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Inferring Molecular Phylogenies in the Post-genomic Era

Research Project

Project/Area Number 19300099
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Statistical science
Research InstitutionThe Institute of Statistical Mathematics

Principal Investigator

ADACHI Jun  The Institute of Statistical Mathematics, モデリング研究系, 准教授 (30370092)

Co-Investigator(Kenkyū-buntansha) CAO Ying  統計数理研究所, モデリング研究系, 助教 (20370091)
Co-Investigator(Renkei-kenkyūsha) HASEGAWA Masami  統計数理研究所, モデリング研究系, 名誉教授 (60011657)
NISHIHARA Hidenori  東京工業大学, 大学院・生命理工学研究科, 助教 (10450727)
MATSUI Atsushi  京都大学, 霊長類研究所・遺伝子情報分野・gCOE, 研究員
YONEZAWA Takahiro  復旦大学(中国), 生命科学学院, 講師
Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000)
Fiscal Year 2009: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2008: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2007: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
Keywordsゲノム系統学 / 分子進化 / 分子系統樹 / 最尤法 / モデル選択
Research Abstract

The availability of large genomic sequence datasets allows us to perform the maximum likelihood analysis of the eutherian phylogenetic relationship. We demonstrate that the better model which takes into account the different tempos and modes of evolution among genes, should be used for phylogenetic inference in cases of large variation in evolutionary features among different genes, such as for genome-scale data.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (18 results)

All 2009 2008 2007

All Journal Article (16 results) (of which Peer Reviewed: 16 results) Presentation (2 results)

  • [Journal Article] Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs2009

    • Author(s)
      A. Matsui, F. Rakotondraparany, I. Munechika, M. Hasegawa, S. Horai
    • Journal Title

      Gene 441

      Pages: 53-66

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The monophyletic origin of sea lions and fur seals (Carnivora; Otariidae) in the Southern Hemisphere2009

    • Author(s)
      T. Yonezawa, N. Kohno, M. Hasegawa
    • Journal Title

      Gene 441

      Pages: 89-99

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications2009

    • Author(s)
      Z. Ren, B. Zhu, E. Ma, J. Wen, T. Tu, Y. Cao, M. Hasegawa, Y. Zhong
    • Journal Title

      Gene 441

      Pages: 148-155

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Adaptive evolution of rbcL in Conocephalum (Hepaticae, Bryophytes)2009

    • Author(s)
      H. Miwa, I.J. Odrzykoski, A. Matsui, M. Hasegawa, H. Akiyama, Y. Jia, R. Sabirov, H. Takahashi, D.E. Boufford, N. Murakami
    • Journal Title

      Gene 441

      Pages: 169-175

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Chronology of the extant African elephant species and case study of the species identification of the small African elephant with the molecular phylogenetic method2009

    • Author(s)
      Y. Murata, T. Yonezawa, I. Kihara, T. Kashiwamura, Y. Sugihara, M. Nikaido, N. Okada, H. Endo, M. Hasegawa
    • Journal Title

      Gene 441

      Pages: 176-186

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications2009

    • Author(s)
      Zhumei Ren
    • Journal Title

      Gene 441

      Pages: 148-155

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The monophyletic origin of sea lions and fur seals(Carnivora ; Otariidae)in the Southern Hemisphere2009

    • Author(s)
      Takahiro Yonezawa
    • Journal Title

      Gene 441

      Pages: 88-99

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs2009

    • Author(s)
      Atsushi Matsui
    • Journal Title

      Gene 441

      Pages: 53-66

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Adaptive evolution of rbcL in Conocephalum(Hepaticae, bryophytes)2009

    • Author(s)
      Hidetsugu Miwa
    • Journal Title

      Gene 441

      Pages: 160-175

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Chronology of the extant African elephant species and case study of the species identification of the small African elephant with the molecular phylogenetic method2009

    • Author(s)
      Yumie Murata
    • Journal Title

      Gene 441

      Pages: 176-186

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar2008

    • Author(s)
      A. Kurabayashi, M. Sumida, H. Yonekawa, F. Glaw, M. Vences, M. Hasegawa
    • Journal Title

      Mol. Biol. Evol. 25

      Pages: 874-891

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-2008

    • Author(s)
      Zhumei Ren
    • Journal Title

      Gene doi : 10.1016/j. gene. 2008.09.010

      Pages: 1-8

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 鰭脚類の起源と進化2008

    • Author(s)
      米澤隆弘
    • Journal Title

      統計数理 56

      Pages: 81-99

    • NAID

      120006019014

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ゲノム系統学的手法の応用と課題-真獣類の起源に関する解析を例として-2008

    • Author(s)
      西原秀典
    • Journal Title

      統計数理 56

      Pages: 19-35

    • NAID

      120006019012

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rooting the eutherian tree: the power and pitfalls of phylogenomics2007

    • Author(s)
      H. Nishihara, N. Okada, M. Hasegawa
    • Journal Title

      Genome Biology 8:R199

      Pages: 1-10

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Molecular phylogenetic study on the origin and evolution of Mustelidae2007

    • Author(s)
      T. Yonezawa, M. Nikaido, N. Kohno, Y. Fukumoto, N. Okada, M. Hasegawa
    • Journal Title

      Gene 396

      Pages: 1-12

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Presentation] Molecular phylogeny and evolution of river dolphins: integration of mitochondrial DNA and SINE flanking sequences2007

    • Author(s)
      Y. Cao
    • Organizer
      Evolution 2007 Conference
    • Place of Presentation
      Christchurch, New Zealand
    • Year and Date
      2007-06-18
    • Related Report
      2009 Final Research Report 2007 Annual Research Report
  • [Presentation] MolPhy: new software for phylogenetic analyses using maximum likelihood2007

    • Author(s)
      J. Adachi
    • Organizer
      Evolution 2007 Conference
    • Place of Presentation
      Christchurch, New Zealand
    • Year and Date
      2007-06-17
    • Related Report
      2009 Final Research Report 2007 Annual Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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