Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data

Understanding the evolution and phylogenetic distribution of morphologic traits is fundamental to macroevolutionary research. Despite decades of major advances and key insights from molecular systematics, organismal anatomical features remain a key source of biological data for both inferring phylogenies and investigating patterns of trait evolution among fossil and extant species. In palaeobiology, morphologic characters are typically the only source of information available for reconstructing evolutionary trees. Systematists working with fossil data must make decisions regarding how morphological characters are modeled, whether they are coded as continuous or categorical, and how to address biological sources of rate variation. To determine the impact of how different models of morphological evolution influence phylogenetic inferences and downstream comparative analyses of fossil data, we compared a series of increasingly complex model configurations of character evolution to a dataset of Cambrian-Ordovician trilobites containing both discrete morphological characters and continuous traits. Model configurations vary in complexity, ranging from simple constant rate scenarios with only discrete categorical traits, to complex evolutionary models including both discrete and quantitative traits across multiple ecological partitions while accounting for multiple sources of rate variation. We compared topological distributions across model configurations by visualizing their distances in multidimensional treespace. Results indicate support for rate-variable models and partitioning characters. However, inclusion of continuous traits dramatically alters macroevolutionary inferences. Character model complexity also has a major impact on which regions of treespace are explored, suggesting a critical need to carefully model morphologic evolution even when systematists are only interested in patterns of phylogenetic relationships alone.