Data from: Empirical and Bayesian approaches to fossil-only divergence times: a study across three reptile clades

Estimating divergence times on phylogenies is critical in paleontological
and neontological studies. Chronostratigraphically-constrained fossils are
the only direct evidence of absolute timing of species divergence. Strict
temporal calibration of fossil-only phylogenies provides minimum
divergence estimates, and various methods have been proposed to estimate
divergences beyond these minimum values. We explore the utility of
simultaneous estimation of tree topology and divergence times using BEAST
tip-dating on datasets consisting only of fossils by using relaxed
morphological clocks and birth-death tree priors that include serial
sampling (BDSS) at a constant rate through time. We compare BEAST results
to those from the traditional maximum parsimony (MP) and undated Bayesian
inference (BI) methods. Three overlapping datasets were used that span 250
million years of archosauromorph evolution leading to crocodylians. The
first dataset focuses on early Sauria (31 taxa, 240 chars.), the second on
early Archosauria (76 taxa, 400 chars.) and the third on Crocodyliformes
(101 taxa, 340 chars.). For each dataset three time-calibrated trees
(timetrees) were calculated: a minimum-age timetree with node ages based
on earliest occurrences in the fossil record; a 'smoothed'
timetree using a range of time added to the root that is then averaged
over zero-length internodes; and a tip-dated timetree. Comparisons within
datasets show that the smoothed and tip-dated timetrees provide similar
estimates. Only near the root node do BEAST estimates fall outside the
smoothed timetree range. The BEAST model is not able to overcome limited
sampling to correctly estimate divergences considerably older than sampled
fossil occurrence dates. Conversely, the smoothed timetrees consistently
provide node-ages far older than the strict dates or BEAST estimates for
morphologically conservative sister-taxa when they sit on long ghost
lineages. In this latter case, the relaxed-clock model appears to be
correctly moderating the node-age estimate based on the limited
morphological divergence. Topologies are generally similar across
analyses, but BEAST trees for crocodyliforms differ when clades are deeply
nested but contain very old taxa. It appears that the constant-rate
sampling assumption of the BDSS tree prior influences topology inference
by disfavoring long, unsampled branches.