Bayesian tests of topology hypotheses with an example from diving beetles.
Bayesian tests of topology hypotheses with an example from diving beetles.
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DOI：
10.1093/sysbio/syt029
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发表时间：
2013-09
影响因子：
6.5
通讯作者：
Ronquist F
中科院分区：
文献类型：
--
作者：
Bergsten J;Nilsson AN;Ronquist F
我们回顾贝叶斯方法模型测试一般和评估的拓扑假设。我们表明，标准的方式设置贝叶斯因子测试的单系的一组，或放置一个样本序列在一个已知的参考树，可以是误导。其原因与贝叶斯因子对模型特定先验的众所周知的依赖性有关。具体来说，当测试树假设时，重要的是每个假设都与先验中的适当树空间相关联。这可以通过使用适当约束的搜索或通过在后验样本中过滤树来实现，但比通常实现的方式更复杂。如果很难找到合适的树集进行对比，那么后验模型几率可能比贝叶斯因子更有信息量。我们说明了推荐的技术，使用经验的测试案例解决的问题，是否两个属的潜水甲虫（鞘翅目：Dytismartae），Suphrodytes和Hydroporus，应synchronized。我们改进的贝叶斯因子检验，与标准分析相反，表明有强烈的支持Suphrodytes嵌套内Hydroporus，属，因此synchronized。[贝叶斯因子;鞘翅目;异翅目;边际似然;模型检验;后验概率;可逆跳MCMC;垫脚石抽样。]
We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized. [Bayes factor; Coleoptera; Dytiscidae; marginal likelihood; model testing; posterior odds; reversible-jump MCMC; stepping-stone sampling.]
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