Data from: Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Echinoids are key components of modern marine ecosystems. Despite a
remarkable fossil record, the emergence of their crown group is documented
by few specimens of unclear affinities, rendering their early history
uncertain. The origin of sand dollars, one of its most distinctive clades,
is also unclear due to an unstable phylogenetic context. We employ
eighteen novel genomes and transcriptomes to build a phylogenomic dataset
with a near-complete sampling of major lineages. With it, we revise the
phylogeny and divergence times of echinoids, and place their history
within the broader context of echinoderm evolution. We also introduce the
concept of a chronospace—a multidimensional representation of node
ages—and use it to explore methodological decisions involved in time
calibrating phylogenies. We find the choice of clock model to have the
strongest impact on divergence times, while the use of site-heterogeneous
models and alternative node prior distributions showing minimal effects.
The choice of loci has an intermediate impact, affecting mostly deep
Paleozoic nodes, for which clock-like genes recover dates more congruent
with fossil evidence. Our results reveal that crown group echinoids
originated in the Permian and diversified rapidly in the Triassic, despite
the relative lack of fossil evidence for this early diversification. We
also clarify the relationships between sand dollars and their close
relatives and confidently date their origins to the Cretaceous, implying
ghost ranges spanning approximately 50 million years, a remarkable
discrepancy with their rich fossil record.