A likelihood method for assessing molecular divergence time estimates and the placement of fossil calibrations

Abstract

Estimating divergence times using molecular sequence data has become a common application of statistical phylogenetics. However, disparities between estimated ages for clades produced in different studies have become equally commonplace. Here, I propose a method for the objective assessment of the likelihood of inferred divergence times to evaluate the placement of fossil constraints using information from the broader fossil record. The inclusion of nodes from the Tree of Life for which credible age ranges are known, in addition to the fossil constraints used in the ingroup, will allow for the comparison of alternate fossil placements when the phylogenetic affinity of a fossil is ambiguous as well as provide a heuristic assessment of the global likelihood of estimated divergence times. The use of these "likelihood checkpoints" will allow for the comparison of inferred dates across data sets and across taxonomic groups to place divergence time estimates into a broader evolutionary timescale. The method is illustrated with an example using an expanded phylogenetic estimate of the Gnathostomata, inferred with relaxed-clock molecular dating methods.