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Phylogenetic Evolution of Vertebrate Mitochondrial DNA

Research Project

Project/Area Number 09640739
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field 遺伝
Research InstitutionInstitute of Statistical Mathematics

Principal Investigator

HASEGAWA Masami  ISM Professor, 予測制御研究系, 教授 (60011657)

Co-Investigator(Kenkyū-buntansha) HASHIMOTO Tetsuo  ISM Associate professor, 助教授 (50208451)
Project Period (FY) 1997 – 1998
Project Status Completed (Fiscal Year 1998)
Budget Amount *help
¥2,900,000 (Direct Cost: ¥2,900,000)
Fiscal Year 1998: ¥1,200,000 (Direct Cost: ¥1,200,000)
Fiscal Year 1997: ¥1,700,000 (Direct Cost: ¥1,700,000)
Keywordsmitochondrial DNA / protein / molecular phylogeny / ND1 / vertebrate / eutheria / lamprey / shark / NDI / ヤツメウナギ / ND1遺伝子 / 肺魚 / シ-ラカンス / 収斂進化
Research Abstract

Several cases of misleading molecular phylogenies estimated from mitochondrial DNA-encoded proteins have been known. In order to clarify the causes of these misleading phylogenies, we conducted several new analyses.
1) ND1 gene gives contradictory tree from that estimated from other genes of mitochondria concerning phylogeny among eutherian orders. In order to distinguish stochastic error due to to small species sampling from convergent substitutions due to some adaptive evolution, we sequenced ND1 gene from several eutherian species as well as several outgroup marsupials.
It turned out that convergent evolution has occurred in ND1 between primates and rodents or between ferungulates and outgroup.
2) By using lamprey as an outgroup in the analysis of mitochondrial proteins, a bizarre tree is obtained in which lamprey groups with lungfish in the vertebrate tree. In order to clarify the reason of this, we sequenced complete mtDNA from shak. With this data as an outgroup, morphologically acceptable tree was obtained, demonstrating that something strange occurred in the lamprey and/or lungflsh lineages.

Report

(3 results)
  • 1998 Annual Research Report   Final Research Report Summary
  • 1997 Annual Research Report
  • Research Products

    (25 results)

All Other

All Publications (25 results)

  • [Publications] Y.Cao, M.Hasegawa: "Comment on the quartet puzzling method for finding maximum-likelihood tree topologies" Mol. Biol. Evol.,. 15. 87-89 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] Y.Cao, M.Hasegawa: "Conflict among individual mitochondorial proteins in resolving the phylogeny of eatherian orders" J. Mol. Evol.47. 307-322 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] R.Zardoya,M.Hasegawa: "Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data" Mol. Biol. Evol.15. 506-517 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] M.Hasegawa, Y.Cao: "Preponderance of slightly deleterious polymorphism in mitochondrial DNA: Non-Synonyinous/synonyrnous rate ratio is higher within species than between syeties" Mol. Biol. Evol.15. 1499-1505 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] Z.Yang, M.Hasegawa: "Models of amino acid substitution and application to mitochondrial protein evolution" Mol. Biol. Evol.15. 1600-1611 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] Y.Cao, M.Hasegawa: "The complete mitochondrial DNA sequence of the shark Mustelus marazo: Resolving verterate phylogemy with mitochondrial genase sequece when all 〓 〓 fail 〓" Mol. Biol. Evol.15. 1637-1646 (1998)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] Y.Cao, N.Okada, and M.Hasegawa: "Phylogenetic position of guinea-pigs revisited." Mol.Biol.Evol.14. 461-464 (1997)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] Y.Cao, J.Adachi, and M.Hasegawa: "Comment on the quartet puzzling method for finding maximum-likelihood tree topologies." Mol.Biol.Evol.15. 87-89 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] Y.Cao, A.Janke, P.J.Waddell, M.Westerman, O.Takenaka, S.Murata, N.Okada, S.Paabo, and M.Hasegawa: "Conflict amongst individual mitochondrial proteins in resolving the phylogeny of eutherian orders." J.Mol.Evol.47. 307-322 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] T.Hashimoto, L.Sanchez, T.Shirakura, M.Muller, and M.Hasegawa: "Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny." Proc.Natl.Acad.Sci.USA.95. 6860-6865 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] R.Zardoya, Y.Cao, M.Hasegawa, and A.Meyer: "Searching for the closest living relative (s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data." Mol.Biol.Evol.15. 506-517 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] M.Hasegawa, Y.Cao, and Z.Yang: "Preponderance of slightly deleterious polymorphism in mitochondrial DNA : Nonsynony-mous/synonymous rate ratio is much higher within species than between species." Mol.Biol.Evol.15. 1499-1505 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] Z.Yang, R.Nielsen, and M.Hasegawa: "Models of amino acid substitution and applications to mitochondrial protein evolution." Mol.Biol.Evol.15. 1600-1611 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] Y.Cao, P.J.Waddell, N.Okada, and M.Hasegawa: "The complete mitochondrial DNA sequence of the shark Mustelus manazo : Resolving vertebrate phylogeny with mitochondrial genome sequences when all known methods fail completely." Mol.Biol.Evol.15. 1637-1646 (1998)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      1998 Final Research Report Summary
  • [Publications] Y.Cao,M.Hasegawa: "Comment on the quartet puzzling method for finding maximum-likelihood tree topologies" Mol.Biol.Evol.15. 87-89 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Y.Cao,M.Hasegawa: "Conflict among individual mitochondorial proteins in resolving the phylogeny of entherian orders" J.Mol.Evol.47. 307-322 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] R.Zardoya,M.Hasegawa: "Searching for the closest living relative(s) of tetrapods through evolutionary analyses of mitochondrial and nuclear data" Mol.Biol.Evol.15. 506-517 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] M.Hasegawa,Y.Cao: "Preponderance of slightly deleterious polymorphism in mitchondrial DNA:Non-synonymous/synonymous rate ratio is higher within species than between species." Mol.Biol.Evol.15. 1499-1505 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Z.Yang,M.Hasegawa: "Models of amino acid substitution and application to mitochondrial protein evolution" Mol.Biol.Evol.15. 1600-1611 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Y.Cao,M.Hasegawa: "The complete mitochondrial DNA sequence of the shark Mustelus manazo:Resolving verterate phylogeny with mitochondrial genome sequence. When all known method fail completely." Mol.Biol.Evol.15. 1637-1646 (1998)

    • Related Report
      1998 Annual Research Report
  • [Publications] Penny,D., Hasegawa,M.: "The platypus put its place" Nature. 387. 549-550 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Zardoya,R., Hasegawa,M.: "Searching for the closest licing relatives of tetrapods" Molecular Biology and Evolution. (印刷中).

    • Related Report
      1997 Annual Research Report
  • [Publications] Cao,Y., Hasegawa,M.: "Phylogenetic position of guineapigs reuisited" Malecular Biology and Evalution. 14. 461-464 (1997)

    • Related Report
      1997 Annual Research Report
  • [Publications] Cao,Y., Hasegawa,M.: "Comments on the quartet puzzling method" Molecular Biology and Evolution. 15. 87-89 (1998)

    • Related Report
      1997 Annual Research Report
  • [Publications] Cao,Y., Hasegawa,M.: "Conflict amongst individual proteins" Journal of Molecular Evolation. (印刷中). (1998)

    • Related Report
      1997 Annual Research Report

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Published: 1997-04-01   Modified: 2016-04-21  

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