Data from: 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 competed 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. Competed models 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 competed models 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.