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 much of their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context and discrepancies between molecular divergence times and fossil evidence. We employ seventeen 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 the effects of using alternative gene samples, models of molecular evolution, and clock priors. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models shows little effects. The choice of loci shows 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 among sand dollars and their close relatives, showing that the genusApatopygusrepresents a relict lineage with a deep Jurassic origin. Surprisingly, the origin of sand dollars is confidently dated to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.