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2004 Fiscal Year Final Research Report Summary

Mitochondrial Genomic Analysis of the Percomorph Fish Phytogenies : Resolving Polytomies Using Large Datasets

Research Project

Project/Area Number 15570090
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Biodiversity/Systematics
Research InstitutionNatural History Museum and Institute, Chiba

Principal Investigator

MIYA Masaki  Natural History Museum & Institute, Chiba, Department of Zoology, 動物学研究科, 上席研究員 (30250137)

Project Period (FY) 2003 – 2004
Keywordslarge data set / mitochondrial genome / higher classification / molecular phylogeny / Bayesian method / Actinopterygii / polytomy / fish
Research Abstract

A series of recent molecular phylogenetic studies based on whole mitochondrial genome (mitogenome) sequences (Inoue et al.,2003a, b, 2004 ; Ishiguro, Miya & Nishida,2003 ; Miya et al., 2003 ; Saitoh et al., 2003), however, have shed a new light on our concepts of actinopterygian higher-level relationships. These six mitogenomic studies plus previous pioneering works (Chang, Huang & Lo, 1994 ; Johansen & Bakke, 1996,Miya & Nishida,1999,2000b ; Noack, Zardoya & Meyer,1996 ; Saitoh et al., 2000 ; Tzeng et al., 1992 ; Zardoya, Garrido-Pertierra & Bautista,1995) together sampled all major lineages of actinopterygians at the ordinal level, with their data sets partially overlapping each other. Also they were all based on the same sets of strictly homologous characters, with no potential for paralogous comparisons among sampled genes owing to ancient genome duplication (Martin & Burg,2002) as recently suggested for actinopterygian nuclear genomes (e.g., Taylor et al., 2003 ; Van de Peer, Tayl … More or & Meyer,2003). In addition, it should be noted that the resultant phylogenies were well resolved and many basal clades received high statistical support irrespective of analytical methods (see Simmons & Miya, 2004). Accordingly the whole mitogenome sequences have afforded a new comprehensive perspective on the higher-level relationships of actinopterygians, portions of which have been supported by recent molecular phylogenetic studies based on different markers (Chen, Bonillo & Lecointre,2003 ; Wiley, Johnson & Dimmick,2000). Exception to this is relationships of the Percomorpha, known as "bush at the top of the tree"(Nelson, 1989).
In this study, I attempted at resolving relationships of the Percomorpha based on the whole mitochondrial genome sequences. First I successfully demonstrated a phylogenetic position of toadfish (order Batrachoidiformes) using whole mitochondrial genome sequences from 102 actinopterygians (Miya et al., 2005). I am further analyzing large datasets comprising 336 actinopterygians to correctly determine limits of the Percomorpha and resolve their intrarelationships. The analyses have been conducted using two parallel computing systems and will be finished within this year. Less

  • Research Products

    (27 results)

All 2005 2004 2003

All Journal Article (26 results) Book (1 results)

  • [Journal Article] The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences2005

    • Author(s)
      M.Miya, T.P.Satoh, M.Nishida
    • Journal Title

      Biological Journal of the Linnean Society 85(In press)

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences.2005

    • Author(s)
      Minegishi, Y., J.Aoyama, J.G.Inoue, M.Miya, M.Nishida, K.Tsukamoto
    • Journal Title

      Molecular Phylogenetics and Evolution 34(1)

      Pages: 134-146

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] A PCR-based approach for sequencing the mitochondrial genomes of decapod crustaceans, with a practical example from kuruma prawn Marsupenaeus japonicus.2005

    • Author(s)
      Yamauchi, M.M., M.Miya, R.J.Machida, M.Nishida
    • Journal Title

      Marine Biotechnology (In press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Evolution of the mitochondrial genome in Cephalochordata as inferred from complete nucleotide sequences from two Epigonichthys species.2005

    • Author(s)
      Nohara, M., M.Nishida, M.Miya, T.Nishikawa
    • Journal Title

      Journal of Molecular Evolution (In press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii : Coelacanthiformes) and divergence time estimation between the two coelacanths.2005

    • Author(s)
      Inoue, J.G., M.Miya, B.Venkatesh, M.Nishida
    • Journal Title

      Gene (In press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Sundasalanx (Sundasalangidae) is a progenetic clupeiform, not a closely-related group of salangids (Osmeriformes) : Mitogenomic evidence.2005

    • Author(s)
      Ishiguro, N.B., M.Miya, J.G.Inoue, M.Nishida
    • Journal Title

      Journal of Fish Biology (In press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences.2005

    • Author(s)
      Miya, M., T.P.Satoh, M.Nishida
    • Journal Title

      Biological Journal of the Linnean Society (In press)

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfishes (Teleostei : Perciformes : Scaridae)2004

    • Author(s)
      Mabuchi, K., M.Miya, T.P.Satoh, M.W.Westneat, M.Nishida
    • Journal Title

      Journal of Molecular Evolution 59(3)

      Pages: 287-297

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] How meaningful are Bayesian support values?2004

    • Author(s)
      Simmons, M.P., K.M.Pickett, M.Miya
    • Journal Title

      Molecular Biology and Evolution 21(1)

      Pages: 188-199

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches : A case study using 100 complete mitochondrial DNA sequences from higher teleost fishes.2004

    • Author(s)
      Simmons, M.P., M.Miya
    • Journal Title

      Molecular Phylogenetics and Evolution 31(1)

      Pages: 351-362

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Large-scale gene rearrangements in the mitochondrial genomes of two calanoid copepods Eucalanus bungii and Neocalanus cristatus (Crustacea), with notes on new versatile primers for the srRNA and COI genes.2004

    • Author(s)
      Machida, R.J., M.Miya, M.M.Yamauchi, M.Nishida, S.Nishida
    • Journal Title

      Gene 332

      Pages: 71-78

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva.2004

    • Author(s)
      Inoue, J.G., M.Miya, K.Tsukamoto, M.Nishida
    • Journal Title

      Molecular Phylogenetics and Evolution 32(1)

      Pages: 274-286

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Organization of the mitochondrial genome of antarctic krill, Euphausia superba (Crustacea : Malacostraca).2004

    • Author(s)
      Machida, R.J., M.Miya, M.M.Yamauchi, M.Nishida, S.Nishida
    • Journal Title

      Marine Biotechnology 6(3)

      Pages: 238-250

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Use of a PCR-based approach for sequencing whole mitochondrial genomes of insects : Two examples (cockroach and dragonfly) based on the method developed for decapod crustaceans.2004

    • Author(s)
      Yamauchi, M.M., M.Miya, M.Nishida
    • Journal Title

      Insect Molecular Biology 13(4)

      Pages: 435-442

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Mitochondrial genomes and phylogeny of the ocean sunfishes (Tetraodontiformes : Molidae).2004

    • Author(s)
      Yamanoue, Y., M.Miya, K.Matsuura, M.Katoh, H.Sakai, M.Nishida
    • Journal Title

      Ichthyological Research 51(3)

      Pages: 269-273

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfishes (Teleostei : Perciformes : Scaridae).2004

    • Author(s)
      Mabuchi, K., M.Miya, T.P.Satoh, M.W.Westneat, M.Nishida
    • Journal Title

      Journal of Molecular Evolution 59(3)

      Pages: 287-297

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Basal actinopterygian relationships : A mitogenomic perspective on the phylogeny of the "ancient fish"2003

    • Author(s)
      Inoue, J.G., M.Miya, K.Tsukamoto, M.Nishida
    • Journal Title

      Molecular Phylogenetics and Evolution 26(1)

      Pages: 110-120

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Major patterns of higher teleostean phylogenies : A new perspective based on 100 complete mitochondrial DNA sequences2003

    • Author(s)
      M.Miya, H.Takeshima, H.Endo et al.(12 coauthors)
    • Journal Title

      Molecular Phylogenetics and Evolution 26(1)

      Pages: 121-138

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Mitochondrial genomics of ostariophysan fish : Perspectives on phylogeny and biogeography2003

    • Author(s)
      Saitoh, K., M.Miya, J.G.Inoue, N.B.Ishiguro, M.Nishida
    • Journal Title

      Journal of Molecular Evolution 56(4)

      Pages: 464-472

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Basal euteleostean relationships : A mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii"2003

    • Author(s)
      Ishiguro, N.B., M.Miya, M.Nishida
    • Journal Title

      Molecular Phylogenetics and Evolution 27(3)

      Pages: 476-488

    • Description
      「研究成果報告書概要(和文)」より
  • [Journal Article] Basal actinopterygian relationships : A mitogenomic perspective on the phytogeny of the "ancient fish."2003

    • Author(s)
      Inoue, J.G., M.Miya, K.Tsukamoto, M.Nishida
    • Journal Title

      Molecular Phylogenetics and Evolution 26(1)

      Pages: 110-120

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Major patterns of higher teleostean phylogenies : A new perspective based on 100 complete mitochondrial DNA sequences.2003

    • Author(s)
      Miya, M., H.Takeshima, H.Endo, N.B.Ishiguro, J.G.Inoue, T.Mukai, T.P.Satoh, M.Yamaguchi, A.Kawaguchi, K.Mabuchi, S.M.Shirai, M.Nishida
    • Journal Title

      Molecular Phylogenetics and Evolution 26(1)

      Pages: 121-138

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Mitochondrial genomics of ostariophysan fish : Perspectives on phylogeny and biogeography.2003

    • Author(s)
      Saitoh, K., M.Miya, J.G.Inoue, N.B.Ishiguro, M.Nishida
    • Journal Title

      Journal of Molecular Evolution 56(4)

      Pages: 464-472

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Basal euteleostean relationships : A mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii."2003

    • Author(s)
      Ishiguro, N., M.Miya, M.Nishida
    • Journal Title

      Molecular Phylogenetics and Evolution 27(3)

      Pages: 476-488

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (Crustacea : Decapoda).2003

    • Author(s)
      Yamauchi, M.M., M.Miya, M.Nishida
    • Journal Title

      Gene 311(1)

      Pages: 129-135

    • Description
      「研究成果報告書概要(欧文)」より
  • [Journal Article] Evolution of the deep-sea gulper eel mitochondrial genomes : Large-scale gene rearrangements originated within the eels.2003

    • Author(s)
      Inoue, J.G., M.Miya, K.Tsukamoto, M.Nishida
    • Journal Title

      Molecular Biology and Evolution 20(11)

      Pages: 1911-1917

    • Description
      「研究成果報告書概要(欧文)」より
  • [Book] 魚類の大系統:ミトコンドリアゲノミクスによるアプローチ『海洋の生命史』(西田 睦編著)2005

    • Author(s)
      宮 正樹, 西田 睦
    • Publisher
      東海大学出版(印刷中)(所収)
    • Description
      「研究成果報告書概要(和文)」より

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Published: 2006-07-11  

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