1989 Fiscal Year Annual Research Report

遺伝情報の解析

Research Project

Project/Area Number	01618003
Research Institution	The Institute of Statistical Mathematics
Principal Investigator	長谷川政美統計数理研究所, 予測制御研究系, 教授 (60011657)
Co-Investigator(Kenkyū-buntansha)	次田晧東京理科大学, 総合研究所, 教授 (00028284) 安永照雄理化学研究所, 電算機歇, 研究員舘野義男国立遺伝学研究所, 遺伝資源, 助手 (00202424) 五條堀孝国立遺伝学研究所, 集団遺伝系, 助教授 (50162136) 宮田隆九州大学, 理学部, 助教授 (20022692)
Keywords	DNA / 塩基配列 / たんぱく質 / アミノ酸配列 / 系統樹 / 最尤法 / 古細菌 / 突然変異
Research Abstract	最尤法に基づき、DNA塩基配列デ-タあるいはたんぱく質のアミノ酸配列デ-タから進化の系統樹を推定するための方法を開発した。最尤法で得られた系統樹がどの程度まで信頼できるものであるかを示す指標としてブ-トストラップ確率を考え、これを簡単に計算できる方法を開発した。更に、一つの遺伝子だけではなく、複数のさまざまなタイプの遺伝子や蛋白質のデ-タのもつ情報を総合的に活用して、系統樹のブ-トストラップ確率が計算できるようになった。最尤法の一般化である情報量基準AICを用いて、必ずしも分子進化速度が一定でない場合でも、系統樹における枝分かれの年代が推定できるようになった。これらの方法をさまざまのデ-タに適用することにより、以下の知見を得た。第一に、霊長類ミトコンドリアDNAの進化において、原猿類のキツネザルの系統で異常にトランジションの速度が減少していることが見出され、ミトコンドリアDNAの突然変異の機構をさぐる上で貴重な知見が得られた。第二に、ATPア-ゼや伸長因子(TuとG)など現存生物の共通祖先において重複した遺伝子を用いて、古細菌、真正細菌、真核生物の間の系統関係を調べた結果、古細菌は真核生物に近いことが明らかになった。このことは真核生物の起原をさぐる上で、貴重な知見を与えるものである。このほかにも、生物進化や遺伝子の進化を明らかにする上で重要な知見がいくつか得られた。統計約2300種の遺伝子(cDNA)塩基配列デ-タがコンピュ-タに入力された。このほとんどはGenBankなどの最新のデ-タベ-スに入力されていないものであり、チェックが厳重になされているので信頼度が高い。塩基配列デ-タを翻訳し、たんぱく質デ-タベ-スにも格納した。新しいデ-タを附加したたんぱく質デ-タベ-スがホモロジ-探査に利用され、いくつかの成果を得た。

Research Products

(27 results)

All Other

All Publications (27 results)

[Publications] Hasegawa M.,Kishino H.: "Confidence limits on the maximumーlikelihood estimate of the hominoid tree from mitochondrialーDNA sequences" Evolution. 43. 672-677 (1989)
[Publications] Kishino H.,Hasegawa M.: "Evaluation of the maximum likehood estimate of the evolutionary tree topologies from DNA sequence data,and the branching order in Hominoidea" Journal of Molecular Evolution. 29. 170-179 (1989)
[Publications] Hasegawa M.,Kishino H.Yano T.: "Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in Hominoidea" Journal of Human Evolution. 18. 461-476 (1989)
[Publications] Hasegawa M.,Kishino H.: "Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders" Japanese Journal of Genetics. 64. 243-258 (1989)
[Publications] Iwabe N.,Kuma K.,Hasegawa M.,Osawa S.,Miyata T.: "Evolution relationship of archaebacteria,eubacteria,and eukaryーotes inferred from phylogenetic trees of duplicated genes" Proceedings of National Academy of Sciences,USA. 86. 9355-9359 (1989)
[Publications] Kishino H.,Hasegawa M.: "Converting distance to time:Application to human evolution" Methods in Enzymology. 183. 550-570 (1990)
[Publications] Kishino H.,Hasegawa M.: "Maximum likelihood inference of protein phylogeny and the origin of chloroplasts" Journal of Molecular Evolution. 30. (1990)
[Publications] Hasegawa M.,Kishino H.,Hayasaka K.,Horai S.: "Mitochondrial DNA evolutin in primates: Transition rate has been extremely low lemur" Journal of Molecular Evolution. 31. (1990)
[Publications] Watanabe Y.,Saitou N.,Hayashida H.,Miyata T.,Hisajima H.,Honjo T.,Ueda S.: "Nucleotide sequences of immunoglobulin epsilon pseudogenes in man and apes and their phylogenetic relationships" Journal of Molecular Biology. 205. 85-90 (1989)
[Publications] Sakaguchi T.,Toyoda T.,Gotoh B.,Inoceio.N.M.,Kuma K.,Miyata T.,Nagai Y.: "Newcastle disease virus evolution.I.Multiple lineages denined by sequence variability of the hemagglutininーneuraminidase gene" Virology. 169. 273-282 (1989)
[Publications] Toyoda T.,Sakaguchi T.,Hirose H.,Gotoh B.,Kuma K.,Miyata T.,Nagai Y.: "Newcastle disease virus evolution.II.Lack of gene recombination in generating virulent and avirulent strains" Virology.
[Publications] Hatakeyama M.,Tsudo M.,Minamoto S.,Kono T.,Doi,Miyata T.,Miyasaka M.,Taniguchi T.: "Interleukinー2 receptor β chain gene: Generation of three receptor forms by cloned human α and β chain cDNA's" Science. 244. 551-556 (1989)
[Publications] Kodaira K.,Miyata T.,Suzuki K.,Nakano K.,Taketo A.: "Possible finger structure in gene A protein of Microvidiae" Biochem.Biophy.Acta. 1008. 123-124 (1989)
[Publications] Harada H.,Fujita T.,Miyamoto M.,Kimura Y.,Maruyama M.,Furia A.,Miyata T.,Taniguchi T.: "Structurally similar but functionally distinct factors,IRFー1 and IRFー2,bind to the same regulatory elements of IFN and IFNーinducible genes" Cell. 58. 729-739 (1989)
[Publications] Miyata T.,Kuma K.,Iwabe N.,Hayashida H.,Yasunaga T.: "Different rates of evolution of autosomeー,X chromosomeーand Y chromosomeーlinked genes:Hypothesis of maleーdriven molecular evolution" Population Biology of Genes and Molecules(ed.Ohta,T.).
[Publications] Kaupp.U.B.,Niidome T.,Tanabe T.,Terada S.,Boenigk W.,Struhmer W.,Kangawa K.,Matsuo H.,Hirose T.,Miyata T.,Numa S.: "Primary structure and functional expression from complementary DNA of the rod photoreceptor for cGMPーgated channel" Nature. 342. 762-766 (1989)
[Publications] Yokoyama S.,Imoto K.,Kawamura T.,Higashida H.,Iwabe N.,Miyata T.,Numa S.: "Potassium channels from NG108ー15 neuroblastomaーglioma hybrid cells." FEBS Letters. 259. 37-42 (1989)
[Publications] Iwabe N.,Kuma K.,Miyata T.: "Sequence similarity of bacteriophage SP02 DNA polymerase with E.coli DNA polymerase" Nucleic Acids Research. 17. 8866-8866 (1989)
[Publications] Iwabe N.,Kuma K.,Saitou N.,Tsuda M.,Miyata T.: "Evolution of rhodopsin supergene family:Independent divergence of visual pigments in vertebrates and insects and possibly in mollusks" Proceedings of Japan Academy. 65B. 195-198 (1989)
[Publications] Kuma K.,Iwabe N.,Kawanishi Y.,Miyata T.: "RNAーbinding proteinーrelated sequence in a malaria antigen,clusterd asparagineーrich protein" FEBS Letter.
[Publications] Iwabe N.,Kuma K.,Kishino H.,Hasegawa M.,Miyata T.: "Compartmentalized isozyme genes and the origin of introns" Journal of Molecular Evolution.
[Publications] Kono T.,Doi T.,Yamada G.Hatakeyama M.,Minamoto S.Tsudo M.,Miyasaka M.,Miyata T.,Taniguchi T.: "The murine ILー2 receptor β chain:Dysregulated gene expression in a lymphoma line ELー4 caused by a promotor insertion" Proceedings of National Academy of Sciences,USA.
[Publications] Fukami K.,Tateno Y.: "On the maximum likelihood method for estimating molecular trees:Uniqueness of the likelihood point" Journal of Molecular Evolution. 28. 460-464 (1989)
[Publications] Fukami K.,Tateno Y.: "Maximum likelihood tree estimation against differnt patterns of base substitutions" Journal of Molecular Evolution.
[Publications] Satake K.,Yugi M.,Kamo M.,Kihara H.,Tsugita A.: "Hemerythrin from Lingula unguis consists of two different subunits.and β" Protein Sequencec & Data Analysis. 3. 1-5 (1990)
[Publications] Moriyama E.N.,Gojobori T.: "Evolution of nested genes with special reference to cuticle proteins in Drosophila melanogaster" Journal of Molecular Evolution. 28. 391-397 (1989)
[Publications] Gojobori T.,Moriyama E.N.,Kimura M.: "Statistical methods for estimating sequence divergence" Methods in Enzymology. 183. 531-550 (1990)

1989 Fiscal Year Annual Research Report

遺伝情報の解析

Principal Investigator

長谷川 政美 統計数理研究所, 予測制御研究系, 教授 (60011657)

Research Products

[Publications] Hasegawa M.,Kishino H.: "Confidence limits on the maximumーlikelihood estimate of the hominoid tree from mitochondrialーDNA sequences" Evolution. 43. 672-677 (1989)

[Publications] Kishino H.,Hasegawa M.: "Evaluation of the maximum likehood estimate of the evolutionary tree topologies from DNA sequence data,and the branching order in Hominoidea" Journal of Molecular Evolution. 29. 170-179 (1989)

[Publications] Hasegawa M.,Kishino H.Yano T.: "Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in Hominoidea" Journal of Human Evolution. 18. 461-476 (1989)

[Publications] Hasegawa M.,Kishino H.: "Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders" Japanese Journal of Genetics. 64. 243-258 (1989)

[Publications] Iwabe N.,Kuma K.,Hasegawa M.,Osawa S.,Miyata T.: "Evolution relationship of archaebacteria,eubacteria,and eukaryーotes inferred from phylogenetic trees of duplicated genes" Proceedings of National Academy of Sciences,USA. 86. 9355-9359 (1989)

[Publications] Kishino H.,Hasegawa M.: "Converting distance to time:Application to human evolution" Methods in Enzymology. 183. 550-570 (1990)

[Publications] Kishino H.,Hasegawa M.: "Maximum likelihood inference of protein phylogeny and the origin of chloroplasts" Journal of Molecular Evolution. 30. (1990)

[Publications] Hasegawa M.,Kishino H.,Hayasaka K.,Horai S.: "Mitochondrial DNA evolutin in primates: Transition rate has been extremely low lemur" Journal of Molecular Evolution. 31. (1990)

[Publications] Watanabe Y.,Saitou N.,Hayashida H.,Miyata T.,Hisajima H.,Honjo T.,Ueda S.: "Nucleotide sequences of immunoglobulin epsilon pseudogenes in man and apes and their phylogenetic relationships" Journal of Molecular Biology. 205. 85-90 (1989)

[Publications] Sakaguchi T.,Toyoda T.,Gotoh B.,Inoceio.N.M.,Kuma K.,Miyata T.,Nagai Y.: "Newcastle disease virus evolution.I.Multiple lineages denined by sequence variability of the hemagglutininーneuraminidase gene" Virology. 169. 273-282 (1989)

[Publications] Toyoda T.,Sakaguchi T.,Hirose H.,Gotoh B.,Kuma K.,Miyata T.,Nagai Y.: "Newcastle disease virus evolution.II.Lack of gene recombination in generating virulent and avirulent strains" Virology.

[Publications] Hatakeyama M.,Tsudo M.,Minamoto S.,Kono T.,Doi,Miyata T.,Miyasaka M.,Taniguchi T.: "Interleukinー2 receptor β chain gene: Generation of three receptor forms by cloned human α and β chain cDNA's" Science. 244. 551-556 (1989)

[Publications] Kodaira K.,Miyata T.,Suzuki K.,Nakano K.,Taketo A.: "Possible finger structure in gene A protein of Microvidiae" Biochem.Biophy.Acta. 1008. 123-124 (1989)

[Publications] Harada H.,Fujita T.,Miyamoto M.,Kimura Y.,Maruyama M.,Furia A.,Miyata T.,Taniguchi T.: "Structurally similar but functionally distinct factors,IRFー1 and IRFー2,bind to the same regulatory elements of IFN and IFNーinducible genes" Cell. 58. 729-739 (1989)

[Publications] Miyata T.,Kuma K.,Iwabe N.,Hayashida H.,Yasunaga T.: "Different rates of evolution of autosomeー,X chromosomeーand Y chromosomeーlinked genes:Hypothesis of maleーdriven molecular evolution" Population Biology of Genes and Molecules(ed.Ohta,T.).

[Publications] Kaupp.U.B.,Niidome T.,Tanabe T.,Terada S.,Boenigk W.,Struhmer W.,Kangawa K.,Matsuo H.,Hirose T.,Miyata T.,Numa S.: "Primary structure and functional expression from complementary DNA of the rod photoreceptor for cGMPーgated channel" Nature. 342. 762-766 (1989)

[Publications] Yokoyama S.,Imoto K.,Kawamura T.,Higashida H.,Iwabe N.,Miyata T.,Numa S.: "Potassium channels from NG108ー15 neuroblastomaーglioma hybrid cells." FEBS Letters. 259. 37-42 (1989)

[Publications] Iwabe N.,Kuma K.,Miyata T.: "Sequence similarity of bacteriophage SP02 DNA polymerase with E.coli DNA polymerase" Nucleic Acids Research. 17. 8866-8866 (1989)

[Publications] Iwabe N.,Kuma K.,Saitou N.,Tsuda M.,Miyata T.: "Evolution of rhodopsin supergene family:Independent divergence of visual pigments in vertebrates and insects and possibly in mollusks" Proceedings of Japan Academy. 65B. 195-198 (1989)

[Publications] Kuma K.,Iwabe N.,Kawanishi Y.,Miyata T.: "RNAーbinding proteinーrelated sequence in a malaria antigen,clusterd asparagineーrich protein" FEBS Letter.

[Publications] Iwabe N.,Kuma K.,Kishino H.,Hasegawa M.,Miyata T.: "Compartmentalized isozyme genes and the origin of introns" Journal of Molecular Evolution.

[Publications] Kono T.,Doi T.,Yamada G.Hatakeyama M.,Minamoto S.Tsudo M.,Miyasaka M.,Miyata T.,Taniguchi T.: "The murine ILー2 receptor β chain:Dysregulated gene expression in a lymphoma line ELー4 caused by a promotor insertion" Proceedings of National Academy of Sciences,USA.

[Publications] Fukami K.,Tateno Y.: "On the maximum likelihood method for estimating molecular trees:Uniqueness of the likelihood point" Journal of Molecular Evolution. 28. 460-464 (1989)

[Publications] Fukami K.,Tateno Y.: "Maximum likelihood tree estimation against differnt patterns of base substitutions" Journal of Molecular Evolution.

[Publications] Satake K.,Yugi M.,Kamo M.,Kihara H.,Tsugita A.: "Hemerythrin from Lingula unguis consists of two different subunits.and β" Protein Sequencec & Data Analysis. 3. 1-5 (1990)

[Publications] Moriyama E.N.,Gojobori T.: "Evolution of nested genes with special reference to cuticle proteins in Drosophila melanogaster" Journal of Molecular Evolution. 28. 391-397 (1989)

[Publications] Gojobori T.,Moriyama E.N.,Kimura M.: "Statistical methods for estimating sequence divergence" Methods in Enzymology. 183. 531-550 (1990)

長谷川政美統計数理研究所, 予測制御研究系, 教授 (60011657)