Data from: Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution

Molecular sequence data provide information about relative times only, and
fossil-based age constraints are the ultimate source of information about
absolute times in molecular clock dating analyses. Thus, fossil
calibrations are critical to molecular clock dating, but competing methods
are difficult to evaluate empirically because the true evolutionary time
scale is never known. Here, we combine mechanistic models of fossil
preservation and sequence evolution in simulations to evaluate different
approaches to constructing fossil calibrations and their impact on
Bayesian molecular clock dating, and the relative impact of fossil versus
molecular sampling. We show that divergence time estimation is impacted by
the model of fossil preservation, sampling intensity and tree shape. The
addition of sequence data may improve molecular clock estimates, but
accuracy and precision is dominated by the quality of the fossil
calibrations. Posterior means and medians are poor representatives of true
divergence times; posterior intervals provide a much more accurate
estimate of divergence times, though they may be wide and often do not
have high coverage probability. Our results highlight the importance of
increased fossil sampling and improved statistical approaches to
generating calibrations, which should incorporate the non-uniform nature
of ecological and temporal fossil species distributions.