Aaron A. King, Ph.D.

Nelson G. Hairston Collegiate Professor of
Ecology & Evolutionary Biology, Complex Systems, and Mathematics
University of Michigan

Phylogenetic comparative analysis: a modeling approach for adaptive evolution

M. A. Butler and A. A. King
The American Naturalist 164 : 683–695, 2004.

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. OU 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 which formalize the notion of adaptive zone. In this paper, 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, test the models against data using maximum-likelihood-based model-selection techniques, and 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 datasets 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.


The official version of the paper is here.   Please contact Prof. King if you'd like a reprint.

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