Assessing the Goodness of Fit of Phylogenetic Comparative Methods: A Meta-Analysis and Simulation Study |
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Authors: | Dwueng-Chwuan Jhwueng |
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Affiliation: | Department of Statistics, Feng-Chia University, Taichung, Taiwan, Republic of China.; University of California, San Diego, United States of America, |
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Abstract: | BackgroundPhylogenetic comparative methods (PCMs) have been applied widely in analyzing data from related species but their fit to data is rarely assessed.QuestionCan one determine whether any particular comparative method is typically more appropriate than others by examining comparative data sets?DataI conducted a meta-analysis of 122 phylogenetic data sets found by searching all papers in JEB, Blackwell Synergy and JSTOR published in 2002–2005 for the purpose of assessing the fit of PCMs. The number of species in these data sets ranged from 9 to 117.Analysis MethodI used the Akaike information criterion to compare PCMs, and then fit PCMs to bivariate data sets through REML analysis. Correlation estimates between two traits and bootstrapped confidence intervals of correlations from each model were also compared.ConclusionsFor phylogenies of less than one hundred taxa, the Independent Contrast method and the independent, non-phylogenetic models provide the best fit.For bivariate analysis, correlations from different PCMs are qualitatively similar so that actual correlations from real data seem to be robust to the PCM chosen for the analysis. Therefore, researchers might apply the PCM they believe best describes the evolutionary mechanisms underlying their data. |
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