Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters
Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters
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DOI：
10.1016/0025-5564(95)00172-7
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发表时间：
1996-06-01
影响因子：
4.3
通讯作者：
Chang, JT
中科院分区：
文献类型：
--
作者：
Chang, JT
重建一组物种的进化历史的一个基本问题是推断与这些物种相关的进化树的拓扑结构。如果给定来自越来越多字符的数据，从字符数据估计此类拓扑的统计方法一定会收敛到真实拓扑，则该方法称为一致的。许多流行的方法都是基于将每个角色的进化建模为沿着进化树的马尔可夫过程。标准模型进一步假设每个角色实际上都是根据相同的马尔可夫过程进化的。这种同质性假设是不现实的；例如，已知不同类型的角色会以不同的速率经历替换。拓扑估计的某些距离和最大似然方法已被证明在同质性假设下是一致的。在这里，我们给出的例子表明，当同质性假设放松时，这些方法可能无法保持一致。这些例子非常简单，只需要四个分类单元、二进制字符和以不同速率进化的字符。
A fundamental problem in reconstructing the evolutionary history of a set of species is to infer the topology of the evolutionary tree that relates those species. A statistical method for estimating such a topology from character data is called consistent if, given data from more and more characters, the method is sure to converge to the true topology. A number of popular methods are based on modeling the evolution of each character as a Markov process along the evolutionary tree. The standard models further assume that each character has in fact evolved according to the same Markov process. This homogeneity assumption is unrealistic; for example, different types of characters are known to experience substitutions at different rates. Certain distance and maximum likelihood methods for topology estimation have been shown to be consistent under the homogeneity assumption. Here we give examples showing that these methods can fail to be consistent when the homogeneity assumption is relaxed. The examples are very simple, requiring only four taxa, binary characters, and characters that evolve at mio different rates.