Rabosky Daniel L, Goldberg Emma E
Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48103.
Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, 55108.
Evolution. 2017 Jun;71(6):1432-1442. doi: 10.1111/evo.13227. Epub 2017 Apr 4.
It is widely assumed that phenotypic traits can influence rates of speciation and extinction, and several statistical approaches have been used to test for correlations between character states and lineage diversification. Recent work suggests that model-based tests of state-dependent speciation and extinction are sensitive to model inadequacy and phylogenetic pseudoreplication. We describe a simple nonparametric statistical test ("FiSSE") to assess the effects of a binary character on lineage diversification rates. The method involves computing a test statistic that compares the distributions of branch lengths for lineages with and without a character state of interest. The value of the test statistic is compared to a null distribution generated by simulating character histories on the observed phylogeny. Our tests show that FiSSE can reliably infer trait-dependent speciation on phylogenies of several hundred tips. The method has low power to detect trait-dependent extinction but can infer state-dependent differences in speciation even when net diversification rates are constant. We assemble a range of macroevolutionary scenarios that are problematic for likelihood-based methods, and we find that FiSSE does not show similarly elevated false positive rates. We suggest that nonparametric statistical approaches, such as FiSSE, provide an important complement to formal process-based models for trait-dependent diversification.
人们普遍认为表型性状会影响物种形成和灭绝的速率，并且已经使用了几种统计方法来检验性状状态与谱系多样化之间的相关性。最近的研究表明，基于模型的状态依赖物种形成和灭绝检验对模型不充分和系统发育伪重复很敏感。我们描述了一种简单的非参数统计检验（“FiSSE”），以评估二元性状对谱系多样化速率的影响。该方法涉及计算一个检验统计量，该统计量比较具有和不具有感兴趣性状状态的谱系的分支长度分布。将检验统计量的值与通过在观察到的系统发育树上模拟性状历史生成的零分布进行比较。我们的测试表明，FiSSE可以可靠地推断数百个末端系统发育树上的性状依赖物种形成。该方法检测性状依赖灭绝的能力较低，但即使净多样化速率恒定，也可以推断出物种形成中状态依赖的差异。我们构建了一系列对基于似然性的方法有问题的宏观进化场景，并且我们发现FiSSE没有显示出类似的高假阳性率。我们建议，非参数统计方法，如FiSSE，为基于正式过程的性状依赖多样化模型提供了重要补充。
