Empirical evidence and robustness of clock models with spikes

<jats:p>Time-calibrated phylogenies provide information on past macroevolutionary history. Time calibration can be obtained from fossil ages or node calibrations in combination with a clock model describing evolutionary rates. Relaxed clocks, which allow rates of evolution to vary across lineages, are widely used in phylogenetic research but lack a mechanistic link between rate variation and the evolutionary process. A recently developed class of clock models attempts to introduce biological mechanisms by coupling speciation events with spikes of evolutionary change. However, their empirical support and overall impact on phylogenetic inference remain underexplored. Here, we evaluate the support for spike clock models across a range of empirical datasets and use simulations to quantify the effects of model misspecification and missing data across clock models. We find that spike clock models are supported as the best-fitting model in six of the seven datasets analyzed, suggesting widespread evidence of a punctuated mode of evolution. Although the choice of clock models does not strongly affect the resulting divergence time estimates, spike clock models tend to give more constrained uncertainty intervals of speciation and extinction rate estimates in some empirical analyses. We interpret this as the consequence of information transfer from sequence evolution into the inferred branching process. Our simulations show that a general clock model that incorporates both branch-specific clock rates and spikes is the most robust across simulated datasets. In particular, models with spikes are robust to missing data, capable of accurately estimating speciation and extinction rates even when fossil data is completely absent. In summary, we highlight here that evolutionary spikes leave a detectable signal in the alignment data, and correctly accounting for them leads to improved estimates of the branching parameters and tree topologies.</jats:p>