Inferring Molecular Phylogenies in the Post-genomic Era

• Project/Area Number: 19300099
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Statistical science
• Research Institution: The 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: ¥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.

Research Products

• [Journal Article] Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs (2009)
  • Author(s): A. Matsui, F. Rakotondraparany, I. Munechika, M. Hasegawa, S. Horai
  • Journal Title: Gene 441 Pages: 53-66
  • Peer Reviewed
• [Journal Article] The monophyletic origin of sea lions and fur seals (Carnivora; Otariidae) in the Southern Hemisphere (2009)
  • Author(s): T. Yonezawa, N. Kohno, M. Hasegawa
  • Journal Title: Gene 441 Pages: 89-99
  • Peer Reviewed
• [Journal Article] Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications (2009)
  • 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
  • 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
  • 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 method (2009)
  • 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
  • Peer Reviewed
• [Journal Article] Complete nucleotide sequence and gene arrangement of the mitochondrial genome of the crab-eating frog Fejervarya cancrivora and evolutionary implications (2009)
  • Author(s): Zhumei Ren
  • Journal Title: Gene 441 Pages: 148-155
  • Peer Reviewed
• [Journal Article] The monophyletic origin of sea lions and fur seals(Carnivora ; Otariidae)in the Southern Hemisphere (2009)
  • Author(s): Takahiro Yonezawa
  • Journal Title: Gene 441 Pages: 88-99
  • Peer Reviewed
• [Journal Article] Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs (2009)
  • Author(s): Atsushi Matsui
  • Journal Title: Gene 441 Pages: 53-66
  • Peer Reviewed
• [Journal Article] Adaptive evolution of rbcL in Conocephalum(Hepaticae, bryophytes) (2009)
  • Author(s): Hidetsugu Miwa
  • Journal Title: Gene 441 Pages: 160-175
  • 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 method (2009)
  • Author(s): Yumie Murata
  • Journal Title: Gene 441 Pages: 176-186
  • Peer Reviewed
• [Journal Article] Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar (2008)
  • Author(s): A. Kurabayashi, M. Sumida, H. Yonekawa, F. Glaw, M. Vences, M. Hasegawa
  • Journal Title: Mol. Biol. Evol. 25 Pages: 874-891
  • 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
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Rooting the eutherian tree: the power and pitfalls of phylogenomics (2007)
  • Author(s): H. Nishihara, N. Okada, M. Hasegawa
  • Journal Title: Genome Biology 8:R199 Pages: 1-10
  • Peer Reviewed
• [Journal Article] Molecular phylogenetic study on the origin and evolution of Mustelidae (2007)
  • Author(s): T. Yonezawa, M. Nikaido, N. Kohno, Y. Fukumoto, N. Okada, M. Hasegawa
  • Journal Title: Gene 396 Pages: 1-12
  • Peer Reviewed
• [Presentation] Molecular phylogeny and evolution of river dolphins: integration of mitochondrial DNA and SINE flanking sequences (2007)
  • Author(s): Y. Cao
  • Organizer: Evolution 2007 Conference
  • Place of Presentation: Christchurch, New Zealand
  • Year and Date: 2007-06-18
• [Presentation] MolPhy: new software for phylogenetic analyses using maximum likelihood (2007)
  • Author(s): J. Adachi
  • Organizer: Evolution 2007 Conference
  • Place of Presentation: Christchurch, New Zealand
  • Year and Date: 2007-06-17