Development of statistical methods for phylogeny reconstruction using multilocus sequence data

• Project/Area Number: 18770216
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Evolutionary biology
• Research Institution: The University of Tokyo
• Principal Investigator: SEO Tae-kun The University of Tokyo, 大学院農学生命科学研究科, 特任助教 (60401189)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥270,000); Fiscal Year 2008: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2007: ¥1,200,000 (Direct Cost: ¥1,200,000); Fiscal Year 2006: ¥1,400,000 (Direct Cost: ¥1,400,000)
• Keywords: 分子系統樹 / 距離行列法 / 分子進化 / ブートストラップ確率

Research Abstract

複数の遺伝子の塩基配列を結合せずに、個別に解析する新しい分子系統樹推定法を開発した。また遺伝子と配列サイトを再抽出する2段階サンプリング方式を提案し、この方法の妥当性を哺乳類の核遺伝子の解析で検証した。新しい方法の適用により、遺伝子ごとに違う進化的特徴を保ちながら系統樹の不確実性を測ることができるようになった。分子進化モデルと分岐年代推定法の開発も並行して行い、哺乳類の分岐年代とミトコンドリアタンパク質コード遺伝子の同義置換・非同義置換の変動パタンを推定した。

Research Products

• [Journal Article] Classification of nucleotide sequences using Support Vector Machines (2009)
  • Author(s): Seo T-K
  • Journal Title: (submitted)
• [Journal Article] Statistical comparison of nucleotide-, amino-acid-, and codon-substit ution models for evolutionary analysis of protein-coding sequences (2009)
  • Author(s): Tae-Kun Seo and Hirohisa Kishino
  • Journal Title: Systematic Biology (未定)(in press)
  • Peer Reviewed
• [Journal Article] Rates of nucleotide substitution in Cornaceae (Cornales)-correlation between molecular variation and morphological change, Mol (2008)
  • Author(s): Xiang, Q-Y, Thorne, J, Seo, T-K, Zhang, W., Thomas, D.,Ricklefs, R
  • Journal Title: Phylogenet. Evol. 49 Pages: 327-342
• [Journal Article] Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins (2008)
  • Author(s): Seo T-K, Kishino H
  • Journal Title: Syst. Biol. 57 Pages: 367-377
• [Journal Article] コドンモデルを用いた分岐年代のベイズ推定 (2008)
  • Author(s): 徐 泰健, 岸野 洋久, Jeffrey L. Thorne
  • Journal Title: 統計数理 56 Pages: 37-54
  • NAID: 120006019013
• [Journal Article] 遺伝子型の分子進化と表現型の適応進化 (2008)
  • Author(s): 渡部 輝明, 徐 泰健, 岸野 洋久
  • Journal Title: 統計数理 56 Pages: 55-66
  • NAID: 120006019009
• [Journal Article] Calculating bootstrap probabilities of phylogeny using multilocus sequence data (2008)
  • Author(s): Seo T-K
  • Journal Title: Mol. Biol. Evol. 25 Pages: 960-971
• [Journal Article] Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data (2008)
  • Author(s): Tae-Kun Seo
  • Journal Title: Molecular Biology and Evolution 25 Pages: 960-971
  • Peer Reviewed
• [Journal Article] Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins (2008)
  • Author(s): Tae-Kun Seo and Hirohisa Kishino
  • Journal Title: Systematic Biology 57 Pages: 367-377
  • Peer Reviewed
• [Journal Article] Rates of nucleotide substitution in Cornaceae (Cornales)-correlation between molecular variation and morphological change (2008)
  • Author(s): Xiang, Q-Y, Thorne, J, Seo, T-K, Zhang, W., Thomas, D.,Ricklefs, R.
  • Journal Title: Molecular Phylogenetics and Evolution 49 Pages: 327-342
  • Peer Reviewed
• [Journal Article] コドンモデルを用いた分岐年代のベイズ推定 (2008)
  • Author(s): 徐泰健、岸野洋久、Jeffrey Thorne
  • Journal Title: 統計数理 56 Pages: 37-54
  • NAID: 120006019013
  • Peer Reviewed
• [Journal Article] 遺伝子型の分子進化と表現型の適応進化 (2008)
  • Author(s): 渡部輝明、徐泰健、岸野洋久
  • Journal Title: 統計数理 56 Pages: 55-66
  • NAID: 120006019009
  • Peer Reviewed
• [Journal Article] Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins (2008)
  • Author(s): Tae-Kun Seo and Hirohisa Kishino
  • Journal Title: Systematic Biology (未定)(in press)
  • Peer Reviewed
• [Journal Article] コドンモデルを用いた分岐年代のベイズ推定 (掲載決定) (2008)
  • Author(s): 徐泰健、岸野洋久、Jeffrey Thorne
  • Journal Title: 統計数理 (未定)
  • Peer Reviewed
• [Journal Article] 遺伝子型の分子進化と表現型の適応進化(掲載決定) (2008)
  • Author(s): 渡部輝明、徐泰健、岸野洋久
  • Journal Title: 統計数理 (未定)
  • Peer Reviewed
• [Journal Article] Statistical comparison of nucleotide, amino acid, and codon substitution models for evolutionary analysis of protein-coding sequences
  • Author(s): Seo T-K, Kishino H
  • Journal Title: Syst. Biol. (in press)
• [Presentation] Statistical comparison of nucleotide-, amino-acid-, and codon-substit ution models for evolutionary analysis of protein-coding sequences (2008)
  • Author(s): Tae-Kun Seo and Hirohisa Kishino
  • Organizer: 日本進化学会
  • Place of Presentation: 東京
  • Year and Date: 2008-08-25
• [Presentation] Statistical comparison of nucleotide-, amino-acid-, and codon-substit ution models for evolutionary analysis of protein-coding sequences (2008)
  • Author(s): Tae-Kun Seo and Hirohisa Kishino
  • Organizer: Annual Meeting of SMBE 2008
  • Place of Presentation: Barcelona, Spain
  • Year and Date: 2008-06-06
• [Presentation] Statistical Comparison of Nucleotide-, Amino-Acid-, and Codon-Substitution Models for Evolutionary Analysis of Protein-Coding Sequences (2008)
  • Author(s): Seo, T-K, Kishino, H
  • Organizer: SMBE meeting
• [Presentation] Statistical Comparison of Nucleotide-, Amino-Acid-, and Codon-Substitution Models for Evolutionary Analysis of Protein-Coding Sequences (2008)
  • Author(s): Seo, T-K, Kishino, H
  • Organizer: 日本進化学会
• [Presentation] Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins (2007)
  • Author(s): 徐泰健
  • Organizer: 第九回日本進化学会
  • Place of Presentation: 京都
  • Year and Date: 2007-09-01
• [Presentation] Bayesian Divergence Time Estimation Using Codon Models (2007)
  • Author(s): Tae-Kun Seo
  • Organizer: Annual meeting of the Korean Society of Biological Sciences
  • Place of Presentation: Seoul, Korea
  • Year and Date: 2007-08-17
• [Presentation] Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins (2007)
  • Author(s): Tae-Kun Seo
  • Organizer: Annual meeting of the Society of Molecular Biology and Evolution
  • Place of Presentation: Halifax, Canada
  • Year and Date: 2007-06-27
• [Presentation] Synonymous substitution substantially improve evolutionary inference from highly diverged proteins (2007)
  • Author(s): Seo, T-K., Kishino, H
  • Organizer: SMBE meeting
• [Presentation] Synonymous substitution substantially improve evolutionary inference from highly diverged proteins (2007)
  • Author(s): Seo, T-K, Kishino, H
  • Organizer: 日本進化学会
• [Presentation] Calculating bootstrap probabilities of phylogeny using multilocus sequence data (2006)
  • Author(s): Seo, T-K
  • Organizer: SMBE meeting
• [Presentation] Thorne Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences (2006)
  • Author(s): Seo T-K, Kishino H. Jeffrey L
  • Organizer: 日本進化学会