Czelusniak J, Goodman M, Moore G W
J Mol Evol. 1978 May 12;11(1):75-85. doi: 10.1007/BF01768027.
Goodman et al.'s (1974) populous path algorithm for estimating hidden mutational change in protein evolution is designed to be used as an adjunct to the maximum parsimony method. When the algorithm is so used, the augmented maximum parsimony distances, far from being overestimates, are underestimates of the actual number of nucleotide substitutions which occur in Tateno and Nei's (1978) computer simulation by the Poisson process model, even when the simulation is carried out at two and a half times the sequence density. Although underestimates, our evidence shows that they are nevertheless more accurate than estimates obtained by a Poisson correction. In the maximum parsimony reconstruction, there is a bias towards overrepresenting the number of shared nucleotide identities between adjacent ancestral and descendant nodal sequences with the bias being stronger in those portions of the evolutionary tree sparser in sequence data. Because of this particular property of maximum parsimony reconstructed sequences, the conclusions of Tateno and Nei concerning the statistical properties of the populous path algorithm are invalid. We conclude that estimates of protein evolutionary rates by the maximum parsimony--populous path approach will become more accurate rather than less as larger numbers of closely related species are included in the analysis.
古德曼等人（1974年）用于估计蛋白质进化中隐藏突变变化的多路径算法旨在用作最大简约法的辅助方法。当该算法这样使用时，增强的最大简约距离远非高估，而是在塔泰诺和内（1978年）通过泊松过程模型进行的计算机模拟中，对实际发生的核苷酸替换数量的低估，即使模拟是在序列密度为原来2.5倍的情况下进行的。尽管是低估，但我们的证据表明，它们仍然比通过泊松校正获得的估计更准确。在最大简约重建中，存在一种偏向，即过度表示相邻祖先和后代节点序列之间共享的核苷酸同一性数量，并且在进化树中序列数据较稀疏的那些部分，这种偏向更强。由于最大简约重建序列的这种特殊性质，塔泰诺和内关于多路径算法统计性质的结论是无效的。我们得出结论，随着分析中纳入更多密切相关的物种，通过最大简约 - 多路径方法对蛋白质进化速率的估计将变得更准确而不是更不准确。
