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Use of mitochondrial genomic information in telestean molecular phylogenetics: A new approach using long PCR technique

Research Project

Project/Area Number 11640705
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field 系統・分類
Research InstitutionNatural History Museum and Institute, Chiba

Principal Investigator

MIYA Masaki  Natural History Museum and Institute, Chiba, Department of Zoology, Secior Research Scientist, 自然誌・歴史研究部・動物学研究科, 上席研究員 (30250137)

Project Period (FY) 1999 – 2000
Project Status Completed (Fiscal Year 2001)
Budget Amount *help
¥3,800,000 (Direct Cost: ¥3,800,000)
Fiscal Year 2000: ¥1,300,000 (Direct Cost: ¥1,300,000)
Fiscal Year 1999: ¥2,500,000 (Direct Cost: ¥2,500,000)
KeywordsMolecular phylogeny / Mitochondrial genome / Fish / Teleostei / Maximum parsimony / Large date set / Phulogenetic analysis / ミトコンドリアゲノミクス / ロングPCR / 分子系統学 / モデル系統樹 / tRNA
Research Abstract

I explored the phylogenetic utility and limits of the individual and concatenated mitochondrial genes for reconstructing the higher-level relationships of teleosts, using the complete (or nearly complete) mitochondrial DNA (mtDNA) sequences of eight teleosts (including those three newly-determined sequences), whose relative phylogenetic positions were noncontroversial. Maximum-parsimony analyses of the nucleotide and amino acid sequences of 13 protein-coding genes from the above eight teleosts, plus two outgroups (bichir and shark), indicated that all of the individual protein-coding genes, with the exception of ND5, failed to recover the expected phylogeny, although unambiguously aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem regions only) recovered the expected phylogeny successfully with moderate statistical support. The phylogenetic performance of the 13 protein-coding genes in recovering the expected phylogeny was roughly classified into five groups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Although the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order revealed that the combined data sets comprising nucleotide sequences from the several top ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only), best recovered the expected phylogeny, with all internal branches being supported by bootstrap values >90%. We concluded that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are prerequisites for resolving higher-level relationships in teleosts under the maximum-parsimony optimality criterion.

Report

(3 results)
  • 2001 Final Research Report Summary
  • 2000 Annual Research Report
  • 1999 Annual Research Report
  • Research Products

    (24 results)

All Other

All Publications (24 results)

  • [Publications] Miya, M., M.Nishida: "Organization of the mitochondrial genome of a deep-sea fish Gonostoma gracile : First example of transfer RNA gene rearrangements in bony fishes"Marine Biotechnology. 1(5). 416-426 (1999)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Miya, M., M.Nishida: "Molecular systematics of the deep-sea fish genes Gonostoma : Two paraphyletic clades and resurrection of Sigmops"Copeia. 2000(2). 378-389 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Miya, M., M.Nishida: "Use of mitogenomic information in tereostean molecular phylogenetics : A tree-based exploration under the maximum-parsimony optimality criterion"Molecular Phylogenetics and Evolution. 17(3). 437-455 (2000)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Inoue, J., M.Miya, K.Tsuka et al.: "Complete mitochondrial DNA sequence of Conger myriaster : Novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for arguilliform families"Journal of Molecular Evolution. (印刷中). (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Ishiguro, N., M.Miya, M.Nishida: "Complete mitochondrial DNA sequence of ayu, Plecoglossus altivelis"Fisheries Science. (印刷中). (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Kawaguchi, A., M.Miya, M.Nishida: "Complete mitochondrial DNA sequence of Aulopus japonicus a basal Eurypterygii : Longer DNA sequences and the higher-level relationships"Ichthyological Research. (印刷中). (2001)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Miya, M. and M. Nishida: "Organization of the mitochondrial genome of a deep-sea fish Gonostoma gracile (Teleostei : Stomiiformes) : First example of transfer RNA gene rearrangements in bony fishes"Marine Biolechnology. 1(5). 416-426 (1999)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Yamaguchi, M., M. Miya, M. Okiyama and M. Nishida: "Molecular phylogeny and larval morphological diversity of the lantemfish genus Hygophum (Teleostei : Myctophidae)"Molecular Phylogenelics and Evolution. 15(1). 103-114 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Miya, M. and M. Nishida: "Moleeular systematics of the deep-sea fish genus Gonostoma (Stomiifonnes : Gonostomatidae) : Two paraphyletic clades and resurrection of Simops"Copeia. 2000(2). 378-389 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Inoue, J. G., M. Miya, K. Tsukamoto and M. Nishida: "Complete mitochondrial DNA sequence of the Japanese sardine, Sardinops melanostictus"Fisheries Science. 66(6). 924-932 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Miya, M. and M. Nishida: "Use of mitogenomic information in teleostean molecular phylogenetics : A tree-based exploration under the maximum-parsimony optimality criterion"Molecular Phylogenelics and Evolution. 17(3). 437-455 (2000)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Inoue, J. G., M. Miya, J. Aoyama, S. Ishikawa, K. Tsukamoto and M. Nishida: "Complete mitochondrial DNA sequence of the Japanese eel, Anguilla japonica"Fisheries Science. 67(1). 118-125 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Inoue, J. G., M. Miya, K. Tsukamoto and M. Nishida: "Complete mitochondrial DNA sequence of Conger myriaster (Teleostei : Anguillioformes) : Novel, gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families"NJournal of Molecular Evolution. 52. 311-320 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] lshiguro, N., M. Miya and M. Nishida: "Complete mitochondrial DNA sequence of ayu, Plecoglossus altivelis"Fisheries Science. 67. 474-481 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] kawaguchi, A., M. Miya and M. Nishida: "Complete mitocliondrial DNA sequence of Aulopus japonicus (Teleostei : Aulopiformes), a basal Eurypterygii : Longer DNA sequences and the higher-level relationships"Ichthyological Reseach. 48(3). 213-223 (2001)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2001 Final Research Report Summary
  • [Publications] Miya,M.and M.Nishida: "Organization of the mitochondrial genome of a deep-sea fish Gonostoma gracile ; First example of transfer RNA gene rearrangements in bony fishes."Marine Biotechnology. 1(5). 416-426 (1999)

    • Related Report
      2000 Annual Research Report
  • [Publications] Miya,M.and M.Nishida: "Molecular systematics of the deep-sea fish genus Gonostoma : Two paraphyletic clades and resurrection of sigmops."Copeia. 2000(2). 378-389 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Miya,M.and M.Nishida: "Use of mitogenomic information in teleostean molecular phylogenetics : A tree-based exploration under the maximum-paraimory optimality criterion."molecular Phylogenetice and Evolution. 17(3). 437-455 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Inoue,J.,M.Miya,K.Tsukamoto: "Complete mitochondrial DNA sequence of Conger myriaster : novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families."Journal of Molecular Evolution. (印刷中). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Ishiguro,N.,M Miya,and M.Nishida: "Complete mitochondrial DNA sequence of ayu, Plecoglossus altivelis,"Fisheries Science. (印刷中). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Kawaguchi,A.,M.Miya,and M.Nishida: "Complete mitochondrial DNA sequence of Aulopus japonicus, a basal Eurypterygili Longer DNA sequences and the higher-level relationships."Ichthyological Research. (印刷中). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Ogiwara I.,M.Miya et al.: "Retropositional parasitism of SINES on LINES : Identification of SINES and LINES in Elasmobranchs"Molecular Biology and Evolution. 16巻9号. 1238-1250 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Miya M.and M.Nishida: "Organization of the mitochondrial genome of a deep-Sea fish Gonostoma gracile : First example transfer RNA gene rearrangements in bony fishes"Marine Biotechnology. 1巻5号. 416-426 (1999)

    • Related Report
      1999 Annual Research Report
  • [Publications] Miya M.and M.Nishida: "Molecular systematics of the deep-sea fish genes Gonostoma(stomiiformes:Gonost***)******"Copeia. 2000巻2号. 378-389 (2000)

    • Related Report
      1999 Annual Research Report

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Published: 1999-04-01   Modified: 2016-04-21  

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