Data from: Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

Much of our understanding of the history of life hinges upon time
calibration, the process of assigning absolute times to cladogenetic
events. Bayesian approaches to time scaling phylogenetic trees have
dramatically grown in complexity, and depend today upon numerous
methodological choices. Arriving at objective justifications for all of
these is difficult and time consuming. Thus, divergence times are
routinely inferred under only one or a handful of parametric conditions,
often times chosen arbitrarily. Progress towards building robust
biological timescales necessitate the development of better methods to
visualize and quantify the sensitivity of results to these decisions.
Here, we present an R package that assists in this endeavor through the
use of chronospaces, i.e., graphical representations summarizing variation
in the node ages contained in time-calibrated trees. We further test this
approach using three empirical datasets spanning widely differing
timeframes. Our results reveal large differences in the impact of many
common methodological decisions, with the choice of clock (uncorrelated
vs. autocorrelated) and loci having strong effects on inferred ages. Other
decisions have comparatively minor consequences, including the use of the
computationally intensive site-heterogeneous model CAT-GTR. Notably, these
conclusions are as valid for Cenozoic divergences as they are for the
deepest eukaryote nodes. The package chronospace implements a
range of graphical and analytical tools that assist in the exploration of
sensitivity and the prioritization of computational resources in the
inference of divergence times.