Data from: Assessing the effect of time-scaling methods on phylogeny-based analyses in the fossil record

Phylogeny-based approaches can be used to infer diversification dynamics
and the rate and pattern of trait change. Applying these analyses to
fossil data often requires time-scaling a cladogram of morphotaxon
relationships. Although several time-scaling methods have been developed
for this purpose, the incomplete sampling of the fossil record can distort
the apparent timing of branching. It is unclear how well different
time-scaling methods reconstruct the true temporal relationships or how
any such inaccuracy could affect tree-based evolutionary analyses. I
developed process-based simulations of the fossil record that allow the
comparison of approximated time-scaled trees to true time-scaled trees. I
used this simulation framework to test the effect of time-scaling methods
on the fidelity of several commonly applied tree-based analyses, across a
range of simulation conditions. When the fidelity of time-scaling methods
differed, the stochastic “cal3” time-scaling method with ancestral
assignment produced preferable results. Estimating rates and models of
continuous trait evolution was particularly sensitive to bias from
scenarios that forced the insertion of many short branch lengths, a bias
that is not solved by any of the considered time-scaling methods in all
scenarios. The cal3 method of time-scaling can be recommended as the
preferred time-scaling method among those tested, but caution must be
exercised because tree-based analyses are prone to easily overlooked
biases.