Phylogenies, the comparative method, and the conflation of tempo and mode

The comparison of mathematical models that represent alternative hypotheses about the tempo and mode of evolutionary change is a common approach for assessing the evolutionary processes underlying phenotypic diversification. However, because model parameters are estimated simultaneously, they are inextricably linked, such that changes in tempo, the pace of evolution, and mode, the manner in which evolution occurs, may be difficult to assess separately. This may potentially complicate biological interpretation, but the extent to which this occurs has not yet been determined. In this study, we examined 160 phylogeny × trait empirical data sets, and conducted extensive numerical phylogenetic simulations, to investigate the efficacy of phylogenetic comparative methods to distinguish between models that represent different evolutionary processes in a phylogenetic context. We observed that, in some circumstances, a high uncertainty exists when attempting to distinguish between alternative evo...