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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

A co-first authored paper has been published in Marine Biology! Read here: https://rdcu.be/bmGJr <br /> By using images over a five years period from a cabled deep-sea observatory placed in colony of Phreagena spp. vesicomyid clams in Sagami Bay, Japan, we show that their density showed an overall decline across the time period from natural disturbances (and a ROV visit), and earthquake-induced disturbances wiped out the population in the end. This implies vesicomyid clams, a dominant taxa in many deep-sea chemosynthetic ecosystems, are unlikely to survive potential impacts of deep-sea mining. <br /> <br /> Abstract: <br /> Cabled seafloor platforms can overcome many constraints of stand-alone systems and archived long-term seafloor monitoring, and their advantages include unlimited power, real time communication, a synchronized clock, and virtually unlimited data storage. Using monthly images from a fixed camera on a cabled deep-sea observatory in the Off Hatsushima seep site in Sagami Bay, Japan, fluctuations in clam density (Phreagena soyoae and P. okutanii) were observed over five years, March 1994–July 1999. Eight disturbances were seen, including five phytodetritus deposition events associated with seasonal blooms, two earthquake-associated turbid flows, and one caused by a maintenance visit by a remotely operated vehicle. Overall, these observations indicate that the vesicomyids experienced an ongoing decline throughout the observation series, and strong disturbance events such as earthquakes appeared to be too severe for the clams to survive. As such, vesicomyid clams are unlikely to survive the forseeable impacts of deep-sea mining. These results show that long-term observations of deep-sea chemosynthetic communities are useful for understanding their resilience and for making an environmental impact assessment.<br /> <br /> Nakajima R#*, Chen C#, Iwase R, Yamamoto H, Fujikura K (2019). Clams after storms: the impact of multiple disturbances on seep vesicomyid clams revealed by long-term monitoring. Marine Biology, 166: 35. DOI: 10.1007/s00227-019-3484-6
A co-authored paper on gut microbiota of the giant deep-sea trench isopod Hirondellea gigas (Birstein & Vinogradov, 1955) from Mariana Trench and Japan Trench has been published in Applied and Environmental Microbiology: https://aem.asm.org/content/85/1/e02032-18<br /> <br /> Abstract: <br /> Hadal environments sustain diverse microorganisms. A few studies have investigated hadal microbial communities consisting of free-living or particle-associated bacteria and archaea. However, animal-associated microbial communities in hadal environments remain largely unexplored, and comparative analyses of animal gut microbiota between two isolated hadal environments have never been done so far. In the present study, 228 Gb of gut metagenomes of the giant amphipod Hirondellea gigas from two hadal trenches, the Mariana Trench and Japan Trench, were sequenced and analyzed. Taxonomic analysis identified 49 microbial genera commonly shared by the gut microbiota of the two H. gigas populations. However, the results of statistical analysis, in congruency with the alpha and beta diversity analyses, revealed significant differences in gut microbial composition across the two trenches. Abundance variation of Psychromonas, Propionibacterium, and Pseudoalteromonas species was observed. Microbial cooccurrence was demonstrated for microbes that were overrepresented in the Mariana trench. Comparison of functional potential showed that the percentage of carbohydrate metabolic genes among the total microbial genes was significantly higher in the guts of H. gigas specimens from the Mariana Trench. Integrating carbon input information and geological characters of the two hadal trenches, we propose that the differences in the community structure might be due to several selective factors, such as environmental variations and microbial interactions. <br /> <br /> Zhang W, Watanabe HK, Ding W, Lan Y. Tian R-M, Sun J, Chen C, Cai L, Li Y, Oguri K, Toyofuku T, Kitazato H, Drazen JC, Bartlett D, Qian P-Y (2018). Gut microbial divergence between two populations of the hadal amphipod Hirondellea gigas. Applied and Environmental Microbiology, 85(1): e02032-18. DOI: 10.1128/AEM.02032-18
Our new paper published in Zootaxa yesterday introduces a new chiton (polyplacophoran mollusc), Hanleyella henrici Sigwart & Chen, 2018, from deep-sea hydrothermal vents in Okinawa Trough! https://www.mapress.com/j/zt/article/view/zootaxa.4531.3.7<br /> <br /> Abstract: <br /> Recent expeditions exploring deep-sea hydrothermal vent ecosystems in the Okinawa Trough, East China Sea resulted in the collection of a hitherto undescribed species of polyplacophoran mollusc found living at three different vent fields at depths of 950–1178 m. This new chiton is a member of the small lepidopleuran family Protochitonidae and is morphologically similar to Hanleyella japonica Saito, 1997. The two species differ in small morphological differences of the valve shape and elevation, are divergent in the standard molecular barcoding mitochondrial gene cytochrome oxidase I (COI), and furthermore the known distribution range of H. japonica is considerably more northern and also shallower. The new species is described herein as Hanleyella henrici n. sp. Additional in situ observations taken in the course of collecting material for this study indicates that chitons are more abundant in the vicinity of hydrothermal vents than was previously appreciated, and perhaps more speciose.<br /> <br /> As always, please let me know if you would like to have a PDF copy of the paper. <br /> <br /> Sigwart JD, Chen C (2018). A new deep water chiton (Mollusca: Polyplacophora) from hydrothermal vent ecosystems in the Okinawa Trough, Japan. Zootaxa, 4531(3): 430-436. DOI: 10.11646/zootaxa.4531.3.7
A new co-authored article has been published in the Open Access journal eLife! Read for free: https://elifesciences.org/articles/41319<br /> <br /> Here, we present our thoughts that our ability to come up with a conservation framework for managing and developing deep-sea resources exploitation is constrained by the fact that we don't even know what lives there -- and hence it is not (yet) feasible to model how ecosystems will be affected by such activities. We make a case that a taxon-focused approach with high-throughput taxonomy (like describing 1000 species in 5 years) is achievable, and needs to, be done for regions with foreseeable industrial activity. <br /> <br /> Thanks goes to Adrian, Helena, and Thomas for including me in this work! It was a real pleasure : D <br /> <br /> Abstract: <br /> Ensuring that the wealth of resources contained in our oceans are managed and developed in a sustainable manner is a priority for the emerging 'blue economy'. However, modern ecosystem-based management approaches do not translate well to regions where we know almost nothing about the individual species found in the ecosystem. Here, we propose a new taxon-focused approach to deep-sea conservation that includes regulatory oversight to set targets for the delivery of taxonomic data. For example, a five-year plan to deliver taxonomic and genomic knowledge on a thousand species in regions of the ocean earmarked for industrial activity is an achievable target. High-throughput, integrative taxonomy can, therefore, provide the data that is needed to monitor various ecosystem services (such as the natural history, connectivity, value and function of species) and to help break the regulatory deadlock of high-seas conservation. <br /> <br /> Glover AG, Wiklund H, Chen C, Dahlgren TG (2018). Managing a sustainable deep-sea ‘blue economy’ requires knowledge of what actually lives there. eLife, 7: e41319. DOI: 10.7554/eLife.41319
Co-authored paper with Yukiko Nagai, Takashi Toyofuku, and others published in the journal Biogeosciences reveals how foraminifera "weave" their tests ('shells') with fine threads of cytoplasm, using high-res microscopy and time-lapse imaging. This has implications on how geochemical signatures in foraminifera tests are shaped, and thus contribute to interpreting such signatures from fossils and using them as biogeochemical proxies. This paper is Open Access: https://www.biogeosciences.net/15/6773/2018/bg-15-6773-2018.html<br /> <br /> Abstract: <br /> Elemental and/or isotopic signatures of calcareous tests of foraminifera are commonly used to reconstruct paleoenvironmental conditions. A major problem, often referred to as the "vital effect", is that such geochemical signatures stored in inorganic calcium carbonates differ greatly under the same environmental conditions, as well as between taxa, species, individuals, etc. This effect was previously explained by relative contributions between passive vs. active ion transport patterns, but their details are still under investigation. In this study, the functional role of pseudopodial structures during chamber formation is elucidated by detailed observation of Ammonia beccarii (Linnaeus, 1758) using a time-lapse optical imaging system and high-resolution electron microscopy. We document triple organic layers sandwiching carbonate precipitation sites for the first time. The three major organic layers (outer organic layer, primary organic sheet, and inner organic layer) are formed by an initial framework of pseudopodia overlaid with further layer-like pseudopodia. The primary organic sheet seems to facilitate early calcium carbonate nucleation, then entrapped by double precipitation sites. We further show that calcification starts when outer or inner organic layers still exhibit tiny gaps (holes within the framework) that may serve as pathways for passive ion exchange (e.g. Mg2+) between seawater and the confined precipitation space. Nevertheless, the majority of wall thickening occurs when the precipitation site is completely isolated from seawater, which implies active ion exchange. This may explain the differences in Mg∕Ca ratios in early and later stages of calcification observed in previous studies. Our study provides insight into resolving a key "missing piece" in understanding foraminiferal calcification through culture experiments and in-depth observations of living animals. Our findings contribute to interpreting and understanding biogeochemical proxies by showing that the "vital effect", specifically elemental and isotopic ratios along chamber walls, is directly linked to spatio-temporal organization of the "biomineralization sandwich" controlled by the three major organic layers.<br /> <br /> Nagai Y, Uematsu K, Chen C, Wani R, Tyszka J, Toyofuku T (2018). Weaving of biomineralization framework in rotaliid foraminifera: Implications for paleoceanographic proxies. Biogeosciences, 15: 6773-6789. DOI: 10.5194/10.5194/bg-15-6773-2018
A co-authored paper reviewing the cold seep systems in the South China Sea has been published online in Journal of Asian Earth Sciences: https://doi.org/10.1016/j.jseaes.2018.09.021 <br /> This review comprehensively covers various relevant diciplines, and I was responsible for the macroecology section. <br /> <br /> Abstract: <br /> Three decades after the discovery of cold seep systems, various sites of hydrocarbon seepage have been found in the South China Sea (SCS). Over the past decade, these sites have become model systems for understanding the variability of hydrocarbon seepage and associated biogeochemical processes. In this review, we describe the cold seep systems of the SCS with an emphasis on seafloor manifestations, fluid sources, biogeochemical processes, and macroecology. Seafloor features associated with seeps include mud volcanoes, pockmarks, and carbonate deposits. A common characteristic of cold seeps is the occurrence of authigenic (i.e., in situ precipitated) carbonate minerals. These carbonates commonly exhibit low δ13C and high δ18O values, suggesting the incorporation of methane-derived carbon and oxygen derived from gas hydrate water. Biogeochemical processes such as sulfate-driven anaerobic oxidation of methane (SD-AOM), the key process at seeps, have been studied in detail with the aim of establishing geochemical proxies to trace these processes into the geological past. We also detail the features characterizing seep ecosystems. Understanding the impact of decomposing methane hydrate on the marine carbon budget remains challenging and requires additional seafloor observations as well as models predicting how gas hydrate responds to changing conditions such as temperature increase, sea level rise, and episodic mass wasting. <br /> <br /> Feng D, Qiu J-W, Hu Y, Peckmann J, Guan H, Tong H, Chen C, Chen J, Gong S, Li N, Chen D (2018). Cold seep systems in the South China Sea: An overview. Journal of Asian Earth Sciences. DOI: 10.1016/j.jseaes.2018.09.021
The first paper on the physiology of Indian Ocean vent animals has been published in The Biological Bulletin! Link: https://www.journals.uchicago.edu/doi/abs/10.1086/699326<br /> <br /> We used closed-chamber respirometry to investigate whether the scaly-foot snail (Chrysomallon squamiferum)'s strategy of having an internal symbiont-housing organ increased its routine metabolism. By comparing the oxygen consumption of both Chrysomallon and Alviniconcha marisindica at different temperatures, we show that housing symbionts in an internal organ does not fundamentally increase the oxygen requirement. The Scaly-foot, however, was able to maintain a steady metabolic demand across experiment temperatures, while Alviniconcha showed stress responses at low temperature. Vent habitats have steep temperature gradients between the superheated vent fluid and the cold surrounding seawater, and such physiological constraints likely play important roles in defining niches in these environments. <br /> <br /> Abstract: <br /> Physiological traits are the foundation of an organism’s success in a dynamic environment, yet basic measurements are unavailable for many taxa and even ecosystems. We measured routine metabolism in two hydrothermal vent gastropods, Alviniconcha marisindica (n = 40) and the scaly-foot gastropod Chrysomallon squamiferum (n = 18), from Kairei and Edmond vent fields on the Central Indian Ridge (23–25°S, about 3000 meter depth). No previous studies have measured metabolism in any Indian Ocean vent animals. After recovering healthy animals to the surface, we performed shipboard closed-chamber respirometry experiments to compare oxygen uptake at different temperatures (10, 16, and 25 °C) at surface pressure (1 atm). The physiology of these species is driven by the demands of their chemoautotrophic symbionts. Chrysomallon has very enlarged respiratory and circulatory systems, and endosymbionts are housed in its trophosome-like internal esophageal gland. By contrast, Alviniconcha has chemoautotrophic bacteria within the gill and less extensive associated anatomical adaptations. Thus, we predicted that routine oxygen consumption of Chrysomallon might be higher than that of Alviniconcha. However, oxygen consumption of Chrysomallon was not higher than that of Alviniconcha, and, further, Chrysomallon maintained a steady metabolic demand in two widely separated experimental temperatures, while Alviniconcha did not. We interpret that these findings indicate that (1) the “trophosome” does not fundamentally increase oxygen requirement compared to other gastropod holobionts, and (2) cold temperatures (10 °C) induce a stress response in Alviniconcha, resulting in aberrantly high uptake. While these two large gastropod species co-occur, differences in oxygen consumption may reflect the separate niches they occupy in the vent ecosystem.<br /> <br /> Sigwart JD, Chen C (2018). Comparative oxygen consumption of gastropod holobionts from deep-sea hydrothermal vents in the Indian Ocean. The Biological Bulletin, 235(2). DOI: 10.1086/699326
A paper using genome-wide SNPs to elucidate population genetic of the deep-sea mussel Bathymodiolus platifrons that I co-authored is now available for free (Open Access) online! Many thanks for the lead author Ting Xu and the co-authors, including Jin Sun, Hiromi Watanabe-Kayama, Masako Nakamura, among others. Link: https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12696<br /> <br /> Abstract: <br /> Studying population genetics of deep‐sea animals helps us understand their history of habitat colonization and population divergence. Here, we report a population genetic study of the deep‐sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) widely distributed in chemosynthesis‐based ecosystems in the Northwest Pacific. Three mitochondrial genes (i.e., atp6, cox1, and nad4) and 6,398 genomewide single nucleotide polymorphisms (SNPs) were obtained from 110 individuals from four hydrothermal vents and two methane seeps. When using the three mitochondrial genes, nearly no genetic differentiation was detected for B. platifrons in the Northwest Pacific. Nevertheless, when using SNP datasets, all individuals in the South China Sea (SCS) and three individuals in Sagami Bay (SB) together formed one genetic cluster that was distinct from the remaining individuals. Such genetic divergence indicated a genetic barrier to gene flow between the SCS and the open Northwest Pacific, resulting in the co‐occurrence of two cryptic semi‐isolated lineages. When using 125 outlier SNPs identified focusing on individuals in the Okinawa Trough (OT) and SB, a minor genetic subdivision was detected between individuals in the southern OT (S‐OT) and those in the middle OT (M‐OT) and SB. This result indicated that, although under the influence of the Kuroshio Current and the North Pacific Intermediate Water, subtle geographic barriers may exist between the S‐OT and the M‐OT. Introgression analyses based on these outlier SNPs revealed that Hatoma Knoll in the S‐OT represents a possible contact zone for individuals in the OT‐SB region. Furthermore, migration dynamic analyses uncovered stronger gene flow from Dai‐yon Yonaguni Knoll in the S‐OT to the other local populations, compared to the reverse directions. Taken together, the present study offered novel perspectives on the genetic connectivity of B. platifrons mussels, revealing the potential interaction of ocean currents and geographic barriers with adaption and reproductive isolation in shaping their migration patterns and genetic differentiation in the Northwest Pacific. <br /> <br /> Xu T, Sun J, Watanabe HK, Chen C, Nakamura M, Ji R, Feng D, Lv J, Wang S, Bao Z, Qian P-Y, Qiu J-W (2018). Population genetic structure of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific. Evolutionary Applications. DOI: 10.1111/eva.12696
A new co-authored proceedings paper on using micro-CT scans to visualise molluscs is now published! It is Open Access and can be read for free here: https://dx.doi.org/10.1007/978-981-13-1002-7_9<br /> <br /> Abstract: <br /> Three-dimensional (3D) reconstruction is an essential approach in morphological studies in biology and paleontology. Seeking an optimized protocol for nondestructive observations, we attempted 3D visualization of various molluscan shells and animals with X-ray micro-computed tomography (micro-CT). Calcified parts of molluscs were easily visualized except for cases with marked differences in thickness heterogeneity. 3D imaging of shell microstructure was difficult. Visualization of soft tissue requires staining to enhance the image contrast. Especially for soft tissues, synchrotron X-ray microtomography is the most advanced method to generate clear 3D images. 3D data facilitates morphological quantification, enabling calculations of length and volume even for very complex forms. X-ray micro-CT is extremely useful in the morphologic examination of mineralized and soft tissues, although microstructural and histological details should be supplemented by other microscopic techniques. <br /> <br /> Sasaki T, Maekawa Y, Takeda Y, Atsushiba M, Chen C, Noshita K, Uesugi K, Hoshino M (2018). 3D visualization of calcified and non-calcified molluscan tissues using computed tomography. In: Endo K, Kogure T, Nagasawa H (eds.) Biomineralization: From Molecular and Nano-structural Analyses to Environmental Science, pp. 83-93. Springer, Singapore. DOI: 10.1007/978-981-13-1002-7_9
A new co-authored paper with Tomomi Ogura and Hiromi Watanabe-Kayama (among others) has been published in the open-access journal PeerJ! We investigated the genetic connectivity and population history of five deep-sea abyssochrysoid snails in the genus Provanna from vents and seeps. Read for free here: https://peerj.com/articles/5673/<br /> <br /> Abstract: <br /> Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. We investigated the population history and connectivity of five Provanna species in the northwestern Pacific through population genetic analyses using partial sequences of the cytochrome c oxidase subunit I gene. We found that P. subglabra, the most abundant and genetically diverse species, is genetically segregated by depth. Among the five species, the three comparatively shallower species (P. lucida, P. kuroshimensis, P. glabra) had a more constant demographic history compared to the deeper species (P. subglabra, P. clathrata).<br /> <br /> Ogura T, Watanabe HK, Chen C, Sasaki T, Kojima S, Ishibashi J-i, Fujikura K (2018). Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific. PeerJ. DOI: 10.7717/peerj.5673
A new lead-authored paper has been published in Proceedings of the Royal Society B: Biological Sciences ( http://bit.ly/2JcwlOF )! In this paper, we reveal a previously undocumented type of metamorphosis exhibited by the deep-sea vent snail Gigantopelta using synchrotron micro-CT. Please let me know if you would like a PDF copy. <br /> <br /> Metamorphosis, such as the transformation from caterpillar to butterfly or tadpole to frog, is one of the most exquisite phenomena in animal life history, and has been thought to always involve a clearly correlated transformation in both external and internal morphology. We used state-of-the-art 3D reconstruction to reveal that the snail Gigantopelta chessoia from deep-sea hydrothermal vents goes through a further internal transformation in anatomy after settlement, which is not apparent from external morphology. Termed ‘cryptometamorphosis’, this newly discovered phenomenon allows Gigantopelta to switch from ingesting food to relying entirely on symbionts. The possibility of an additional, ‘hidden’, metamorphosis as adults also have a profound impact on understanding the energy flow in ecosystems, as it means we may not be able to tell the trophic role of an animal without detailed anatomical observations. Modelling food webs and the energetic flow in ecosystems is crucial in their conservation, especially in a time of rapid environmental changes, and our results highlight the importance of in-depth knowledge on the life history of animal species in order to model ecosystems accurately. <br /> <br /> Chen C*, Linse K, Uematsu K, Sigwart JD (2018). Cryptic niche switching in a chemosymbiotic gastropod. Proceedings of the Royal Society B: Biological Sciences, 285(1882): 20181099. DOI: 10.1098/rspb.2018.1099
Another lead-authored paper published in Venus (Journal of the Malacological Society of Japan) this week describes Thermomya sulcata new genus and new species from a hydrothermal vent almost 2500 m deep in the southern Mariana Trough. It differs from other cuspidariids mainly by its sharp and upturned commarginal ribs resembling the sculpture in some venerids. This is the first cuspidariid or Anomalodesmata bivalve found from any chemosynthetic ecosystems in the deep-sea. <br /> <br /> Abstract: <br /> Cuspidariidae is a family of bizarre heterodont bivalves with a specialized carnivorous lifestyle. An unusual cuspidariid bivalve was discovered from 2,489 m depth in the Snail hydrothermal vent site, Southern Mariana Trough, and is described herein as Thermomya sulcata n. gen. & n. sp. Although cuspidariids are well-known from the deep sea, until now none were known to inhabit chemosynthetic ecosystems. In fact, this is also the first member of the clade Anomalodesmata found in hydrothermal vent ecosystems. <br /> <br /> Chen C*, Okutani T, Watanabe HK, Kojima S (2018). The first cuspidariid bivalve associated with hydrothermal vents discovered from the Southern Mariana Trough. Venus (Journal of the Malacological Society of Japan), 76: 39-44. DOI: 10.18941/venus.76.1-4_39
A new first-authored publication in Venus (Journal of the Malacological Society of Japan) describes 'Calyptogena' marissinica Chen, Okutani, Liang & Qiu, 2018 from a hydrocarbon seep over 1300 m deep in the South China Sea. We left this species in Calyptogena sensu lato for the time being, due to the genus assignment being unclear in the current flux of vesicomyid taxonomy. Please let me know if you would like to have a PDF of this paper. <br /> <br /> Abstract<br /> “Calyptogena” marissinica n. sp. is described from the Haima cold seep on the northwestern slope of the South China Sea, China, at depths of 1,372 m and 1,398 m. Phylogenetic reconstruction using the cytochrome oxidase c subunit I (COI) gene shows that it is sister to Calyptogena similaris but distinct from that species by a pairwise distance of 3.9%, larger than the average intraspecific variation within the genus Calyptogena sensu lato. Morphologically, the new species is distinguished from C. similaris in having a less elongate shell, with nearly straight ventral margin, and no apparent anterior lateral tooth. <br /> <br /> Chen C*, Okutani T, Liang Q, Qiu J-W (2018). A noteworthy new species of the family Vesicomyidae from the South China Sea (Bivalvia: Glossoidea). Venus (Journal of the Malacological Society of Japan), 76: 29-37. DOI: 10.18941/venus.76.1-4_29
A new co-authored paper in BMC Genomics led by Yi Lan uses transcriptomics to look at molecular adaptation in the deep-sea fish Aldrovandia affinis (Günther, 1877) (Actinopterygii: Halosauridae). Open Access: https://doi.org/10.1186/s12864-018-4720-z<br /> <br /> Abstract<br /> <br /> High hydrostatic pressure and low temperatures make the deep sea a harsh environment for life forms. Actin organization and microtubules assembly, which are essential for intracellular transport and cell motility, can be disrupted by high hydrostatic pressure. High hydrostatic pressure can also damage DNA. Nucleic acids exposed to low temperatures can form secondary structures that hinder genetic information processing. To study how deep-sea creatures adapt to such a hostile environment, one of the most straightforward ways is to sequence and compare their genes with those of their shallow-water relatives. We captured an individual of the fish species Aldrovandia affinis, which is a typical deep-sea inhabitant, from the Okinawa Trough at a depth of 1550 m using a remotely operated vehicle (ROV). We sequenced its transcriptome and analyzed its molecular adaptation. We obtained 27,633 protein coding sequences using an Illumina platform and compared them with those of several shallow-water fish species. Analysis of 4918 single-copy orthologs identified 138 positively selected genes in A. affinis, including genes involved in microtubule regulation. Particularly, functional domains related to cold shock as well as DNA repair are exposed to positive selection pressure in both deep-sea fish and hadal amphipod. Overall, we have identified a set of positively selected genes related to cytoskeleton structures, DNA repair and genetic information processing, which shed light on molecular adaptation to the deep sea. These results suggest that amino acid substitutions of these positively selected genes may contribute crucially to the adaptation of deep-sea animals. Additionally, we provide a high-quality transcriptome of a deep-sea fish for future deep-sea studies.
A new co-authored paper published in Royal Society Open Science led by Hiromi Watanabe-Kayama describes a new species of deep-sea stalked barnacle from Indian Ocean hydrothermal vents: Neolepas marisindica Watanabe, Chen & Chan in Watanabe et al., 2018. Furthermore, we also carried out phylogeographic investigation of deep-sea eolepadid stalked barnacles, leading to a better understanding of their evolution and biogeography. The paper is Open Access and available here: http://rsos.royalsocietypublishing.org/content/5/4/172408<br /> <br /> Abstract: <br /> Phylogeography of animals provides clues to processes governing their evolution and diversification. The Indian Ocean has been hypothesized as a ‘dispersal corridor’ connecting hydrothermal vent fauna of Atlantic and Pacific oceans. Stalked barnacles of the family Eolepadidae are common associates of deep-sea vents in Southern, Pacific and Indian oceans, and the family is an ideal group for testing this hypothesis. Here, we describe Neolepas marisindica sp. nov. from the Indian Ocean, distinguished from N. zevinae and N. rapanuii by having a tridentoid mandible in which the second tooth lacks small elongated teeth. Morphological variations suggest that environmental differences result in phenotypic plasticity in the capitulum and scales on the peduncle in eolepadids. We suggest that diagnostic characters in Eolepadidae should be based mainly on more reliable arthropodal characters and DNA barcoding, while the plate arrangement should be used carefully with their intraspecific variation in mind. We show morphologically that Neolepas specimens collected from the South West Indian Ridge, the South East Indian Ridge and the Central Indian Ridge belong to the new species. Molecular phylogeny and fossil evidence indicated that Neolepas migrated from the southern Pacific to the Indian Ocean through the Southern Ocean, providing key evidence against the ‘dispersal corridor’ hypothesis. Exploration of the South East Indian Ridge is urgently required to understand vent biogeography in the Indian Ocean.<br /> <br /> Watanabe HK*, Chen C, Marie DP, Takai K, Fujikura K, Chan BKK* (2018). Phylogeography of hydrothermal vent stalked barnacles: a new species fills a gap in the Indian Ocean ‘dispersal corridor’ hypothesis. Royal Society Open Science, 5: 172408. DOI: 10.1098/rsos.172408
A co-author paper of mine, led by Dr. Tomoyuki Komai from Chiba Natural History Museum and Institute, has been published in the journal Zootaxa. In this paper, we describe two new species of shrimps in genus Metacrangon (Caridea: Crangonidae) from hydrothermally influenced areas in Okinawa Trough, Japan. Please let me know if you would like to see the PDF. http://www.mapress.com/j/zt/article/view/zootaxa.4410.1.5 <br /> <br /> Abstract: <br /> Two new species of the crangonid shrimp genus Metacrangon Zarenkov, 1965, are described and illustrated on the basis of materials collected from the Okinawa Trough, Ryukyu Islands, southern Japan, during diving operations of remotely operated vehicles (ROVs): M. ryukyu n. sp. from off Iheya Island, at depth of 986 m; and Metacrangon kaiko n. sp. from NE of Yonaguni Island, at depth of 2205 m. The two new species resemble members of the M. munita (Dana, 1852) species group, but are both characteristic in having setose dactyli on pereopods 4 and 5. Some minor differences in morphology and genetic analysis using partial sequences of the barcoding mitochondrial COI gene support the recognition of the two new species. Holotypes of the two new species were collected from hydrothermally influenced areas, representing a previously unknown habitat for species of Metacrangon. <br /> <br /> Komai T*, Chen C, Watanabe HK (2018). Two new species of the crangonid genus Metacrangon Zarenkov, 1965 (Crustacea: Decapoda: Caridea) from the Okinawa Trough, Japan. Zootaxa, 4410(1): 97-112. DOI: 10.11646/zootaxa.4410.1.5
A paper I co-authored has been published in Molecular Phylogenetics and Evolution! In this work led by Yanjie Zhang, we sequenced mitochondrial genomes from deep-sea scale worms (Annelida: Aphroditiformia) to study their phylogeny and evolution. Here's a link that gives you free access to the full paper for the next 50 days: https://authors.elsevier.com/c/1Wt5g3m3nMqWNm<br /> <br /> Highlights<br /> <br /> - We recovered 15 mitochondrial genomes and 16 18S and 28S genes from 16 scale worms.<br /> - Eulepethidae and Aphroditidae are sister to the other families.<br /> - Branchinotogluminae and Macellicephalinae are paraphyletic.<br /> - Mitochondrial gene orders of deep-sea species have two novel arrangement patterns.<br /> - Mitochondrial genomes of deep-sea species show relaxed purifying selection. <br /> <br /> Zhang Y, Sun J, Rouse GW, Wiklund H, Pleijel F, Watanabe HK, Chen C, Qian P-Y, Qiu J-W* (2018). Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Molecular Phylogenetics and Evolution, 125: 220-231. DOI: 10.1016/j.ympev.2018.04.002
Co-authored paper describing hydrothermal vent scale worms (Polychaeta: Polynoidae) has been just published in Frontiers in Marine Science (sorry its not molluscs this time)! It is Open Access and free for all to read here: https://www.frontiersin.org/articles/10.3389/fmars.2018.00112/<br /> <br /> In this paper, we described two new vent polynoides including Levensteiniella undomarginata Zhang, Chen & Qiu, 2018 and Branchinotogluma elytropapillata Zhang, Chen & Qiu, 2018; and also redescribed Lepidonotopodium okinawae Sui & Li, 2017 and Branchinotogluma japonicus Miura &Hashimoto, 1991 to include both sex forms. These scale worms are highly sexually dimorphic and in many cases the two sexes have been described as separate species or even genera, highlighting the importance of describing morphological characteristics of both sexes. <br /> <br /> Zhang Y, Chen C, Qiu J-W* (2018). Sexually dimorphic scale worms (Annelida: Polynoidae) from deep-sea hydrothermal vents in the Okinawa Trough: Two new species and two new sex morphs. Frontiers in Marine Science, 5: 112. DOI: 10.3389/fmars.2018.00112
Our short paper describing the strange behaviour of forming hanging 'stacks' exhibited by the vent snail genus Gigantopelta has been published in the journal Plankton and Benthos Research! This behaviour is probably related to reproduction. The paper is open access and available for view here: https://doi.org/10.3800/pbr.13.25<br /> <br /> “Mating stacks” have been widely documented in calyptraeid slipper limpets, which are protandric and exhibit sequential hermaphroditism. Gigantopelta is a genus of peltospirid snails endemic to deep-sea hydrothermal vents containing two species, one distributed on the East Scotia Ridge in the Southern Ocean and another on the Southwest Indian Ridge in the Indian Ocean. Here, we report the observation that both species form extensive (often >15 individuals) “snail chains”. These chains are potentially analogous to ‘mating stacks’ of calyptraeids, or alternatively, maybe a behaviour to facilitate spermatophore transfer. Both Gigantopelta species apparently have separate sexes and are sexually mature at a small size. However, it remains unclear whether they undergo sex change during their life. <br /> <br /> Chen C*, Marsh L, Copley JT (2018). Is it sex in chains? Potential mating stacks in deep-sea hydrothermal vent snails. Plankton and Benthos Research, 13(1): 25-27.
A co-authored paper with Muricidae experts Roland Houart and Chris Moe, describing three new muricid gastropods from the western Pacific, has been published in The Nautilus! This is my last paper for 2017 and the 13th this year! <br /> <br /> Of the three muricids described in this paper, one is a Chicomurex from the Philippines and Kwajalein Atoll – Chicomurex excelsus Houart, Moe & Chen, 2017. With live-taken specimens known from 150~200 m deep (dead shells have been found as shallow as 60 m), this species is characterised by a long siphonal canal which carries intricately webbed fronds but lacks in strong recurved spines. This unique siphonal canal sculpture, as well as a lower spire and a more angular final teleoconch whorl, separate it from C. gloriosus (Shikama, 1977), the closest congener which it co-occurs with. The other two species described are from Fiji and in the genus Chicoreus (Triplex) – Chicoreus kaitomoei Houart, Moe & Chen, 2017 and Chicoreus aquilus Houart, Moe & Chen, 2017, both being small-sized (<40 mm) for the genus. Although C. kaitomoei has been confused with C. aculeatus (Lamarck, 1822) and C. nobilis Shikama, 1977, these two species have multispiral protoconchs implying planktotrophic development unlike C. kaitomoei which has a pausispiral protoconch implying lecithotrophic development. The teleoconch of C. kaitomoei is by very short variceal spines (except those from P1-3) and a siphonal canal with three abapically bent spines concentrated on the anterior half. This species inhabit shallow waters around 9~30 m deep and is named after Kaito Moe, son of Chris Moe. Finally, C. aquilus which is only known from the holotype taken from 31~40 m deep in Fiji, is a highly distinctive species closest to C. rubescens (Broderip, 1833) and a few other species belonging to Chicoreus “group 2” (sensu Houart, 1992) but easily distinguished by differences in varice and aperture characteristics. <br /> <br /> Houart R*, Moe C, Chen C (2017). Description of three new muricids (Gastropoda: Muricidae: Muricinae) from the Philippines and Fiji. The Nautilus, 131(4): 207-216.
A new paper on the discovery of a new hydrothermal vent field has been published in the peer-reviewed Open Access journal Royal Society Open Science! I acted as the corresponding author. Read for free here: http://rsos.royalsocietypublishing.org/content/4/12/171570<br /> <br /> We report, in this paper, the discovery of the “Yokosuka” site – the deepest and hottest hydrothermal vent field in the Okinawa Trough, Japan. At 2190 m deep, this new vent field is highly active and exhibit vigorous focused venting from ‘black smoker’ chimneys, the highest temperature recorded being 364°C. We named the new vent site after R/V Yokosuka, the supporting vessel of DSV Shinkai6500 and AUV URASHIMA.<br /> <br /> Fauna and microbiota in the new site were generally similar to other Okinawa Trough vents, although with some different characteristics. For fauna, the dominance of the deep-sea mussel Bathymodiolus aduloides is surprising given other nearby vent sites are usually dominated by B. platifrons and/or B. japonicus, and a sponge field in the periphery dominated by Poecilosclerida is unusual for vents in this region. In terms of microbiota, the H2-rich vent fluids in one of the chimneys resulted in the dominance of hydrogenotrophic chemolithoautotrophs such as Thioreductor and Desulfobacterium. In terms of vent fluid, notable Cl depletion (130 mM) and high concentrations of both H2 and CH4 (~10 mM) probably result from subcritical phase separation and thermal decomposition of sedimentary organic matter. Our insights from the Yokosuka site implies that although the distribution of vent animal species may be linked to depth, the constraint is perhaps not water pressure and resulting chemical properties of the vent fluid but instead physical properties of the surrounding seawater. <br /> <br /> Miyazaki J, Kawagucci S, Makabe A, Takahashi A, Kitada K, Torimoto J, Matsui Y, Tasumi E, Shibuya T, Nakamura K, Horai S, Sato S, Ishibashi J, Kanzaki H, Nakagawa S, Hirai M, Takaki Y, Okino K, Watanabe HK, Kumagai H, Chen C* (2017). Deepest and hottest hydrothermal activity in the Okinawa Trough: Yokosuka site at Yaeyama knoll. Royal Society Open Science, 4: 171570. http://dx.doi.org/10.1098/rsos.171570
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