The consistency of several phylogeny-inference methods under varying evolutionary rates.
The consistency of several phylogeny-inference methods under varying evolutionary rates.
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几种系统发育推断方法在不同进化速率下的一致性。
DOI：
10.1093/oxfordjournals.molbev.a040740
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发表时间：
1992
影响因子：
10.7
通讯作者：
DeBry,RW
中科院分区：
文献类型：
--
作者：
DeBry,RW
系统发育方法是系统发育的一致估计，当且仅当它保证给出正确的树，给定足够的（可能是无限的）独立数据进行检查。检查以下方法的一致性：UPGMA（未加权对组方法，平均值），NJ（相邻连接），MF（修改的Farris）和P（简约）。使用了一个核苷酸序列替换的双参数模型，并计算了字符状态的期望分布。如果没有对叠加替换的完美校正，如果只有一个分支以比其他分支更快的速率进化，则所有四种方法都可能不一致。观测距离的部分校正提高了NJ方法对速率变化的鲁棒性，并且完美校正使得NJ方法对于所检查的速率的所有组合是一致的估计。所有方法对不等比率的敏感性在很大范围内变化，因此相对比率检验不太可能成为接受或拒绝基于简约分析的重复性的可靠指南。
A phylogenetic method is a consistent estimator of phylogeny if and only if it is guaranteed to give the correct tree, given that sufficient (possibly infinite) independent data are examined. The following methods are examined for consistency: UPGMA (unweighted pair-group method, averages), NJ (neighbor joining), MF (modified Farris), and P (parsimony). A two-parameter model of nucleotide sequence substitution is used, and the expected distribution of character states is calculated. Without perfect correction for superimposed substitutions, all four methods may be inconsistent if there is but one branch evolving at a faster rate than the other branches. Partial correction of observed distances improves the robustness of the NJ method to rate variation, and perfect correction makes the NJ method a consistent estimator for all combinations of rates that were examined. The sensitivity of all the methods to unequal rates varies over a wide range, so relative-rate tests are unlikely to be a reliable guide for accepting or rejecting phylogenies based on parsimony analysis.