Inferring the root of a phylogenetic tree
Inferring the root of a phylogenetic tree
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DOI：
10.1080/106351502753475862
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发表时间：
2002-01-01
影响因子：
6.5
通讯作者：
Levine, AM
中科院分区：
文献类型：
--
作者：
Huelsenbeck, JP;Bollback, JP;Levine, AM
系统发育树可以以许多标准为根基。在这里，我们介绍了一种贝叶斯方法，通过使用以下几个标准中的一个来推断系统发育树的根：外群、分子时钟和DNA替换的不可逆模型。我们执行模拟分析来检验这三个标准正确识别树根的相对能力。外群和分子时钟标准最能识别树根，而不可逆模型只有在替换过程高度不可逆的情况下才能识别树根。我们还检查了由四个树种组成的树的标准的性能，这些树的拓扑结构和根位置得到了很好的支持。这些数据的分析结果与仿真结果是一致的。
Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.