Molecular Biology of Organismal Diversity

分子进化与生物进化的关系是分子进化领域中有待阐明的一个重要问题，人们与来自分子进化、分子发育生物学和分子生理学三个研究领域的研究人员合作，对分子进化与生物进化的关系进行了研究。我们这个项目的成果如下。(1)Takashi Miyata(京都大学)，“生物多样性的分子基础”：对几个特定于动物的基因家族进行的基于分子系统学的分析表明，基因多样化在副偶氮虫-真氮分裂之前就已经完成，因此在基因多样化和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”：对使用敲入技术构建的小鼠模型进行的功能分析表明，视觉色素的多样化与视觉功能的多样化之间存在密切的关系。(3)T…更多Akashi GOJOBORI(National Inst.遗传学)，《通过比较基因组学研究生物多样性和脊椎动物脑中表达的基因数据库》：耳朵和眼睛中共同表达的基因的模式表明，耳朵和眼睛的共同祖先器官在这两个器官分化之前就存在了。(4)Hiroshi Hori(名古屋大学)，“活跃的青竹转座子和基因组重排”：我们成功地分离出青竹鱼转座子元件Tol2，并描述了青竹基因组中涉及这些mRNAs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”：我们分离了七鳃鳗中已知的参与下颌模式形成的调控基因的同源基因，并表明七鳃鳗中的口腔模式是基于与下颌口目动物相比，上皮和冠状突起的外胚间组织之间的细胞-细胞相互作用的移位。(6)Kiyokazu Agata(RIKEN CDB)，《揭开大脑发育的基本遗传程序并研究其在脑进化过程中的变化》：利用EST、DNA微阵列、原位杂交和RNAi技术，我们成功地分离到了参与脊椎动物脑形成的新基因noudarake。(7)长谷川正美(Inst.统计数学)，《分子系统发育方法的发展及其在哺乳动物进化中的应用》：发展了基于最大似然法的各种分子系统发育推断方法。将这些方法应用到哺乳动物和原生动物的进化中，我们发现在形态水平上经常出现收敛进化。(8)Yoichi Matsuda(北海道大学)，《从基因组结构推断鸟类和爬行动物的进化》：用EST克隆构建了中国甲鱼和日本四纹鼠蛇的比较细胞遗传学图谱。细胞遗传学图谱显示，海龟与鸟类的亲缘关系比与蛇的亲缘关系更近。我们还发现，鸟类和蛇性Z染色体来源于共同祖先的不同染色体。(9)Norihiro Okada(东京Inst.)，“非洲维多利亚湖鱼类多样性和物种形成机制”：我们在东非维多利亚湖200多种特有单色素鱼的长波长敏感(LWS)视蛋白基因座上发现了种群特有的变异，这将为物种形成提供洞察。较少

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