Data from: Bayesian phylogenetic estimation of clade ages supports trans-atlantic dispersal of cichlid fishes

Divergence-time estimation based on molecular phylogenies and the fossil
record has provided insights into fundamental questions of evolutionary
biology. In Bayesian node dating, phylogenies are commonly time calibrated
through the specification of calibration densities on nodes representing
clades with known fossil occurrences. Unfortunately, the optimal shape of
these calibration densities is usually unknown and they are therefore
often chosen arbitrarily, which directly impacts the reliability of the
resulting age estimates. As possible solutions to this problem, two
non-exclusive alternative approaches have recently been developed, the
“fossilized birth-death” model and “total-evidence dating”. While these
approaches have been shown to perform well under certain conditions, they
require including all (or a random subset) of the fossils of each clade in
the analysis, rather than just relying on the oldest fossils of clades. In
addition, both approaches assume that fossil records of different clades
in the phylogeny are all the product of the same underlying fossil
sampling rate, even though this rate has been shown to differ strongly
between higher-level taxa. We here develop a flexible new approach to
Bayesian age estimation that combines advantages of node dating and the
fossilized birth-death model. In our new approach, calibration densities
are defined on the basis of first fossil occurrences and sampling rate
estimates that can be specified separately for all clades. We verify our
approach with a large number of simulated datasets, and compare its
performance to that of the fossilized birth-death model. We find that our
approach produces reliable age estimates that are robust to model
violation, on par with the fossilized birth-death model. By applying our
approach to a large dataset including sequence data from over 1000 species
of teleost fishes as well as 147 carefully selected fossil constraints, we
recover a timeline of teleost diversification that is incompatible with
previously assumed vicariant divergences of freshwater fishes. Our results
instead provide strong evidence for trans-oceanic dispersal of cichlids
and other groups of teleost fishes.