An approximately unbiased test of phylogenetic tree selection
An approximately unbiased test of phylogenetic tree selection
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DOI：
10.1080/10635150290069913
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发表时间：
2002-05-01
影响因子：
6.5
通讯作者：
Shimodaira, H
中科院分区：
文献类型：
--
作者：
Shimodaira, H
一个近似无偏（Au）的测试，使用一个新设计的多尺度自举技术开发的一般假设检验的地区，试图减少测试偏差。将其应用于最大似然树选择，得到树的置信集。Au测试基于Efron等人的理论（Proc.Natl. Acad. Sci. USA 93：13429-13434; 1996），但是新方法提供了更高阶的精度，但实现更简单。Au检验与Shimodaira-Hasegawa（SH）检验一样，调整了标准使用的自助概率和Kishino-Hasegawa检验中忽略的选择偏倚。选择偏差来自于同时比较多棵树，通常会导致对错误的树过度自信。SH检验虽然使用安全，但可能会出现另一种类型的偏倚，使其显得保守。在这里，我表明，Au测试是偏见比其他方法在典型的情况下，树的选择。这些点都说明了在模拟研究，以及在哺乳动物线粒体蛋白质序列的分析。理论论证提供了一个简单的公式，涵盖了自举概率检验、岸野-长谷川检验、Au检验和Zharkikh-Li检验。对于在特定情况下应采用哪种检验标准，提出了切实可行的建议。
An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias. It was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron et al. (Proc. Natl. Acad. Sci. USA 93: 13429-13434; 1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability and Kishino-Hasegawa tests. The selection bias comes from comparing many trees at the same time and often leads to overconfidence in the wrong trees. The SH test, though safe to use, may exhibit another type of bias such that it appears conservative. Here I show that the AU test is less biased than other methods in typical cases of tree selection. These points are illustrated in a simulation study as well as in the analysis of mammalian mitochondrial protein sequences. The theoretical argument provides a simple formula that covers the bootstrap probability test, the Kishino-Hasegawa test, the AU test, and the Zharkikh-Li test. A practical suggestion is provided as to which test should be used under particular circumstances.