Likelihood-based tests of topologies in phylogenetics
Likelihood-based tests of topologies in phylogenetics
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DOI：
10.1080/106351500750049752
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发表时间：
2000-12-01
影响因子：
6.5
通讯作者：
Rodrigo, AG
中科院分区：
文献类型：
--
作者：
Goldman, N;Anderson, JP;Rodrigo, AG
基于可能性的竞争进化假说（树拓扑）的统计测试已经有大约十年了。目前最常用的是岸野-长谷川试验。然而，为确保岸野-长谷川检验标准的有效性而必须作出的假设对其适用性造成了重大限制。特别地，它仅在被比较的拓扑被先验地指定时才有效。不幸的是，这意味着岸野-长谷川检验在许多现在常用的情况下可能会有严重的偏差：例如，在任何情况下，其中一个竞争拓扑被选择用于测试，因为它是手头数据集的最大李克图拓扑。我们回顾了岸野长谷川测试的理论，并认为对于大多数流行的应用程序，这个测试不应该使用。以前发表的Kishino-Hasegawa试验无效应用的结果应极其谨慎地对待，未来的应用应使用适当的替代试验。我们回顾这种替代检验，非参数和参数，并给出两个例子来说明我们的论点的重要性。
Likelihood-based statistical tests of competing evolutionary hypotheses (tree topologies) have been available for approximately a decade. By far the most commonly used is the Kishino-Hasegawa test. However, the assumptions that have to be made to ensure the validity of the Kishino-Hasegawa test place important restrictions on its applicability. In particular, it is only valid when the topologies being compared are specified a priori. Unfortunately, this means that the Kishino-Hasegawa test may be severely biased in many cases in which it is now commonly used: for example, in any case in which one of the competing topologies has been selected for testing because it is the maximum Likelihood topology for the data set at hand. We review the theory of the Kishino-Hasegawa test and contend that for the majority of popular applications this test should not be used. Previously published results from invalid applications of the Kishino-Hasegawa test should be treated extremely cautiously, and future applications should use appropriate alternative tests instead. We review such alternative tests, both nonparametric and parametric, and give two examples which illustrate the importance of our contentions.