ArticleeLife2022
Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 49 citations in OpenAlex.
- The tuxedo sea urchinbioRxiv : the preprint server for biology · 2026Article
- Genomic Distortion of Jawed Vertebrate Phylogeny.bioRxiv : the preprint server for biology · 2026Article
- Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes.Nature ecology & evolution · 2026Article
- But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating.Systematic biology · 2026Article
- The first complete mitochondrial genome and phylogenetic analysis of Clypeaster virescens (Clypeasteroida, Clypeasteridae).Scientific reports · 2026Article
- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- Phylogenomics establishes an Early Miocene reconstruction of reef vertebrate diversity.Science advances · 2025Article
- Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758).DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- The brittle star genome illuminates the genetic basis of animal appendage regeneration.Nature ecology & evolution · 2024Article
- Convergent Adaptation of True Crabs (Decapoda: Brachyura) to a Gradient of Terrestrial Environments.Systematic biology · 2024Article
- Colonization of the ocean floor by jawless vertebrates across three mass extinctions.BMC ecology and evolution · 2024Article
- Two Notorious Nodes: A Critical Examination of Relaxed Molecular Clock Age Estimates of the Bilaterian Animals and Placental Mammals.Systematic biology · 2024Article
- Reply to: Embracing the taxonomic and topological stability of phylogenomics.Scientific reports · 2024Article
- Embracing the taxonomic and topological stability of phylogenomics.Scientific reports · 2024Article
- The mitochondrial genome of the deep-sea pyramid urchinMitochondrial DNA. Part B, Resources · 2024Article
- Article
- Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Confusion will be my epitaph: genome-scale discordance stifles phylogenetic resolution of Holothuroidea.Proceedings. Biological sciences · 2023Article
- Phylogeny, ancestral ranges and reclassification of sand dollars.Scientific reports · 2023Article
- Analysis of theCell genomics · 2023Article
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Authors and funding
11 authors at 9 institutions in 5 countries.
Funding
Abstract
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.
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