Unidad Ejecutora Lillo, Fundación Miguel Lillo, CONICET, Miguel Lillo 251, 4000 San Miguel de Tucumán, Argentina.
Department of Life Sciences, Natural History Museum, London SW7 5BD, United Kingdom.
Mol Phylogenet Evol. 2018 May;122:95-101. doi: 10.1016/j.ympev.2018.01.020. Epub 2018 Jan 31.
This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with maximum parsimony or maximum likelihood. Exhaustive enumeration of cases up to 20 taxa for binary characters, and up to 12 taxa for 4-state characters, shows that the same tree is recovered (as unique most likely or most parsimonious tree) as long as the number of extra steps is within 1/4 of the number of taxa. This dependence, 1/4 of the number of taxa, is discussed with a general argumentation, in terms of the spread of the character changes on the tree used to select character state distributions. The present finding allows creating matrices which have as much homoplasy as possible for the most parsimonious or likely tree to be predictable, and examination of these matrices with hill-climbing search algorithms provides additional evidence on the (lack of a) necessary relationship between homoplasy and the ability of search methods to find optimal trees.
本文讨论了在给定树 T 上创建一个具有固定数量（或额外数量）步骤的所有字符状态组合的矩阵，然后使用最大简约法或最大似然法进行分析时，是否会产生相同的树 T 的问题。对于二元字符，对 20 个分类单元的情况进行穷尽枚举，对于 4 状态字符，对 12 个分类单元的情况进行穷尽枚举，结果表明，只要额外步骤的数量在分类单元数量的 1/4 以内，就可以恢复相同的树（作为唯一最可能或最简约的树）。根据用于选择字符状态分布的树的字符变化的分布情况，用一般的论证来讨论这种依赖性，即分类单元数量的 1/4。目前的发现允许创建具有尽可能多的同源相似性的矩阵，以便预测最简约或最可能的树，并且使用爬山搜索算法对这些矩阵进行检查，为同源相似性与搜索方法找到最优树的能力之间（缺乏）必要关系提供了额外的证据。
