摘要
研究基于生物信息学的方法以36种鲑科鱼类的线粒体基因COX1、Cytb和ND4为材料对其系统发育信息效率进行分析。用Clustal W软件进行对比,然后用MEGA 6.06软件分析DNA序列差异,并生成系统发育树。选择胡瓜鱼(Osmerus mordax)、香鱼(Plecoglossus altivelis)作为外群,用邻接法(neighbor-joining method,NJ法)和最大似然法(maximum likelihood,ML法)重建系统发育树,随后,统计节点支持率并进行分析。脊椎动物线粒体DNA的不同区域的进化速率不同,线粒体各个基因的系统发育信息表现也有所不同。系统发育树表明,最早分化的一枝是白鲑亚科(Coregonidaeinae),处于祖先位置,鲑亚科(Salmoninae)和茴鱼亚科(Thymallinae)互为姐妹群。在鲑亚科中,形成单系群的有聚集在一起的鲑属(Salmo),组成姐妹群的有红点鲑属(Salvelinus)和大麻哈鱼属(Oncorhynchus)。细鳞鲑、多瑙哲罗鲑、哲罗鲑等淡水鱼种类处于系统发育树的基部位置,与距离方法——NJ法构建的系统进化树进行对比,发现系统发育树的拓扑结构完全一致,但是利用ML法构建的系统发育树的节点支持率都有不同程度的下降,尤其是在茴鱼属(Thymallus)和白鲑属(Coregonus)、柱白鲑属(Prosopium)、北鲑属(Stenodus)的部分节点,支持率从100~79下降到41,但与NJ法构建的系统发育树比较,属、种亲缘关系程度没有明显变化。
Based on bioinformatics method, mitochondrial genes of COX1, cytochrome b and ND4 in 36 species of Salmonidae were used to analyze the phylogeny efficiency of information. Phylogenetic trees were generated based on aligning sequences by Clustal W software and analyzing the difference of DNA sequences by MEGA 6.06. The neighbor joining method(NJ) and maximum likelihood method(ML) were used to construct the phylogenetic trees with the outgroup of smelt(Osmerus mordax) and Ayu(Plecoglossus altivelis). Subsequently, statistics of nodes support rate were analyzed. The evolution rates of different regions of the mitochondrial DNA in vertebrates were different, and the phylogeny information of the different mitochondrial genes were also different. According to the phylogenetic trees, the earliest differentiation was whitefish subfamily(Coregonidaeinae) which was in the ancestors position. Salmon subfamily(Salmoninae) and grayling subfamily(Thymallinae) were sister groups. In whitefish subfamily(Coregonidaeinae),Salmo was monophyletic group, while Salvelinus and Oncorhynchus were sister group.Brachymystax lenok, Hucho hucho and whitefish genera(Coregonus)were in the base position of phylogenetic trees. Compared with the phylogenetic tree constructed by NJ method(distance method), topologies were exactly consistent, but node support rate of phylogenetic trees generated by ML method had a different degree of decline, especially in the Thymallus, Coregonus,Prosopium and Stenodus, the support rate of which declined from 79-100 to 41. However,there were no significant changes in the genera and species genetic relationship compared with those exhibited in phylogenetic trees generated by NJ method.
出处
《畜牧与饲料科学》
2015年第9期9-17 61,61,共10页
Animal Husbandry and Feed Science
