Bayesian Divergence Time Analyses of Ruminantia (Artiodactyla, Mammalia): An Example of the Impact of Fossil Taxon Sampling on the Morphological Clock

Abstract Bayesian tip-dating under fossilized birth-death process has become an increasingly popular approach to reconstruct time-scaled phylogenies. This method implements the ages of fossils included in the analysis to calibrate clock models used to estimate divergence times. The use of morphological data and morphological clock models are fundamental in the reconstruction of the positions of fossil taxa and in the timing of their evolution in Bayesian tip-dating, but how morphological clocks perform with calibration types other than the ages from fossil tips are currently unknown. We tested the impact of varying fossil taxon sampling approaches and clock models on divergence time estimations under the morphological clock using a newly constructed matrix of ruminants. Our results indicate that increased fossil taxon sampling had only a minor effect on morphological divergence times; choice of implementing an independent or autocorrelated rate clock model revealed generally similar age estimates. Comparison among tip-dated and fossil calibrated node-dated analyses reveal both approaches estimated node ages generally consistent with previous age estimates from the molecular clock. However, increased sampling did improve precision of age estimates and prevented root age artefacts like deep-root attraction, the tendency for the root age in clock analyses to be much older than expected from the fossil record. Also, the inclusion of more fossil taxa nesting within nodes dominated by extant taxa recovered more realistic ages for these nodes. With the analysis of the largest morphological dataset of fossil and extant ruminants, the first to assess the phylogenetics of the primitive “traguline” and derived crown pecoran ruminants together, we confirm the monophyly of the total-groups of each living family, the inclusion of the blastomerycines in Moschidae and the separation of Palaeomerycidae and Dromomerycidae in addition to clarifying the positions of many fossil ruminant taxa. We discuss the most notable issues within ruminant systematics including the origin of the group, the position of the most controversial fossil taxa (i.e. Archaeomeryx, Palaeomerycidae, Dromomerycidae) and the origin of their cranial appendages. Our analyses highlight the importance of using a genomic backbone in morphological/total evidence analysis of Ruminantia because of the conflicting signals between different datatypes and from within datatypes; we further extend this to analyses of other groups with similar conflicts among data.