Molecular mechanisms of speciation and macroevolution

2013 Fiscal Year Final Research Report

• Project/Area Number: 21227002
• Research Category: Grant-in-Aid for Scientific Research (S)
• Allocation Type: Single-year Grants
• Research Field: Biodiversity/Systematics
• Research Institution: Foundation for Advancement of International Science (2013); Tokyo Institute of Technology (2009-2012)
• Principal Investigator: OKADA Norihiro 公益財団法人国際科学振興財団, その他部局等, 主席研究員 (60132982)
• Co-Investigator(Kenkyū-buntansha): NIKAIDO Masato 東京工業大学, 大学院・生命理工学研究科, 助教 (70432010) ; NISHIHARA Hidenori 東京工業大学, 大学院・生命理工学研究科, 助教 (10450727) ; KAJIKAWA Masaki 東京工業大学, 大学院・生命理工学研究科, 講師 (90361766) ; TERAI Yohey 総合研究大学院大学, 助教 (30432016)
• Project Period (FY): 2009-05-11 – 2014-03-31
• Keywords: 生物多様性 / 進化

Research Abstract

We investigated the genetic mechanism of speciation by focusing on the Lake Victoria cichlid species and that of the evolution of mammalian morphological characteristics. We found, 1) the unique sex determination system caused by the B chromosome, 2) highly dimorphic allelic diversity of pheromone receptor genes, and 3) the clear correlation between nuptial colors and visual sensitivities tuned by opsins. In addition, by constructing a genetic linkage map, we identified the putative sex determination region in the autosome of the Lake Victoria cichlids. For mammalian evolution, we identified several AmnSINE1-derived distal enhancers for developmental genes expressed in mammalian diencephalon and callosal projection neurons. We revealed the detailed molecular function and evolutionary process of the enhancers. Our findings concerning the molecular mechanisms of speciation and large-scale morphological evolution are expected to be applicable in broad animals in general.

Research Products

• [Journal Article] Multiple episodic evolution events in V1R receptor genes of East-Africancichlids (2014)
  • Author(s): Nikaido M, Ota T, Hirata T, Satta Y, Saito Y, Aibara M, Mzighani SI, Hagino-Yamagishi K, Sturmbauer C, Okada N
  • Journal Title: Genome Biol Volume: Evol (in press)
  • Peer Reviewed
• [Journal Article] Coelacanth genomes reveal signatures for evolutionary transition from water to land (2013)
  • Author(s): Nikaido M(27 co-authors)
  • Journal Title: Genome Res Volume: 23 Pages: 1740-1748
  • DOI: 10.1101/gr.158105.113
  • Peer Reviewed
• [Journal Article] Lineage specifice xpansion of V2R receptor (OlfC) genes in cichlids may contribute to diversification in amino acid detection (2013)
  • Author(s): Nikaido M, Suzuki H, Toyoda A, FujiyamaA, Hagino-Yamagishi K, Kocher TD, Carleton KL, Okada N
  • Journal Title: Genome Biol Volume: Evol.5 Pages: 711-722
  • DOI: 10.1093/gbe/evt041
  • Peer Reviewed
• [Journal Article] A SINE-Derived Element Constitutes a Unique Modular Enhancer for Mammalian Diencephalic Fgf8 (2012)
  • Author(s): Nakanishi A, Kobayashi N, Suzuki-Hirano A, Nishihara H, Sasaki T, Hirakawa M, Sumiyama K, Shimogori T, Okada N
  • Journal Title: PLoS One Volume: 7 Pages: e43785
  • DOI: 10.1371/journal.pone.0043785
  • Peer Reviewed
• [Journal Article] Correlation between nuptial colors and visual sensitivities tuned by opsins leads to species richness in sympatric Lake Victoria cichlid fishes (2012)
  • Author(s): Miyagi R, Terai Y, Aibara M, Sugawara T, Imai H, Tachida H, Mzighani SI, Okitsu T, Wada A, Okada N
  • Journal Title: Mol Biol Evol Volume: 29 Pages: 3281-96
  • DOI: 10.1093/molbev/mss139
  • Peer Reviewed
• [Journal Article] A Mammalian Conserved Element Derived from SINE Displays Enhancer Properties Recapitulating Satb2 Expression in Early-Born Callosal Projection Neurons (2011)
  • Author(s): Tashiro K, Teissier A, Kobayashi N, Nakanishi A, Sasaki T, Yan K, Tarabykin V, Vigier L, Sumiyama K, Hirakawa M, Nishihara H, Pierani A, Okada N
  • Journal Title: PLoS One Volume: 6(12) Pages: e28497
  • DOI: 10.1371/journal.pone.0028497
  • Peer Reviewed
• [Journal Article] Genetically distinct coelacanth population off the northern Tanzanian coast (2011)
  • Author(s): Nikaido M, Sasaki T, Emerson JJ, Aibara M, Mzighani SI, Budeba YL, Ngatunga BP, Iwata M, Abe Y, Li WH, Okada N
  • Journal Title: Proc Natl Acad Sci USA Volume: 108 Pages: 18009-13
  • DOI: 10.1073/pnas.1115675108
  • Peer Reviewed
• [Journal Article] B chromosomes have a functional effect on female sex determination in lake victoria cichlid fishes (2011)
  • Author(s): Yoshida K, Terai Y, Mizoiri S, Aibara M, Nishihara H, Watanabe M, Kuroiwa A, Hirai H, Hirai Y, Matsuda Y, Okada N
  • Journal Title: PLoS Genet Volume: 7(8) Pages: e1002203
  • DOI: 10.1371/journal.pgen.1002203
  • Peer Reviewed
• [Journal Article] Reverse evolution in RH1 for adaptation of cichlids to water depth in Lake Tanganyika (2011)
  • Author(s): Nagai H, Terai Y, Sugawara T, Imai H, Nishihara H, Hori M, Okada N
  • Journal Title: Mol Biol Evol Volume: 28 Pages: 1769-76
  • DOI: 10.1093/molbev/msq344
  • Peer Reviewed
• [Journal Article] Emergence of mammals by emergency : exaptation (2010)
  • Author(s): Okada N, Sasaki T, Shimogori T, Nishihara H
  • Journal Title: Genes Cells Volume: 15(8) Pages: 801-12
  • DOI: 10.1111/j.1365-2443.2010.01429.x
  • Peer Reviewed
• [Journal Article] Vertebrate Rhodopsin Adaptation to Dim Light via Rapid Meta-II Intermediate Formation (2010)
  • Author(s): Sugawara T, Imai H, Nikaido M, Imamoto Y, Okada N
  • Journal Title: Mol Biol Evol Volume: 27(3) Pages: 506-19
  • DOI: 10.1093/molbev/msp252
  • Peer Reviewed
• [Journal Article] Genetic Variation and Demographic History of the Laparogramma Cichlid Species Group of Lake Victoria-An Analysis Based on SINEs and Mitochondrial DNA (2010)
  • Author(s): Mzighani SI, Nikaido M, Takeda M, Seehausen O, Budeba YL, Ngatunga BP, Katunzi EFB, Aibara M, Mizoiri S, Sato T, Tachida H, Okada N
  • Journal Title: Gene Volume: 450 Pages: 39-47
  • DOI: 10.1016/j.gene.2009.10.002
  • Peer Reviewed
• [Journal Article] Genetic evidence that the non-homologous end-joining repair pathway is involved in LINE retrotransposition (2009)
  • Author(s): Suzuki J, Yamaguchi K, Kajikawa M, Ichiyanagi K, Adachi N, Koyama H, Takeda S, Okada N
  • Journal Title: PLoS Genet Volume: 5 Pages: e1000461
  • DOI: 10.1371/journal.pgen.1000461
  • Peer Reviewed
• [Journal Article] Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals (2009)
  • Author(s): Nishihara H, Maruyama S, Okada N
  • Journal Title: Proc NatlAcad Sci USA Volume: 106(13) Pages: 5235-40
  • DOI: 10.1073/pnas.0809297106
  • Peer Reviewed
• [Journal Article] Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes (2009)
  • Author(s): Hirakawa M, Nishihara H, Kanehisa M, Okada N
  • Journal Title: Gene Jul 15 Volume: 441(1-2) Pages: 100-10
  • DOI: 10.1016/j.gene.2008.12.009
  • Peer Reviewed
• [Presentation] Exaptation by Emergency Hypothesis (2012)
  • Author(s): Norihiro Okada
  • Organizer: 63rd FUJIHARA SEMINAR -- A new horizon of retroposon research
  • Place of Presentation: Kyoto
  • Year and Date: 2012-08-03
• [Presentation] Mammalian exaptation burst (2012)
  • Author(s): Norihiro Okada
  • Organizer: Genomic Impact of Eukaryotic Transposable Elements
  • Place of Presentation: アシロマ
  • Year and Date: 2012-02-25
  • Invited
• [Presentation] Speciation by Sensory Drive : its Generality in Cichlids of Lake Victoria (2011)
  • Author(s): Norihiro Okada
  • Organizer: Molecular Evolution in the Genomic Era
  • Place of Presentation: ローマ
  • Year and Date: 2011-09-30
  • Invited
• [Presentation] SINE Exaptation Reprogramming the Mammalian Brain (2011)
  • Author(s): Norihiro Okada
  • Organizer: FASEB Summer Research Conferences
  • Place of Presentation: アメリカ
  • Year and Date: 2011-08-11
  • Invited
• [Book] シクリッドの視覚の適応と種分化 : 現代の生態学9巻「淡水生態学のフロンティア」 (2012)
  • Author(s): 寺井洋平, 岡田典弘
  • Total Pages: 46-60
  • Publisher: 共立出版