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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 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 genus Apatopygus represents 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.

Lamellibrachia columna Southward was originally described from hydrothermal vents of the Lau Basin, between Fiji and Tonga. This study utilizes phylogenetic and morphological analyses to confirm the collection of Lamellibrachia columna from cold seeps on the Hikurangi Margin off New Zealand, thereby extending its geographic range southward by approximately 1900 km. We also propose, based on molecular evidence, that specimens previously reported from vents in the Nankai Trough, Japan and seeps off southern and eastern Japan are L. columna. Furthermore, we suggest that Lamellibrachia sagami Kobayashi et al. described from cold seeps off southern and eastern Japan is a junior synonym of Lamellibrachia columna. Our work confirms that L. columna is found at two types of chemosynthetic habitat over a wide geographic range in the western Pacific Ocean.

Bathymodiolus Kenk and Wilson, 1985 includes fourteen currently recognized species from deep-sea chemosynthetic environments in the Pacific, Atlantic, and Indian oceans. In this study, phylogenetic analyses of mytilid mussels sampled from seeps along the Costa Rica margin reveal the presence of three new Bathymodiolus species, sampled from depths across ~1000–1900 m. Bathymodiolus billschneideri n. sp., B. earlougheri n. sp., and B. nancyschneiderae n. sp. differ genetically from congeneric species of Bathymodiolus and show some stratification by depth. The depth ranges of Bathymodiolus billschneideri n. sp., B. nancyschneiderae n. sp., and B. earlougheri n. sp. were ~1400–1900 m, 1000–1100 m, and ~1000–1900m, respectively. Bathymodiolus billschneideri n. sp. and B. earlougheri n. sp. were found to be closely related to Bathymodiolus thermophilus Kenk and Wilson, 1985, while B. nancyschneiderae n. sp. exhibited closer relationships to non-East-Pacific taxa. Bathymodiolus thermophilus was the first Bathymodiolus mussel discovered, sampled from a vent along the Galapagos Rift Zone in 1985 and later recorded along much of the East Pacific Rise. This study confirms the presence of B. thermophilus at the Costa Rica margin, representing the first DNA and morphological samples of B. thermophilus at a seep environment. Analysis of habitat evolution suggests that B. thermophilus and its closest relative, B. antarcticus Johnson and Vrijenhoek, 2013, are of seep ancestry.

Lamellibrachia Webb, 1969 has eight currently recognized species reported from chemosynthetic environments in the Pacific, Atlantic, and Mediterranean. Of these, Lamellibrachia barhami Webb, 1969 has been reported in the eastern Pacific from Canada to Costa Rica. In this study, phylogenetic analyses of Lamellibrachia tubeworms sampled from the Costa Rica margin confirm the large geographic range of L. barhami and reveal a new Lamellibrachia species from a single methane seep between 999 and 1,040 meters. Lamellibrachia donwalshi sp. nov. differs genetically and morphologically from all congeneric species. Despite its geographic proximity to the eastern Pacific L. barhami, L. donwalshi sp. nov. formed a clade with Atlantic and Mediterranean Lamellibrachia species. This suggests a vicariant event may have occurred after an Atlantic radiation of Lamellibrachia.

The scale-worm family Iphionidae consists of four genera. Of these, Thermiphione has two accepted species, both native to hydrothermal vents in the Pacific Ocean; T.fijiensis Miura, 1994 (West Pacific) and T.tufari Hartmann-Schröder, 1992 (East Pacific Rise). Iphionella is also known from the Pacific, and has two recognized species; Iphionellarisensis Pettibone, 1986 (East Pacific Rise, hydrothermal vents) and I.philippinensis Pettibone, 1986 (West Pacific, deep sea). In this study, phylogenetic analyses of Iphionidae from various hydrothermal vent systems of the Pacific Ocean were conducted utilizing morphology and mitochondrial (COI and 16S rRNA) and nuclear (18S and 28S rRNA) genes. The results revealed a new iphionid species, described here as Thermiphionerapanuisp. n. The analyses also demonstrated the paraphyly of Thermiphione, requiring Iphionellarisensis to be referred to the genus, as Thermiphionerisensis (Pettibone, 1986).