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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 18 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 show 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. 

The archaeocidarids comprise the most derived stem group echinoids and have long been regarded as closely related to the crown group. The fossil record of echinoids in the Palaeozoic is, however, poor, so details surrounding the initial divergence of crown group echinoids are not well constrained. In order to better understand the phylogenetic relationships of the most derived stem group and most basal crown group echinoids, a phylogenetic analysis was undertaken of the Archaeocidaridae, including the generaNortonechinus,Devonocidaris,Lepidocidaris,PolytaxicidarisandArchaeocidarisand the Palaeozoic miocidarid cidaroids from the genusEotiaris. We found thatArchaeocidarisappears to be paraphyletic with respect to crown group echinoids. Furthermore, we mapped character evolution along our phylogeny and found that the diversification of archaeocidarids and miocidarids may be linked to large‐scale macroecological changes taking place in the late Palaeozoic, including increasing predation pressure and echinoid encrustation by epibionts. We compared the stratigraphical distribution of archaeocidarid and miocidarid occurrences to our resulting phylogenies, and found that the fit of our cladograms to the stratigraphic record of archaeocidarid occurrences is worse than other echinoid groups, supporting the idea that the imbricate plated archaeocidarids have a poor fossil record. In the course of carrying out these analyses, we also felt it necessary to describe a new species ofArchaeocidaris,Archaeocidaris ivanovisp. nov. We also provide novel descriptions and interpretations forDevonocidaris primaevus,Archaeocidaris brownwoodensis,Archaeocidaris aphelesand revise the synonymy ofArchaeocidaris legrandensisand ?Eotiaris meurevillensis, which may be a crown group echinoid.