Abstract
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 (in addition to using scattered primary sources and copying from each other). Using a recent example of a large node-dated timetree inferred from molecular data, I reevaluate all 30 calibrations in detail, present the current state of knowledge on them with its various uncertainties, rerun the dating analysis, and conclude that calibration dates cannot be taken from published compendia or other secondary or tertiary sources without risking strong distortions to the results, because all such sources become outdated faster than they are published: 50 of the (primary) sources I cite to constrain calibrations were published in 2019, half of the total of 280 after mid-2016, and 90% after mid-2005. It follows that 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, and that literature is not optimized for that task, but largely has other objectives.
Highlights
This work is not intended as a review of the theory or practice of node dating with calibration dates inferred from the fossil record; as the most recent reviews of methods and sources of error, I recommend those by Barido-Sottani et al (2019), Barido-Sottani et al (2020), Marshall (2019), Matschiner (2019), Guindon (2020), Pardo et al (2020), Powell et al (2020), and, with caveats of which I will address two
I discuss wider implications, the scope of this work is narrow: to evaluate each of the 30 calibrations used in the largest vertebrate timetree yet published, that by Irisarri et al (2017), and the total impact of the errors therein on the results
Irisarri et al (2017: supplementary table 8) cited 15 works as sources for their calibrations, six of them compilations made by paleontologists to help molecular biologists calibrate timetrees
Summary
This work is not intended as a review of the theory or practice of node (or tip) dating with calibration dates (or tip dates) inferred from the fossil record; as the most recent reviews of methods and sources of error, I recommend those by Barido-Sottani et al (2019), Barido-Sottani et al (2020), Marshall (2019), Matschiner (2019), Guindon (2020), Pardo et al (2020), Powell et al (2020), and, with caveats of which I will address two I have tried to present, and use, the current state of knowledge on each of these calibrations
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