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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 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
We carried out a comprehensive survey of the Sumisu Caldera deep-sea hot vent about 500 km southeast of Tokyo, increasing the known animal species diversity from 9 to 54 -- making it the most species-rich vent in the NW Pacific! These are key data for the conservation of these vulnerable 'oases' eyed for deep-sea mining. Just out in Aquatic Conservation, free for everyone to read (Open Access): https://doi.org/10.1002/aqc.70009<br /> <br /> Abstract: <br /> Hydrothermal vents are biodiversity hotspots on the deep seafloor powered by chemosynthetic primary production, inhabited by a specially adapted fauna whose composition varies between regions. Sumisu Caldera, located approximately 500 km south of Tokyo, hosts a hot vent with an unusual species composition among the Izu–Ogasawara Arc sites and has been suggested as a priority site for conservation in light of upcoming deep-sea mining for massive sulfides. However, this was based on just five species serendipitously recorded from geological surveys. Here, we carried out the first comprehensive biological sampling of Sumisu using two dives of the human-occupied vehicle Shinkai 6500. Together with literature records, we count a total of 54 animal species of which at least 25 are endemic to chemosynthetic ecosystems, drastically increasing the known faunal diversity—including three sponges, one cnidarian, 12 molluscs, 23 annelids, 13 arthropods, one echinoderm, and one fish. The presence of sediments facilitating the occurrence of burrowing species and three non-endemic predators contribute to the high species richness. Our findings make Sumisu the most species-rich vent community in the entire northwestern Pacific and our work serves as a prime example for detailed faunal surveys to obtain key piece of baseline data for future environmental assessments. Although the apparent lack of massive sulfide deposits means Sumisu is unlikely to be an immediate target of mining, its close distance to Bayonnaise Knoll with a major deposit and the possibility that it acts as a critical stepping-stone population for many species, as well as the presence of several endangered ones, presents a case for its protection.<br /> <br /> Chen C*, Hookabe N, Hashimoto R, Shimooka S, Shiraki S, Uyeno D, Kawagucci S (2024). Faunal composition of the Sumisu Caldera hydrothermal vent field as a key baseline for conservation in light of deep-sea mining. Aquatic Conservation: Marine and Freshwater Ecosystems, 34(11): e70009. DOI: 10.1002/aqc.70009
Our new paper In Systematic Biology uses hundreds of newly captured ultra-conserved elements (UCEs) on over 50 families of bivalve molluscs from all six major clades, revealing new topologies. Many were historical museum specimens! Link: https://doi.org/10.1093/sysbio/syae052<br /> <br /> Abstract: <br /> Despite significant advances in phylogenetics over the past decades, the deep relationships within Bivalvia (phylum Mollusca) remain inconclusive. Previous efforts based on morphology or several genes have failed to resolve many key nodes in the phylogeny of Bivalvia. Advances have been made recently using transcriptome data, but the phylogenetic relationships within Bivalvia historically lacked consensus, especially within Pteriomorphia and Imparidentia. Here, we inferred the relationships of key lineages within Bivalvia using matrices generated from specifically designed ultraconserved elements (UCEs) with 16 available genomic resources and 85 newly sequenced specimens from 55 families. Our new probes (Bivalve UCE 2k v.1) for target sequencing captured an average of 849 UCEs with 1085 bp in mean length from in vitro experiments. Our results introduced novel schemes from 6 major clades (Protobranchina, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata, and Imparidentia), though some inner nodes were poorly resolved, such as paraphyletic Heterodonta in some topologies potentially due to insufficient taxon sampling. The resolution increased when analyzing specific matrices for Pteriomorphia and Imparidentia. We recovered 3 Pteriomorphia topologies different from previously published trees, with the strongest support for ((Ostreida + (Arcida + Mytilida)) + (Pectinida + (Limida + Pectinida))). Limida were nested within Pectinida, warranting further studies. For Imparidentia, our results strongly supported the new hypothesis of (Galeommatida + (Adapedonta + Cardiida)), while the possible non-monophyly of Lucinida was inferred but poorly supported. Overall, our results provide important insights into the phylogeny of Bivalvia and show that target enrichment sequencing of UCEs can be broadly applied to study both deep and shallow phylogenetic relationships. <br /> <br /> Li Y-X, Ip JC-H, Chen C, Xu T, Zhang Q, Sun Y, Ma P-Z, Qiu J-W* (2024). Phylogenomics of Bivalvia using ultraconserved elements (UCEs) reveal new topologies for Pteriomorphia and Imparidentia. Systematic Biology, Advance Article: syae052. DOI: 10.1093/sysbio/syae052 <br /> PDF: https://www.researchgate.net/publication/384077062_Phylogenomics_of_Bivalvia_Using_Ultraconserved_Elements_UCEs_Reveal_New_Topologies_for_Pteriomorphia_and_Imparidentia
We described and named Lebbeus parvirostris Komai & Chen, 2024, a new thorid shrimp species discovered from the Amami Rift deep-sea hydrothermal vent field off Amami Ōshima Island, Japan! Link to the paper in Zootaxa: https://doi.org/10.11646/zootaxa.5523.2.7<br /> <br /> Abstract: <br /> A new species of the thorid shrimp genus Lebbeus White, 1847, is described and illustrated on the basis of two specimens collected from the recently discovered Amami Rift hot vent field in the Ryukyu region in southwestern Japan, at a depth of 628 m. Lebbeus parvirostris sp. nov. is morphologically similar to L. microceros (Krøyer, 1841), L. mundus Jensen, 2006, L. saldanhae (Barnard, 1947), L. schrencki (Bražnikov, 1907), L. spongiaris Komai, 2001, and L. tosaensis Hanamura & Abe, 2003, but differs from all of them in the lack of a pterygostomial tooth on the carapace in the female. Other diagnostic characters useful in differentiating the new species from the aforementioned close relatives are also discussed. Genetic analyses using sequences of two mitochondrial markers, including cytochrome c oxidase subunit I (COI) and 16S rRNA, are also presented to provide preliminary support for the status of the new species. Lebbeus parvirostris sp. nov. is the second representative of Lebbeus known from active hydrothermal vents in the Ryukyu region. <br /> <br /> Komai T*, Chen C* (2024). A new species of the thorid shrimp genus Lebbeus White, 1847 (Decapoda: Caridea) from the Amami Rift hydrothermal vent field in the Ryukyu region, Japan. Zootaxa, 5523(2): 254-268. DOI: 10.11646/zootaxa.5523.2.7<br /> PDF: https://www.researchgate.net/publication/384904322_A_new_species_of_the_thorid_shrimp_genus_Lebbeus_White_1847_Decapoda_Caridea_from_the_Amami_Rift_hydrothermal_vent_field_in_the_Ryukyu_region_Japan
We revisited Mokuyo Seamount deep-sea vent field on the Izu-Ogasawara Arc 30 years after its discovery, finding significant changes in hydrothermal activities. Our survey also updated its faunal list from three to 18 species! Link: https://doi.org/10.1111/1440-1703.12528<br /> <br /> Abstract: <br /> Deep-sea hydrothermal vents are biological hotspots driven by microbial chemosynthetic primary production and characterized by a high proportion of endemic, specially adapted species. Vent communities can be unstable depending on the geological setting, as the underlying geofluid supply may change in location and chemical composition over a decadal timescale. Although the Izu-Ogasawara Arc in Japan is home to many vent fields within an Ecologically or Biologically Significant Marine Area (EBSA), no observations of decadal changes have been conducted. On Mokuyo Seamount, venting was first confirmed by several submersible dives between 1990 and 1993, but only fragmentary information has been published on its biodiversity. Here, we revisited Mokuyo on two dives between 2021 and 2024, three decades after its discovery. We found changes in venting activities, with the fluid supply on the northern caldera wall almost completely waned, while the northeastern face of the central cone has become increasingly active. The northwestern ridge of the central cone was covered in a dense white plume, under which xenophyophores (giant protists) thrive. The first comprehensive faunal sampling at Mokuyo greatly updated the faunal list from three to 18 species. Our results suggest vent communities on the Izu-Ogasawara Arc shift on a decadal scale, providing key baseline data for future conservation planning of the EBSA. <br /> <br /> Chen C*, Methou P, Yamamoto D, Kayamori M, Nomaki H (2024). There and there again: Hydrothermal vent communities at Mokuyo Seamount, 30 years apart. Ecological Research, 39: Early View. DOI: 10.1111/1440-1703.12528<br /> https://www.researchgate.net/publication/384395462_There_and_there_again_Hydrothermal_vent_communities_at_Mokuyo_Seamount_30_years_apart
Our new paper in PEPS measured natural radiocarbon (14C) in cold seep clams and tubeworms to reveal their carbon sources! ~9% of carbon in clams come from seep fluid vs >40% for tubeworms, likely due to different CO2 uptake mechanisms. OPEN ACCESS, read for FREE here: https://doi.org/10.1186/s40645-024-00648-5<br /> <br /> Abstract:<br /> Cold seeps, where geofluids containing methane and other hydrocarbons originating from the subseafloor seeps through the sediment surface, play important roles in the elemental and energy flux between sediment and seawater. These seep sites often harbor communities of endemic animals supported by chemolithoautotrophic bacteria, either through symbiosis or feeding. Despite these animal communities being intensively studied since their discovery in the 1980’s, the contribution of carbon from seep fluid to symbiotic microbes and subsequently host animals remains unclear. Here, we used natural-abundance radiocarbon to discern carbon sources: the ambient bottom water or the seeping geofluid. The 14C concentrations were measured for vesicomyid clams, a parasitic calamyzine polychaete, and a siboglinid tubeworm species from four different cold seep sites around Japan. We found most vesicomyid clams exhibiting 14C concentrations slightly lower than that of the ambient bottom water, suggesting up to 9% of C for chemolithoautotrophy originates from geofluid DIC. The different extent of fluid contribution across species may be explained by different routes to incorporate DIC and/or different DIC concentrations in the geofluid at each seep site. Stable nitrogen isotopic compositions further suggested N incorporation from geofluids in these clams, where the burrowing depth may be a key factor in determining their δ15N values. The siboglinid tubeworm showed a clear dependency for geofluid DIC, with a contribution of >40%. Our results demonstrate the effectiveness of 14C analyses for elucidating the nutritional ecology of cold seep animals and their symbionts, as was previously shown for hydrothermal vent ecosystems.<br /> <br /> Nomaki H*, Kojima S, Miyairi Y, Yokoyama Y, Chen C (2024). Natural 14C abundances and stable isotopes suggest discrete uptake routes for carbon and nitrogen in cold seep animals. Progress in Earth and Planetary Science, 11: 51. DOI: 10.1186/s40645-024-00648-5
We collaborated with Sony to develop a new method to evaluate organismal behaviour and particle dynamics using the Event‐based Vision Sensor (EVS)! By focusing on brightness shifts, EVS is a new type of camera sensor that can reach 10,000 fps even under low-light. Read this OPEN ACCESS paper for free: https://doi.org/10.1002/ece3.70150<br /> <br /> Abstract:<br /> The Event-based Vision Sensor (EVS) is a bio-inspired sensor that captures detailed motions of objects, aiming to become the ‘eyes’ of machines like self-driving cars. Compared to conventional frame-based image sensors, the EVS has an extremely fast motion capture equivalent to 10,000-fps even with standard optical settings, plus high dynamic ranges for brightness and also lower consumption of memory and energy. Here, we developed 22 characteristic features for analysing the motions of aquatic particles from the EVS raw data and tested the applicability of the EVS in analysing plankton behaviour. Laboratory cultures of six species of zooplankton and phytoplankton were observed, confirming species-specific motion periodicities up to 41 Hz. We applied machine learning to automatically classify particles into four categories of zooplankton and passive particles, achieving an accuracy up to 86%. At the in situ deployment of the EVS at the bottom of Lake Biwa, several particles exhibiting distinct cumulative trajectory with periodicities in their motion (up to 16 Hz) were identified, suggesting that they were living organisms with rhythmic behaviour. We also used the EVS in the deep sea, observing particles with active motion and periodicities over 40 Hz. Our application of the EVS, especially focusing on its millisecond-scale temporal resolution and wide dynamic range, provides a new avenue to investigate organismal behaviour characterised by rapid and periodical motions. The EVS will likely be applicable in the near future for the automated monitoring of plankton behaviour by edge computing on autonomous floats, as well as quantifying rapid cellular-level activities under microscopy.<br /> <br /> Takatsuka S# / Miyamoto N#, Sato H, Morino Y, Kurita Y, Yabuki A, Chen C, Kawagucci S* (2024). Milli-second-scale behaviours of plankton quantified in vitro and in situ using the Event-based Vision Sensor. Ecology and Evolution, 14: e70150. DOI: 10.1002/ece3.70150 [Preprint available on bioRxiv, DOI: 10.1101/2023.01.11.523686]
New Species Alert! 1 new genus, 11 new species, and 1 redescription/reinstatement, to be exact. Including two deep-sea hydrothermal vent gastropods contributed by myself and collaborators -- Lepetodrilus marianae and Shinkailepas gigas. The paper is OPEN ACCESS: https://bdj.pensoft.net/article/128431/<br /> <br /> The Ocean Species Discoveries (OSD) is a new publication format from @oceanspecies of concise and high-quality species descriptions that aims to accelerate the pace at which new marine invertebrate species are described and published. The species in the OSD originate from all over the globe, at depths from 5.2 to 7081 meters and were contributed by 25 researchers from 10 countries.<br /> <br /> Reducing the time it takes to get from discovering a new animal to a public species description is crucial in our era of increasing biodiversity loss. A scientific name and description help us better understand and protect animals like the deep-sea snails Lepetodrilus marianae and Shinkailepas gigas.<br /> <br /> Learn more about the OSD, the 13 new marine invertebrate taxa included, and how it helps accelerate the discovery of more species in our OPEN ACCESS paper: https://bdj.pensoft.net/article/128431/<br /> <br /> #OceanSpeciesDiscoveries<br /> <br /> Senckenberg Ocean Species Alliance (SOSA), Brandt A, Chen C, Engel L, Esquete P, Horton T, Jażdżewska AM, Johannsen N, Kaiser S, Kihara TC, Knauber H, Kniesz K, Landschoff J, Lörz A-N, Machado FM, Martínez-Muñoz CA, Riehl T*, Serpell-Stevens A, Sigwart JD, Tandberg A-H, Tato R, Tsuda M, Vončina K, Watanabe HK, Wenz C, Williams JD (2024). Ocean Species Discoveries 1-12 – A primer for accelerating marine invertebrate taxonomy. Biodiversity Data Journal, 12: e128431. DOI: 10.3897/BDJ.12.e128431
We sequenced a draft genome of the deep-sea volutid snail Fulgoraria chinoi Bail, 2000, the first genomic data for superfamily Volutoidea -- and used it to improve the existing Neogastropoda phylogeny! Out now in Zoologica Scripta: https://doi.org/10.1111/zsc.12687<br /> <br /> Abstract: <br /> Neogastropoda is a large order of predominantly marine gastropod molluscs, typically predatory or parasitic on other animals. It includes over 16,000 species representing a large post-Cretaceous radiation, but the internal phylogenetic relationships of contained taxa are far from resolved, with inconsistent results from nuclear genes, mitogenomes, and morphology. One major issue in reconstructing the molecular phylogeny is the lack of high-quality sequences for early-diverging families and superfamilies such as Volutidae (Volutoidea). Here, we examine the superfamily-level phylogenetic relationships in Neogastropoda, aided by newly sequenced draft genome and mitogenome of the volutid snail Fulgoraria chinoi from the deep sea off Japan. The genome of F. chinoi is relatively large at 1.54&amp;#x02009;Gb but exhibits low genome heterozygosity; over 54% of this genome constitutes of repeat contents, and we find evidence for active insertion of transposable elements, particularly LINEs and SINEs. A total of 50,792 protein-coding genes (PCGs) were predicted from the nuclear genome, and a circular mitogenome was also assembled and annotated. Our phylogenetic analyses using mitogenomes recovered each neogastropod superfamily as monophyletic, though also revealed inconsistent phylogenetic signals within superfamilies. Phylogenetic reconstructions using the PCGs resulted in a robust tree from different models and data matrices, recovering Volutoidea as the earliest diverging superfamily (among those for which comparable data is available) within a monophyletic Neogastropoda. Dated phylogenetic analysis revealed an early Cretaceous radiation of Neogastropoda, congruent with the fossil record. Our study provides a robust internal evolutionary framework for the speciose but genomically undersampled Neogastropoda, and expands the available genomic resources for this order. Genomic data for key missing lineages such as Mitroidea, Olivoidea, and Cancellariidae are much sought in the future for a full understanding of Neogastropoda evolution.<br /> <br /> Wang H, He X, Chen C, Gao K, Dai Y, Sun J* (2024). New insights into the phylogeny of Neogastropoda aided by draft genome sequencing of the volutid snail Fulgoraria chinoi. Zoologica Scripta, Early View. DOI: 10.1111/zsc.12687
Our paper in Marine Ecology Progress Series presents new data on alvinocaridid shrimps from deep-sea hot vents and cold seeps off Aotearoa / New Zealand, revealing their genetic connectivity and isotopic niches! We also name a new species and synonymise two names. <br /> <br /> Abstract: <br /> Chemosynthetic ecosystems off Aotearoa/New Zealand comprise both hydrothermal vents on the Kermadec Arc and methane seeps on the Hikurangi Margin which host rich communities of specialized fauna including 4 alvinocaridid shrimp species. The systematic positions of these New Zealand alvinocaridid shrimps have not been studied using genetic tools and little is known about their habitat use and feeding habits. Here, we re-evaluate the taxonomy of alvinocaridid shrimps from New Zealand using genetic barcoding and characterize their connectivity and isotopic niches across 8 localities. We describe a new species, Alvinocaris webberi sp. nov., previously confused with A. longirostris. We also show that A. alexander and A. chelys are junior synonyms of A. dissimilis, revealing a high genetic connectivity across hydrothermal vents and methane seeps from Japan to New Zealand, greatly extending its range. Finally, we find clear niche separation in co-occurring alvinocaridid shrimps, suggesting different diets and/or habitat use. Nevertheless, all species rely on chemosynthetic resources, regardless of the habitat depth, which ranges from 380 to 1650 m. <br /> <br /> Methou P*, Ogawa NO, Nomaki H, Ohkouchi N, Chen C, Schnabel K (2024). Genetic connectivity and isotopic niches of alvinocaridid shrimps from chemosynthetic habitats in Aotearoa/New Zealand, with a new Alvinocaris species. Marine Ecology Progress Series, 739: 85-109. DOI: 10.3354/meps14611
Our paper in Zoosystematics and Evolution names a new giant worm-mollusc from deep-sea cold seeps in South China Sea! Chaetoderma shenloong is the 2nd largest member of class Caudofoveata and the first aplacophoran mollusc associated with cold seeps! Its name was inspired by the magical dragon in the manga Dragon Ball. The paper is OPEN ACCESS and free to read: https://doi.org/10.3897/zse.100.125409<br /> <br /> Abstract: <br /> Caudofoveata is a class of worm-like molluscs (aplacophorans) that typically have an infaunal lifestyle, burrowing in soft bottoms in a wide range of marine habitats from shallow to deep waters. Here, we describe a very large new species of caudofoveate from South China Sea methane seeps growing up to 154 mm in length: Chaetoderma shenloong sp. nov. It is the first caudofoveate to be named from a chemosynthetic ecosystem and the first aplacophoran mollusc associated with seeps. Our new species stands out from other Pacific Chaetoderma species by its large size, a wide body relative to its length, a barely sclerotised radula, and the presence of isosceles-triangular sclerites. Phylogenetic reconstruction using the mitochondrial cytochrome c oxidase subunit I (COI) gene placed it within a paraphyletic clade comprising Chaetodermatidae and Limifossoridae, in line with a previous phylogenetic analysis. This also revealed that C. shenloong sp. nov. is conspecific with a Chaetoderma sp. whose whole genome was recently sequenced and assembled but remained undescribed until now. The most closely related species with an available COI sequence was C. felderi, the largest caudofoveate species recorded. Our discovery suggests caudofoveates may be present in other seeps globally but so far neglected; a potential example is C. felderi from the Gulf of Mexico, where seeps are abundant but whose exact habitat remains unclear. <br /> <br /> Chen C# / Liu X#, Gu X, Qiu J-W, J Sun* (2024). Integrative taxonomy of a new giant deep-sea caudofoveate from South China Sea cold seeps. Zoosystematics and Evolution, 100(3): 841-850. DOI: https://doi.org/10.3897/zse.100.125409
We published a commentary on a paper by Mao et al. (2024) in Frontiers in Marine Science., pointing out a highly problematic misidentification of their main study species -- a deep-sea hot vent barnacle. OPEN ACCESS: https://doi.org/10.3389/fmars.2023.1269411<br /> <br /> Abstract: <br /> Mao et al. (2024) recently published an article comparing the mitochondrial genome and transcriptome of the deep-sea hydrothermal vent barnacle Vulcanolepas fijiensis and the relatively shallower barnacle Scalpellum stearnsi (contradictory to the title, no new species was described). This paper concluded that the mitogenomes and key genes found in the transcriptomic analysis were subjected to positive selection related to high-temperature and high-pressure conditions, allowing V. fijiensis to adapt to the deep-sea environment. However, the neolepadid hydrothermal vent barnacle used in their study was misidentified and actually represents a different species, Neolepas marisindica. We present our evidence and reasoning for this below. Although the main conclusions presented by Mao et al. (2024) still stand because N. marisindica is also a deep-sea vent species, their misidentification has connotations on the context, interpretation, and of course future use of their data. <br /> <br /> Chan BKK, Watanabe-Kayama H, Chen C* (2024). Commentary: “Comparative omics analysis of a new deep-sea barnacle species (Cirripedia, Scalpellomorpha) and shallow-water barnacle species provides insights into deep-sea adaptation”. Frontiers in Marine Science, 11: 1374419. DOI: 10.3389/fmars.2024.1374419
We describe and name three new neomphaline limpet species from deep-sea hot vents of the SW Pacific in a new paper in the Zoological Journal of the Linnean Society! Read for FREE: https://bit.ly/CHUBACARC2<br /> <br /> Abstract: <br /> Neomphaloidean gastropods are endemic to chemosynthesis-based ecosystems ranging from hot vents to organic falls, and their diversity and evolutionary history remain poorly understood. In the southwestern Pacific, deep-sea hydrothermal vents on back-arc basins and volcanic arcs are found in three geographically secluded regions: a western region around Manus Basin, an eastern region around North Fiji and Lau Basins, and the intermediate Woodlark Basin where active venting was confirmed only recently, on the 2019 R/V L’Atalante CHUBACARC expedition. Although various lineages of neomphaloidean snails have been detected, typically restricted to one of the three regions, some of these have remained without names. Here, we use integrative taxonomy to describe three of these species: the neomphalid Symmetromphalus mithril sp. nov. from Woodlark Basin and the peltospirids Symmetriapelta becki sp. nov. from the eastern region and Symmetriapelta radiata sp. nov. from Woodlark Basin. A combination of shell sculpture and radular characters allow the morphological separation of these new species from their described congeners. A molecular phylogeny reconstructed from 570 bp of the mitochondrial cytochrome c oxidase subunit I gene confirmed the placement of the three new species in their respective genera and the superfamily Neomphaloidea. The finding of these new gastropods, particularly the ones from the Woodlark Basin, provides insights and implications on the historical role of Woodlark as a dispersing centre, in addition to highlighting the uniqueness of the Woodlark faunal community.<br /> <br /> Chen C*, Poitrimol C, Matabos M (2024). Integrative taxonomy of new neomphaloidean gastropods from deep-sea hot vents of the southwestern Pacific. Zoological Journal of the Linnean Society, Advance Access: zlae064. DOI: 10.1093/zoolinnean/zlae064<br /> PDF: https://www.researchgate.net/publication/380818411_Integrative_taxonomy_of_new_neomphaloidean_gastropods_from_deep-sea_hot_vents_of_the_southwestern_Pacific
My serendipitous (re)discovery of the "Living Fossil" monoplacophoran mollusc Neopilina galatheae off Galápagos is now out in Journal of Molluscan Studies! This is the first bona fide specimen of this legendary mollusc collected since 1959. The paper is OPEN ACCESS: https://doi.org/10.1093/mollus/eyae014<br /> <br /> Abstract: <br /> Monoplacophoran molluscs have been dubbed ‘living fossils’ due to their absence in the fossil record for about 375 million years, until Neopilina galatheae Lemche, 1957 was trawled off Costa Rica in 1952. Since then, over 35 species of living monoplacophorans have been discovered. Nevertheless, in situ observations of these rare deep-sea animals remain scant. Here, I observed and collected an intact specimen of N. galatheae using a remotely operated vehicle from 2460 m deep on the Eastern Galápagos Spreading Center. The animal was found attached to the glassy surface of solidified basalt lava flow, and no feeding trails were found near the animal. Such hard substrate is in contrast with previous records that were trawled on sand and mud, suggesting Neopilina can be found on a wide range of substrates. This is the first time this species was collected since 1959, and represents a southeast range extension of about 1000 km for the species. <br /> <br /> Chen C* (2024). In situ observation and range extension of the first discovered monoplacophoran Neopilina galatheae. Journal of Molluscan Studies, 90(2): eyae014. DOI: 10.1093/mollus/eyae014 [Preprint available on bioRxiv, DOI: 10.1101/2023.11.08.566290]
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