquatic Sciences Meeting
  • Place of Presentation: Lake Biwa, Otsu, Shiga, Japan
• [Presentation] 福井県三方湖周辺水域におけるフナの遺伝的個体群構造 (2012)
  • Author(s): 武島弘彦・松崎慎一郎・高田未来美・児玉晃治・前田英章・西田 睦
  • Organizer: 第19回信州魚類研究会
  • Place of Presentation: 信州大農学部付属野辺山農場，長野県南佐久郡
• [Presentation] 遺伝分析から見た三方湖周辺水域におけるフナの種内系統構成 (2012)
  • Author(s): 武島弘彦
  • Organizer: 三方湖自然再生フォーラム
  • Place of Presentation: 福井県三方青年の家，福井県
• [Presentation] 琉球列島におけるフナの分布と生息場所：在来フナと移植フナの比較（日本魚類学会論文賞） (2012)
  • Author(s): 高田未来美・立原一憲・西田 睦
  • Organizer: 2012年度日本魚類学会年会
  • Place of Presentation: 水産大学校，山口県下関市
• [Presentation] ベトナムで採集された分布域最南端のアユの遺伝的特徴 (2012)
  • Author(s): 武島弘彦・Hau D. TRAN・木下 泉・井口恵一朗・西田 睦
  • Organizer: 2012年度日本魚類学会年会
  • Place of Presentation: 水産大学校，山口県下関市
• [Presentation] 核遺伝子配列から推定された日本産ヨシノボリ属魚類の系統関係 (2012)
  • Author(s): 山﨑 曜・西田 睦・鈴木寿之・向井貴彦・渡辺勝敏
  • Organizer: 2012年度日本魚類学会年会
  • Place of Presentation: 水産大学校，山口県下関市
• [Presentation] Multiplex PCR判別法を用いた琉球列島在来・移植フナの判別とそれらの分布の詳細 (2012)
  • Author(s): 高田未来美・立原一憲・西田 睦
  • Organizer: 2012年度日本魚類学会年会
  • Place of Presentation: 水産大学校，山口県下関市
• [Presentation] ミトコンドリアゲノム全長配列から推定されたダルマガレイ科魚類の系統関係 (2012)
  • Author(s): 佐藤 崇・宮 正樹・西田 睦
  • Organizer: 2012年度日本魚類学会年会
  • Place of Presentation: 水産大学校，山口県下関市
• [Presentation] バイカルカジカ類の進化研究の面白さ. 2012年度日本魚類学会年会（シンポジウム「バイカル湖におけるカジカ類の起源，適応放散と種分化」総合議論） (2012)
  • Author(s): 西田睦
  • Organizer: 2012年度日本魚類学会年会
  • Place of Presentation: 水産大学校，山口県下関市
• [Presentation] 馬渕浩司：バイカルカジカ類の種間系統を解く試みから. 2012年度日本魚類学会年会（シンポジウム「バイカル湖におけるカジカ類の起源，適応放散と種分化」総合議論） (2012)
  • Author(s): 馬渕浩司
  • Organizer: 2012年度日本魚類学会年会
  • Place of Presentation: 水産大学校，山口県下関市
• [Presentation] Phylogenetic analysis of syngnathoid fishes based on whole mitochondrial genome sequences : a contribution to understanding fish diversity (2011)
  • Author(s): Hayeun SONG, Kohji MABUCHI, Takashi SATOH, Masaki MIYA, Mutsumi NISHIDA
  • Organizer: 第3回日韓(AORI-KIOS)海洋科学シンポジウム
  • Place of Presentation: 東京大学大気海洋研究所,千葉県柏市
  • Year and Date: 2011-11-10
• [Presentation] 魚類のミトコンドリア進化ゲノミクス:10年の軌跡と到達点 (2011)
  • Author(s): 宮正樹・西田睦
  • Organizer: 2011年度日本魚類学会年会「セッション:ミトコンドリアゲノミクスにもとづく魚類の系統進化研究:成果と展望」
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-10-01
• [Presentation] ミトコンドリアゲノム全長塩基配列に基づくヨウジウオ亜目魚類の系統解析:亜目の枠組みと内部の系統関係 (2011)
  • Author(s): ソンハヨン・馬渕浩司・佐藤崇・宮正樹・西田睦
  • Organizer: 2011年度日本魚類学会年会「セッション:ミトコンドリアゲノミクスにもとづく魚類の系統進化研究:成果と展望」
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-10-01
• [Presentation] ミトコンドリアゲノム全長配列によるハゼ亜目魚類の分子系統解析:幼形進化的シラスウオ属魚類の起源を中心に (2011)
  • Author(s): 昆健志・宮正樹・佐土哲也・Lukas Ruber・中谷将典・佐藤崇・吉野哲夫・西田睦
  • Organizer: 2011年度日本魚類学会年会「セッション:ミトコンドリアゲノミクスにもとづく魚類の系統進化研究:成果と展望」
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-10-01
• [Presentation] ミトコンドリアゲノム全長塩基配列にもとづくフグ目魚類の系統解析:姉妹群探索から淡水種の起源推定まで (2011)
  • Author(s): 山野上祐介・宮正樹・松浦啓一・酒井治己・西田睦
  • Organizer: 2011年度日本魚類学会年会「セッション:ミトコンドリアゲノミクスにもとづく魚類の系統進化研究:成果と展望」
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-10-01
• [Presentation] 魚類のミトコンドリアゲノムにおける遺伝子配置の多様性とその進化 (2011)
  • Author(s): 佐藤崇・宮正樹・馬渕浩司・西田睦
  • Organizer: 2011年度日本魚類学会年会「セッション:ミトコンドリアゲノミクスにもとづく魚類の系統進化研究:成果と展望」
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-10-01
• [Presentation] ミトコンドリアゲノム全長配列に基づく魚類の分岐年代推定 (2011)
  • Author(s): 井上潤・宮正樹・西田睦
  • Organizer: 2011年度日本魚類学会年会「セッション:ミトコンドリアゲノミクスにもとづく魚類の系統進化研究:成果と展望」
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-10-01
• [Presentation] 魚類のミトコンドリア進化ゲノミクス:今後の展望 (2011)
  • Author(s): 西田睦・武島弘彦・馬渕浩司・宮正樹
  • Organizer: 2011年度日本魚類学会年会「セッション:ミトコンドリアゲノミクスにもとづく魚類の系統進化研究:成果と展望」
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-10-01
• [Presentation] 福井県三方湖周辺水域におけるフナ地域個体群の種内系統構成 (2011)
  • Author(s): 武島弘彦・松崎慎一郎・児玉晃治・前田英章・西田睦
  • Organizer: 2011年度日本魚類学会年会
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-09-30
• [Presentation] フナ種群Carassius auratus-complexにおける主要系統のさらなる探索 (2011)
  • Author(s): 高田未来美・酒井治己・高橋洋・井口恵一朗・横山良太・渡辺勝敏・柿岡諒・伊藤明・山崎裕治・張春光・趙亜輝・S.F.Safronov・V.G.Sideleva・立原一憲・後藤晃・西田睦
  • Organizer: 2011年度日本魚類学会年会
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-09-30
• [Presentation] ミトゲノム解析に基づくコイ科ウグイ亜科魚類の系統地理 (2011)
  • Author(s): 井元順一・斉藤憲治・佐々木剛・足立淳・K.Yuri・宮正樹・西田睦・半澤直人
  • Organizer: 2011年度日本魚類学会年会
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-09-30
• [Presentation] マイクロサテライト隣接領域の一塩基多型を用いたコイの在来系統の識別 (2011)
  • Author(s): 馬渕浩司・ソンハヨン・武島弘彦・中井克樹・瀬能宏・西田睦
  • Organizer: 2011年度日本魚類学会年会
  • Place of Presentation: 弘前大学,青森県弘前市
  • Year and Date: 2011-09-30
• [Presentation] 孵化酵素の環境適応～1つのアミノ酸変異による至適塩濃度の違い～ (2011)
  • Author(s): 川口眞理・井内一郎・西田睦・安増茂樹
  • Organizer: 日本動物学会第82回旭川大会
  • Place of Presentation: 旭川市大雪クリスタルホール,北海道旭川市
  • Year and Date: 2011-09-21
• [Presentation] ミトゲノム超行列による巨大クレードの包括的な進化史解明:コイ目魚類を例に (2011)
  • Author(s): 宮正樹・佐土哲也・斎藤憲治・西田睦
  • Organizer: 日本進化学会第13回大会
  • Place of Presentation: 京都大学百周年時計台記念館,京都市
  • Year and Date: 2011-07-30
• [Presentation] 孵化酵素と卵膜の分子共進化 (2011)
  • Author(s): 川口眞理・西田睦・安増茂樹
  • Organizer: 日本進化学会第13回大会
  • Place of Presentation: 京都大学百周年時計台記念館,京都市
  • Year and Date: 2011-07-30
• [Presentation] リュウキュウアユと私たち (2011)
  • Author(s): 西田睦
  • Organizer: リュウキュウアユを蘇生させる会20周年記念,シンポジウムin沖縄
  • Place of Presentation: 名護市民会館中ホール,沖縄県
  • Year and Date: 2011-06-11
• [Presentation] 生物学的比較の基礎としての系統枠 (2011)
  • Author(s): 西田睦
  • Organizer: 第11回東京大学生命科学シンポジウム
  • Place of Presentation: 東京大学安田講堂(東京都)(招待講演)
  • Year and Date: 2011-06-04
• [Presentation] カタナメクジウオ属Epigonichthys(頭索動物亜門)の分子系統解析と琉球列島からの日本記録種発見 (2011)
  • Author(s): 昆健志・西田睦・西川輝昭
  • Organizer: 沖縄生物学会第48回大会
  • Place of Presentation: 琉球大学理学部複合棟102教室・大学会館,沖縄県
  • Year and Date: 2011-06-04