Recalibrating the transcriptomic timetree of jawed vertebrates

Molecular divergence dating has the potential to overcome the incompleteness of the fossil record in inferring when cladogenetic events (splits, divergences) happened, but needs to be calibrated by the fossil record. Ideally but unrealistically, this would require practitioners to be specialists in molecular evolution, in the phylogeny and the fossil record of all sampled taxa, and in the chronostratigraphy of the sites the fossils were found in. Paleontologists have therefore tried to help by publishing compendia of recommended calibrations, and molecular biologists unfamiliar with the fossil record have made heavy use of such works. Using a recent example of a large timetree inferred from molecular data, I demonstrate that calibration dates cannot be taken from published compendia without risking strong distortions to the results, because compendia become outdated faster than they are published. The present work cannot serve as such a compendium either; in the slightly longer term, it can only highlight known and overlooked problems. Future authors will need to solve each of these problems anew through a thorough search of the primary paleobiological and chronostratigraphic literature on each calibration date every time they infer a new timetree; over 40% of the sources I cite were published after mid-2016. Treating all calibrations as soft bounds results in younger nodes than treating all calibrations as hard bounds. The unexpected exception are nodes calibrated with both minimum and maximum ages, further demonstrating the widely underestimated importance of maximum ages in divergence dating.