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 topologies with high stratigraphic fit metrics is modulated
by the diversification dynamics of the group under investigation. In
particular, when net diversification rate is low, the tree model favours
trees with a higher Gap Excess Ratio compared to when net diversification
rate is high. Differences in stratigraphic fit and tree topology between
tip dating and other methods are concentrated in parts of the tree with
weaker character signal, as shown by successive deletion of the most
incomplete taxa from two datasets. These results show that tip dating
incorporates stratigraphic data in an intuitive way, with good
stratigraphic fit an expectation that can be overturned by strong evidence
from character data.