Russo C A, Takezaki N, Nei M
Department of Biology, Pennsylvania State University, University Park 16802, USA.
Mol Biol Evol. 1996 Mar;13(3):525-36. doi: 10.1093/oxfordjournals.molbev.a025613.
The relative efficiencies of different protein-coding genes of the mitochondrial genome and different tree-building methods in recovering a known vertebrate phylogeny (two whale species, cow, rat, mouse, opossum, chicken, frog, and three bony fish species) was evaluated. The tree-building methods examined were the neighbor joining (NJ), minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML), and both nucleotide sequences and deduced amino acid sequences were analyzed. Generally speaking, amino acid sequences were better than nucleotide sequences in obtaining the true tree (topology) or trees close to the true tree. However, when only first and second codon positions data were used, nucleotide sequences produced reasonably good trees. Among the 13 genes examined, Nd5 produced the true tree in all tree-building methods or algorithms for both amino acid and nucleotide sequence data. Genes Cytb and Nd4 also produced the correct tree in most tree-building algorithms when amino acid sequence data were used. By contrast, Co2, Nd1, and Nd41 showed a poor performance. In general, large genes produced better results, and when the entire set of genes was used, all tree-building methods generated the true tree. In each tree-building method, several distance measures or algorithms were used, but all these distance measures or algorithms produced essentially the same results. The ME method, in which many different topologies are examined, was no better than the NJ method, which generates a single final tree. Similarly, an ML method, in which many topologies are examined, was no better than the ML star decomposition algorithm that generates a single final tree. In ML the best substitution model chosen by using the Akaike information criterion produced no better results than simpler substitution models. These results question the utility of the currently used optimization principles in phylogenetic construction. Relatively simple methods such as the NJ and ML star decomposition algorithms seem to produce as good results as those obtained by more sophisticated methods. The efficiencies of the NJ, ME, MP, and ML methods in obtaining the correct tree were nearly the same when amino acid sequence data were used. The most important factor in constructing reliable phylogenetic trees seems to be the number of amino acids or nucleotides used.
评估了线粒体基因组不同蛋白质编码基因以及不同建树方法在恢复已知脊椎动物系统发育关系（两种鲸类物种、牛、大鼠、小鼠、负鼠、鸡、青蛙和三种硬骨鱼类物种）方面的相对效率。所考察的建树方法包括邻接法（NJ）、最小进化法（ME）、最大简约法（MP）和最大似然法（ML），同时分析了核苷酸序列和推导的氨基酸序列。一般来说，在获得真实树（拓扑结构）或接近真实树的树方面，氨基酸序列比核苷酸序列更好。然而，当仅使用第一和第二密码子位置的数据时，核苷酸序列能产生相当不错的树。在所考察的13个基因中，对于氨基酸和核苷酸序列数据，在所有建树方法或算法中，Nd5都能产生真实树。当使用氨基酸序列数据时，基因Cytb和Nd4在大多数建树算法中也能产生正确的树。相比之下，Co2、Nd1和Nd41表现不佳。一般而言，大基因产生的结果更好，并且当使用所有基因时，所有建树方法都能产生真实树。在每种建树方法中，使用了几种距离度量或算法，但所有这些距离度量或算法产生的结果基本相同。考察多种不同拓扑结构的ME方法并不比生成单一最终树的NJ方法更好。同样，考察多种拓扑结构的ML方法也不比生成单一最终树的ML星分解算法更好。在ML中，使用赤池信息准则选择的最佳替代模型并不比更简单的替代模型产生更好的结果。这些结果对系统发育构建中当前使用的优化原则的效用提出了质疑。相对简单的方法，如NJ和ML星分解算法，似乎能产生与更复杂方法一样好的结果。当使用氨基酸序列数据时，NJ、ME、MP和ML方法在获得正确树方面的效率几乎相同。构建可靠系统发育树最重要的因素似乎是所使用的氨基酸或核苷酸的数量。
