Bayesian tip-dated phylogenetics in paleontology: topological effects and stratigraphic fit

The incorporation of stratigraphic data into phylogenetic analysis has a long history of debate, but is not currently standard practice for paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic methods have returned these arguments to the spotlight, but how tip dating affects the recovery of evolutionary relationships has yet to be fully explored. Here I show, through analysis of several datasets with multiple phylogenetic methods, that topologies produced by tip dating are outliers when compared to topologies produced by parsimony and undated Bayesian methods, which retrieve broadly similar trees. Unsurprisingly, trees recovered by tip dating have better fit to stratigraphy than trees recovered by other methods under both the Gap Excess Ratio and The Stratigraphic Completeness Index. This is because trees with better stratigraphic fit are assigned a higher likelihood by the fossilized birth-death tree model. However, the degree to which the tree model favours tree t...