Improving phylogenetic regression under complex evolutionary models

Phylogenetic Generalized Least Square (PGLS) is the tool of choice among phylogenetic comparative methods to measure the correlation between species features such as morphological and life-history traits or niche characteristics. In its usual form, it assumes that the residual variation follows a homogenous model of evolution across the branches of the phylogenetic tree. Since a homogenous model of evolution is unlikely to be realistic in nature, we explored the robustness of the phylogenetic regression when this assumption is violated. We did so by simulating a set of traits under various heterogeneous models of evolution, and evaluating the statistical performance (type I error [the percentage of tests based on samples that incorrectly rejected a true null hypothesis] and power [the percentage of tests that correctly rejected a false null hypothesis]) of classical phylogenetic regression. We found that PGLS has good power but unacceptable type I error rates. This finding is important since this method has been increasingly used in comparative analyses over the last decade. To address this issue, we propose a simple solution based on transforming the underlying variance-covariance matrix to adjust for model heterogeneity within PGLS. We suggest that heterogeneous rates of evolution might be particularly prevalent in large phylogenetic trees, while most current approaches assume a homogenous rate of evolution. Our analysis demonstrates that overlooking rate heterogeneity can result in inflated type I errors, thus misleading comparative analyses. We show that it is possible to correct for this bias even when the underlying model of evolution is not known a priori.