The impact of rate heterogeneity on inference of phylogenetic models of trait evolution

Rates of trait evolution are known to vary across phylogenies; however, standard evolutionary models assume a homogeneous process of trait change. These simple methods are widely applied in small-scale phylogenetic studies, whereas models of rate heterogeneity are not, so the prevalence and patterns of potential rate variation in groups up to hundreds of species remain unclear. The extent to which trait evolution is modelled accurately on a given phylogeny is also largely unknown because studies typically lack absolute model fit tests. We investigated these issues by applying both rate-static and variable-rates methods on (i) body mass data for 88 avian clades of 10–318 species, and (ii) data simulated under a range of rate-heterogeneity scenarios. Our results show that rate heterogeneity is present across small-scaled avian clades, and consequently applying only standard single-process models prompts inaccurate inferences about the generating evolutionary process. Specifically, these a...