I am a biologist primarily working on the deep sea and molluscs (incl. snails, clams, octopuses, chitons, etc.). A focus of my research is to document and understand biodiversity and its evolution across multiple levels: from species to ecosystem, and from phenome to genome. Over geological timescales, life has evolved countless ‘novelties’ in order to gain new functions and conquer new environments. Like how wings allowed access to the sky, living in ‘extreme’ habitats such as deep-sea hot vents require novel adaptations. I am interested in 1) the diversity of organisms and their novelties, 2) how they help the organism adapt to the environment, and 3) by what trajectories do these novelties arise (and if there are common laws governing them).
I am currently a Senior Scientist with Tenure at the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), the Japanese national research institute for marine sciences. I am also a visiting scientist of Senckenberg Research Institute and Natural History Museum, Frankfurt, and a member of the IUCN Species Survival Commission, Mollusc Specialist Group. I have dived up to >6,000 m deep in the manned submersibles DSV SHINKAI 6500 and TRITON 3300/3 Mk. II in person to explore hot vents and other deep-sea environments, although I also often work with remotely operated submersibles. I am an avid collector of molluscs (‘shell collector’) and photographer.
PUBLICATIONS
![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 />
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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 />
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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]](https://scontent-lax3-2.xx.fbcdn.net/v/t39.30808-6/650687164_10236005728577909_5210072466921152159_n.jpg?_nc_cat=107&ccb=1-7&_nc_sid=4714a5&_nc_ohc=HWzs3lWoq3YQ7kNvwFtMQ1P&_nc_oc=AdpyUEilkP6z3sUUjYroG3FpyKvc6ZbfVgAdzqvX-GQyABsCV_OtlRbjewIh935oDVY&_nc_zt=23&_nc_ht=scontent-lax3-2.xx&edm=AC7C4-wEAAAA&_nc_gid=zVuaaQfOSAhN1B3KXj_iwA&_nc_tpa=Q5bMBQEDzs-6QEVzHh6_JXfxwWjZg0wqlKZj2P_JgG8wAfh462OmRVGvnTG6PotzlDeR5JZFdo26tSHg&oh=00_Af2R99pCpayC3Gf3Tmo0rpMpSu7_Uw1_CAkaxyG0mBDeZQ&oe=69EF3AA7)
![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 />
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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 />
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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]](https://scontent-lax3-1.xx.fbcdn.net/v/t39.30808-6/646535487_10235863205734927_3528303636189668413_n.jpg?_nc_cat=102&ccb=1-7&_nc_sid=4714a5&_nc_ohc=YzR1QL7bB0IQ7kNvwFDHF0k&_nc_oc=Adqfaid0NzoqqcgpZNXl2UFn7xUfL0lBhLzbf798Wj0KcZU6lPjfrcw3MN-VTQazP84&_nc_zt=23&_nc_ht=scontent-lax3-1.xx&edm=AC7C4-wEAAAA&_nc_gid=zVuaaQfOSAhN1B3KXj_iwA&_nc_tpa=Q5bMBQFWC4xUmnLRCl3QnPYFcVwMN2aZXYFClU_dM6Mqpxgql8EUEHZGk4nBETgeUoP9IJFeufcSp2bw&oh=00_Af2498CQCmOzvGEcqCJVD56RLg5PqEwFx4-4zkduu3Htkg&oe=69EF4120)
![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 />
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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 />
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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]](https://scontent-lax3-2.xx.fbcdn.net/v/t39.30808-6/634675422_10235613625455576_1912082848123759062_n.jpg?_nc_cat=100&ccb=1-7&_nc_sid=4714a5&_nc_ohc=qgXNZTwMAtcQ7kNvwHYqAxD&_nc_oc=AdpCNIS2qQwf7zZlR72A_vmCcRbxQWkyJQTOXITPa0SGT01CHsEEhBHKX50x18kwjLM&_nc_zt=23&_nc_ht=scontent-lax3-2.xx&edm=AC7C4-wEAAAA&_nc_gid=zVuaaQfOSAhN1B3KXj_iwA&_nc_tpa=Q5bMBQF5sC3Mu5_QmO4qCX7jl2_FH-bJn2eLRVKmV6wPVfo1ULZM469a3FnPtem1N5QoMAUingIwoZte&oh=00_Af39_laaB7sf9oNupXWk7Plj00PlkZhkaW_XwzBUaWE0bQ&oe=69EF4C2B)
![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 />
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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 />
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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]](https://scontent-lax7-1.xx.fbcdn.net/v/t39.30808-6/633000884_10235557964544088_5024011605154786945_n.jpg?_nc_cat=101&ccb=1-7&_nc_sid=4714a5&_nc_ohc=mSrrYpPxodgQ7kNvwGwI37k&_nc_oc=AdrCa_2knILHd31u13f_Xp7Z-78zbxtfaxdgbkzttnjREkeZZbJQe9-VLXxFzhnFBSM&_nc_zt=23&_nc_ht=scontent-lax7-1.xx&edm=AC7C4-wEAAAA&_nc_gid=zVuaaQfOSAhN1B3KXj_iwA&_nc_tpa=Q5bMBQFOJzy2U_yDmzwe1rIppMgQBJM9C5pI1lHRW9Dj59ryvPBWbW8-zwz7qCdbvxpwV1VJGJGdOT-U&oh=00_Af37Sx1D45F8P2GM-Pqmta-g_b9RLUdvyt2caTgs5WAnpA&oe=69EF5D88)
FROM THE C. CHEN COLLECTION
![Ferreiraella populi Sigwart in SOSA [Senckenberg Ocean Species Alliance] et al., 2026<br />
FERREIRAELLIDAE<br />
-5506 m, On sunken wood on the abyssal plain near the Izu-Ogasawara Trench off Japan (32°34.6760'N, 143°46.1235'E), Collected by a suction sampler mounted on HOV Shinkai 6500, R/V Yokosuka, 22.1 mm <br />
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Only known from a single sunken wood site on the northwestern Pacific abyssal plain off Japan, Ferreiraella populi is a ferreiraellid chiton characterised by an unusually small tail plate. At 5506 m deep, this sunken wood is currently the world's deepest known natural wood fall (i.e. not artificially deployed for scientific research), and this species is one of the most dominant animals there. All chitons from the family Ferreiraellidae are endemic to sunken wood, they are thought to be secondary consumers that do not directly digest wood and instead rely on gut symbionts that do -- but how exactly members of the genus Ferreiraella obtains nutrition from wood remains unclear. It is currently known from just a handful of specimens collected by a deep-diving manned submersible. <br />
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The aesthetes of F. populi has fewer pores in each bundle where the macrasthetes and micraesthetes are separated by greater distance that typical for the genus. The radula is also diagnostic as the comb-form major uncinus 'sweeper' teeth typical of the genus is much smaller than other known species. These characters, combined with the small tail valve, distinguish F. populi from all other known congeners. Typical body length around 15 mm, very large specimens can attain 25 mm. Like many other species of the genus, the tail valve is often colonised by serpulid tube worms.<br />
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The specific epithet 'populi' means 'of the people', and was the outcome of a public naming competition on YouTube in collaboratio with the internet performance artist and YouTuber Hosea Jan "Ze" Frank, an initiative intended to raise awareness of taxonomy and enhance public engagement with species discovery. This name was sugggest independently 11 times from over 8000 total contributions to the public naming competition.](https://scontent-lax7-1.xx.fbcdn.net/v/t39.30808-6/629228987_10235484502067572_6190716220691244043_n.jpg?_nc_cat=105&ccb=1-7&_nc_sid=4714a5&_nc_ohc=5bAEeg57OPQQ7kNvwEt8aTc&_nc_oc=AdoNFPPkNTh1vuJ-YiDxnZMZzV12VSt9kfa2UVSPDaCJQsu0PnTuQfRQHmgYlYouv0g&_nc_zt=23&_nc_ht=scontent-lax7-1.xx&edm=AC7C4-wEAAAA&_nc_gid=i77Fi4XPo69YvNJeU_3gsw&_nc_tpa=Q5bMBQHVOOO-qthoRtrwYAeLEDovbzrJtsez9LfwjGDDQxAt_M2oYixx34QbWaq5SidiZH2n_F6fjlaN&oh=00_Af0Osq9Gt9ebrZg4EmD9FT_3sj6GQGIxvVb5dsDb4nsq9g&oe=69EF48E7)
NEWS
- Publication: New cleftclams from Mariana (April 16th, 2026)
- Publication: The SOSA concept for marine conservation (April 6th, 2026)
- Publication: Phymorhynchus global barcoding (April 1st, 2026)
- Publication: VEHoP pipeline for phylogenomics (March 10th, 2026)
- Publication: Cleftclam symbiosis (March 4th, 206)
- Publication: 5 new vent limpet species (March 3rd, 2026)
- Publication: Sea of Japan cold seeps (February 25th, 2026)
- Publication: Scaly-foot Snail population genomics (February 11th, 2026)
- Publication: Symbiosis in vent & seep shrimps (February 11th, 2026)
- Publication: Chiton naming competition (February 6th, 2026)
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Scaly-foot Snail
A favourite among my study species is the Scaly-foot Snail (Chrysomallon squamiferum), an ‘armored snail‘ living in hot vents over 2000 m deep, which I formally named in 2015 as a part of my doctorate thesis at the University of Oxford studying peltospirid snails from deep-sea hydrothermal vents of the Indian Ocean and Antarctica. It is the only snail with dermal scales, which along with its shell are often coated in iron sulfide — the only known animal to have a skeleton composed (partly) of iron sulfide. The iron content vary depending on the environment, iron-rich specimens stick to magnet and will rust if not properly cared for.
Chrysomallon squamiferum Chen et al., 2015
The Scaly-foot Snail is now on the IUCN Red List as the first species Endangered by deep-sea mining risks — click here to read our paper in Nature Ecology & Evolution. We also deciphered its whole genome and found clues on how it evolved the unique scale armour — click here to read our paper in Nature Communications.
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