This chapter discusses the fundamental structure and advantages of the approximate Bayesian computation (ABC) algorithm in phylogenetic comparative methods (PCMs). ABC estimates unknown parameters as follows: (1) simulated data are generated under a suite of parameters randomly chosen from their prior distributions; (2) the simulated data are compared with empirical data; (3) parameters are accepted when the distance between the simulated and empirical data is small; and (4) by repeating steps (1)—(3), posterior distributions of parameters will be gained. Because ABC does not necessitate mathematical expression or analytic solution of a likelihood function, ABC is particularly useful when a maximum-likelihood (ML) estimation is difficult to conduct (a common situation when testing complex evolutionary models and/or models with many parameters in PCMs). As an application, we analysed trait evolution in which a specific species exhibits an extraordinary trait value relative to others. The ABC approach detected the occurrence of branch-specific directional selection and estimated ancestral states of internal nodes. As computational power increases, such likelihood-free approaches will become increasingly useful for PCMs, particularly for testing complex evolutionary models that deviate from the standard models based on the Brownian motion.
CITATION STYLE
Kutsukake, N., & Innan, H. (2014). Detecting phenotypic selection by approximate bayesian computation in phylogenetic comparative methods. In Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology (pp. 309–424). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-662-43550-2_17
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