Phylogenetic comparative analysis: A modeling approach for adaptive evolution
Phylogenetic comparative analysis: A modeling approach for adaptive evolution
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DOI：
10.1086/426002
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发表时间：
2004-12-01
影响因子：
2.9
通讯作者：
King, AA
中科院分区：
文献类型：
--
作者：
Butler, MA;King, AA
生物学家采用系统发育比较的方法来研究适应性进化。然而，没有一种流行的方法是直接选择模型的。我们解释并开发了一种基于Hansen首先提出的Ornstein-Uhlenbeck （OU）过程的方法。Ornstein-Uhlenbeck模型同时包含了选择和漂移，因此与基于布朗运动的纯漂移模型在性质上有所不同，而且更一般。最重要的是，OU模型具有选择性最优，使自适应区域的概念形式化。在本文中，我们开发了一个定量特征的方法，讨论了其参数的解释，并提供了实现该方法的代码。我们的方法允许我们将关于不同选择制度下的适应的假设转化为明确的模型，使用基于最大似然的模型选择技术对模型进行数据测试，并推断进化过程的细节。我们用两个实例来说明这种方法。相对于现有方法，我们展示的直接建模方法允许人们探索更详细的假设，并利用比现有方法更多的比较数据集的信息内容。此外，使用模型选择框架来同时比较各种假设，提高了我们评估替代进化解释的能力。
Biologists employ phylogenetic comparative methods to study adaptive evolution. However, none of the popular methods model selection directly. We explain and develop a method based on the Ornstein-Uhlenbeck (OU) process, first proposed by Hansen. Ornstein-Uhlenbeck models incorporate both selection and drift and are thus qualitatively different from, and more general than, pure drift models based on Brownian motion. Most importantly, OU models possess selective optima that formalize the notion of adaptive zone. In this article, we develop the method for one quantitative character, discuss interpretations of its parameters, and provide code implementing the method. Our approach allows us to translate hypotheses regarding adaptation in different selective regimes into explicit models, to test the models against data using maximum-likelihood-based model selection techniques, and to infer details of the evolutionary process. We illustrate the method using two worked examples. Relative to existing approaches, the direct modeling approach we demonstrate allows one to explore more detailed hypotheses and to utilize more of the information content of comparative data sets than existing methods. Moreover, the use of a model selection framework to simultaneously compare a variety of hypotheses advances our ability to assess alternative evolutionary explanations.