The asymptotic behavior of bootstrap support values in molecular phylogenetics.
The asymptotic behavior of bootstrap support values in molecular phylogenetics.
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DOI：
10.1093/sysbio/syaa100
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发表时间：
2020-12
影响因子：
6.5
通讯作者：
Jun Huang;Yuting Liu;Tianqi Zhu;Ziheng Yang
中科院分区：
文献类型：
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作者：
Jun Huang;Yuting Liu;Tianqi Zhu;Ziheng Yang
系统发育自举法是最常用的方法，用于评估非贝叶斯方法（如最大简约法和最大似然法（ML））估计的系统发育的统计置信度。据观察，引导支持往往是高的大型基因组数据集，无论推断的树和分支是正确的。在这里，我们研究了在大型数据集中，当竞争的系统发育树同样正确或同样错误时，ML树的自举支持的渐近行为。我们认为系统发育重建作为一个统计模型选择的问题时，比较模型是非嵌套和错误指定。的引导被发现有定性不同的动态贝叶斯推断，并没有表现出极化行为的后验模型的概率，符合经验观察，引导是比贝叶斯概率更保守。然而，自举支持类似地显示了大数据集之间的波动，当比较的模型同样正确或同样错误时，没有收敛到一个点值。因此，在大型数据集中，很可能会出现对错误树或模型的强支持。我们的分析提供了一个部分解释的高引导支持值不正确的分支在经验数据分析中观察到的。
The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic datasets whether or not the inferred trees and clades are correct. Here we study the asymptotic behavior of bootstrap support for the ML tree in large datasets when the competing phylogenetic trees are equally right or equally wrong. We consider phylogenetic reconstruction as a problem of statistical model selection when the compared models are nonnested and misspecified. The bootstrap is found to have qualitatively different dynamics from Bayesian inference, and does not exhibit the polarized behavior of posterior model probabilities, consistent with the empirical observation that the bootstrap is more conservative than Bayesian probabilities. Nevertheless bootstrap support similarly shows fluctuations among large datasets, with no convergence to a point value, when the compared models are equally right or equally wrong. Thus in large datasets strong support for wrong trees or models is likely to occur. Our analysis provides a partial explanation for the high bootstrap support values for incorrect clades observed in empirical data analysis.