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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

We named two new cleftclam species in the genus Thyasira from serpentine seeps on seamounts of the Mariana Forearc! Both probably host chemosymbiotic bacteria. Out now in Molluscan Research, FREE-to-read link for the first 50: https://www.tandfonline.com/eprint/7FEDH6ZF2IFSRXSJ7NN3/full?target=10.1080/13235818.2026.2642441<br /> <br /> Abstract: <br /> Members of the genus Thyasira host chemoautotrophic bacteria in their gills and are commonly found in hydrocarbon seeps and hydrothermal vents. Here, we report two new species of Thyasira from serpentinite seeps on Mariana Forearc mud volcanoes. One new species, Thyasira chamorroensis n. sp., is described from three articulated specimens recovered from the Summit Site of the South Chamorro Seamount (2915 m). The other new species, Thyasira tesoru n. sp., was collected from the Big Blue seep on the Asùt Tesoru Seamount (1240 m); it is described based on one articulated specimen and 15 disarticulated valves. The finding of two new Thyasira species from serpentinite seeps highlight the uniqueness of the biological community at this previously much-overlooked type of chemosynthetic habitat. These represent the first records of the genus Thyasira from the Mariana region, despite previous surveys of many hydrothermal vent systems there.<br /> <br /> Amano K* 天野和孝, Haga T, Hirayama H, Chen C* (2026). Two new species of Thyasira Lamarck, 1818 (Bivalvia: Thyasiridae) from serpentinite seeps on the Mariana Forearc. Molluscan Research, Online First. DOI: https://doi.org/10.1080/13235818.2026.2642441
Our new paper in Trends in Ecology & Evolution presents the concept of the Senckenberg Ocean Species Alliance - SOSA project, pushing for the acceleration of marine conservation through the synergistic interaction among a "triad": Taxonomy, Red Listing, and Public Engagement! OPEN ACCESS: https://doi.org/10.1016/j.tree.2026.03.004<br /> <br /> Abstract: <br /> The majority of marine invertebrate species are undescribed and absent from biodiversity frameworks, leaving them beyond the reach of conservation mechanisms. We show that three disciplines—taxonomy, International Union for Conservation of Nature Red List assessment, and public engagement—achieve disproportionately greater impact when operated as a coupled system rather than in isolation. Each pillar feeds the others: taxonomic knowledge underpins assessments; assessments attract public and policy attention; and public engagement, in turn, drives commitment to new discovery, evaluation, and actions to recover threatened species. New tools for DNA sequencing, specimen imaging, and data sharing have made this integration achievable at speed and scale. Public engagement amplifies the reach of taxonomy and conservation, generating funding, contributors, and the policy traction needed to protect the ocean’s overlooked life.<br /> <br /> Riehl T*, Böhm M, Brandão SN, Brandt A, Chen C, Edgecombe GD, Frank HJZ, Gallagher AJ, Goldburg R, Hutchings P, Machado FM, Mosbrugger V, Pollom RA, Steger J, Tandberg AH, Thiyagarajan S, Tilic E, Torkov A, Vences M, Wasmund R, Sigwart JD (2026). Marine conservation: linking taxonomy, Red Listing, and public engagement. Trends in Ecology & Evolution, 41: Online Now. DOI: 10.1016/j.tree.2026.03.004
Our new paper in Biology Letters presents a global barcoding (180 individuals) of the deep-sea snail genus Phymorhynchus from hot vents & cold seeps, revealing few species with very broad and sometimes cosmopolitan distributions! The paper is OPEN ACCESS: https://doi.org/10.1098/rsbl.2025.0685<br /> <br /> Abstract: <br /> For rare fauna inhabiting insular habitats, specimens from geographically distant locations are often assumed to be distinct species without a detailed assessment of their genetic diversity. The raphitomid snail genus Phymorhynchus includes a species complex considered endemic to deep-sea hot vents and cold seeps. Despite small morphological differences, existing species hypotheses largely relied on geographic distance to support separation. Here, we present a molecular barcoding study for this complex with a total of 180 specimens sampled across the Atlantic, Pacific and Indian oceans. Our delimitation analyses identified six distinct species supported by morphology, notably egg-capsule characters. They have broader distributions than previously realized, with P. starmeri ranging across the Indo-West Pacific and P. moskalevi apparently cosmopolitan, both showing complex genetic subgroupings. These species are probably also distributed outside vents and seeps, supported by several ambient records. Our results challenge the assumption of fine-scale geographic separation in species inhabiting deep-water insular habitats.<br /> <br /> Zhang M# / Chen C#, Wu M, Copley JT, Poitrimol C, Alfaro-Lucas JM, Watanabe HK, Zhou Y* (2026). Global barcoding of the deep-sea snail genus Phymorhynchus reveals surprising distribution ranges and genetic diversity. Biology Letters, 22: 20250685. DOI: 10.1098/rsbl.2025.0685
We present "VEHoP", a new bioinformatics pipeline capable of inferring protein-coding regions from a diverse and mixed NGS data types and automate phylogenomic reconstructions! OPEN ACCESS in Molecular Ecology Resources: https://doi.org/10.1111/1755-0998.70116<br /> <br /> Abstract: <br /> Phylogenomics is a transformative approach in systematics, conservation biology, and biomedical research, enabling the inference of evolutionary relationships by leveraging hundreds to thousands of genes from genomic or transcriptomic data. However, acquiring high-quality genomes and transcriptomes necessitates samples with intact DNA and RNA, substantial sequencing investments, and extensive bioinformatic processing, such as genome/transcriptome assembly and annotation. This challenge is particularly pronounced for rare or difficult-to-collect species, such as those inhabiting the deep sea, where often only fragmented DNA reads are available due to environmental degradation or suboptimal preservation conditions. To address these limitations, we developed VEHoP (Versatile, Easy-to-use Homology-based Phylogenomic pipeline), a tool designed to infer protein-coding regions from diverse inputs, including raw reads (short and long), draft genomes, transcriptomes, and annotated genomes. VEHoP automates the generation of orthologous sequence alignments, concatenated matrices, and phylogenetic trees, streamlining phylogenomic analyses for researchers across disciplines. The tool expands taxonomic sampling by accommodating a wide range of input data types and simplifies phylogenomic workflows, making them accessible to researchers with varying levels of bioinformatic expertise. We validated VEHoP using datasets from oysters, catfish, and insects, demonstrating its ability to produce robust phylogenetic trees with strong bootstrap support, outperforming assembly-free methods. Additionally, we applied VEHoP to reconstruct the phylogeny of the enigmatic deep-sea gastropod order Neomphalida, resolving a well-supported phylogenetic backbone for this poorly understood group. VEHoP is freely available on GitHub ( https://github.com/ylify/VEHoP ) and easily installable via Bioconda or the configured container image via Docker, Singularity and Apptainer.<br /> <br /> Li Y# / Liu X#, Chen C, Qiu J-W, Kocot K, Sun J* (2026). Reliable inference of phylogenomic relationship via assembly-based strategy accommodating raw reads and proteins. Molecular Ecology Resources, 26(3): e70116. DOI: 10.1111/1755-0998.70116 [Preprint available on bioRxiv, DOI: 10.1101/2024.07.24.604968]
Our new paper in Science Advances reveals intricate mechanisms of chemosynthetic symbiosis in the shallow-water cleftclam Thyasira tokunagai, with carbon fixation rates estimated using radiocarbon. Thyasira clams are widespread globally -- a great model to study chemosymbiosis! OPEN ACCESS: https://doi.org/10.1126/sciadv.adw8163<br /> <br /> Abstract: <br /> Chemosynthetic symbioses between animals and bacteria are common in marine ecosystems, but the symbioses in shallow-water thyasirid clams inhabiting suboxic sediments remain understudied despite their widespread occurrence. Here, we report that the shallow-water thyasirid clam Thyasira tokunagai, dominant in Yellow Sea sediments, harbors sulfur-oxidizing Sedimenticola symbionts in pouch-like structures on the gill; the symbionts exhibit highly consistent genomic content and functionality across the region. Two phylotypes of symbionts are present, differing by a single base in the 16S rRNA gene while sharing key functional genes with minimal differences. Spatial metabarcoding analyses of gills showed that individuals also vary in the level of spatial heterogeneity concerning the two phylotypes. These symbionts exhibit active Calvin cycle gene expressions and close-knit host-symbiont metabolic integration. Furthermore, we estimated the capacity of dissolved inorganic carbon assimilation in the live holobiont by radiocarbon tracing (29.3 ± 8.7 nmol C·clam−1·day−1). Our findings provide the basis for understanding chemosymbiosis in thyasirid clams, highlight the potential of T. tokunagai as a model for studying symbiosis, and underscore the ecological significance of shallow-water chemosymbioses overall.<br /> <br /> Li M# / Li Y# / Mao S-H#, Zhang Z, Chen C, Nie X, Liu X [Xu], Wang H, Liu X [Xiaoshou], Zhang W, Lin Q, Zhuang G-C*, Sun J* (2026). Intricate chemosymbiosis in a widespread shallow-water thyasirid clam. Science Advances, 12: eadw8163. DOI: 10.1126/sciadv.adw8163 [Preprint available on bioRxiv, DOI: 10.1101/2024.02.25.581922]
We are on the COVER of the journal Royal Society Open Science! We name 5 new species of hot vent limpets in the family Lepetodrilidae from Indian Ocean -- phylogenetics indicate this family used Indian Ocean as a corridor to disperse from Pacific to Atlantic. OPEN ACCESS: https://royalsocietypublishing.org/rsos/article/13/3/251392/480673/Unexpectedly-high-diversity-of-lepetodrilid<br /> <br /> Abstract: <br /> Vetigastropod limpets in the family Lepetodrilidae are endemic to deep-sea chemosynthetic ecosystems, exhibiting a near-global distribution. Their diversity in the Indian Ocean has remained critically understudied despite unidentified specimens known from there for decades. Here, we use an integrative approach to characterize and describe these Indian Ocean vent lepetodrilids, based on material collected from the Carlsberg Ridge (CR), Central Indian Ridge (CIR) and Southwest Indian Ridge (SWIR). We name five new species: Lepetodrilus disco sp. nov. and L. timidus sp. nov. from both the CR and the CIR, L. draco sp. nov. and L. speratus sp. nov. from the SWIR, and Pseudorimula protaspa sp. nov. from both the CR and SWIR. A combination of shell, anatomical and radular characters distinguishes these taxa from their known congeners. Phylogenetic reconstruction using a 1522 bp alignment of the mitochondrial cytochrome oxidase c subunit I (COI) gene demonstrates the radiation of genus Lepetodrilus from the Pacific into the Indian Ocean before colonizing the Atlantic and Southern Oceans. Our results reveal an unexpectedly high diversity in the Indian Ocean and the global vent biogeographic history of genus Lepetodrilus. This highlights the Indian Ocean’s role as a crucial ‘dispersal corridor’ and underscores the urgency for the conservation of vent animals in the face of deep-sea mining threats.<br /> <br /> Gu X# / Chen C#, Zhou Y*, Sun J* (2026). Unexpectedly high diversity of lepetodrilid limpets at Indian Ocean deep-sea hot vents sheds light on their global biogeography. Royal Society Open Science, 13: 251392. DOI: 10.1098/rsos.251392
We discovered Acanthotrochus verruciosseous, a new species of namako (holothurian) from >5000 m deep in the Aleutian Trench! We also present a high-resolution CT scan of the whole body, showing the ossicle distribution. Out now in Bulletin of Marine Science: https://doi.org/10.5343/bms.2025.0092<br /> <br /> Abstract: <br /> A new species of the rarely seen myriotrochid holothurian genus Acanthotrochus, Acanthotrochus verruciosseous sp. nov., is described from 5272 to 5325 m deep in the Aleutian Trench, North Pacific Ocean. The new species is morphologically clearly separated from three valid congeners based on acanthotrochid-type wheel ossicles bearing multiple low knobs on the inner and outer rims as well as the outward teeth. The outer, concave side of the acanthotrochid-type wheels also form inwardpointing protrusions at the base of spokes at the inner rim edge. These ossicle features have never been observed in the three described species. Acanthotrochus has a global distribution, in the North Atlantic, Indian Ocean, and Antarctica, with a maximum depth of 3320 m. Our discovery is the first record of Acanthotrochus from the North Pacific and from the lower abyssal zone, which greatly extends the known geographic and bathymetric range of this genus. Partial mitochondrial 16S ribosomal DNA sequences from the type specimens of A. verruciosseous sp. nov. are clearly separated from the type species of the genus, Acanthotrochus mirabilis Danielssen and Koren, 1881. <br /> <br /> Ogawa A*, Chen C, Sigwart JD (2025). A new abyssal species of Acanthotrochus (Holothuroidea: Apodida) from the Aleutian Trench, North Pacific Ocean. Bulletin of Marine Science, 102(1): 23-37. DOI: 10.5343/bms.2025.0092
Our new paper in Journal of Zoological Systematics and Evolutionary Research provides the first description of cold seep fauna in the Sea of Japan, revealing just a few species living in very cold water. We also found a new snail species -- named Provanna cocytus after the icy hell in Dante's "Divine Comedy"! OPEN ACCESS: https://onlinelibrary.wiley.com/doi/10.1155/jzs/4623950<br /> <br /> Abstract: <br /> The Sea of Japan is a semi-enclosed marginal sea in the northwestern Pacific whose bathyal communities exhibit a depauperate species diversity due to anoxic events during the last glacial maximum. Cold seeps associated with chemosynthetic ecosystems were discovered in this region over three decades ago, yet their fauna have not been characterised. Here, we surveyed three bathyal seeps in the northeastern Sea of Japan off Okushiri Island, Hokkaido, to reveal their faunal composition and environmental conditions. We documented only eight macrofaunal species across all sites, of which six are well-known ambient fauna, with just two gastropod species in the genera Provanna and Hyalogyrina being seep endemics. Dissolved oxygen (DO) concentrations were consistently reduced on the seep bacterial mats, while the temperature remained similar to the ambient seawater. The Provanna species was new to science and is named P. cocytus sp. nov., characterised by a smooth shell with very convex whorls and a nearly holostomous aperture and a radula with a truncated central tooth cusp and the lateral teeth lacking a buttress. Phylogenetic reconstruction using the mitochondrial cytochrome c subunit I (COI) gene recovered P. cocytus sp. nov. as sister to all other congeners, indicating this genus did not recolonise the Sea of Japan after the last glacial maximum from seep or vent sources. The low species richness at seeps likely represents a combined effect of shallow connections limiting dispersal and impacts of the very cold Japan Sea Proper Water to larval settlement. Our results contribute to the understanding of the biodiversity in the Sea of Japan and close a major knowledge gap in the biogeography of chemosynthesis-based ecosystems across the western Pacific.<br /> <br /> Chen C*, Watanabe HK, Kawagucci S (2026). Cold seep communities in the Sea of Japan are species-poor and dominated by a new species of provannid snail. Journal of Zoological Systematics and Evolutionary Research, 2026: 4623950. DOI: 10.1155/jzs/4623950
We sequenced chromosome-level genomes of two Alviniconcha hairy snail species from deep-sea hydrothermal vents! Combined with spatial transcriptomics, we reveal intricate details about its endosymbiosis. Read for FREE: https://rdcu.be/e38Fl<br /> <br /> Abstract:<br /> Deep-sea hydrothermal vents are “extreme” environments with constantly fluctuating physicochemical conditions, but dense animal aggregations thrive primarily through symbiosis with chemoautotrophic bacteria to exploit the unusual chemistry. Alviniconcha snails, which harbor symbionts in their enlarged gill at an intermediate state between intracellular and extracellular, are a prime example. Here, we present chromosome-level genomes of two Alviniconcha species (A. adamantis and A. marisindica) to investigate the adaptations of this holobiont. Significant expansion of solute carrier families enhances nutrient transport between the two parties. Alviniconcha lacks complete methionine biosynthesis pathways, likely compensated by symbiont provisioning, highlighting host-symbiont metabolic complementarity. High myoglobin expression levels in the gills contradict previous reports of hemoglobin, suggesting myoglobin-mediated oxygen storage to mitigate fluctuating environmental oxygen levels. Spatial transcriptomics further delineated gill’s functional zones on the gill filament responsible for symbiont digestion via phagocytosis in bacteriocytes, oxygen transport in secretory zones, and ciliary water flow regulation. Our findings elucidate molecular and physiological adaptations underpinning the Alviniconcha holobiont’s success in dynamic vent ecosystems.<br /> <br /> Wang H, Dai Y, Chen C, Li Y, He X, Li M, Zhou Y, Ip JC-H, Sun J* (2026). Multi-omics analyses of the Alviniconcha holobiont reveal multi-faceted adaptations to deep-sea hydrothermal vents. Science China Life Sciences, Online First. DOI: https://doi.org/10.1007/s11427-025-3148-0 [Preprint available on bioRxiv, DOI: 10.1101/2025.05.21.655246]
Our paper in Current Biology presents a population genomics study of the iconic Scaly-foot Snail: 125 genomes from 8 Indian Ocean hot vents! Deep currents drive South→North gene flow, while transform faults act as dispersal barriers. READ FOR FREE: https://authors.elsevier.com/c/1mbW73QW8SDrjI<br /> <br /> Abstract: <br /> How species disperse and have dispersed is a central question in biology, as it governs patterns of genetic isolation and is a key driver of evolutionary processes. Over 600 hydrothermal vents worldwide are grouped into more than 10 biogeographic provinces, but even within each province, the dispersal barriers remain poorly understood. The scaly-foot snail (Chrysomallon squamiferum) is an iconic species with ironclad scales distributed across the Indian Ocean, providing an opportunity to test dispersal across these well-separated insular habitats. Here, we present the first population genomic study of Indian Ocean vents using this species. By analyzing 125 individuals from eight vents using 14 million single-nucleotide polymorphisms, we identify five genetic groups. Among these, the most genetically distinct were Longqi-Duanqiao fields on the Southwest Indian Ridge and the Wocan field on the Carlsberg Ridge. Demographic modeling indicates that contributions from extinct or unsampled “ghost populations” critically facilitated the contemporary genetic structure. Combined with physical ocean modeling, we show that deep currents shape asymmetric gene flow from south to north, whereas transform faults act as dispersal barriers. Furthermore, we identify an extinct vent field on the Central Indian Ridge and an unsampled vent plume signal on the Southwest Indian Ridge as the two most plausible locations representing the key ghost populations. Given its exceptional adaptations and public recognition, the scaly-foot snail is well positioned as a flagship and umbrella species, and our findings thus provide essential baseline data for conservation biology in light of deep-sea mining.<br /> <br /> Chen X# / Jun S# / Chen C#* / Liu R# / Xu T# / Zhang H#, Gao Y, He X, Liu X, Gao K, Gu X, Zhou Y, Takai K, Wang Y*, Qian P-Y*, Won Y-J*, Sun J* (2026). Dispersal and isolation of the scaly-foot snail across abyssal insular habitats and through time. Current Biology, 36. DOI: https://doi.org/10.1016/j.cub.2026.01.033 [Preprint available on bioRxiv, DOI: 10.1101/2025.08.02.668274]
Just out in Royal Society Proceedings B, our paper reveals multiple emergence of symbiosis in alvinocaridid shrimps from deep-sea hot vents and cold seeps! Many species show intermediate reliance on symbionts, illuminating steps towards full dependency. The paper is OPEN ACCESS: https://doi.org/10.1098/rspb.2025.2883<br /> <br /> Abstract: <br /> Convergent evolution offers a powerful lens through which to examine the selective forces shaping life in extreme environments. In deep-sea hot vents and cold seeps, invertebrates have independently evolved symbioses with chemosynthetic bacteria, but repeated origins of such associations within a family remain rare. Here, we investigate the evolutionary emergence of chemosymbiosis in the shrimp family Alvinocarididae across 22 species collected globally. Electron microscopy identified a gradient of epibiotic bacterial colonization within the cephalothoracic cavity, ranging from absent to dense filamentous mats, suggesting distinct trophic strategies. Isotope and lipid trophic markers confirmed differences in reliance on chemosynthetic production among sympatric species with different bacterial colonization from a single vent. Phylogenetic analysis reveals at least two independent origins of chemosymbiosis, suggesting evolutionary convergence. Microhabitat association data further show that symbiotic phenotypes are most common in shrimps occupying the hottest, most geofluid-enriched microhabitats, though exceptions suggest contributions from additional ecological or physiological constraints. Our findings reveal many alvinocaridids as gradually evolving towards reliance on symbiosis, highlighting the importance of intermediate cases to understand the pathways to chemosymbiosis. This study contributes to a broader understanding of the predictability of evolutionary outcomes in dynamic habitats such as vents, with broader implications for resilience of deep-sea ecosystems.<br /> <br /> Methou P*, Mathieu-Resuge M, Michel LN, Cueff-Gauchard V, Watanabe HK, Cowell EJ, Copley JT, Beinart RA, Zbinden M, Pradillon F, Cambon M-A*, Chen C* (2026). Evolutionary convergence and trophic diversity in hot vent and cold seep shrimps showcase a continuum of symbiosis. Proceedings of the Royal Society B: Biological Sciences 292: 20252883. DOI: <br /> https://doi.org/10.1098/rspb.2025.2883<br /> [Preprint available on bioRxiv, DOI: 10.1101/2025.08.27.672534]
Our new paper in Biodiversity Data Journal names three new chiton species -- including one from a sunken wood site 5506 m deep in the NW Pacific. We ran a public naming competition on YouTube in collaboration with Ze Frank, and the name Ferreiraella populi ("chiton of the people") was chosen among over 8000 entries! The paper is OPEN ACCESS: https://doi.org/10.3897/BDJ.14.e180491<br /> <br /> Abstract:<br /> Three new chitons are reported from distinct and underexplored marine habitats: Ferreiraella populi sp. nov. from deep-sea sunken wood off Japan in the western Pacific, Notoplax madagascariensis sp. nov. from Madagascar, and the carnivorous Placiphorella granulosa sp. nov. from Papua New Guinea, occurring from the sublittoral into the bathyal zone. These findings broaden current understanding of chiton diversity and emphasise how much remains undocumented in the deep-sea and tropical systems. The discovery of Notoplax madagascariensis sp. nov. is particularly relevant for ongoing efforts to resolve generic limits within Cryptoplacoidea, where both taxonomic and molecular evidence remain incomplete. The three species described here add substantially to the known diversity and ecological breadth of chitons. The species epithet of the new Ferreiraella species was the outcome of a public naming competition, an initiative intended to raise awareness of taxonomy and enhance public engagement with species discovery. All three chitons illustrate the value of targeted sampling across poorly-studied habitats.<br /> <br /> Senckenberg Ocean Species Alliance (SOSA), Chen C, Frank H, Kraniotis L, Nakadera Y, Schwabe E, Sigwart JD*, Trautwein B, Vončina K (2026). Ocean Species Discoveries 28–30 — new species of chitons (Mollusca: Polyplacophora) and a public naming competition. Biodiversity Data Journal, 14: e180491. DOI: 10.3897/BDJ.14.e180491
We present a proof-of-concept that ultraconserved elements (UCEs) can also be useful for population genomic analyses of marine animals, in addition to phylogenomic reconstructions! OPEN ACCESS in the journal Evolutionary Applications: https://onlinelibrary.wiley.com/doi/10.1111/eva.70195<br /> <br /> Abstract: <br /> Ultraconserved elements (UCEs) have emerged as a powerful tool for resolving deep evolutionary relationships due to their low DNA quality requirements and broad taxonomic applicability. While their utility for intraspecific and shallow-divergence studies is growing, only a few studies have explored their performance in marine taxa, some of them with metapopulations spanning thousands of kilometers. Here, we employed the UCE approach to investigate the population genomics of Gigantidas platifrons—a deep-sea mussel with a long larval dispersal period that exhibits a panmictic genetic structure across its extensive distribution range in the chemosynthetic ecosystems of the Western Pacific. With its published whole genome and prior restriction site-associated DNA sequencing using IIB restriction enzymes (2b-RAD seq) study, this species is an excellent candidate for evaluating the effectiveness of UCEs. We conducted UCE target capture sequencing on 123 individuals collected from two hydrocarbon seeps and four hydrothermal vents, yielding 1960 UCEs. To assess the impact of different reference choices, we identified 11,870 single-nucleotide polymorphisms (SNPs) by mapping against the published genome and 8936 SNPs by mapping to the representative 1960 UCEs. Both datasets were similar, with over 80% of the SNPs located in intronic and intergenic regions. Analyses based on both datasets consistently implied a clear genetic divergence between the South China Sea (SCS) and Okinawa Trough-Sagami Bay (OT-SB) populations, with predominant gene flow from OT to SB, consistent with previously published 2b-RAD seq findings. Additionally, UCE-based SNPs identified a dynamic decline in population size for individuals in the three regions and revealed selective adaptation signals to their environments. Overall, our study serves as a proof-of-concept demonstrating that UCEs provide a comparable resolution to RAD-Seq in detecting shallow-level genetic divergence and delineating conservation units in a high-dispersal marine species, even when lacking a sequenced genome.<br /> <br /> Li Y-X, Xu T, Perez M, Chen C, Watanabe HK, Ip JC-H, Qiu J-W* (2026). Sequencing ultraconserved elements for population genomics: A proof-of-concept using a deep-sea mussel species. Evolutionary Applications, 19(1): e70195. DOI: 10.1111/eva.70195
We identified the mineral coatings on deep-sea hydrothermal vent snails, linking their chemical composition to geological background and distance from active fluid orifices! Find out more here (OPEN ACCESS): https://doi.org/10.1038/s41598-025-29638-3<br /> <br /> Abstract: <br /> Shells of hydrothermal vent gastropods are often covered by inorganic coatings whose chemical composition, formation mechanisms, and possible function remain poorly understood. We investigated the mineral coatings of six vent gastropod specimens (one each of the species Lepetodrilus nux, Cantrainea jamsteci, Desbruyeresia armata, Desbruyeresia marisindica, and two specimens of Alviniconcha marisindica from separate vent sites) from four different localities (Iheya North vent field, Okinawa Trough and Myojin-sho Caldera, Izu-Ogasawara Arc in the Pacific Ocean, and Kairei and Edmond vent fields on the Central Indian Ridge) using SEM/EDS and Raman spectroscopy. The resulting data show that the chemical composition of the coatings corresponds to the chemistry of vent fluids at the respective localities and distance from active venting. There was no evidence of mineral replacement of any of the studied shells. In one specimen the coating was partly overgrown by the shell, showing a contemporary growth of the shell and the coating. The texture of the coating on the Desbruyeresia armata specimen suggests a possible role of microorganisms in its formation. Gastropod fossils from ancient vent sites are preserved by pyrite, with no remaining carbonate shell. We found pyrite only in coatings of the modern gastropods collected near high-temperature vent sites, indicating that close proximity to active venting may be necessary for successful preservation of vent gastropods in the fossil record.<br /> <br /> Bonk A, Hryniewicz K, Bącal P, Smrzka D, Chen C, Little CTS (2025). Diversity of mineral coatings on hydrothermal vent gastropods. Scientific Reports, Early Access. DOI: 10.1038/s41598-025-29638-3
We revealed an unexpectedly high animal diversity at Nankai Trough deep-sea methane seeps off Japan: 80 species including over 10 underscribed ones! This paper is OPEN ACCESS in the journal Ecosphere: https://doi.org/10.1002/ecs2.70451<br /> <br /> ABSTRACT: <br /> Cold seeps are chemosynthesis-based ecosystems powered by microbial primary production that support diverse and specialized faunal assemblages in the deep sea. Despite Nankai Trough in Japan being a geologically active margin hosting numerous seeps, much of the faunal diversity remains undocumented. Here, we present results from the first coordinated biological survey across five methane seep sites in the Nankai Trough with different water depths: Daini Tenryu Knoll (600 m), Ryuyo Canyon (1000 m), Oomine Ridge (2000 m), Yukie Ridge (2500 m), and the Off Cape Muroto 4600 m Site. The seep sites were imaged in situ using a combination of high-definition video cameras and still cameras, and biological samples were taken using suction and scoop sampling in addition to grab samples collected directly using the submersible's manipulator. Our results, together with existing records, together reveal a total of 80 seep-associated macro- and megafaunal animal species in these five Nankai Trough seeps (33 molluscs, 23 annelids, 11 arthropods, five nemerteans, four echinoderms, three cnidarians, and a bryozoan), over a fivefold increase compared to the previous number (14). The species diversity at each site also increased from 1–6 to 15–30. These findings include numerous range extensions, new records at seeps, and previously undocumented associations. Our results shed light on the exceptional and underappreciated diversity of seep fauna along the Nankai Trough. In light of growing interest in methane hydrate exploitation in this region, our findings provide essential biodiversity baselines and highlight the need for site-specific conservation measures to protect endemic, depth-segregated communities from anthropogenic disturbance.<br /> <br /> Chen C*, Watanabe HK, Hookabe N, Shiraki S, Nye V, Fleming JF, Jimi N (2025). Biological surveys reveal unexpectedly high faunal diversity at Nankai Trough methane seeps. Ecosphere, 16(11): e70451. DOI: 10.1002/ecs2.70451
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
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