A mitogenomic supermatrix approach to resolve phylogeny and evolution of species-rich clades: Development of method and its applications to fishes

• Project/Area Number: 22370035
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biodiversity/Systematics
• Research Institution: Natural History Museum and Institute, Chiba
• Principal Investigator: MASAKI Miya 千葉県立中央博物館, 自然誌・歴史研究部・動物学研究科, 科長 (30250137)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥18,720,000 (Direct Cost: ¥14,400,000、Indirect Cost: ¥4,320,000); Fiscal Year 2012: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2011: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2010: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
• Keywords: 遺伝子 / 動物 / ゲノム / 進化 / 分類学 / ミトコンドリアゲノム / 超行列 / 系統解析 / 高次分類 / 最尤法 / 魚類 / 起源

Research Abstract

Resolution of phylogenetic relationships among members of a species-rich clade is inherently difficult because it requires longer sequences from a large number of taxa. Freshwater fishes of the order Cypriniformes represent one of such species-rich clades, with over 4,000 species currently recognized that have been placed in 6+ families, each with poorly defined subfamilies and/or tribes. This study attempted comprehensive resolution of the cypriniform phylogenies by combining a mitogenomic tree as a backbone constraint for the robust higher-level relationships and numerous partial sequences downloaded from GenBank for the reconstruction of lower-level relationships within the constrained clades. Also this supermatrix approaches were applied to fishes of Gobioidei and Otophysi, both including numerous species (ca. 2,000 spp. and 8,000 spp, respectively) and exhibiting different habitat preferences (principally marine vs. freshwater). The mitogenomic tree of the Cypriniformes was based on 602 sequences (including 6 outgroups) and the resulting best-scoring ML tree is congruent with the previous molecular phylogenies based on both mitogenomes and nuclear genes. A total of 17,057 partial sequences from cypriniforms were available from GenBank and they were sorted into 9 mitochondrial genes from 1,073 species, of which 1,039 species were those from the cyt b gene alone. 機関番号：８２５０３ 研究種目：基盤研究 (B) 研究期間：2011～2013 年 課題番号：22370035 研究課題名（和文）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：方法論の確 立と実際 研究課題名（英文）A mitogenomic supermatrix approach to resolve phylogeny and evolution of species-rich clades: Development of method and its applications to fishes 研究代表者 宮 正樹（Masaki Miya） 千葉県立中央博物館・自然誌・歴史研究部・動物学研究科・科長 研究者番号：30250137 The supermatrix was constructed by combining 602 mitogenomic and 1,073 partial sequences and it was subjected to partitioned ML analysis using the mitogenomic tree as a backbone constraint. The best-scoring ML tree derived from 24 runs using a fast bootstrap (BS) option in RAxML places all species from the partial sequences (1,073 spp.) in reasonable positions, with 62.2% of the internal branches being supported by .80% BS probabilities. In addition whole mitogenome sequences from 152 gobioid and 120 otophysan were assembled to provide robust phylogenies for these groups of fishes and the trees will be used in the subsequent supermatrix analyses.

Research Products

• [Journal Article] Mitogenomic evidence for an Indo-West Pacific origin of the Clupeoidei (Teleostei: Clupeiformes) (2013)
  • Author(s): Lavoue, S., Miya, M., Musikasinthorn, P., Chen, W.J. & Nishida, M
  • Journal Title: PloS One Volume: 8
  • 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., Saitoh, K., Sasaki, T., Yonezawa, Adachi, J., Kartavtsev, Y.P., Miya, M., Nishida, M. & Hanzawa, N.
  • Journal Title: Gene Volume: 514 Pages: 112-124
  • 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] 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] Phylogenetic placements of the barbin genera Discherodontus, Chagunius, and Hypselobarbus in the subfamily Cyprininae (Teleostei: Cypriniformes) and their relationships with other barbins. (2012)
  • Author(s): Yang, L., Hirt, M.V., Sado, T., Arunachalam, M., Tang, K.L., Manickam, R., Simons, A.M., Wu, H.-H., Mayden, R.L. & Miya, M.
  • Journal Title: Zootaxa Volume: 3586 Pages: 26-40
  • Peer Reviewed
• [Journal Article] Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes). (2012)
  • Author(s): Yang, L., Arunachalam, M., Sado, T., Levin, B.A., Golubtsov, A.S., Freyhof, J., Friel, J.P., Chen, W.J., Vincent Hirt, M., Manickam, R., Agnew, M.K., Simons, A.M., Saitoh, K., Miya, M., Mayden, R.L. & He, S
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 65 Pages: 362-379
  • 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): Lavoue, S., Miya, M., Moritz, T. & Nishida, M
  • Journal Title: Ichthyological Research Volume: 52 Pages: 1-9
  • NAID: 10030628297
  • Peer Reviewed
• [Journal Article] Inoue, J.G., Rosana, K.M. & Naylor, G.J.P. 2012. 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 Pages: 28-42
  • Peer Reviewed
• [Journal Article] A 'living fossil' eel (Anguilliformes: Protanguillidae, fam. nov.)from an undersea cave in Palau. (2012)
  • Author(s): Johnson, G.D., Ida, H., Sakaue, J., Sado, T., Asahida, T. & Miya, M
  • Journal Title: Proceedings of the Royal Society B Volume: 279 Pages: 934-943
  • Peer Reviewed
• [Journal Article] Phylogenetic placements of the barbin genera Discherodontus, Chagunius, and Hypselobarbus in the subfamily Cyprininae (Teleostei: Cypriniformes) and their relationships with other barbins (2012)
  • Author(s): Yang, L., Hirt, M.V., Sado, T., Arunachalam, M., Tang, K.L., Manickam, R., Simons, A.M., Wu, H.-H., Mayden, R.L. & Miya, M.
  • Journal Title: Zootaxa Volume: 3586 Pages: 26-40
  • Peer Reviewed
• [Journal Article] Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes) (2012)
  • Author(s): Yang, L., Sado, T., Levin, B.A., Golubtsov, A.S., Freyhof, J., Friel, J.P., Chen, W.J., Vincent Hirt, M. & Manickam, R., Agnew, M.K., Saitoh, K., Miya, M., Mayden, R.L. & He, S.
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 65 Issue: 2 Pages: 362-379
  • DOI: 10.1016/j.ympev.2012.06.007
  • 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] 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] A 'living fossil' eel (Anguilliformes : Protanguillidae, fam.nov.) from an undersea cave in Palau (2012)
  • Author(s): Johnson, G.D., Ida, H., Sakaue, J., Sado, T., Asahida, T., Miya, M.
  • Journal Title: Proceedings of the Royal Society B Volume: 279 Issue: 1730 Pages: 934-943
  • DOI: 10.1098/rspb.2011.1289
  • Peer Reviewed
• [Journal Article] Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae) (2011)
  • Author(s): Tang, K.L., Agnew, M.K., Chen, W.J., Hirt, M.V., Raley, M.E., Sado, T., Schneider, L.M., Yang, L., Bart, H.L., He, S., Liu, H., Miya, M., Saitoh, K., Simons, A.M., Wood, R.M. & Mayden, R.L.
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 61 Pages: 103-124
  • 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. & Nishida, M
  • Journal Title: BMC Evolutionary Biology Volume: 11 Pages: 177-177
  • Peer Reviewed
• [Journal Article] Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence (2011)
  • Author(s): Lavoue, S., Miya, M., Arnegard, M.E., McIntyre, P.B., Mamonekene, V. & Nishida, M
  • Journal Title: Proceedings of the Royal Society B Volume: 278 Pages: 1003-1008
  • 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, M.H., Bart, H.L., Inoue, J.G., Nishida, M., Mayden, R.L., Nishida, M. & Miya, M.
  • Journal Title: Zoological Journal of the Linnean Society Volume: 161 Pages: 633-662
  • Peer Reviewed
• [Journal Article] Multiple invasions into freshwater by pufferfishes (Teleostei: Tetraodontidae): a mitogenomic perspective (2011)
  • Author(s): Yamanoue, Y., Miya, M., Doi, H., Mabuchi, K., Sakai, H. & Nishida, M.
  • Journal Title: PloS One Volume: 6
  • Peer Reviewed
• [Journal Article] Phylogeny of the gudgeons (Teleostei : Cyprinidae : Gobioninae) (2011)
  • Author(s): Tang, K.L., Miya, M., Saitoh, K., Simons, A.M., Wood, R.M., Mayden, R.L.
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 61 Issue: 1 Pages: 106-124
  • DOI: 10.1016/j.ympev.2011.05.022
  • 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] Multiple invasions into freshwater by pufferfishes(Teleostei : Tetraodoxrtidae) : a mitogenomic eperspective (2011)
  • Author(s): Yamanoue, Y., Miya, M., Doi, H., Mabuchi, K., Sakai, H., Nishida, M
  • Journal Title: PLoS ONE Volume: 6
  • Peer Reviewed
• [Journal Article] Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time andplace of basal divergence of cypriniform fishes(Actinopterygii : Ostariophysi) (2011)
  • Author(s): Saitoh, K., T.Sado, M.H.Doosey, H.L.Bart, Jr., Jun G.moue, R.L.Mayden, M.Nishida, M.Miya
  • Journal Title: Zoological Journal of the Linnean Society Volume: 161 Pages: 633-662
  • Peer Reviewed
• [Journal Article] Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective (2010)
  • Author(s): Inoue, J.G., Miya, M., Lam, K., Tay, B.-H., Danks, J.A., Bell, J., Walker, T.I. & Venkatesh, B
  • Journal Title: Molecular Biology and Evolution Volume: 27 Pages: 2576-2586
  • Peer Reviewed
• [Journal Article] Molecular phylogeny of the fishes traditionally referred to Cyprinini sensu stricto (Teleostei: Cypriniformes) (2010)
  • Author(s): Yang, L., Mayden, R.L., Sado, T., He, S., Saitoh, K. & Miya, M.
  • Journal Title: Zoologica Scripta Volume: 39 Pages: 527-550
  • Peer Reviewed
• [Journal Article] Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae). (2010)
  • Author(s): Tang, K.L., Conway, K.W., Agnew, M.K., Chen, W.-J., Hirt, M.V., Sado, T., Schneider, L.M., Freyhof, J., Swartz, E., Vidthayanon, C., Bart, H.L., Miya, M., Saitoh, K., Simons, A.M., Wood, R.M. & Mayden, R.L
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 57 Pages: 189-214
  • Peer Reviewed
• [Journal Article] Intron-loss evolution of hatching enzyme genes in Teleostei (2010)
  • Author(s): Kawaguchi, M., Hiroi, J., Miya, M., Nishida, M., Iuchi, I. & Yasumasu, S
  • Journal Title: BMC Evolutionary Biology Volume: 10 Pages: 260-260
  • Peer Reviewed
• [Journal Article] Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation (2010)
  • Author(s): Satoh, T.P., Sato, Y., Masuyama, N., Miya, M. & Nishida, M.
  • Journal Title: BMC Genomics Volume: 11 Pages: 479-479
  • Peer Reviewed
• [Journal Article] Mitochondrial phylogenomics of anchovies (family Engraulidae) and recurrent origins of pronounced miniaturization in the order Clupeiformes (2010)
  • Author(s): Lavoue, S., Miya, M. & Nishida, M
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 56 Pages: 480-485
  • Peer Reviewed
• [Journal Article] Deep-ocean origin of the freshwater eels (2010)
  • Author(s): Inoue, J.G., Miya, M., Miller, M.J., Sado, T., Hanel, R., Hatooka, K., Aoyama, J., Minegishi, Y., Nishida, M. & Tsukamoto, K
  • Journal Title: Biology Letters Volume: 6 Pages: 363-366
  • Peer Reviewed
• [Journal Article] Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes (2010)
  • Author(s): Hirayama, M., Mukai, T., Miya, M., Murata, Y., Sekiya, Y., Yamashita, T., Nishida, M., Watabe, S., Oda, S. & Mitani, H
  • Journal Title: Gene Volume: 457 Pages: 13-24
  • Peer Reviewed
• [Journal Article] Phylogenetic relationships of catostomid Fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences (2010)
  • Author(s): Doosey, M.H., Bart, H.L., Saitoh, K. & Miya, M
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 54 Pages: 1028-1034
  • Peer Reviewed
• [Journal Article] Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective (2010)
  • Author(s): Miya, M., Pietsch, T.W., Orr, J.W., Arnold, R.J., Satoh, T.P., Shedlock, A.M., Ho, H.C., Shimazaki, M., Yabe, M. & Nishida, M
  • Journal Title: BMC Evolutionary Biology Volume: 10 Pages: 58-58
  • Peer Reviewed
• [Journal Article] Biogeography and evolution of the Carassius auratus-complex in East Asia (2010)
  • Author(s): Takada, M., Tachida, K., Kon, T., Yamamoto, G., Iguchi, K.i., Miya, M. & Nishida, M
  • Journal Title: BMC Evolutionary Biology Volume: 10 Pages: 7-7
  • Peer Reviewed
• [Journal Article] Phylogenetic relationships of catostomid Fishes (Actinopterygii : Cyprinifonnes) based on mitochondrial ND4/ND5 gene sequences (2010)
  • Author(s): Doosey, M.H., H.L.Bart, Jr., K.Saitoh, M.Miya
  • Journal Title: Molecular Phylogenetics and Evolution Volume: 54 Pages: 1028-1034
  • Peer Reviewed
• [Journal Article] Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryziaslatipes (2010)
  • Author(s): Hirayama, M., T.Mukai, M.Miya, Y.Murata, Y.Sekiya, T.Yamashita, M.Nishida, S.Watabe, S.Oda, H.Mitani
  • Journal Title: Gene Volume: 457 Pages: 13-24
  • Peer Reviewed
• [Journal Article] Phylogeny-dependent intron-loss evolution of hatching enzyme genes in Teleostei (2010)
  • Author(s): Kawaguchi, M., J.Hiroi, M.Miya, M.Nishida, I.Iuchi, S.Yasumasu
  • Journal Title: BMC Evolutionary Biology Volume: 10 Pages: 260-260
  • Peer Reviewed
• [Journal Article] Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes : a newinsight into gene order conservation (2010)
  • Author(s): Satoh, T.P., Y.Sato, N.Masuyama, M.Miya, M.Nishida
  • Journal Title: BMC Genomics Volume: 11 Pages: 479-479
  • Peer Reviewed
• [Journal Article] Evolutionary origin and phylogeny of the modem holocephalans (Chondrichthyes : Chimaeriformes) : a mitogenomic perspective (2010)
  • Author(s): Inoue, J.G., M.Miya, K.Lam, B.-H.Tay, J.A.Danks, J.Bell, T.I.Walker, B.Venkatesh
  • Journal Title: Molecular Biology and Evolution Volume: 27 Pages: 2576-2586
  • Peer Reviewed
• [Journal Article] Molecular phylogeny of the fishes traditionally referred to Cyprinini sensu stricto (Teleostei : Cyprinifonnes) (2010)
  • Author(s): Yang, L., R.L.Mayden, T.Sado, S.He, K.Saitoh, M.Miya
  • Journal Title: Zoological Scripta Volume: 39 Pages: 527-550
  • Peer Reviewed
• [Journal Article] Systematics of the subfamily Danioninae (Teleostei : Cypriniformes : Cyprinidae) (2010)
  • Author(s): Tang, K.L., K.W.Conway, M.K.Agnew, W.-J.Chen, M.V.Hirt, T.Sado, L.M.Schneider, J.Freyhof, E.Swartz, C.Vidthayanon, H.L.Bart, M.Miya, K.Saitoh, A.M.Simons, R.M.Wood, R.L.Mayden
  • Journal Title: Moleculaz Phylogenetics and Evolution Volume: 57 Pages: 189-214
  • Peer Reviewed
• [Presentation] Undetected evolutionary radiation in the pelagic realm: A novel clade in the percomorph fishes as revealed by bioinformatic and mitogenomic analyses (2013)
  • Author(s): Miya, M., Satoh, T.P., Sado, T. & Nishida, M
  • Organizer: Joint Meeting of Ichthyologists and Herpetologists
  • Place of Presentation: Vancouver, Canada
• [Presentation] Undetected evolutionary radiation in the pelagic realm: A novel clade in the percomorph fishes as revealed by bioinformatic and mitogenomic analyses (2012)
  • Author(s): Miya, M., Satoh, T.P., Sado, T. & Nishida, M
  • Organizer: Congress of Ichthyology
  • Place of Presentation: Liege, Belgium
• [Presentation] Undetected evolutionary radiation in the pelagic realm: A novel clade in the percomorph fishes as revealed by bioinformatic and mitogenomic analyses (2012)
  • Author(s): Miya, M., Satoh, T.P., Sado, T. & Nishida, M.
  • Organizer: European Congress of Ichthyology
  • Place of Presentation: Liége, Belgium
• [Presentation] Undetected evolutionary radiation in the pelagic realm: A novel clade in the percomorph fishes as revealed by bioinformatic and mitogenomic analyses (2012)
  • Author(s): Miya, M., Satoh, T.P., Sado, T. & Nishida, M.
  • Organizer: Joint Meeting of Ichthyologists and Herpetologists
  • Place of Presentation: Vancouver, Canada
• [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
  • Place of Presentation: 弘前大学,弘前
  • 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
  • Place of Presentation: 弘前大学,弘前
  • 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
  • Place of Presentation: 弘前大学,弘前
  • 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
  • Place of Presentation: 弘前大学,弘前
  • 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
  • Place of Presentation: 弘前大学,弘前
  • 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
  • Place of Presentation: 弘前大学,弘前
  • Year and Date: 2011-10-01
• [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
  • Place of Presentation: 弘前大学,弘前
  • Year and Date: 2011-10-01
• [Presentation] 魚類のミトマ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: 日本魚類学会
  • Place of Presentation: 弘前大学
  • 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: 日本魚類学会
  • Place of Presentation: 弘前大学
  • Year and Date: 2011-10-01
• [Presentation] The mitogenomic supermatrices to resolve Cypriniformes Tree of Life: An empirical approach based on 469 complete and 2171 partial mtDNA sequences (2011)
  • Author(s): Miya, M., T. Sado, K. Saitoh, H.L. Bart, Jr., M.H. Doosey, I. Doadrio, Y. Keivany, J. Shrestha, V. Lheknim, R. Zardoya, M. Nishida, R.L. Mayden
  • Organizer: 日本進化学会
  • Place of Presentation: 京都大学,京都
  • Year and Date: 2011-07-30
• [Presentation] The mitogenomic supermatrices to resolve Cypriniformes Tree of Life : An empirical approach based on 469 complete and 2171 partial mtDNA sequences (2011)
  • Author(s): Miya, M., T.Sado, K.Saitoh, H.L.Bart, Jr., M.H.Doosey, I.Doadrio, Y.Keivany, J.Shrestha, V.Lheknim, R.Zardoya, M.Nishida, R.L.Mayden
  • Organizer: 日本進化学会
  • Place of Presentation: 京都大学
  • Year and Date: 2011-07-30
• [Presentation] Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes : Pangaean origin and Mesozoic radiation (2011)
  • Author(s): Masaki M., M.Nakatani, K.Mabuchi, K.Saitoh, M.Nishida
  • Organizer: Joint Meeting of Ichthyologists and Herpetologists
  • Place of Presentation: Minneapolis, Minnesota, USA
  • Year and Date: 2011-07-10
• [Presentation] The mitogenomic supermatrices to resolve Cypriniformes Tree of Life : An empirical approach based on 469 complete and 2171 partial mtDNA sequences (2011)
  • Author(s): Miya, M., T.Sado, K.Saitoh, H.L.Bart, Jr., M.H.Doosey, I.Doadrio, Y.Keivany, J.Shrestha, V.Lheknim, R.Zardoya, M.Nishida, R.L.Mayden
  • Organizer: Evolution 2011
  • Place of Presentation: Norman, Oklahoma, USA
  • Year and Date: 2011-06-07
• [Presentation] Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation (2011)
  • Author(s): Miya, M., Nakatani, K. Mabuchi, K. Saitoh, M. Nishida
  • Organizer: Joint Meeting of Ichthyologists and Herpetologists
  • Place of Presentation: Hilton Minneapolis, Minneapolis, Minnesota, USA
• [Presentation] The mitogenomic supermatrices to resolve Cypriniformes Tree of Life: An empirical approach based on 472 complete and 2171 partial mtDNA sequences (2011)
  • Author(s): Miya, M., T. Sado, K. Saitoh, H.L. Bart, Jr., M.H. Doosey, I. Doadrio, Y. Keivany, J. Shrestha, V. Lheknim, R. Zardoya, M. Nishida, R.L. Mayden.
  • Organizer: Joint Meeting of Ichthyologists and Herpetologists
  • Place of Presentation: Hilton Minneapolis, Minneapolis, Minnesota, USA
• [Presentation] The mitogenomic supermatrices to resolve Cypriniformes Tree of Life: An empirical approach based on 469 complete and 2171 partial mtDNA sequences (2011)
  • Author(s): Miya, M., T. Sado, K. Saitoh, H.L. Bart, Jr., M.H. Doosey, I. Doadrio, Y. Keivany, J. Shrestha, V. Lheknim, R. Zardoya, M. Nishida, R.L. Mayden.
  • Organizer: Evolution 2011. Embassy Suites Norman
  • Place of Presentation: Hotel & Conference Center, Norman, Oklahoma, USA
• [Presentation] ウナギ目の新科を発見:パラオの海底洞窟に生息する「生きた化石」 (2010)
  • Author(s): 宮 正樹・井田 齊・G. David Johnson・坂上治郎・ 佐土哲也・朝日田卓
  • Organizer: 2010 年度日本魚類学会年会
  • Place of Presentation: 三重大学,津
  • Year and Date: 2010-09-24
• [Presentation] ウナギ目の新科を発見:パラオの海底洞窟に生息する「生きた化石」 (2010)
  • Author(s): 宮正樹・井田齊・G.David Johnson・坂上治郎・佐土哲也・朝日田卓
  • Organizer: 日本魚類学会
  • Place of Presentation: 三重県津市
  • Year and Date: 2010-09-24
• [Presentation] Evolutionary History of Anglerfishes(Teleostei : Lophiifomies) : A Mitogenomic Perspective (2010)
  • Author(s): Masaki Miya, Theodore W.Pietsch, James W.Orr, Takashi P.Satoh, Hsuan-Ching Ho, Rachel Arnold, Andrew M.Shedlock, Mitsuomi Shimazaki, Mamoru Yabe, Mutsumi Nishida
  • Organizer: Joint Meeting of Ichthyologists and Harpetologists 2010
  • Place of Presentation: Providence, Rhode Island, USA
  • Year and Date: 2010-07-10
• [Presentation] Deep-ocean origin of the freshwater eels and their evolutionary history : A mitogenomic perspectrve (2010)
  • Author(s): M.Miya
  • Organizer: Evolution 2010
  • Place of Presentation: Portland, Oregon, USA
  • Year and Date: 2010-06-28
• [Presentation] Evolution of the deep-sea fishes : A mitogenomic perspective (2010)
  • Author(s): M.Miya
  • Organizer: DNA Bazcoding of Marine Biodiversity (MarBOL)
  • Place of Presentation: Hazvazd University
  • Year and Date: 2010-05-11
• [Presentation] An extraordinary primitive eel from shallow waters of Palau . new family, living fossil? (2010)
  • Author(s): Johnson G.D., Ida H., Sakaue J., Sado T., Asahida T. & Miya M
  • Organizer: Joint Meeting of Ichthyologists and Herpetologists.
  • Place of Presentation: Rhode Island
• [Presentation] Phylogenetic relationships of the cyprinid subfamily Gobioninae (Teleostei: Cypriniformes) (2010)
  • Author(s): Tang K.L., Agnew, M.K., Chen W.-J., Hirt M.V., Raley, Sado T., Schneider L.M., Yang L., Bart H.L., He, S., Liu H., M.E., Miya M., Saitoh K., Simons A.M., Wood R.M. & Mayden R.L.
  • Organizer: Joint Meeting of Ichthyologists and Herpetologists
  • Place of Presentation: Rhode Island
• [Presentation] Evolutionary history of anglerfishes (Teleostei: Lophiiformes): A mitogenomic perspective (2010)
  • Author(s): Miya, M., T.W. Pietsch, J.W. Orr, T.P. Satoh, H.-C. Ho, R. Arnold, A.M. Shedlock, M. Shimazaki, M. Yabe, M. Nishida
  • Organizer: Joint Meeting of Ichthyologists and Herpetologists.
  • Place of Presentation: Rhode Island
• [Remarks] Masaki Miya Lab
  • URL: https://sites.google.com/site/masakimiyalab/
• [Remarks] MitoFish
  • URL: http://mitofish.ori.u-tokyo.ac.jp/
• [Remarks] 魚類のミトゲノム全長配列と断片配列に絞り込んで構築したデータベース
• [Remarks] Masaki Miya Lab
  • URL: https://sites.google.com/site/masakimiyalab/home
• [Remarks] Google Scholar My Citations "Masaki Miya"
  • URL: http://scholar.google.com/citations?user=aTG4wPQAAAAJ&hl=en
• [Remarks] ResearchGate "Masaki Miya"
  • URL: https://www.researchgate.net/profile/Masaki_Miya/
• [Remarks]
  • URL: http://web.me.com/masaki_miya
• [Remarks]
  • URL: http://web.me.com/masaki_miya