Method and Practice of Phylogenomics

• Project/Area Number: 22570099
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biodiversity/Systematics
• Research Institution: The Institute of Statistical Mathematics
• Principal Investigator: HASEGAWA Masami 統計数理研究所, 名誉教授 (60011657)
• Co-Investigator(Kenkyū-buntansha): ADACHI Jun 統計数理研究所, データ科学研究系, 准教授 (30370092) ; CAO Ying 統計数理研究所, データ科学研究系, 助教 (20370091)
• Co-Investigator(Renkei-kenkyūsha): YONEZAWA Takahiro 復旦大学, 生命科学学院, 副教授
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2012: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2011: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2010: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: 系統樹推定 / 最尤法 / モデル比較 / ゲノム / 連結配列 / ミトコンドリア / ゲノム系統学 / 種系統樹 / 集団系統樹 / 遺伝子系統樹 / ミトコンドリア系統樹 / 種サンプリング / 適応的進化 / 中立的進化 / 家畜化 / UCA仮説 / アラインメント / 分子系統学 / 機能的制約 / モデル / 分子進化 / グネツム / AIC

Research Abstract

Problems misleading in the phylogenetic analyses of genome-scale data were studied, and methods to overcome these problems were developed. (1)The method for testing whether there existed the Universal Common Ancestor for all extant species on Earth was evaluated. (2)Based on a population genetic analysis of nuclear genomes, we obtained an evidence for the hypothesis that the polar bear evolved from a local population of the brown bear, that is, the brown bear is not monophyletic. (3)It was shown that several misleading signals in the eutherian tree of mitochondrial genomes are relieved by increasing the density of taxon sampling.

Research Products

• [Journal Article] Comment on "Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage" (2013)
  • Author(s): Shigeki Nakagome
  • Journal Title: Science Volume: 339 Issue: 6127 Pages: 1522-1522
  • DOI: 10.1126/science.1227339
  • Peer Reviewed
• [Journal Article] Some problems in proving the existence of the universal common ancestor of life on earth (2012)
  • Author(s): T. Yonezawa and M. Hasegawa
  • Journal Title: The Scientific World Journal Volume: 479824 Pages: 1-5
  • DOI: 10.1100/2012/479824
  • Peer Reviewed
• [Journal Article] Stability of mitochondrial membrane proteins in terrestrial vertebrates predicts aerobic capacity and longevity (2011)
  • Author(s): Kitazoe, Y., Kishino, H., Hasegawa, M., Matsui, A., Lane, N., Tanaka, M.
  • Journal Title: Genome Biology and Evolution Volume: 3 Pages: 1233-1244
  • DOI: 10.1093/gbe/evr079
  • Peer Reviewed
• [Journal Article] Was the universal common ancestry proved? (2010)
  • Author(s): T. Yonezawa and M. Hasegawa
  • Journal Title: Nature Volume: 468, E9
• [Journal Article] The position of Gnetales among seed plants : overcoming pitfalls of chloroplast phylogenomics (2010)
  • Author(s): B.Zhong, T.Yonezawa, Y.Zhong, M.Hasegawa
  • Journal Title: Molecular Biology and Evolution Volume: 27 Pages: 2855-2863
  • Peer Reviewed
• [Journal Article] Was the universal common ancestry proved? (2010)
  • Author(s): T.Yonezawa, M.Hasegawa
  • Journal Title: Nature Volume: 468
  • Peer Reviewed
• [Presentation] Divergence and convergence in evolution (2011)
  • Author(s): M. Hasegawa
  • Organizer: Molecular Biology and Evolution Meeting
  • Place of Presentation: Kyoto
  • Year and Date: 2011-07-28
• [Presentation] The human‐chimpanzee‐gorilla problem in the post‐genomic era (2011)
  • Author(s): M. Hasegawa
  • Organizer: Workshop of Molecular Evolutionary Studies in Post-Genomic Era
  • Place of Presentation: Xian, China
  • Year and Date: 2011-06-09
• [Book] 新図説・動物の起源と進化 (2011)
  • Author(s): 長谷川政美
  • Total Pages: 207
  • Publisher: 八坂書房