Phylogeny and the inference of evolutionary trajectories

Most important organismal adaptations are not actually single traits, but complex trait syndromes that are evolutionarily integrated into a single emergent phenotype. Two alternative photosynthetic pathways, C-4 photosynthesis and crassulacean acid metabolism (CAM), are primary plant adaptations of this sort, each requiring multiple biochemical and anatomical modifications. Phylogenetic methods are a promising approach for teasing apart the order of character acquisition during the evolution of complex traits, and the phylogenetic placement of intermediate phenotypes as sister taxa to fully optimized syndromes has been taken as good evidence of an 'ordered' evolutionary trajectory. But how much power does the phylogenetic approach have to detect ordered evolution? This study simulated ordered and unordered character evolution across a diverse set of phylogenetic trees to understand how tree size, models of evolution, and sampling efforts influence the ability to detect an evolutionary trajectory. The simulations show that small trees (15 taxa) do not contain enough information to correctly infer either an ordered or unordered trajectory, although inference improves as tree size and sampling increases. However, even when working with a 1000-taxon tree, the possibility of inferring the incorrect evolutionary model (type I/type II error) remains. Caution is needed when interpreting the phylogenetic placement of intermediate phenotypes, especially in small lineages. Such phylogenetic patterns can provide a line of evidence for the existence of a particular evolutionary trajectory, but they should be coupled with other types of data to infer the stepwise evolution of a complex character trait.