Ortí G, Petry P, Porto J I, Jégu M, Meyer A
Department of Ecology and Evolution, State University of New York at Stony Brook 11794-5245, USA.
J Mol Evol. 1996 Feb;42(2):169-82. doi: 10.1007/BF02198843.
The patterns and rates of nucleotide substitution in mitochondrial ribosomal RNA genes are described and applied in a phylogenetic analysis of fishes of the subfamily Serrasalminae (Teleostei, Characiformes, Characidae). Fragments of 345 bp of the 12S and 535 bp of the 16S genes were sequenced for 37 taxa representing all but three genera in the subfamily. Secondary-structure models based on comparative sequence analysis were derived to characterize the pattern of change among paired and unpaired nucleotides, forming stem and loop regions, respectively. Base compositional biases were in the direction of A-rich loops and G-rich stems. Ninety-five percent of substitutions in stem regions were compensatory mutations, suggesting that selection for maintenance of base pairing is strong and that independence among characters cannot be assumed in phylogenetic analyses of stem characters. The relative rate of nucleotide substitution was similar in both fragments sequenced but higher in loop than in stem regions. In both genes, C-T transitions were the most common type of change, and overall transitions outnumbered transversions by a factor of two in 16S and four in 12S. Phylogenetic analysis of the mitochondrial DNA sequences suggests that a clade formed by the genera Piaractus, Colossoma, and Mylossoma is the sister group to all other serrasalmins and that the genera Myleus, Serrasalmus, and Pristobrycon are paraphyletic. A previous hypothesis concerning relationships for the serrasalmins, based on morphological evidence, is not supported by the molecular data. However, phylogenetic analysis of host-specific helminth parasites and cytogenetic data support the phylogeny of the Serrasalminae obtained in this study and provide evidence for coevolution between helminth parasites and their fish hosts.
描述了线粒体核糖体RNA基因中的核苷酸替换模式和速率，并将其应用于锯脂鲤亚科（硬骨鱼纲、脂鲤目、脂鲤科）鱼类的系统发育分析。对代表该亚科除三个属之外所有属的37个分类单元的12S基因的345bp片段和16S基因的535bp片段进行了测序。基于比较序列分析得出二级结构模型，以表征分别形成茎环区域的配对和未配对核苷酸之间的变化模式。碱基组成偏向富含A的环和富含G的茎。茎区域中95%的替换是补偿性突变，这表明维持碱基配对的选择很强，并且在茎特征的系统发育分析中不能假定性状之间具有独立性。两个测序片段中的核苷酸替换相对速率相似，但环区域高于茎区域。在两个基因中，C-T转换是最常见的变化类型，在16S基因中总体转换比颠换多两倍，在12S基因中多四倍。线粒体DNA序列的系统发育分析表明，由肥脂鲤属、巨脂鲤属和细脂鲤属组成的一个进化枝是所有其他锯脂鲤类的姐妹群，而军脂鲤属、锯脂鲤属和锯啮脂鲤属是并系的。基于形态学证据的先前关于锯脂鲤类关系的假设未得到分子数据的支持。然而，对宿主特异性蠕虫寄生虫的系统发育分析和细胞遗传学数据支持了本研究中获得的锯脂鲤亚科的系统发育，并为蠕虫寄生虫与其鱼类宿主之间的共同进化提供了证据。
