A Simple Method for Estimating and Testing Minimum-Evolution Trees
A Simple Method for Estimating and Testing Minimum-Evolution Trees
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DOI：
10.1093/oxfordjournals.molbev.a040771
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发表时间：
1992-09
影响因子：
10.7
通讯作者：
A. Rzhetsky;M. Nei
中科院分区：
文献类型：
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作者：
A. Rzhetsky;M. Nei
提出了一种基于最小进化原理估计和测试系统发育树的简单方法。该方法的基本步骤是先通过Saitou和Nei的方法得到邻接树（NJ），然后通过检查与NJ树密切相关的所有树来搜索分支长度和S最小的树。一旦确定了ME树，就对该树与其他密切相关的树之间的S差异进行统计检验。进行该测试所需的数学方法是用最小二乘方法开发的。计算机模拟表明，只要检查的核苷酸数量足够大，这种方法就有很高的概率识别出正确的树。研究还表明，NJ树的拓扑结构几乎总是与ME树的拓扑结构相同。给出了给定拓扑下分支长度的最小二乘估计（及其标准误差）的一种方法。该方法可用于测试ME树分支模式的可靠性。然而，S值的统计检验在拒绝不正确的树方面比分支长度检验或自举更强大。此外，还提出了一种计算具有给定NJ树拓扑差值的树数的数学方法和一种识别所有拓扑的计算机算法。
A simple method for estimating and testing phylogenetic trees under the principle of minimum evolution (ME) is presented. The basic procedure of this method is first to obtain the neighbor-joining (NJ) tree by Saitou and Nei’s method and then to search for a tree with the minimum value of the sum (S) of branch lengths by examining all trees that are closely related to the NJ tree. Once the ME tree is identified, a statistical test is conducted for the difference in S between this tree and other closely related trees. The mathematical method required for conducting this test is developed by using the least-squares approach. Computer simulation has shown that this method identifies the correct tree with a high probability, as long as the number of nucleotides examined is sufficiently large. It has also been shown that the topology of the NJ tree is almost always identical with that of the ME tree. A method for obtaining least-squares estimates (and their standard errors) of branch lengths for a given topology is also presented. This method can be used for testing the reliability of the branching pattern of the ME tree. However, the statistical test of S values is more powerful in rejecting incorrect trees than is the branch-length test or bootstrapping. Furthermore, both a mathematical method for computing the number of trees with a given value of topological difference from the NJ tree and a computer algorithm for identifying all the topologies are developed.