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一种用于检测性状依赖多样化的稳健半参数检验。

A Robust Semi-Parametric Test for Detecting Trait-Dependent Diversification.

作者信息

Rabosky Daniel L, Huang Huateng

机构信息

Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109, USA

Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, 1109 Geddes Avenue, Ann Arbor, MI 48109, USA.

出版信息

Syst Biol. 2016 Mar;65(2):181-93. doi: 10.1093/sysbio/syv066. Epub 2015 Sep 22.

Abstract

Rates of species diversification vary widely across the tree of life and there is considerable interest in identifying organismal traits that correlate with rates of speciation and extinction. However, it has been challenging to develop methodological frameworks for testing hypotheses about trait-dependent diversification that are robust to phylogenetic pseudoreplication and to directionally biased rates of character change. We describe a semi-parametric test for trait-dependent diversification that explicitly requires replicated associations between character states and diversification rates to detect effects. To use the method, diversification rates are reconstructed across a phylogenetic tree with no consideration of character states. A test statistic is then computed to measure the association between species-level traits and the corresponding diversification rate estimates at the tips of the tree. The empirical value of the test statistic is compared to a null distribution that is generated by structured permutations of evolutionary rates across the phylogeny. The test is applicable to binary discrete characters as well as continuous-valued traits and can accommodate extremely sparse sampling of character states at the tips of the tree. We apply the test to several empirical data sets and demonstrate that the method has acceptable Type I error rates.

摘要

物种多样化的速率在整个生命之树上差异很大,人们对识别与物种形成和灭绝速率相关的生物体特征有着浓厚的兴趣。然而,要开发出能够检验关于性状依赖多样化的假设的方法框架是具有挑战性的,这些假设要对系统发育伪重复和性状变化的定向偏差率具有鲁棒性。我们描述了一种用于性状依赖多样化的半参数检验,该检验明确要求性状状态和多样化速率之间存在重复关联以检测效应。要使用该方法,需在不考虑性状状态的情况下,在系统发育树上重建多样化速率。然后计算一个检验统计量,以测量物种水平性状与树末端相应多样化速率估计值之间的关联。将检验统计量的经验值与通过系统发育树上进化速率的结构化排列生成的零分布进行比较。该检验适用于二元离散性状以及连续值性状,并且可以适应树末端性状状态的极其稀疏的采样。我们将该检验应用于几个实证数据集,并证明该方法具有可接受的第一类错误率。

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