Data from: Biogeographic dating of speciation times using paleogeographically informed processes

Standard models of molecular evolution cannot estimate absolute speciation
times alone, and require external calibrations to do so, such as fossils.
Because fossil calibration methods rely on the incomplete fossil record, a
great number of nodes in the tree of life cannot be dated precisely.
However, many major paleogeographical events are dated, and since
biogeographic processes depend on paleogeographical conditions,
biogeographic dating may be used as an alternative or complementary method
to fossil dating. I demonstrate how a time-stratified biogeographic
stochastic process may be used to estimate absolute divergence times by
conditioning on dated paleogeographical events. Informed by the current
paleogeographical literature, I construct an empirical dispersal graph
using 25 areas and 26 epochs for the past 540 Ma of Earth’s history.
Simulations indicate biogeographic dating performs well so long as
paleogeography imposes constraint on biogeographic character evolution. To
gauge whether biogeographic dating may be of practical use, I analyzed the
well-studied turtle clade (Testudines) to assess how well biogeographic
dating fares when compared to fossil-calibrated dating estimates reported
in the literature. Fossil-free biogeographic dating estimated the age of
the most recent common ancestor of extant turtles to be from the Late
Triassic, which is consistent with fossil-based estimates. Dating
precision improves further when including a root node fossil calibration.
The described model, paleogeographical dispersal graph, and analysis
scripts are available for use with RevBayes.