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Dr. Chong CHEN

Dr. Chong CHEN

Deep-sea biologist. Malacologist. Evolutionary biologist. "Mollusc collector", photographer.

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Gallery of Publications

Our new paper in Molecular Ecology targeted two deep-sea alvinocaridid shrimp species, Rimicaris loihi and R. cambonae, living side by side at hydrothermal vents — yet remaining genetically distinct. Our genomic data and decadal sampling reveal insights on their demography and speciation! The paper is OPEN ACCESS, read for FREE here: https://doi.org/10.1111/mec.70119<br /> <br /> Abstract: <br /> Hydrothermal vents can serve as natural laboratories to study speciation processes due to their fragmented distribution, often with geographic barriers between habitats. Two sympatric species of Rimicaris shrimps occur at vents on the Izu-Bonin-Mariana volcanic arc: Rimicaris loihi also occurs near Hawai’i and R. cambonae is present on the Tonga Arc. These two species biogeographically co-occur and are genetically similar, raising questions about their speciation mechanisms, how they maintain distinct species, and whether interbreeding occurs. Here, we used barcoding and shotgun sequencing to test their genetic isolation and investigate their speciation process. We also evaluated population demography over 10 years to assess population densities and sex ratios at vents. Our results supported R. cambonae and R. loihi as two distinct species despite sympatry throughout part of their range. We also observed regional-scale genetic structure among R. loihi populations from the Izu-Bonin-Mariana volcanic arc, despite high dispersal potential. Finally, we found concomitant variations of shrimp densities and genetic diversity following fluctuations in geological and venting activities over a decade. A combination of geological instability, ocean currents dynamics and sea-level changes might drive temporary isolation among these local populations. We suggest that similar factors, with longer isolation periods, may also have promoted speciation between the two Rimicaris species, whereas distinct life-history traits could strengthen and maintain reproductive barriers. Overall, we found that the two species with large geographic distributions had significant patterns of genetic partitioning on a volcanic arc; this scenario contrasts with those observed previously at vents from mid-ocean ridges or back-arc basin systems.<br /> <br /> Methou P*, Johnson S, Sherrin J, Shank TM, Chen C, Tunnicliffe V (2025). A Tale of Two Shrimps — Speciation and demography of two sympatric shrimp species from hydrothermal vents. Molecular Ecology, Early View: e70119. DOI: 10.1111/mec.70119 [Preprint available on bioRxiv, DOI: 10.1101/2024.12.18.629080]
We discovered and named Chaetoderma naga, a gigantic (>13 cm) new caudofoveate worm-mollusc from a cold seep -- We named it after Nāga, a group of snake-gods from Asian mythologies! Like its sister-species C. shenloong named last year, it probably relies on endosymbiotic bacteria. Out now in Molluscan Research: https://www.tandfonline.com/eprint/9AUCH5GUIQICIJBCSGVN/full?target=10.1080/13235818.2025.2566524<br /> <br /> Abstract: <br /> Deep-sea chemosynthetic ecosystems such as hydrothermal vents and hydrocarbon seeps are home to numerous endemic species. Despite decades of exploration, the diversity of minor animal groups such as aplacophoran molluscs in these systems remain understudied. The recent discovery of Chaetoderma shenloong, a giant caudofoveate from Haima cold seep in the South China Sea, marked the first aplacophoran from cold seeps and the first caudofoveate from chemosynthetic systems overall. Here, we report another giant caudofoveate species from Haima seep – Chaetoderma naga sp. nov. This new species is morphologically closest to C. shenloong, but differ significantly in spicule morphology where the distribution of isosceles-triangle shaped spicules differ and that the needle-like spicules are much longer and thicker in C. shenloong. Molecular phylogenetic reconstruction based on the mitochondrial cytochrome c oxidase subunit I (COI) gene recovered C. naga n. sp. as sister to C. shenloong among those with data available, with a K2P genetic distance of 17% supporting the status of C. naga n. sp. as a separate species. Our discovery highlights the presence of overlooked biodiversity within sediments of chemosynthetic ecosystems and reinforces the possibility of a high caudofoveate diversity in such environments.<br /> <br /> Liu X, Chen C, Gu X, Sun J* (2025). A second species of giant caudofoveate worm-mollusc from Haima cold seep in the South China Sea. Molluscan Research, Early View: 2566524. DOI: 10.1080/13235818.2025.2566524<br /> PDF: https://www.researchgate.net/publication/396388688_A_second_species_of_giant_caudofoveate_worm-mollusc_from_Haima_cold_seep_in_the_South_China_Sea
Just out in Zootaxa, we named a new genus Lobatoradarea in the amphipod family Calliopiidae, with 10 new species found across a wide range of marine habitats from shallow subtidal waters to a deep-sea hydrothermal vent! Link to the paper: https://mapress.com/zt/article/view/zootaxa.5699.1.1<br /> <br /> Abstract: <br /> Ten new species of calliopiid amphipods were collected from Japanese waters between 0–694 m deep. All specimens commonly exhibit (1) 1-articulate accessory flagellum, (2) developed inner lobes of lower lip, (3) elongate carpus and propodus of gnathopod 2 in both sexes, and (4) entire telson. Among these characters 1, 3 and 4 are shared with the genus Oradarea, but the character 2 is quite different from Oradarea; therefore, Lobatoradarea gen. nov. is established herein to house these species. The ten new species are described in detail, including Lobatoradarea angulata sp. nov., L. anko sp. nov., L. coccina sp. nov., L. inermis sp. nov., L. kagoshimensis sp. nov., L. lignorum sp. nov., L. littoralis sp. nov., L. obliquua sp. nov., L. subinermis sp. nov., and L. thermicola sp. nov. These species can be distinguished from one another mainly by the presence or absence of the posterodorsal projections on pereonite 7 and pleonites 1, 2, and the shapes of the anteroventral corner of head, the dactyli of pereopods 3–7, the ventral margin of coxa 4, the posteroventral corner of epimeral plate 2, and the telson. A key to these species of Lobatoradarea gen. nov. is provided and the diagnosis of Oradarea is emended. <br /> <br /> Ariyama H*, Kohtsuka H, Hoshino O, Kodama M, Moritaki T, Chen C (2025). Lobatoradarea, a new genus of the family Calliopiidae Sars, 1895 (Crustacea: Amphipoda) from Japan, with descriptions of ten new species. Zootaxa, 5669(1): 1-72. DOI: 10.11646/zootaxa.5699.1.1
We studied Pyropelta limpets from the northwestern Pacific, extending the distribution of two species and discovered Pyropelta artemis, a new species from Japan that can shape-shift its shell to fit the substrate shape! Just out in Contributions to Zoology, OPEN ACCESS: https://brill.com/view/journals/ctoz/94/4/article-p371_3.xml<br /> <br /> Abstract:<br /> Hydrothermal vents and other chemosynthetic ecosystems are island-like oases in the deep ocean where microbial primary production supports an unusually high biomass. The small lepetelloidean family Pyropeltidae, with its sole genus Pyropelta containing about 10 described species, specialises in these systems. In the northwestern Pacific two species have been named around Japan, but their ranges have remained uncertain as shells of Pyropelta are typically corroded and difficult to identify morphologically. Here, we collected Pyropelta from three vents and two seeps in the northwestern Pacific, and assess the distribution of each species using molecular barcoding of the mitochondrial cytochrome c oxidase subunit I (COI) gene. As a result, we greatly extend the known distribution ranges of the two known northwestern Pacific species P. yamato and P. ryukyuensis. A lineage found in the Off Hatsushima seep in Sagami Bay was genetically distinct from the two described species and is named as Pyropelta artemis sp. nov. This new species inhabits a variety of substrates including tubes of siboglinid polychaetes as well as snail and mussel shells, and is noteworthy in displaying a great variability in its shell form because the aperture is constricted by substrate morphology. Our findings show that pyropeltids can also ‘shape-shift’ according to the substrate like many other limpet-formed gastropods, which excludes shell shape as a broadly useful taxonomic character in this family. <br /> <br /> Chen C*, Tsuda M, Watanabe HK (2025). Distribution of the deep-sea limpet genus Pyropelta in the northwestern Pacific, with the description of a new species. Contributions to Zoology, 94(4): 371-394. DOI: 10.1163/18759866-bja10083
We found a SECOND SNAIL with HARD SCALES on the foot -- Ifremeria nautilei makes chitinous scales not by secretion but by cell differentiation, like our own skin! READ FOR FREE: https://doi.org/10.1098/rspb.2025.1220<br /> <br /> Abstract: <br /> Animals produce diverse hard structures for critical functions such as protection, feeding and detoxification. Most animals use the polysaccharide chitin as a framework for this, while vertebrates have switched to using fibrous proteins like collagen and keratin. Vertebrates make structures like skin and horns through a cellular differentiation process called keratinization where cells accumulating keratin die and compact into hard layers—drastically different from chitinous structures, which are secreted directly by living cells. Here, we report remarkable chitinous dermal sclerites that are not secreted but instead produced by a keratinization-like process, in the deep-sea hot-vent snail Ifremeria nautilei. These scales bundle to form ‘warts’ on the foot, the framework of which we show to be β-chitin. Microscopic observations reveal that Ifremeria scales are not formed by uniform, secreted layers but instead involve cells going through a series of unusual differentiation steps strongly resembling keratinization. The only other gastropod with chitinous dermal sclerites is the phylogenetically distant scaly-foot snail Chrysomallon squamiferum, but the scales of Chrysomallon form by secretion. Our finding of a chitinous convergence for keratinization opens a new avenue to unveil how such complex terminal cell differentiation processes evolve and may also inspire biomimetic innovation in material sciences.<br /> <br /> Chen C*, Okada S, Watanabe HK, Uematsu K, Isobe N (2025). Keratinisation-like differentiation process forms chitinous dermal sclerites in the hot vent snail Ifremeria nautilei. Proceedings of the Royal Society B: Biological Sciences, 292(2053): 20251220. DOI: 10.1098/rspb.2025.1220
We discovered the world's deepest true limpet from almost 6 km deep! Meet Bathylepeta wadatsumi -- a giant-sized (4 cm) limpet for this depth named after the god of sea in Japan & also the Large Monk “Wadatsumi” from the manga series ONE PIECE! Read for FREE: https://doi.org/10.3897/zse.101.156207<br /> <br /> Abstract: <br /> True limpets in the gastropod subclass Patellogastropoda are familiar members of shallow-water rocky environments but are much rarer in the deep, with just three families adapted to bathyal depths or more. Of these, Lepetidae is the only one found on ambient seafloor habitats, and Bathylepeta is a very deep genus known from two species off Chile and Antarctica. Here, we report a giant Bathylepeta up to a shell length of 40.5 mm from 5922 m deep in the northwestern Pacific and name it Bathylepeta wadatsumi sp. nov. Phylogenetic reconstruction using the mitochondrial cytochrome c oxidase subunit I (COI) gene supports the placement of this new species in Bathylepeta. Our new species is most similar to B. linseae from the Weddell Sea but can be distinguished by its much more developed second lateral and marginal teeth, as well as a larger size. Bathylepeta wadatsumi sp. nov. also has slightly imbricating radular basal plates, a feature previously unknown from this genus; we therefore emend the genus diagnosis. Our finding not only extends the distribution of this enigmatic limpet genus to Japan but also marks the deepest bathymetric record for the entire Patellogastropoda.<br /> <br /> Chen C*, Tsuda M, Ishitani Y (2025). A new large-sized lepetid limpet from the abyssal northwestern Pacific is the deepest known patellogastropod. Zoosystematics and Evolution 101(3): 1249-1258. DOI: 10.3897/zse.101.156207
Our new paper in European Journal of Taxonomy names one new genus and three new species of xenophyophores -- giant single-celled foraminifera! We integrate in situ imagery, dissection, SEM, micro-CT, and molecular phylogeny for unprecedentedly detailed descriptions of this understudied group. Read this OPEN ACCESS paper for free: https://doi.org/10.5852/ejt.2025.1004.2973<br /> <br /> Abstract: Xenophyophores dominate the abyssal megafauna across many areas of the Pacific Ocean. These giant agglutinated foraminifera have been studied mainly in the tropics, including within the Clarion-Clipperton Zone (CCZ), from where the majority of recently described taxa have originated. Here, we describe three new species, one of them assigned to a new genus, from an area further north (30–32.5° N) near the Japanese Archipelago. Specimens were collected in pushcores during dives of the manned submersible Shinkai 6500 and preserved in the cores after removal of fragments for genetic analyses, allowing them to be examined in life position using X-ray micro-computed tomography (µCT). The three species have basically plate-like tests composed largely of mineral grains. Two, both from 32.5° N, are assigned to the genus Psammina. They are closely related to each other and to P. tenuis from the western CCZ. In Psammina yokosukae sp. nov., the test comprises curved plates, whereas in Psammina contorta sp. nov., it comprises a confusing array of contorted plates and other poorly defined structures. The third new species, Laminarena variabilis gen. et sp. nov., is genetically distinct from the others. In typical specimens from 30° N, the plates are large, curved or sinuous, relatively thin, and marked by a distinct surface pattern of concentric zones, traversed by closely spaced, radial ridges that correspond to internal partitions. A form from 32.5° N is shown to be conspecific with the 30° N specimens based on molecular evidence but is morphologically more complex, comprising elongate bar- and plate-like elements, some with fan-like terminations. A fourth taxon, resembling a bumpy pebble and occupied by bubble-like internal compartments, is described informally. These new taxa enhance our knowledge of Pacific xenophyophores, as well as our understanding of the morphological diversity of xenophyophores in general.<br /> <br /> Gooday AJ*, Y Ishitani, Chen C, Holzmann M, Richirt J, Seike K, Yamashita M, Tsuchiya M, Nomaki H (2025). Integrative taxonomy of new xenophyophores (Rhizaria, Foraminifera) from the abyssal northwest Pacific. European Journal of Taxonomy, 1004(1): 144-189. DOI: 10.5852/ejt.2025.1004.2973
We used genetic data from 444 individuals to reveal 4 distinct metapopulations in the hot vent mussel Bathymodiolus septemdierum across the Indo-W Pacific -- with implications for conservation in the face of upcoming deep-sea mining! Read this OPEN ACCESS paper for FREE in Journal of Biogeography: https://doi.org/10.1111/jbi.70017<br /> <br /> Abstract: Genetic diversity and connectivity are crucial to informing the conservation strategy for deep-sea organisms, especially those threatened by deep-sea mining. The vent mussel Bathymodiolus septemdierum has an extraordinary trans-oceanic distribution range across the Indo-West Pacific including numerous sites eyed for exploitation. Here, we aimed to assess the connectivity of B. septemdierum across its entire range, for the first time: hydrothermal vent fields on the Carlsberg Ridge (CR), Central Indian Ridge (CIR), Southwest Indian Ridge (SWIR), as well as those in the Mariana Trough and the Southwest Pacific. Combining new and published data, we studied the genetic structure, historical demography and gene flow of B. septemdierum using three mitochondrial and two nuclear genes from a total of 444 individuals across 16 vent fields. Bathymodiolus septemdierum populations are structured with four regional metapopulations including (1) the whole Western Pacific, (2) CR in the northern Indian Ocean, (3) vents on the SWIR and southern CIR (CIR + SWIR) and (4) Onnuri field on the northern CIR. IMa3 analysis shows divergence first occurred between WP and the Indian Ocean, and then between CR and CIR + SWIR metapopulations. The gene flow towards CR from both CIR + SWIR and WP is higher than the reverse directions, while Onnuri received exceptionally high migrations from both CIR + SWIR and CR metapopulations. Our findings support a large-scale dispersal scenario where larvae are carried westwards from the Pacific Ocean into the western Indian Ocean through Indonesia, and then separated into northern and southern Indian Ocean clades. The CR acts as an isolated gene pool for this species among others, and the Onnuri field serves as a key transition zone in the Indian Ocean, and we urge for the prioritised protection of these vents currently targeted by deep-sea mining.<br /> <br /> Mao Q# / Chen C#, Sun J, Liang J, Sun Y, Wang Y, Zeng C, Li M, Xin S, Zhang D, Zhou Y* (2025). Genetic structure in a trans-oceanic hot vent mussel reveals four metapopulations with implications for conservation. Journal of Biogeography, Early View: e70017. DOI: 10.1111/jbi.70017
Just out in Progress in Oceanography, our paper reports mollusc eggs collected from the Aleutian Trench! Most are gastropod eggs, with one cirrate octopus (likely Dumbo Octopus) egg. Read for FREE here: https://www.sciencedirect.com/science/article/pii/S0079661125001235<br /> <br /> Abstract: <br /> Many deep-sea molluscs are in taxonomic groups known to deposit demersal egg capsules, but limited information is available on the morphology of egg capsules from abyssal and hadal depths. During the 2022 “AleutBio” expedition (R/V SONNE, SO293) to the Aleutian Trench, we collected egg capsules from depths ranging between 4,220 and 7,142 m. Morphological analysis revealed eight distinct egg types, ranging from translucent capsules to large, grape-like yolky eggs, and those containing no discernible development to visible embryos. Six of these could be tentatively attributed to known taxa based on co-occurrence and morphology: caenogastropod egg capsules with protoconchs morphologically matching the buccinid Bayerius knudseni (Bouchet & Warén, 1986), different capsules likely belonging to Cancellariidae and Eulimidae, stalked yolky eggs postulated as being from the rare trench volutid Tenebrincola frigida Harasewych & Kantor, 1991, and droplet-shaped egg causules consistent with cirrate octopuses of which the emperor’s dumbo octopus (Grimpoteuthis imperator Ziegler & Sagorny, 2021) is the only species known with certainty from the region. Two other egg types — a small ovate egg with metallic sheen and a cluster of seven grape-like capsules — remain taxonomically unresolved and may or may not be molluscan. Our findings represent the first records of molluscan egg capsules from abyssal to hadal parts of the Aleutian Trench and add to the limited knowledge of deep-sea mollusc spawns. <br /> <br /> Chen C*, Sigwart JD (2025). Diversity and potential parentage of molluscan (and likely-molluscan) eggs from the Aleutian Trench. Progress in Oceanography, Early View. DOI: 10.1016/j.pocean.2025.103535
Just out in Cladistics, our new paper uses phylogenomics to resolve how deep-sea symbiotic vesicomyid clams in the subfamily Pliocardiinae evolved to conquer the abyss; revising some of the genus-level taxonomy along the way! Read for FREE here: https://onlinelibrary.wiley.com/share/author/VUSHSJUBIX3998HZXAI9?target=10.1111/cla.70001<br /> <br /> Abstract: Vesicomyid clams in the subfamily Pliocardiinae are chemosymbiotic and specific to deep-sea chemosynthetic ecosystems with wide bathymetric and geographic ranges, making them a suitable model to study molecular adaptation and biogeography. Its phylogeny, however, still remains contentious due to limited molecular markers. Here, we elucidate the evolutionary relationships among pliocardiines based on phylogenomics data. By testing a wide range of matrices with methods including maximum likelihood, maximum parsimony, Bayesian inference, and a coalescent approach, we present a robust phylogenomic tree at the genus level supported by AU-test and GLS analyses. We revise the genus-level taxonomy of pliocardiines updating from Johnson et al. (Syst. Biodivers. 2017, 15, 346) synonymising a number of species in the “gigas-group” with Archivesica—also supported by a mitogenome phylogeny. Our fossil-calibrated tree based on the phylogenomic backbone reveals that Pliocardiinae originated earlier than [41.06, 42.00] Ma in the middle Eocene, while its diversification has been concurrent with global climatic cooling events. Ancestral state reconstruction analyses found two independent invasions into the abyssal zone, and a shift from harbouring the Ca. Ruthia symbionts to Ca. Vesicomyosocius symbionts. Our results present a solid backbone for future investigations into molecular adaptation, biogeography and symbiosis in this fascinating group of molluscs.<br /> <br /> Gao K, He X, Wang H, Chen C, Gu X, Lai Q, Perez M, Kojima S, Amano K, Sun J* (2025). Phylogenomic analyses of Pliocardiinae (Bivalvia: Vesicomyidae) update genus-level taxonomy and shed light on trait evolution. Cladistics, Early View. DOI: 10.1111/cla.70001
We found three species of annelid worms in the family Capitellidae from Indian Ocean hydrothermal vents -- Two of them are described as new species Capitella longqiensis and Decamastus branchiatus! Read for free: https://academic.oup.com/zoolinnean/article/doi/10.1093/zoolinnean/zlaf058/8161711?utm_source=authortollfreelink&utm_campaign=zoolinnean&utm_medium=email&guestAccessKey=5a4d8ea7-2c55-4451-85aa-49a38ac1a13e<br /> <br /> Abstract:<br /> Capitellidae constitute an important family of polychaetes valued for their usefulness as indicators of environmental health in many ecosystems, yet their diversity at mid-ocean ridges remains largely unexplored. Here, we report three species of Capitellidae across three genera from Indian Ocean ridges and formally describe two of them, including Capitella longqiensis sp. nov. from the inactive zones near the active vents of the Longqi vent field on the Southwest Indian Ridge, Notomastus sp. TVG12 from organic matter-rich sediments on the same ridge, and Decamastus branchiatus sp. nov. collected on an active vent chimney in the Edmond vent field on the Central Indian Ridge. Phylogenetic analyses support their assignment to three different genera. Within Capitella, C. longqiensis and the whale-fall species Capitella iatapiuna fell in separate subclades, indicating two independent historical colonizations of chemosynthetic ecosystems. Decamastus branchiatus is sister to an undescribed capitellid from a Red Sea vent, and Notomastus sp. TVG12 was closely related to Notomastus from Pacific nodule fields, supporting a potential biogeographical linkage between these regions. These new capitellids add to the diversity of annelids in the Indian Ocean, underlining the need for further sampling efforts to understand in full the biodiversity at these vents eyed for deep-sea mining.<br /> <br /> Sun Y*, Bao Q, Chen C, Wu X, Ju Y, Liao S, Zhou Y* (2025). New species of capitellid polychaetes add to the unique biodiversity of Indian Ocean hot vents. Zoological Journal of the Linnean Society, 204(2): zlaf058. DOI: 10.1093/zoolinnean/zlaf058
Our new paper in The Nautilus with Roland Houart and Chris Moe describes Naquetia confusa, a new muricid snail from Province of Palawan in the Philippines! Read here: https://www.researchgate.net/publication/392558618_Description_of_a_new_species_of_Naquetia_Jousseaume_1880_Gastropoda_Muricidae_Muricinae_from_the_Philippines<br /> <br /> Abstract: <br /> Naquetia confusa new species, assigned to the genus Naquetia Jousseaume, 1880, is described from a limited distribution area in the Philippines. It is compared with Naquetia vokesae (Houart, 1986) from the western Indian Ocean, with which it has been confused, and with Naquetia triqueter (Born, 1778), a similar species ranging from the Pacific to the southeastern Indian Ocean.<br /> <br /> Houart R*, Moe C, Chen C* (In press). Description of a new species of Naquetia Jousseaume, 1880 (Gastropoda: Muricidae: Muricinae) from the Philippines. The Nautilus, 139(2): 70-77.
Presenting two deep-sea vent snails from the Atlantic in Zoological Journal of the Linnean Society! Being giants for their genera, they're named after the giants "Gargantua and Pantagruel" in 16th Century French novels by François Rabelais. Peltospira gargantua is likely to have symbionts! <br /> <br /> Abstract: Deep-sea hydrothermal vents host lush communities of animals relying on bacterial chemosynthetic primary production, where intimate symbioses often form. Peltospiridae are a family of gastropods endemic to hot vents, whose members exhibit a variety of feeding strategies ranging from bacterial grazing to total reliance on endosymbiosis. Here, we report and describe two new peltospirid snails, Peltospira gargantua sp. nov. and Lirapex pantagruel sp. nov., from two recently discovered vent fields on the Mid-Atlantic Ridge. Peltospira gargantua is clearly distinct from other congeners by its much larger size, differences in the number and arrangement of epipodial tentacles, and notably, a hypertrophied oesophageal gland. Lirapex pantagruel is also the largest known species in the genus, differing from other species also by shell shape and sculpture. Phylogenetic reconstructions using the mitochondrial cytochrome c oxidase subunit I (COI) gene agree with their respective generic placements. An expanded oesophageal gland in peltospirids was known only from the endosymbiotic genera Chrysomallon and Gigantopelta, where it is used to host symbionts, indicating that P. gargantua is probably also endosymbiotic. This would represent another case of likely convergently acquired oesophageal endosymbiosis in the family, and the first record of endosymbiotic gastropod from Mid-Atlantic Ridge vents.<br /> <br /> Chen C*, Pradillon F, Lorenzo CD-R, Alfaro-Lucas JM (2025). Integrative taxonomy of two new peltospirid gastropods from Mid-Atlantic Ridge hot vents including a potentially symbiotic species. Zoological Journal of the Linnean Society, 204(2): zlaf055. DOI: 10.1093/zoolinnean/zlaf055
Our paper in Ecology reveals deep-sea snails in the extremely rare family Laubierinidae as obligate associates of crinoids (likely parasitic), including the first-ever in situ observations of ALL FOUR genera! This relationship where a whole gastropod family specialised in crinoids was last seen in fossils >200 mil years old -- a famed association between stalked crinoids and the snail family Platyceratidae which went extinct in the Permian–Triassic extinction event! READ FOR FREE HERE: https://onlinelibrary.wiley.com/share/author/IPVKHJHXW5FSEXQBHQD8?target=10.1002/ecy.70061<br /> <br /> Abstract: <br /> Crinoids flourished in the Ordovician, and with that appeared platyceratid gastropods intimately associated with them (Bowsher 1955). This relationship was long-lasting and continued at least to the Permian (Ponder and Lindberg 2008). A classic example of biotic interactions in the fossil record, the prevailing view is that platyceratids were parasites or fed on the excrements of sea lilies (Baumiller and Gahn 2018). Though the phylogenetic affinity of Platyceratidae remains unsettled, anatomical and conchological evidences indicate it is most likely a member of subclass Neritimorpha (Sutton et al. 2006, Nützel et al. 2023). Despite crinoids narrowly surviving the end-Permian extinction, Platyceratidae died out. Since then, no gastropod family has been observed to be specifically linked with crinoids as a whole. The enigmatic gastropod family Laubierinidae is restricted to the deep sea, and because almost all of its sparse records are from dredge hauls and beam trawlings, little information has been available on its ecology (Warén and Bouchet 1990). Here, we demonstrate, based on the first in situ observations covering all four genera, that this family is an obligate associate of crinoids and a modern analogue of platyceratids.<br /> <br /> Chen C, Zhang R, Zhang, D, Qiu J-W, Zhou Y* (2025). Laubierinid snails are associates of crinoids and a modern analogue of Paleozoic platyceratids. Ecology, 106(3): e70061. DOI: 10.1002/ecy.70061
In a Communications Biology paper, we extracted and analysed the scale and shell proteomes (total protein contents) of the Scaly-foot Snail! We show the scale largely contains co-opted proteins found in shells of other molluscs -- and surprisingly the shell actually has more novel proteins than the scale. OPEN ACCESS: https://doi.org/10.1038/s42003-025-07785-7<br /> <br /> Abstract: <br /> Biomineralization, a key driving force underlying dramatic morphological diversity, is widely adopted by metazoans to incorporate inorganic minerals into their organic matrices. The scaly-foot snail Chrysomallon squamiferum from deep-sea hot vents uniquely possesses hundreds of sclerites on its foot in addition to a coiled shell, providing an exclusive case to study the formation of evolutionarily novel hard parts. Here, we identified the matrix proteins present in the exoskeletons of C. squamiferum and Gigantopelta aegis, a confamilial species from the same vent habitat but lacking sclerites, to uncover the genes and proteins presumably involved in the sclerite formation processes. Comparative multi-omics analyses suggest that C. squamiferum co-opted a diverse range of metazoan biocalcifying proteins through sclerite formation in a possibly deep homology scenario, and the up-regulated biomineralization-related genes in the foot imply alternative sources of sclerite proteins. The sclerite-secreting epithelium employs and utilizes genes considerably older than those in the mantle, which supports the predominant contribution of co-option in C. squamiferum sclerite formation. Our results highlight the importance of gene co-option in shaping novel hard parts in C. squamiferum and indicate that lineage-specific gene incorporation is a possible key factor leading to the rapid evolution of a novel hard structure in this vent-endemic species. <br /> <br /> Wong WC, Kwan YH, He X, Chen C, Xiang S, Xiao Y, Long L, Gao K, Wang N, Wu L, Qian P-Y*, Sun J* (2025). Proteomic analyses reveal the key role of gene co-option in the evolution of the scaly-foot snail scleritome. Communications Biology, 8: 337. DOI: 10.1038/s42003-025-07785-7
Just out in SCIENCE today: We present the FIRST genome-phylogeny of Mollusca complete with ALL classes — including the mythical "living fossil" Monoplacophora — revealing how they evolved the most diverse body forms of all animals! Read our OPEN ACCESS paper for FREE here: https://doi.org/10.1126/science.ads0215<br /> <br /> Abstract: <br /> Extreme morphological disparity within Mollusca has long confounded efforts to reconstruct a stable backbone phylogeny for the phylum. Familiar molluscan groups—gastropods, bivalves, and cephalopods—each represent a diverse radiation with myriad morphological, ecological, and behavioral adaptations. The phylum further encompasses many more unfamiliar experiments in animal body-plan evolution. In this work, we reconstructed the phylogeny for living Mollusca on the basis of metazoan BUSCO (Benchmarking Universal Single-Copy Orthologs) genes extracted from 77 (13 new) genomes, including multiple members of all eight classes with two high-quality genome assemblies for monoplacophorans. Our analyses confirm a phylogeny proposed from morphology and show widespread genomic variation. The flexibility of the molluscan genome likely explains both historic challenges with their genomes and their evolutionary success. <br /> <br /> Chen Z, Baeza JA, Chen C, Gonzalez MT, González VL, Greve C, Kocot KM, Martinez Arbizu P, Moles J, Schell T, Schwabe E, Sun J, Wong LWS, Yap-Chiongco M, Sigwart JD* (2025). A genome-based phylogeny for Mollusca is concordant with fossils and morphology. Science, 387(6737): 1001-1007. DOI: 10.1126/science.ads0215
Our new paper in Progress in Oceanography reveals distribution patterns of deep-sea molluscs from Bering Sea and Aleutian Trench using 212 species (>4200 specimens) -- collected between 3500~7300 m deep on-board RV SONNE, "AleutBio" cruise in 2022! Read this OPEN ACCESS paper for free: https://doi.org/10.1016/j.pocean.2025.103440<br /> <br /> Abstract: <br /> The Aleutian Trench, a canyon-like structure in the deep sea floor that parallels the southern fringe of the Aleutian Islands off Alaska, has only been studied by a few previous expeditions. The trench itself and the adjacent island archipelago both present potential dispersal barriers to marine species, which may shape the regional biogeography. We report new findings on the molluscan fauna of the trench and adjacent regions, from the recent “AleutBio” expedition in summer 2022 on the German research vessel Sonne. We recovered over 4300 individual mollusc specimens representing 212 identified taxa in 7 classes (all living taxonomic classes except Polyplacophora), of which 180 could be assigned to a species-level morphospecies. Highlights from our new material include: one monoplacophoran, the dumbo octopus Grimpoteuthis imperator re-collected for the first time since its description, the deepest record for the large-bodied solenogaster family Neomeniidae at 6612 m, the very rare columbariid gastropod Tropidofusus aequilonius, and new hadal records for several bivalves: Rengea murrayi, Limatula cf. vancouverensis, Neilonella abyssopacifica, Neilonella politissima, Catillopecten squamiformis, Parvamussium pacificum, and Setigloma japonica and the bivalve family Sareptidae. Comparing records from the Bering Sea (3490–3655 m), the north rim of the trench (4220–4641 m), the hadal depths of the trench bottom (6181–7287 m), and the southern rim (4790–5330 m), provides a test of potential barriers to the distributions of species across these regions. Of the species found in the Bering Sea, 63 % are also found in the broader Aleutian Trench region. Similarly, of the mollusc species found on the south rim of the trench, 68 % cross the Aleutian Trench and are found on the north rim and/or in the Bering Sea. The dispersal potential of most mollusc species is apparently not restricted by deep-sea trenches or island chains in the North Pacific.<br /> <br /> Sigwart JD*, Chen C, Kamenev G, Machado FM, Schwabe E (2025). Distribution patterns of deep-sea molluscs from the Bering Sea and Aleutian Trench. Progress in Oceanography, 233: 103440. DOI: 10.1016/j.pocean.2025.103440
Our new paper in Invertebrate Systematics names Delectopecten thermus, a new species of Glass Scallop from a deep-sea hot vent in Okinawa Trough, Japan! We also present its mitogenome, the first for this early-diverging pectinid genus; providing key insights to gene order evolution in this family. Link: https://doi.org/10.1071/IS24091<br /> <br /> Abstract: <br /> Delectopecten is a small genus of the family Pectinidae (Bivalvia: Pectinida) that remains poorly studied in terms of both morphology and phylogeny. Here, we describe the first member of this genus from deep-sea hydrothermal vent ecosystems, D. thermus sp. nov., based on morphological investigations and molecular analyses of a specimen collected from the Higashi–Ensei vent field (962-m depth) in the northern Okinawa Trough. Morphologically, this new species resembles D. vancouverensis and D. gelatinosus in shell size, shape, auricle size and sculpture. However, D. thermus sp. nov. can be distinguished from its congeneric species (including 9 extant and 12 fossil species) by its unequal auricles (the anterior one being larger than the posterior), inwardly recurved anterior auricle of the left valve and a large byssal notch angle of ~90°. Comparisons of genetic sequences from three mitochondrial and three nuclear gene fragments supported the placement of the new species in the genus Delectopecten. Further phylogenetic analyses using these gene markers support that Delectopecten is monophyletic and positioned as an early diverging clade of the family Pectinidae. Additionally, the mitogenome of D. thermus sp. nov. was assembled and annotated, a first for its genus – revealing significant divergences in gene order compared to other pectinids. The 16S rRNA amplicon analysis of the gill tissue indicated that this vent-dwelling scallop does not exhibit symbiosis with chemosynthetic bacteria. A key to all known species of Delectopecten is provided to aid the identification of species in this understudied genus.<br /> <br /> Lin Y-T, Peng Y-B, Chen C, Xu T, Qiu J-W* (2025). Integrative morphological, mitogenomic, and phylogenetic analyses reveal new vent-dwelling scallop species. Invertebrate Systematics, 39: IS24091. DOI: 10.1071/IS24091 <br /> <br /> PDF: https://www.researchgate.net/publication/388836581_Integrative_morphological_mitogenomic_and_phylogenetic_analyses_reveal_new_vent-dwelling_scallop_species
Our new paper in Proceedings of the Royal Society B reveals dominant circatidal biological clock (~12.4 hr) in the deep-sea hot vent shrimp Rimicaris leurokolos, through a 72 hr free-running experiment + transcriptomic analyses! LINK: https://doi.org/10.1098/rspb.2024.2970<br /> <br /> Abstract: <br /> Biological clocks are a ubiquitous feature of all life, enabling the use of natural environmental cycles to track time. Although studies on circadian rhythms have contributed greatly to the knowledge of chronobiology, biological rhythms in dark biospheres such as the deep sea remain poorly understood. Here, based on a free-running experiment in the laboratory, we reveal potentially endogenous rhythms in the gene expression of the deep-sea hydrothermal vent shrimp Rimicaris leurokolos. Oscillations with approximately 12 h periods, probably reflecting tidal influence, greatly prevail over others in the temporal transcriptome, indicating R. leurokolos probably depends on a circatidal clock consisting of at least some components independent from the circadian clocks. The tidal transcripts exhibit an antiphased expression pattern divided into two internally synchronized clusters, correlated with wide-ranging biological processes that occur in the nucleus and cytoplasm, respectively. In addition, the tidal transcripts showed great similarities with genes in fruit flies and mice exhibiting approximately 12 h ultradian rhythms, indicating that the tide probably had a broad impact on the evolution of approximately 12 h oscillations found across the Metazoa. These findings not only provide new insights into the temporal adaptations in deep-sea organisms but also highlight hydrothermal vent organisms as intriguing models for chronobiological studies, particularly those linked to approximately 12 h ultradian rhythms. <br /> <br /> Zhang H# / Yahagi T#, Miyamoto N, Chen C, Jiang Q, Qian P-Y, Sun J* (2025). Circatidal control of gene expression in the deep-sea hot vent shrimp Rimicaris leurokolos. Proceedings of the Royal Society B: Biological Sciences, 292(2040): 20242970. DOI: 10.1098/rspb.2024.2970 [Preprint available on bioRxiv, DOI: 10.1101/2024.01.12.575359]<br /> <br /> PDF: https://www.researchgate.net/publication/388684923_Circatidal_control_of_gene_expression_in_the_deep-sea_hot_vent_shrimp_Rimicaris_leurokolos
Our new paper describing and naming two new deep-sea limpets in the genus Shinkailepas from Indian Ocean hydrothermal vents is now out in Zoological Journal of the Linnean Society!Molecular phylogeny revealed these two species invaded Indian Ocean separately. It "only" took ~25 years to name them since the first report of undescribed Shinkailepas by an American team in 2001! Link: https://doi.org/10.1093/zoolinnean/zlae167<br /> <br /> Abstract: <br /> Red-blooded neritimorph gastropods in the subfamily Shinkailepadinae are specialists of chemosynthesis-based ecosystems, with the most diverse genus Shinkailepas endemic to deep-sea hydrothermal vents. All described Shinkailepas species have so far been from the western Pacific, despite reports of unidentified Shinkailepas from the Indian Ocean in the literature for decades. Here, we use an integrative approach to characterize and describe these Indian Ocean vent neritimorphs for the first time, based on material collected from the Carlsberg Ridge (CR) and the Central Indian Ridge (CIR). We name two new species: Shinkailepas tiarasimia sp. nov. from both the CR and the CIR, and Shinkailepas cornuthauma sp. nov. from the CR. A combination of shell and epipodial lobe characters reliably separate these new species from their described congeners. A phylogenetic reconstruction of all known Shinkailepas species using 658 bp of the mitochondrial COI gene reveal two separate major clades within the genus, each with an Indian Ocean species—implying two independent colonizations of Indian Ocean vents by separate lineages. Our finding of two new species on the CR, including one not known anywhere else, underscores the unique biodiversity at these vents and strengthens the case for protecting them from potential deep-sea mining activities. <br /> <br /> Gu X# / Chen C#, Gao K, Zhou Y*, Sun J* (2025). Integrative taxonomy of new neritimorph limpets from Indian Ocean deep-sea hot vents shed light on their biogeographic history. Zoological Journal of the Linnean Society, 203(1): zlae167. DOI: 10.1093/zoolinnean/zlae167<br /> PDF: https://www.researchgate.net/publication/387689752_Integrative_taxonomy_of_new_neritimorph_limpets_from_Indian_Ocean_deep-sea_hot_vents_shed_light_on_their_biogeographic_history
It's snowing... sea cucumbers! Our paper "A herd of sea cucumber, flock together" is now out in Marine Biodiversity -- reporting for the first time that deep-sea elpidiid holothurians can swim together in large groups! These holothurians have been known to swim, but previous sightings were all of one to just a few individuals. Link: https://doi.org/10.1007/s12526-024-01487-9<br /> <br /> Abstract: <br /> Holothurians are the most conspicuous epifauna on the typical deep seafloor and a key bioturbator in marine systems. Dense aggregations of various sea cucumbers (‘herds’) of up to 50 individuals per metre square have been reported from deep-sea habitats around the world (Billett and Hansen 1982), and aggregating behaviour is also known for some swimming members of families Elpidiidae and Pelagothuridae (Billett 1991). Swimming has been hypothesised as an adaptation to optimise energetic costs in searching for high-quality food in the form of sediment with rich organic content (Rogacheva et al. 2012), among other theories such as escape behaviour and dispersal (Miller and Pawson 1990). These benthopelagic holothurians only feed on the seafloor, after which they defecate to drop the ‘ballast’ and then relocate by swimming and drifting with the current (Gebruk and Kremenetskaia 2024). Although numerous short trails on the seafloor have been attributed to swimming species, all observed cases of such behaviour have involved one or few individuals only. Here, we present the first observation of a dense flocking herd of swimming holothurians (Fig. 1). <br /> <br /> Chen C, Kawamura K, Ogawa A* (2024). A herd of sea cucumber, flock together. Marine Biodiversity, 55: 4. DOI: 10.1007/s12526-024-01487-9 <br /> PDF: https://www.researchgate.net/publication/387459363_A_herd_of_sea_cucumber_flock_together
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