Molecular Biology of Organismal Diversity

分子进化与生物进化的关系是分子进化领域亟待澄清的一个重要问题，我们与来自分子进化、分子发育生物学和分子生理学三个研究领域的研究人员进行了合作研究。我们这个项目的结果如下。(1)Takashi MIYATA（京都大学），“The molecular bases of organisaldiversity”：对几个动物特异性基因家族的分子系统发育分析表明，基因多样化在寄生虫-真菌性动物分裂之前就已经完成，因此基因多样化与寒武纪大爆发之间没有直接联系。(2)Yoshinori SHICHIDA（京都大学），“视觉色素的功能多样性及其与视觉多样性的关系”：使用敲入技术构建的小鼠模型的功能分析揭示了视觉色素的多样性与视觉功能的多样性之间的密切关系。(3)T . More akashi GOJOBORI (National institute . Genetics)，“通过比较基因组学和planarian brain表达cDNA数据库研究生物多样性”：耳和眼共同表达基因的模式表明，耳和眼在分化之前就存在共同的祖先器官。(4)Hiroshi HORI (Nagoya university)，“medaka转座子和基因组重排”：我们成功分离了medaka鱼转座子元件Tol2，并表征了medaka基因组中涉及这些mrna表达的调控机制。(5)Shigeru KURATANI (RIKEN CDB)，“脊椎动物颌骨进化的分子发育研究”：我们分离出已知参与颌口颌模式的调控基因的七鳃鳗同源，并表明与颌口相比，七鳃鳗的口腔模式是基于上皮和冠源外间质之间转移的细胞-细胞相互作用。(6)Kiyokazu AGATA (RIKEN CDB)，“揭示大脑发育的基本遗传程序并研究其在大脑进化过程中的变化”：使用EST， DNA微阵列，原位杂交和RNAi技术，我们成功地分离出了一个新的基因，noudarake，它参与了planaria大脑的形成。(7)Masami HASEGAWA（统计数学研究所），“分子系统发育方法的发展及其在哺乳动物进化中的应用”：基于最大似然方法的各种推断分子系统发育的方法得到了发展。将这些方法应用于哺乳动物和原生动物的进化，我们发现在形态水平上有频繁的趋同进化。(8)Yoichi MATSUDA（北海道大学），“从基因组结构推断的鸟类和爬行动物的进化”：用EST克隆构建了中国软壳龟和日本四条纹鼠蛇的比较细胞遗传学图谱。细胞遗传学图谱揭示了海龟与鸟类的亲缘关系，而不是蛇。我们还发现，鸟类和蛇的性Z染色体来源于共同祖先的不同染色体。(9)Norihiro OKADA（东京工业大学），“非洲维多利亚湖稚鱼的多样化和物种形成机制”：我们从东非维多利亚湖200多种特有的单色胺鱼类中发现了长波敏感（LWS）视蛋白位点的种群特异性变异，这将为物种形成提供见解。少

Relationship between molecular evolution and organismal evolution, an important problem left to be clarified in molecular evolution field, have been studied in collaboration with researchers from three research fields, molecular evolution, molecular developmental biology, and molecular physiology. Our results of this project are as follows. (1)Takashi MIYATA (Kyoto Univ.), "The molecular bases of organismal diversity" : A molecular phylogeny-based analysis of several animal-specific gene families revealed that gene diversification had been completed before the parazoan-eumetazoan split and therefore there is no direct link between gene diversification and the Cambrian explosion. (2)Yoshinori SHICHIDA (Kyoto Univ.), "Functional diversity of visual pigments and its relationship with diversity of vision" : Functional analyses of the mouse models constructed using knock-in technology revealed close relationship between diversification of a visual pigment and that of a visual function. (3)T … More akashi GOJOBORI (National Inst. Genetics), "Study for biodiversity by comparative genomics and the database for expressed cDNA on planarian brain" : The pattern of commonly expressed genes in ear and eye suggested the common ancestral organs of ear and eye existed before diversification of those two organs. (4)Hiroshi HORI (Nagoya Univ.), "Active medaka transposon and genome rearrangement" : We succeeded in isolating the medaka fish transposable element, Tol2, and characterized the regulatory mechanism in the medaka genome, involving the expression of these mRNAs. (5)Shigeru KURATANI (RIKEN CDB), "Molecular developmental studies on vertebrate jaw evolution" : We isolated lamprey cognates of regulatory genes known to be involved in jaw patterning in gnathostomes and showed that oral patterning in the lamprey is based on the shifted cell-cell interactions between the epithelium and crest-derived ectomesenchyme as compared to that in gnathostomes. (6)Kiyokazu AGATA (RIKEN CDB), "Unraveling a fundamental genetic program for brain development and investigating the change of it in the brain evolution process" : Using EST, DNA microarray, in situ hybridization, and RNAi technologies, we succeeded in isolating a novel gene, noudarake, which involved in planarian brain formation. (7)Masami HASEGAWA (Inst. Statistical Math.), "Development of methods for molecular phylogenetics and their application to mammalian evolution" : Various methods for inferring molecular phylogenies based on the maximum likelihood method were developed. Applying these methods to mammalian and protistan evolution, we found frequent convergent evolution in morphological level. (8)Yoichi MATSUDA (Hokkaido Univ.), "Evolution of birds and reptiles inferred from genome structure" : Comparative cytogenetic maps of the Chinese soft-shelled turtle and the Japanese four-striped rat snake were constructed with EST clones. The cytogenetic maps revealed the close relatedness of turtles to birds rather than to snakes. We also showed that the avian and snake sex Z chromosomes were derived from the different chromosomes of the common ancestor. (9)Norihiro OKADA (Tokyo Inst. Tech.), "Diversification and speciation mechanism of cichlid fishes of Lake Victoria in Africa" : We found population-specific variation at the long wavelength-sensitive (LWS) opsin locus from more than 200 endemic species of haplochromine fishes in the East African Lake Victoria which would provide an insight into species formation. Less