Variability and scale-dependence in molecular evolution rate impacts interpretation of eukaryotic evolutionary histories

Molecular evolution is often modeled as proceeding at consistent rates over time, with some deviations accommodated by relaxed molecular clock models. Here, we quantify the full extent of variability in branch-specific substitution rates across relatively well-calibrated eukaryotic phylogenies, confirming that punctuated change at the molecular level underlies evolution at the morphological level where punctuated dynamics are more commonly recognized. We also show how inferred substitution rates decrease systematically when measured across increasing time intervals. This scale-dependence persists across alternative clock models, calibration strategies, and prior assumptions, but disappears in simulated data evolved under a constant rate - suggesting that the phenomenon arises from time-varying substitution rates and reflects genuine properties of evolutionary histories rather than model artifacts. The observed pattern is analogous to the Sadler effect in sedimentary geology, where time-averaged rates decline with increasing measurement interval because sedimentation is episodic, with longer hiatuses occurring less frequently. The recognized scale-dependent bias in molecular evolution is not captured in current molecular clock models and significantly impacts inferences of evolutionary history, such as estimating the age of Metazoa and understanding the timing and nature of the Cambrian Explosion.