Data from: Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

Background Bayesian relaxed-clock dating has significantly influenced our
understanding of the timeline of plant evolution. This approach requires
the use of priors on the branching process, yet little is known about
their impact on divergence time estimates. We investigated the effect of
branching priors using the iconic cycads. We conducted phylogenetic
estimations for 237 cycad species using three genes and two calibration
strategies incorporating up to six fossil constraints to (i) test the
impact of two different branching process priors on age estimates, (ii)
assess which branching prior better fits the data, (iii) investigate
branching prior impacts on diversification analyses, and (iv) provide
insights into the diversification history of cycads. Results Using Bayes
factors, we compared divergence time estimates and the inferred dynamics
of diversification when using Yule versus birth-death priors. Bayes
factors were calculated with marginal likelihood estimated with
stepping-stone sampling. We found striking differences in age estimates
and diversification dynamics depending on prior choice. Dating with the
Yule prior suggested that extant cycad genera diversified in the Paleogene
and with two diversification rate shifts. In contrast, dating with the
birth-death prior yielded Neogene diversifications, and four rate shifts,
one for each of the four richest genera. Nonetheless, dating with the two
priors provided similar age estimates for the divergence of cycads from
Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes
factors clearly supported the birth-death prior. Conclusions These results
suggest the choice of the branching process prior can have a drastic
influence on our understanding of evolutionary radiations. Therefore, all
dating analyses must involve a model selection process using Bayes factors
to select between a Yule or birth-death prior, in particular on ancient
clades with a potential pattern of high extinction. We also provide new
insights into the history of cycad diversification because we found (i)
periods of extinction along the long branches of the genera consistent
with fossil data, and (ii) high diversification rates within the Miocene
genus radiations.