A Likelihood Method for Detecting Trait-Dependent Shifts in the Rate of Molecular Evolution
A Likelihood Method for Detecting Trait-Dependent Shifts in the Rate of Molecular Evolution
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DOI：
10.1093/molbev/msq263
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发表时间：
2011-01-01
影响因子：
10.7
通讯作者：
Otto, Sarah P.
中科院分区：
文献类型：
--
作者：
Mayrose, Itay;Otto, Sarah P.
即使在检查密切相关的分类单元时，已知生物体群体内的速率异质性也存在。人们已经开发了多种系统发育和年代测定方法，旨在测试速率变异的存在或纠正其偏差。然而，现有的方法都没有跟踪解释观察到的速率异质性的特征的演变。在这里，我们提出了一个似然模型，假设速率变化部分是由物种的内在特征引起的，例如特定的生活史特征、形态特征或栖息地关联。该模型结合了序列模型和字符状态演化模型，使得序列变化率取决于谱系在每个时间点的字符状态。我们使用模拟测试模型的能力和准确性，以确定分子进化速率是否取决于特定的特征状态，并使用嗜盐和淡水水蚤的经验示例证明其实用性。
Rate heterogeneity within groups of organisms is known to exist even when closely related taxa are examined. A wide variety of phylogenetic and dating methods have been developed that aim either to test for the existence of rate variation or to correct for its bias. However, none of the existing methods track the evolution of features that account for observed rate heterogeneity. Here, we present a likelihood model that assumes that rate variation is caused, in part, by species' intrinsic characteristics, such as a particular life-history trait, morphological feature, or habitat association. The model combines models of sequence and character state evolution such that rates of sequence change depend on the character state of a lineage at each point in time. We test, using simulations, the power and accuracy of the model to determine whether rates of molecular evolution depend on a particular character state and demonstrate its utility using an empirical example with halophilic and freshwater daphniids.