Evolutionary characteristics of the fish mitochondrial DNA and its utilization for analysis of population and phylogeny

虽然线粒体DNA作为遗传标记的主要来源已被应用于鱼类种群和系统发育分析，但其进化特征还没有得到足够的阐明。本研究通过对两个核糖体RNA基因、几个蛋白质编码基因和控制区的分析，研究了线粒体DNA的进化特征。此外，利用这些基因的序列数据，对鱼类近缘种和远缘种进行了种群结构分析和系统发育分析。主要结果如下。1)控制区由于其高度的变异性，对于种内种群或近缘种的种群和生殖分析是有用的，但也有一些例外，即该区域的变异性不是很大。2)来自核糖体RNA基因的系统发育信息有时不足以解决远缘群体（如家庭）之间的系统发育关系。3)对于深分支的分析，来自许多蛋白质编码基因的数据汇编似乎是有用的。4)一对蛋白质编码基因的“分子钟”被校准用于鱼类。本研究利用长链PCR技术建立了一种有效的鱼类线粒体全基因组扩增和测序方法。在下一步的研究中，新的方法可以充分利用获得和表征完整的线粒体DNA序列从许多鱼类，所产生的序列数据将有效地用于详细检查主要群体的鱼类系统发育关系。

Though the mitochondrial DNA (mtDNA) has been utilized for population and phylogeny analysis of fishes as a primary source of genetic markers, its evolutionary characteristics have not been clarified enough. In this project, evolutionary characteristics of the mtDNA were examined through analyzing the two ribosomal RNA genes, several protein-coding genes, and the control region. In addition, by using sequence data from these genes, population structure analysis and phylogenetic analysis of closely related species as well as distantly related species of fishes were made. Main points of the results are as follows. 1) The control region is useful for population and phylogeny analysis of intraspecific populations or closely related species because of its high variability, but there are some .exceptions that this region is not so variable. 2) Phylogenetic information from the ribosomal RNA genes is sometimes not enough for resolving phylogenetic relationships among distantly related groups such as families. 3) For analysis of deep-branches, compilation of data from many protein-coding genes appears to be useful. 4) A "molecular clock" from a couple of protein-coding genes was calibrated for fishes. During this study, an effective method for amplifying and sequencing of a total mitochondrial genome of fishes was established by utilizing so-called the long PCR techniques. In the next step of this study, the new method can be fully utilized in obtaining and characterizing complete mtDNA sequences from many fishes, and the resulting sequence data will be effectively used for examining phylogenetic relationships of major groups of fishes in detail.