Evolution by loss of genes that have become redundant in relation to changing environments

• Project/Area Number: 16107001
• Research Category: Grant-in-Aid for Scientific Research (S)
• Allocation Type: Single-year Grants
• Research Field: Genetics/Genome dynamics
• Research Institution: The Graduate University for Advanced Studies
• Principal Investigator: TAKAHATA Naoyuki The Graduate University for Advanced Studies, 学長 (30124217)
• Co-Investigator(Kenkyū-buntansha): SATTA Yoko 総合研究大学院大学, 先導科学研究科, 教授 (20222010) ; OTA Tatsuya 総合研究大学院大学, 先導科学研究科, 准教授 (30322100)
• Co-Investigator(Renkei-kenkyūsha): GO Yasuhiro 総合研究大学院大学, 葉山高等研究センター, 上級研究員 (50377123) ; SAWAI Hiromi 総合研究大学院大学, 葉山高等研究センター, 上級研究員 (60377124) ; KANEKO Satoko 総合研究大学院大学, 葉山高等研究センター, 上級研究員 (30456339) ; KIM Hie Lim 総合研究大学院大学, 葉山高等研究センター, 上級研究員 (60507200) ; IGAWA Takeshi 総合研究大学院大学, 葉山高等研究センター, 上級研究員 (00507197) ; IWASE Mineyo 総合研究大学院大学, 葉山高等研究センター, センター研究員 (30155048)
• Project Period (FY): 2004 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥104,260,000 (Direct Cost: ¥80,200,000、Indirect Cost: ¥24,060,000); Fiscal Year 2008: ¥20,800,000 (Direct Cost: ¥16,000,000、Indirect Cost: ¥4,800,000); Fiscal Year 2007: ¥20,800,000 (Direct Cost: ¥16,000,000、Indirect Cost: ¥4,800,000); Fiscal Year 2006: ¥20,800,000 (Direct Cost: ¥16,000,000、Indirect Cost: ¥4,800,000); Fiscal Year 2005: ¥20,800,000 (Direct Cost: ¥16,000,000、Indirect Cost: ¥4,800,000); Fiscal Year 2004: ¥21,060,000 (Direct Cost: ¥16,200,000、Indirect Cost: ¥4,860,000)
• Keywords: 偽遺伝子 / 遺伝子発現 / 環境と生物 / ゲノム / ヒト特異的発現抑制遺伝子 / 皮膚発現遺伝子 / 霊長類 / 極限環境 / 自然選択の緩和 / 近縁種 / 家禽化 / ヒフ発現遺伝子 / 種分化 / 分子時計 / 進化 / 適応 / 性染色体の進化 / 人類進化 / 発現プロファイル / 苦味受容体遺伝子の退化 / マコリン遺伝子の発現調節 / 家禽の遺伝的多様性 / ノトセニア / 遺伝子の退化 / 分子進化、集団遺伝学 / 苦味受容体遺伝子 / 家禽

Research Abstract

生物進化の道筋は、その生物を取り巻く生物的・物理的環境によって決められてきた。種の個別性とは既存の遺伝子の発現をその生息環境に適応させて整理した結果である。本研究では、このような作業仮説に基づき、数百万年の期間に獲得されたヒトの個別性に関する遺伝的変容を探った。また、同様の観点から、家禽化に伴うニワトリの遺伝的変容を研究し、作業仮説の一般性を検証した。

Research Products

• [Journal Article] 人間の由来と病気 (2009)
  • Author(s): 高畑尚之
  • Journal Title: 日経サイエンス 39 Pages: 56-63
• [Journal Article] ological implication for loss of function at major histocompatibility complex loci (2008)
  • Author(s): Sawai, H., Go, Y. and Satta, Y. Bi
  • Journal Title: Immunogenetics 60 Pages: 295-302
  • Peer Reviewed
• [Journal Article] Biological implication for loss of function at major histocompatibility complex loci. (2008)
  • Author(s): Sawai, H., Go, Y. Satta, Y
  • Journal Title: Immunogenetics 60 Pages: 295-302
  • Peer Reviewed
• [Journal Article] ダーウィンと現代集団遺伝学 (2008)
  • Author(s): 高畑尚之
  • Journal Title: 生物の科学「遺伝」 62 Pages: 26-30
• [Journal Article] Population genetic analysis of the N-acylsphingosine amidohydrolase gene associated with mental activity in humans (2008)
  • Author(s): Kim, H.L., Satta, Y.
  • Journal Title: Genetics 178 Pages: 1505-1515
  • Peer Reviewed
• [Journal Article] Gene conversion during primate evolution. (2008)
  • Author(s): Satta, Y.
  • Journal Title: Encyclopedia of Life Sciences (http://www.els.net/)
• [Journal Article] Biological implication for loss of function at Major Histocompatibility Complex loci. Immunogenetics (2008)
  • Author(s): Sawai, H., Go, Y., Satta, Y.
  • Journal Title: Immunogenetics (印刷中)
  • Peer Reviewed
• [Journal Article] J. Gene flow between species of Lake Victoria haplochromine fishes (2007)
  • Author(s): Samonte, I. E., Satta, Y. Sato, A., Tichy, H., Takahata, N.and Klein
  • Journal Title: Mol. Biol. Evol 24 Pages: 2069-2080
  • Peer Reviewed
• [Journal Article] mtDNA sequenc es show Japanese native chickens have multiple origins (2007)
  • Author(s): Oka, T., Ino, Y., Nomura, K.,Ka washima, S., Kuwatama, T., Han ada, H., Amano, T., Takada,M., Takahata, N., Hayashi, Y.and Ak ishinomiya, F
  • Journal Title: Animal Genet 38 Pages: 287-293
  • Peer Reviewed
• [Journal Article] Evolutionary history of sex-linked mammalian amelogenin genes (2007)
  • Author(s): Iwase, M., Kaneko, S., Kim, H., Satta, Y. and Takahata, N
  • Journal Title: Cells Tissues Organs 186 Pages: 49-59
  • Peer Reviewed
• [Journal Article] Molecular clock : An anti-neo-Darwinian legacy (2007)
  • Author(s): Takahata, N
  • Journal Title: Genetics 176 Pages: 1-6
  • Peer Reviewed
• [Journal Article] An Al u retrotrans-position-mediated deletio n of CHD7 in a patient with CH ARGE syndrome (2007)
  • Author(s): Udaka, T., Okamoto, N., Aramaki, M., Torii, C., Kosaki, R., Hosokai, N., Hayakawa, T.,, Takahata, N., Ta kahashi, T. and Kosaki, K
  • Journal Title: Am. J. Med. Genet. A 147 Pages: 721-726
  • Peer Reviewed
• [Journal Article] The origin and evolutio n of human ampliconic gene familie s and ampliconic structure (2007)
  • Author(s): Bhowmick, B. K., Satta, Y. and Ta kahata, N
  • Journal Title: Genome Res 17 Pages: 441-450
  • Peer Reviewed
• [Journal Article] Molecular clock: an anti-neo-Darwinian legacy (2007)
  • Author(s): Takahata, N.
  • Journal Title: Genetics 176 Pages: 1-6
• [Journal Article] The origin and evolution of human ampliconic gene families and ampliconic structure. (2007)
  • Author(s): Bhomick, B. K., Satta, Y., Takahata, N.,
  • Journal Title: Genome Res. 17 Pages: 441-450
  • Peer Reviewed
• [Journal Article] An Alu retrotransposition-mediated deletion of CHD7 in a patient with CHARGE syndrome. (2007)
  • Author(s): Udaka, T., Okamoto, N., Aramaki, M., Torii, C., Kosaki, R., Hosokai, N., Hayakawa, T., Takahata, N., Takahashi, T. Kosaki, K
  • Journal Title: Am. J. Med. Genet. A.143 Pages: 721-726
  • Peer Reviewed
• [Journal Article] mtDNA sequences show Japanese native chickens have multiple origins. (2007)
  • Author(s): Oka, T., Ino, Y., Nomura, K., Kawashima, S., Kuwatama, T., Hanada, H., Amano, T., Takada, M., Takahata, N., Hayashi, Y. and Fumihito, A.
  • Journal Title: Animal Genet. 38 Pages: 287-293
  • Peer Reviewed
• [Journal Article] Evolutionary history of sex-linked mammalian amelogenin genes (2007)
  • Author(s): Iwase, M., Kaneko, S., Kim, H., Satta, Y., Takahata, N.
  • Journal Title: Cells Tissues Organs 186 Pages: 49-59
  • Peer Reviewed
• [Journal Article] Gene flow between species of Lake Victoria haplochromine fishes. (2007)
  • Author(s): Samonte, IE, Satta, Y., Sato, A., Tichy, H., Takahata N., Klein J
  • Journal Title: Mol Biol Evol 24 Pages: 2069-2080
  • Peer Reviewed
• [Journal Article] Identification of CTL epitopes in hepatitis C virus by a genome-wide computational scanning and a rational design of peptide vaccine. (2007)
  • Author(s): Mashiba, T., Udaka, K., Hirachi, Y., Hiasa, Y., Miyakawa, T., Satta, Y. Osoda, T., Kataoka, S., Kohara, M., Onji, M.
  • Journal Title: Immunogenetics 59 Pages: 197-209
  • Peer Reviewed
• [Journal Article] Further evid ence for recombina- tion between m ouse hemoglobin-beta b1 and b2 ge nes based on the nucleotide sequenc es of intron, UTR, and intergenic spacer regions. (2006)
  • Author(s): Sato, J. J., Tsuru, Y., Hirai, K., Ya maguchi, Y., Mekada, K., Takahata,N. and Moriwaki, K
  • Journal Title: Genes, Genet. Syst 81 Pages: 201-209
  • Peer Reviewed
• [Journal Article] Origin and evolution of processed pseudoge nes that stabilize functional Makorin1 mRNAs in mice (2006)
  • Author(s): Kaneko, S., Aki, I., Tsuda, K. Mekada, K., Moriwaki, K, Takahata N.,and Satta, Y
  • Journal Title: primates and other mammals. Genetics 172 Pages: 2421-2429
  • Peer Reviewed
• [Journal Article] Fixation of the human-specific CMP-N-acetylneuraminic acid hydroxylase pseudogene and implications of haplotype diversity for human evolution (2006)
  • Author(s): Hayakawa, T., Aki, I., Varki, A.,Satta, Y., and Takahata, N
  • Journal Title: Genetics 172 Pages: 1139-1146
  • Peer Reviewed
• [Journal Article] Origin and evolution of processed pseudogenes that stabilize functional Makorin1 mRNAs in mice, primates and other mammals (2006)
  • Author(s): Kaneko, S. et al.
  • Journal Title: Genetics 172 Pages: 2421-2429
• [Journal Article] Fixation of the human-specific CMP-N-acetylneuraminic acid hydroxylase pseudogene and implications of haplotype diversityfor human evolution. (2006)
  • Author(s): Hayakawa, T. et al.
  • Journal Title: Genome Research 172 Pages: 1139-1146
• [Journal Article] MHC偽遺伝子化の生物学的意義 (2006)
  • Author(s): 颯田 葉子
  • Journal Title: MHC 13・1 Pages: 19-24
  • NAID: 130005509822
• [Journal Article] 五感の遺伝子からみたヒトの進化 (2006)
  • Author(s): 郷 康広, 颯田 葉子
  • Journal Title: 日経サイエンス 36・3 Pages: 32-41
• [Journal Article] Lineage-specific loss of function of bitter taste receptor genes in humans and non-human primates (2005)
  • Author(s): Go, Y., Satta, Y., Takenaka, O.,and Takahata, N
  • Journal Title: Genetics 170 Pages: 313-326
  • Peer Reviewed
• [Journal Article] Lineage-specific loss of function of bitter taste receptor genes in humans and non-human primates. (2005)
  • Author(s): Go, Y.et al.
  • Journal Title: Genetics 170 Pages: 313-326
• [Journal Article] Fixation of the human-specific CMP-N-acetylneuraminic acid hydroxylase pseudogene and implications of haplotype diversity for human evolution. (2005)
  • Author(s): Hayakawa, T. et al.
  • Journal Title: Genetics 172 Pages: 1139-1146
• [Journal Article] Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and B AC end sequences (2004)
  • Author(s): Satta, Y., Hickerson, M., Watanabe,H., O'hUigin, C., and Klein, J
  • Journal Title: J. Mol. Evol 59 Pages: 478-487
  • Peer Reviewed
• [Journal Article] The distribution of the ancestral haplotype in finite stepping-stone models with population expansion (2004)
  • Author(s): Satta, Y., and Takahata, N
  • Journal Title: Mol. Ecol 13 Pages: 877-886
  • Peer Reviewed
• [Journal Article] Evolutionary relationships of major histocompatibility complex class I genes in simian prima tes (2004)
  • Author(s): Sawai, H., Kawamoto, Y., Takahata,N., and Satta, Y
  • Journal Title: Genetics 166 Pages: 1897-1907
  • Peer Reviewed
• [Journal Article] Evolutionary relationships of major histocompatibility complex class I genes in simian primates (2004)
  • Author(s): SAWAI, H., KAWAMOTO, Y., TAKAHATA, N., SATTA, Y.
  • Journal Title: Genetics 166 Pages: 1897-1907
• [Journal Article] The distribution of the ancestral haplotype in finite stepping-stone models with population expansion. (2004)
  • Author(s): SATTA, Y., TAKAHATA, N.
  • Journal Title: Mol.Ecol. 13 Pages: 877-886
• [Journal Article] Ancestral population size and species divergence times in the primate lineage on the basis of intron and BAC end sequences (2004)
  • Author(s): SATTA, Y., et al.
  • Journal Title: J.Mol.Evol. 59 Pages: 478-487
• [Journal Article] Phylogenetic relationships among East African haplochromine fish as revealed by short interspersed elements (SINEs) (2004)
  • Author(s): TERAI, Y., et al.
  • Journal Title: J.Mol.Evol. 58 Pages: 64-78
• [Journal Article] The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear loci (2004)
  • Author(s): TAKEZAKI, N., et al.
  • Journal Title: Mol.Biolo.Evol. 21(8) Pages: 1512-1524
• [Journal Article] Origin and evolution of processed pseudogenes that stabilize functional Makorin1 mRNAs in mice, primates and other mammals
  • Author(s): Kaneko, S. et al.
  • Journal Title: Genetics (印刷中)
• [Journal Article] Lineage-specific loss of function of bitter taste receptor genes in humans and non-human primates
  • Author(s): GO, Y., Y.SATTA, O.TAKENAKA, N.TAKAHATA
  • Journal Title: Genetics (印刷中)
• [Presentation] 極限環境におけるノトセニア亜目硬骨魚類の分子進化 (2008)
  • Author(s): 大田竜也
  • Organizer: 第77回岩手大学COEフォーラム
  • Place of Presentation: 岩手大学
  • Year and Date: 2008-11-28
• [Presentation] 皮膚発現遺伝子プロファイルのヒトとチンパンンジー間の比較 (2008)
  • Author(s): 颯田葉子
  • Organizer: 日本遺伝学会第80回大会
  • Place of Presentation: 名古屋
  • Year and Date: 2008-09-05
• [Presentation] 哺乳類VCXファミリーの形成過程 (2008)
  • Author(s): 岩瀬峰代, 颯田葉子, 高畑尚之
  • Organizer: 日本遺伝学会第80回大会
  • Place of Presentation: 名古屋
  • Year and Date: 2008-09-03
• [Presentation] ヒト特異的に発現量が低下している遺伝子群の進化 (2008)
  • Author(s): 金子聡子, 颯田葉子, 高畑尚之
  • Organizer: 日本遺伝学会第80回大会
  • Place of Presentation: 名古屋
  • Year and Date: 2008-09-03
• [Presentation] ヒト特異的偽遺伝子の起源と進化における意義 (2008)
  • Author(s): 井川武, 颯田葉子, 高畑尚之
  • Organizer: 日本遺伝学会第80回大会
  • Place of Presentation: 名古屋
  • Year and Date: 2008-09-03
• [Presentation] 機能を失った遺伝子の進化-偽遺伝子の生物学的意味 (2008)
  • Author(s): 颯田葉子
  • Organizer: 日本バイオインフォマティクス学会、第19回システムバイオロジー研究会
  • Place of Presentation: 横浜
  • Year and Date: 2008-06-27
• [Presentation] Biological implication for loss of function at Major Histo- compatibility Complex loci. (2008)
  • Author(s): Sawai, H., Go, Y., Satta, Y
  • Organizer: SMBE 2008
  • Place of Presentation: バルセロナ、スペイン
  • Year and Date: 2008-06-08
• [Presentation] Evolutionary origin of peptideglycan recognition proteins in the vertebrate innate innate immune system. (2008)
  • Author(s): Montano, A., Tsujino, F., Takahata, N., Satta, Y.
  • Organizer: 22^<nd> European Immunogenetics and Histocompatibility Conference
  • Place of Presentation: ツールズ、フランス
  • Year and Date: 2008-04-02
• [Presentation] 環境とゲノム (2008)
  • Author(s): 高畑尚之
  • Organizer: 生態学会シンポジウム『ゲノム進化学と生態学』
  • Place of Presentation: 福岡
  • Year and Date: 2008-03-15
• [Presentation] 遺伝子の退化によるヒトの進化-尿酸酸化酵素遺伝子を例として (2008)
  • Author(s): 高畑尚之
  • Organizer: 第41回日本痛風・核酸代謝学会
  • Place of Presentation: 福井
  • Year and Date: 2008-02-14
• [Presentation] 遺伝子の退化によるヒトの進化-尿酸酸化酵素遺伝子を例として (2008)
  • Author(s): 高畑尚之
  • Organizer: 第41回日本痛風・核酸代謝学会、ランチョンセミナー
  • Place of Presentation: 福井
• [Presentation] Evolutionary origin of peptideglycan recognition proteins in the vertebrate innate immune system」22^nd European Immunogenetics and Histocompatibility Conference (2008)
  • Author(s): Satta, Y
  • Organizer: Satellite Symposium "MHC gene polymorphism and evolution"
  • Place of Presentation: Toulouse
• [Presentation] 人類特異的な遺伝的変化と人類進化 (2007)
  • Author(s): 颯田葉子
  • Organizer: 人間行動進化研究会
  • Place of Presentation: 葉山
  • Year and Date: 2007-12-08
• [Presentation] 偽遺伝子と進化医学 (2007)
  • Author(s): 颯田葉子
  • Organizer: 国立遺伝学研究所シンポジウム『ヒトゲノム多様性に基づく進化医学の発展』
  • Place of Presentation: 三島
  • Year and Date: 2007-10-03
• [Presentation] The current status of the neutral theory of molecular evolution (2007)
  • Author(s): 高畑尚之
  • Organizer: 遺伝学会ミニシンポジウム『分子進化の中立説 : これまでの40年とこれから』
  • Place of Presentation: 岡山
  • Year and Date: 2007-09-19
• [Presentation] 分子進化の中立説の意味と課題 (2007)
  • Author(s): 高畑 尚之
  • Organizer: 第79回日本遺伝学会大会
  • Place of Presentation: 岡山
  • Year and Date: 2007-09-19
• [Presentation] Motoo Kimura: An original thinker on evolution in Japan (2007)
  • Author(s): 高畑尚之
  • Organizer: JSPSサマープログラム
  • Place of Presentation: 葉山
  • Year and Date: 2007-07-18
• [Presentation] ヒト特異的な遺伝的変化 (2007)
  • Author(s): 颯田葉子
  • Organizer: BRCセミナー
  • Place of Presentation: 筑波
  • Year and Date: 2007-05-31
• [Presentation] 人間の由来と病気 (2006)
  • Author(s): 高畑尚之
  • Organizer: 日本文学研究専攻特別講義
  • Year and Date: 2006-12-14
• [Presentation] 生物の進化と病気 (2006)
  • Author(s): 高畑尚之
  • Organizer: 人間行動進化研究会
  • Place of Presentation: 東京
  • Year and Date: 2006-12-02
• [Presentation] アミノ酸の合成酵素と味覚受容体遺伝子群の進化と退化 (2006)
  • Author(s): 高畑尚之
  • Organizer: ICAAS「アミノ酸の科学シリーズ講演会」第六回-進化の視点から栄養を考える-
  • Place of Presentation: 東京
  • Year and Date: 2006-04-13
• [Presentation] Evolution of primate sex chromosomes and sex-linked genes (2006)
  • Author(s): Takahata, N.
  • Organizer: Masatoshi Nei Legacy Symposium, Genomes, Evolution & Bioinformatics 2006 (SMBE)
  • Place of Presentation: Arizona State University
• [Presentation] 集団遺伝学理論および分子進化に関する研究 (2006)
  • Author(s): 高畑尚之
  • Organizer: 第8回進化学会、木村賞受賞講演
  • Place of Presentation: 東京
• [Presentation] スズキ類ノトセニア亜目魚類における多重遺伝子族の進化 (2006)
  • Author(s): 大田竜也
  • Organizer: 日本分子生物学会2006フォーラム、シンポジウム「生物進化の遺伝メカニズム-生物環境適応と重複遺伝子の分子進化」
  • Place of Presentation: 名古屋
• [Presentation] Reduced repertoires of olfactory receptor genes in marine mammals, Cetacea. Annual meeting for Society for Molecular Biology and Evolution (2005)
  • Author(s): Go, Y., Satta, Y., Kuno, K., and Takahata, N.
  • Organizer: Auckland Convention Center
  • Place of Presentation: New Zealand
• [Presentation] A large ancestral population size and the origin of domestic chickens (2005)
  • Author(s): Sawai, H., Satta, Y., and Takahata, N
  • Organizer: Annual meeting for Society for Molecular Biology and Evolution, Auckland Convention Center
  • Place of Presentation: New Zealand
• [Presentation] Origin and evolution of processed pseudogenes that stabilize functional Makorin1 mRNAs in mice, primates and other mammals. Annual meeting for Society for Molecular Biology and Evolution (2005)
  • Author(s): Kaneko, S., Tsuda, K., Mekada, K., Moriwaki, K, Takahata N., and Satta, Y
  • Organizer: Auckland Convention Center
  • Place of Presentation: New Zealand
• [Book] 環境を〈感じる〉岩波サイエンスライブラリー (2009)
  • Author(s): 郷康広・颯田葉子
  • Total Pages: 114
  • Publisher: 岩波書店
• [Book] 「遺伝子からみたヒトの進化」シリーズ進化学第2巻「ヒトの進化」第2章 (2006)
  • Author(s): 颯田葉子・斎藤成也
  • Publisher: 岩波書店
• [Book] シリーズ「進化学」第5巻 ヒトの進化 第2章「遺伝子からみたヒトの進化」 (2006)
  • Author(s): 颯田葉子, 斉藤成也
  • Publisher: 岩波書店
• [Book] Molecular Medicines vol.41臨時増刊号ヒトゲノム(ゲノムと種、ヒト) (2004)
  • Author(s): 高畑尚之
  • Publisher: 中山書店
• [Book] 崩れるゲノムの常識(生命科学の新展開)「遺伝子の退化がヒトを生み出した」 (2004)
  • Author(s): 高畑尚之
  • Publisher: 日経サイエンス
• [Remarks] Webページを現在整備中