A phylogenomic resolution of the sea urchin tree of life

Nicolás Mongiardino Koch, Simon E. Coppard, Harilaos A. Lessios, Derek E. G. Briggs, Rich Mooi, Greg W. Rouse

Research output: Contribution to journalArticlepeer-review

32 Scopus citations


Background: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved. Results: We performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We show that phylogenetic signal for novel resolutions of these lineages is strong and distributed throughout the genome, and fail to recover systematic biases as drivers of our results. Conclusions: Our investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.
Original languageEnglish (US)
JournalBMC Evolutionary Biology
Issue number1
StatePublished - Dec 13 2018
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2021-04-13
Acknowledgements: Many thanks to Tim Ravasi for providing resources and collection facilities to GWR via King Abdullah University of Science and Technology (KAUST). We thank Chief Scientist Erik Cordes, the captain and crew of the RV Atlantis and the crew of the HOV Alvin for assistance in specimen collection off Costa Rica. Thanks also to David Clague (Monterey Bay Aquarium and Research Institute) for inviting GWR to Juan de Fuca and to the captain and crew of the RV Western Flyer and the crew of the ROV Doc Ricketts for specimen collection. The authors are also grateful to Gustav Paulay, Phil Zerofski, Fredrik Pleijel, Frédéric Ducarme and Alejandra Melo for their sampling efforts; Josefin Stiller, Ekin Tilic and Avery Hiley for their help with molecular work; Charlotte Seid for the handling and cataloging of specimens at Scripps; and Casey Dunn, Kaylea Nelson and Benjamin Evans for computational assistance. Specimens of Mellita tenuis were purchased from Gulf Specimen Marine Laboratory. Conolampas sigsbei was collected in the submersible “Curasub” on time donated by Adrian “Dutch” Schrier, and identified by David L. Pawson. Kevin Kocot and two anonymous reviewers provided insightful comments that significantly improved this manuscript.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics


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