Huelsenbeck John P, Kirkpatrick Mark
Department of Zoology, University of Texas, Austin, Texas, 78712.
Evolution. 1996 Aug;50(4):1418-1424. doi: 10.1111/j.1558-5646.1996.tb03915.x.
We examine whether phylogenetic methods provide biased estimates of tree shape with respect to the random branching model. We investigate the performance of five commonly used phylogenetic methods using computer simulation: (1) maximum parsimony; (2) neighbor joining; (3) UPGMA with an outgroup taxon; (4) UPGMA without an outgroup taxon; and (5) maximum likelihood. All methods provide estimates of tree shape that are, on average, more asymmetrical than the true tree, especially when rates of evolution are high. We suggest a simple explanation for the bias and propose a modified test of tree shape that corrects for it.
我们检验了系统发育方法对于随机分支模型在树形状估计上是否存在偏差。我们使用计算机模拟研究了五种常用系统发育方法的性能：(1) 最大简约法；(2) 邻接法；(3) 有外类群分类单元的加权分组平均法（UPGMA）；(4) 无外类群分类单元的加权分组平均法（UPGMA）；以及(5) 最大似然法。所有方法所估计的树形状平均而言比真实树更不对称，尤其是在进化速率较高时。我们对这种偏差提出了一个简单解释，并提出了一种修正的树形状检验方法来对其进行校正。
