Data from: Comparing cal3 and other a posteriori time-scaling approaches in a case study with the Pterocephaliid Trilobites

Reconstructing the tree of life involves more than identifying relationships among lineages, but also accurately estimating when lineages diverged. Paleontologists typically ‘a posteriori’ scale cladograms to time by direct reference to first appearances of taxa in the stratigraphic record. Recent approaches, such as the cal3 method, return samples of trees dated using probabilistic models of branching, extinction and sampling processes. However, these models require estimates of the rates of those processes, which may be hard to obtain, particularly for sampling. Here, we contrast the use of cal3 and other a posteriori time-scaling approaches by examining a previous study which documented a decelerating rate of morphological evolution in pterocephaliid trilobites. Although aspects of the dataset make estimation of branching, extinction, and sampling rates difficult, we use a multifaceted approach to calculate and evaluate the rate estimates needed for applying cal3. In agreement with previous simulation studies, we find that the choice of phylogenetic dating method impacts downstream macroevolutionary conclusions. We also find contradictory evolutionary inferences between analyses on ancestor-descendant contrasts (based on ancestor trait reconstruction methods) and maximum-likelihood parameter estimates. Ancestral taxon inference in cal3 corroborates previously hypothesized ancestor-descendant sequences, although cal3 suggests greater support for budding cladogenesis than proposed. This case study demonstrates the potential and wide applicability of the cal3 method, as well as the benefits allotted by choosing cal3 over simpler a posteriori time-scaling approaches.