A total-evidence dated phylogeny of Echinoidea combining phylogenomic and paleontological data

Phylogenomic and paleontological data constitute complementary resources
for unravelling the phylogenetic relationships and divergence times of
lineages, yet few studies have attempted to fully integrate them. Several
unique properties of echinoids (sea urchins) make them especially useful
for such synthetizing approaches, including a remarkable fossil record
that can be incorporated into explicit phylogenetic hypotheses. We revisit
the phylogeny of crown group Echinoidea using a total-evidence dating
approach that combines the largest phylogenomic dataset for the clade, a
large-scale morphological matrix with a dense fossil sampling, and a novel
compendium of tip and node age constraints. To this end, we develop a
novel method for subsampling phylogenomic datasets that selects loci with
high phylogenetic signal, low systematic biases and enhanced clock-like
behavior. Our results demonstrate that combining different data sources
increases topological accuracy and helps resolve conflicts between
molecular and morphological data. Notably, we present a new hypothesis for
the origin of sand dollars, and restructure the relationships between stem
and crown echinoids in a way that implies a long stretch of unidscovered
evolutionary history of the crown in the late Paleozoic. Our efforts help
bridge the gap between phylogenomics and phylogenetic paleontology,
providing a model example of the benefits of combining the two.