Modeling of Molecular Evolution and Development of the Methods for Phylogenetic Inference
| Project/Area Number |
16300089
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Statistical science
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| Research Institution | Institute of Statistical Mathematics |
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Principal Investigator |
HASEGAWA Masami Institute of Statistical Mathematics, Department of Modeling, Professor, モデリング研究系, 教授 (60011657)
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| Co-Investigator(Kenkyū-buntansha) |
ADACHI Jun Institute of Statistical Mathematics, Department of Modeling, Associate professor, モデリング研究系, 助教授 (30370092)
CAO Ying Institute of Statistical Mathematics, Department of Modeling, Assistant professor, モデリング研究系, 助手 (20370091)
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| Project Period (FY) |
2004 – 2006
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| Project Status |
Completed (Fiscal Year 2006)
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| Budget Amount *help |
¥14,300,000 (Direct Cost: ¥14,300,000)
Fiscal Year 2006: ¥3,200,000 (Direct Cost: ¥3,200,000)
Fiscal Year 2005: ¥4,600,000 (Direct Cost: ¥4,600,000)
Fiscal Year 2004: ¥6,500,000 (Direct Cost: ¥6,500,000)
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| Keywords | Modeling / Molecular evolution / Molecular phylogeny / Maximum likelihood / Codon-substitution model / Model selection / 分子系統樹推定 / モデル / ミススペシフィケーション / ゲノム統計学 / 真獣類 / 推定の偏り / ミトコンドリア / ゲノムデータ / 分子進化のモデル / ヒゲクジラ / ハクジラ / 真核生物 |
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| Research Abstract |
In order to infer the phylogenetic tree from the sequence data of nucleotides and amino acids, it is prerequisite to use statistical methods based on stochastic models. The first step of the phylogenetic inference is how to well approximate the process of molecular evolution. In this research project, we demonstrated the usefulness of the codon-substitution model. The most widely used method in inferring the molecular phylogeny assumes independence among nucleotides. However, this assumption grossly violates the underlying process during evolution. Alternative way is to use amino acid sequences when the data is from a protein-encoding gene. However, this does not take account of the information from synonymous nucleotide substitutions, and therefore it is not an appropriate way in analyzing closely related species. We used a codon-substitution model in real data analyses, and demonstrated that the model is very useful in resolving long-standing phylogenetic problems (Sasaki et al., 2005 ; Yonezawa et al.,2007).
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Report
(4 results)
Research Products
(20 results)
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[Journal Article] Mitochondrial phylogenetics and evolution of Mysticete whales2005
Author(s)
T.Sasaki, M.Nikaido, H.Hamilton, M.Goto, H.Kato, N.Kanda, L.A.Pastene, Y.Cao, R.E.Fordyce, M.Hasegawa, N.Okada
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Journal Title
Systematic Biology 54
Pages: 77-90
Description
「研究成果報告書概要(和文)」より
Related Report
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[Journal Article] Cyanobacterial Genes Transmitted to the Nucleus Before Divergence of Red Algae in the Chromista2004
Author(s)
Nozaki, H., Matsuzaki, M., Misumi, O., Kuroiwa, H., Hasegawa, M., Higashiyama, T., Shin-i, T., Kohara, Y., Ogasawara, N., Kuroiwa, T.
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Journal Title
Journal of Molecular Evolution 59
Pages: 103-113
Related Report
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[Journal Article] Mitochondrial phylogenetics and evolution of Mysticete whales
Author(s)
T.Sasaki, M.Nikaido, H.Hamilton, M.Goto, H.Kato, N.Kanda, L.A.Pastene, Y.Cao, R.E.Fordyce, M.Hasegawa, N.Okada
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Journal Title
Syst.Biol. 54
Pages: 77-90
Description
「研究成果報告書概要(欧文)」より
Related Report
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