Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock.
Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock.
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DOI：
10.1093/oxfordjournals.molbev.a040782
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发表时间：
1992-11
影响因子：
10.7
通讯作者：
Andrey Zharkikh;Wen-Hsiung Li
中科院分区：
文献类型：
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作者：
Andrey Zharkikh;Wen-Hsiung Li
通过使用具有外类群的三个分类单元的模型树，并假设核苷酸替换速率恒定，研究了从核苷酸序列样本中对系统发育变异性进行样本估计和自助法估计的统计特性。采用了最大简约法进行树的重建。推导出一个解析公式，用于估计如果从抽样序列中获得真实树的概率\(P\)等于或高于给定值时所需的序列长度。自助法估计被表述为一个两步抽样过程：（1）从进化过程中对序列进行抽样；（2）对原始序列样本进行重抽样。发现对原始序列样本进行自助法重抽样将支持真实树的概率取决于模型树、序列长度以及随机选取的核苷酸位点是信息位点的概率。当使用三叉树作为模型树时，三个二叉树中的一个在\(\geq95\%\)的自助法重复中出现的概率，如果进行了超过\(50\)次自助法重复，则为\(\geq95\%\)。然而，如果在比如说\(\geq1000\)次自助法重复中观察到一个特定的二叉树。当使用二叉树作为模型树时，当序列很短时，自助法往往会高估\(P\)，但当序列很长时，它往往会低估该概率。此外，模拟结果表明，如果只有当一棵树在\(\geq95\%\)的自助法重复中出现时才被接受为真实树，那么即使\(P = 95\%\)，即即使来自进化过程的\(95\%\)的样本将支持真实树，不接受任何二叉树的概率也可能高达\(58\%\)。因此，如果速率恒定假设成立，自助法是一种用于估计四个分类单元推断的系统发育可靠性的保守方法。
The statistical properties of sample estimation and bootstrap estimation of phylogenetic variability from a sample of nucleotide sequences are studied by using model trees of three taxa with an outgroup and by assuming a constant rate of nucleotide substitution. The maximum-parsimony method of tree reconstruction is used. An analytic formula is derived for estimating the sequence length that is required if P, the probability of obtaining the true tree from the sampled sequences, is to be equal to or higher than a given value. Bootstrap estimation is formulated as a two-step sampling procedure: (1) sampling of sequences from the evolutionary process and (2) resampling of the original sequence sample. The probability that a bootstrap resampling of an original sequence sample will support the true tree is found to depend on the model tree, the sequence length, and the probability that a randomly chosen nucleotide site is an informative site. When a trifurcating tree is used as the model tree, the probability that one of the three bifurcating trees will appear in > or = 95% of the bootstrap replicates is or = 95% of the bootstrap replicates and if more than 50 bootstrap replications are conducted. However, if a particular bifurcating tree is observed in, say, or = 1,000 bootstrap replications are conducted. When a bifurcating tree is used as the model tree, the bootstrap approach tends to overestimate P when the sequences are very short, but it tends to underestimate that probability when the sequences are long. Moreover, simulation results show that, if a tree is accepted as the true tree only if it has appeared in > or = 95% of the bootstrap replicates, then the probability of failing to accept any bifurcating tree can be as large as 58% even when P = 95%, i.e., even when 95% of the samples from the evolutionary process will support the true tree. Thus, if the rate-constancy assumption holds, bootstrapping is a conservative approach for estimating the reliability of an inferred phylogeny for four taxa.