Data from: But the clock, tick-tock: The preeminence of relaxed clock models in total-evidence dated phylogenetics

Phylogenetic clock models translate inferred amounts of evolutionary
change (calculated from either genotypes or phenotypes) into estimates of
elapsed time, providing a mechanism for time scaling phylogenetic trees.
Relaxed clock models, which accommodate variation in evolutionary rates
across branches, are one of the main components of Bayesian dating, yet
their consequences for total-evidence phylogenetics have not been
thoroughly explored. Here, we combine morphological, molecular (both
transcriptomic and Sanger-sequenced), and stratigraphic datasets for all
major lineages of echinoids (sea urchins, heart urchins, sand dollars). We
then perform total-evidence dated inference under the fossilized
birth-death prior, varying two analytical conditions: the choice between
autocorrelated and uncorrelated relaxed clocks, which enforce (or not)
evolutionary rate inheritance; and the ability to recover
ancestor-descendant relationships. Our results show that the latter has no
impact on either topology or node ages and highlight a previously
unnoticed interaction between the tree and clock models, with analyses
implementing an autocorrelated clock precluding the recovery of direct
ancestry. On the other hand, tree topology, fossil placement, divergence
times, and downstream macroevolutionary inferences (e.g., ancestral state
reconstructions) in sea urchins are all strongly affected by the type of
relaxed clock implemented. In regions of the tree where molecular rate
variation is pervasive and morphological signal relatively uninformative,
fossil tips seem to play little to no role in informing divergence times,
and instead passively move in and out of clades depending on the ages
imposed upon them by molecular data. Our results highlight the extent to
which the phylogenetic and macroevolutionary conclusions of total-evidence
dated analyses are contingent on the choice of relaxed clock model,
highlighting the need for either careful methodological validation or a
thorough assessment of sensitivity. Our efforts continue to illuminate the
echinoid tree of life, supporting the erection of the order-level clade
Apatopygoida to include three living species last sharing a common
ancestor with other extant lineages in the Jurassic. Furthermore, they
also illustrate how the phylogenetic placement of extinct clades hinges
upon the modelling of molecular data, evidencing the extent to which the
fossil record remains subservient to phylogenomics.