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

Nicolás Mongiardino Koch*, Jeffrey R. Thompson, Avery S. Hiley, Marina F. McCowin, A. Frances Armstrong, Simon E. Coppard, Felipe Aguilera, Omri Bronstein, Andreas Kroh, Rich Mooi, Greg W. Rouse

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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 affin-ities, 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 discrep-ancy with their rich fossil record.

Original languageEnglish
Article numbere72460
StatePublished - Mar 2022


FundersFunder number
Agencia Nacional de Investigación
Austrian Science Fund project
Department of Geology and Palaeontology
Departmental Council of Mayotte
Libby Liggins
PAI Inserción en la AcademiaPAI79170033
National Science FoundationDEB-2036298, DEB-2036186
Yale University
National Museum of Natural History
Institut français de recherche pour l'exploitation de la mer
Institute for Biospheric Studies, Yale University
Central Research Laboratory
Aneurysm and AVM Foundation
Leverhulme Trust
Royal Society
European Commission
Austrian Science FundP 29508-B25
King Abdullah University of Science and Technology
Muséum national d'histoire naturelle
Terres Australes et Antarctiques Françaises
Agence Française de Développement
Agencia Nacional de Investigación y Desarrollo


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