Rohlf F James, Wooten Michael C
Department of Ecology and Evolution, State University of New York, Stony Brook, NY, 11794.
Evolution. 1988 May;42(3):581-595. doi: 10.1111/j.1558-5646.1988.tb04162.x.
Comparisons are made of the accuracy of the restricted maximum-likelihood, Wagner parsimony, and UPGMA (unweighted pair-group method using arithmetic averages) clustering methods to estimate phylogenetic trees. Data matrices were generated by constructing simulated stochastic evolution in a multidimensional gene-frequency space using a simple genetic-drift model (Brownian-motion, random-walk) with constant rates of divergence in all lineages. Ten differentphylogenetic tree topologies of 20 operational taxonomic units (OTU's), representing a range of tree shapes, were used. Felsenstein's restricted maximum-likelihood method, Wagner parsimony, and UPGMA clustering were used to construct trees from the resulting data matrices. The computations for the restricted maximum-likelihood method were performed on a Cray-1 supercomputer since the required calculations (especially when optimized for the vector hardware) are performed substantially faster than on more conventional computing systems. The overall level of accuracy of tree reconstruction depends on the topology of the true phylogenetic tree. The UPGMA clustering method, especially when genetic-distance coefficients are used, gives the most accurate estimates of the true phylogeny (for our model with constant evolutionary rates). For large numbers of loci, all methods give similar results, but trends in the results imply that the restricted maximum-likelihood method would produce the most accurate trees if sample sizes were large enough.
对限制最大似然法、瓦格纳简约法和UPGMA（算术平均非加权配对组法）聚类方法估计系统发育树的准确性进行了比较。数据矩阵是通过使用简单的遗传漂变模型（布朗运动、随机游走）在多维基因频率空间中构建模拟随机进化生成的，所有谱系的分歧率恒定。使用了代表一系列树形的20个操作分类单元（OTU）的10种不同系统发育树拓扑结构。费尔斯滕森的限制最大似然法、瓦格纳简约法和UPGMA聚类法用于从所得数据矩阵构建树。限制最大似然法的计算在Cray - 1超级计算机上进行，因为所需计算（特别是针对向量硬件进行优化时）比在更传统的计算系统上执行得快得多。树重建的总体准确程度取决于真实系统发育树的拓扑结构。UPGMA聚类方法，特别是在使用遗传距离系数时，能给出对真实系统发育关系最准确的估计（对于我们具有恒定进化速率的模型）。对于大量基因座，所有方法给出的结果相似，但结果趋势表明，如果样本量足够大，限制最大似然法将产生最准确的树。
