Model Misspeci(cid:142)cation and Probabilistic Tests of Topology: Evidence from Empirical Data Sets
Model Misspeci(cid:142)cation and Probabilistic Tests of Topology: Evidence from Empirical Data Sets
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拓扑模型 Missspec(cid:142) 阳离子和概率测试：来自经验数据集的证据
DOI：
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发表时间：
2002
期刊：
影响因子：
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通讯作者：
Uckley
中科院分区：
文献类型：
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作者：
Homas;B. R.;Uckley
．-概率测试-软拓扑学为评估相互竞争的系统发育假说提供了强大的手段。研究了非参数Shimodaira-Hasegawa （SH）检验、参数Swofford-Olsen-Waddell-Hillis （SOWH）检验和贝叶斯后验概率对（cid:142） 5个数据集的性能，这些数据集的所有系统发育关系都具有非常高的确定性。这些结果与先前的模拟研究一致，这些研究表明，由于模型错配（cid:142）阳离子加上分支长度异质性，SOWH测试容易产生1型错误。这些结果还表明，当零假设实际上是正确的时，SOWH检验可能符合真实拓扑的过度信任（cid:142）。相比之下，即使在高取代率和分支长度异质性的情况下，SH检验也更为保守。对于那些SOWH测试被证明具有误导性的数据集，贝叶斯后验概率也具有误导性。所有试验的结果都被精确的取代模型假设强烈地影响（cid:143）。简单的模型，特别是那些假设站点之间的概率均匀性的模型，具有较高的1型错误率，并且更有可能产生误导性的后验概率。对于其中一些数据集，常用的替代模型似乎不足以用SOWH测试和贝叶斯方法估计适当的不确定性水平。讨论了两种最大似然检验之间统计能力差异的原因，并与贝叶斯方法进行了对比。(贝叶斯
.— Probabilistictestsoftopologyofferapowerfulmeansofevaluatingcompetingphylogenetic hypotheses. The performance of the nonparametric Shimodaira–Hasegawa (SH) test, the parametric Swofford–Olsen–Waddell–Hillis (SOWH) test, and Bayesian posterior probabilities were explored for (cid:142)ve data sets for which all the phylogenetic relationships are known with a very high degree of cer-tainty. These results are consistent with previous simulation studies that have indicated a tendency for the SOWH test to be prone to generating Type 1 errors because of model misspeci(cid:142)cation coupled with branch length heterogeneity. These results also suggest that the SOWH test may accord overcon- (cid:142)dence in the true topology when the null hypothesis is in fact correct. In contrast, the SH test was observedto be much moreconservative, even under high substitution ratesand branch length hetero- geneity. For some of those data sets where the SOWH test proved misleading, the Bayesian posterior probabilities were also misleading. The results of all tests were strongly in(cid:143)uenced by the exact sub- stitution model assumptions. Simple models, especially those that assume rate homogeneity among sites, had a higher Type 1 error rate and were more likely to generate misleading posterior probabili- ties. For some of these data sets, the commonly used substitution models appear to be inadequate for estimating appropriate levels of uncertainty with the SOWH test and Bayesian methods. Reasons for the differences in statistical power between the two maximum likelihood tests are discussed and are contrasted with the Bayesian approach. [Bayesian
影响因子：
10.7
作者：
Yang, ZH;Rannala, B
通讯作者：
Rannala, B
影响因子：
4.1
作者：
Goodman, M;Porter, CA;Groves, CP
通讯作者：
Groves, CP