Data from: An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae)

Time-calibrated phylogenies based on molecular data provide a framework
for comparative studies. Calibration methods to combine fossil information
with molecular phylogenies are, however, under active development, often
generating disagreement about the best way to incorporate paleontological
data into these analyses. This study provides an empirical comparison of
the most widely used approach based on node-dating priors for relaxed
clocks implemented in the programs BEAST and MrBayes, with two recently
proposed improvements: one using a new fossilized birth–death process
model for node dating (implemented in the program DPPDiv), and the other
using a total-evidence or tip-dating method (implemented in MrBayes and
BEAST). These methods are applied herein to tetraodontiform fishes, a
diverse group of living and extinct taxa that features one of the most
extensive fossil records among teleosts. Previous estimates of
time-calibrated phylogenies of tetraodontiforms using node-dating methods
reported disparate estimates for their age of origin, ranging from the
late Jurassic to the early Paleocene (ca. 150–59 Ma). We analyzed a
comprehensive dataset with 16 loci and 210 morphological characters,
including 131 taxa (95 extant and 36 fossil species) representing all
families of fossil and extant tetraodontiforms, under different molecular
clock calibration approaches. Results from node-dating methods produced
consistently younger ages than the tip-dating approaches. The older ages
inferred by tip dating imply an unlikely early-late Jurassic (ca. 185–119
Ma) origin for this order and the existence of extended ghost lineages in
their fossil record. Node-based methods, by contrast, produce time
estimates that are more consistent with the stratigraphic record,
suggesting a late Cretaceous (ca. 86–96 Ma) origin. We show that the
precision of clade age estimates using tip dating increases with the
number of fossils analyzed and with the proximity of fossil taxa to the
node under assessment. This study suggests that current implementations of
tip dating may overestimate ages of divergence in calibrated phylogenies.
It also provides a comprehensive phylogenetic framework for
tetraodontiform systematics and future comparative studies.