ACCURACY OF ESTIMATED PHYLOGENETIC TREES FROM MOLECULAR-DATA .2. GENE-FREQUENCY DATA
ACCURACY OF ESTIMATED PHYLOGENETIC TREES FROM MOLECULAR-DATA .2. GENE-FREQUENCY DATA
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DOI：
10.1007/bf02300753
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发表时间：
1983-01-01
影响因子：
3.9
通讯作者：
TATENO, Y
中科院分区：
文献类型：
--
作者：
NEI, M;TAJIMA, F;TATENO, Y
通过计算机模拟，检验了三种不同的从基因频率数据制作系统发育树的方法的准确性和效率。研究的方法有UPGMA、Farris（1972）方法和Tateno等人（1982）改进的Farris方法。在计算机模拟中，假设8个物种（或种群）按照给定的模型树进化，并采用无限等位基因模型跟踪等位基因频率的进化变化。在模拟进化结束时，计算所有对物种的5种遗传距离度量（Nei’s标准距离和最小距离、Rogers’s距离、Cavalli-Sforza’s fλ和改进的Cavalli-Sforza距离），并利用每个距离度量得到的距离矩阵重建系统发育树。将得到的系统发育树与模型树进行比较。结果表明，在所有研究的造树方法中，当使用的基因座数小于20时，重建树（有根树）的拓扑和分支长度的精度都很低，但随着基因座数的增加而逐渐提高。当最短分支的期望基因替换数(M)为每个位点0.1或更多，使用30或更多位点时，以扭曲指数（dT）衡量的拓扑误差并不大，但即使使用60个位点，获得正确拓扑的概率(P)也小于0.5。当M小于0.004时，P显著降低。在获得良好的拓扑结构（小电阻率和高P值）方面，UPGMA和改进的法里斯方法通常比法里斯方法表现出更好的性能。即使使用服从三角不等式的罗杰斯距离，法里斯方法的性能也很差。造成这种情况的主要原因似乎是法里斯方法经常高估分支长度。对于估计真树的期望分支长度，UPGMA表现出最好的性能。由于Nei的标准距离与基因替换的数量呈线性关系，因此其结果优于其他方法。Rogers或Cavalli-Sforza的距离给出了一个系统发育树，其中靠近根的部分被压缩，而其他部分被拉长。建议使用30个以上的基因座，包括多态性和单态基因座。这项研究的结论似乎也适用于限制性内切酶技术获得的核苷酸差异数据。
The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's fλ, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dTand high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogentic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.