Okinawa Churashima Foundation

The concept of the ecological niche, defined as the basic habitat requirements for a species, is central to understanding species geographic distributions and predicting their responses to environmental change. However, identifying the essential niche for large regional communities remains a challenge because niche axes can be "hidden" by the complexity of the underlying ecological processes. Here, applying advanced species distribution modelling to nationwide environmental DNA survey data, we identified hidden niche axes of the Japanese coastal fish community and investigated the response diversity to these axes. Our survey detected 1,220 coastal fish species. The hidden niche axes collectively explained most of the variation in fish biodiversity and revealed five biogeographic boundaries for the regional community. These niches of the Japanese fish community may primarily relate to several processes due to ocean currents, such as environmental filters, transport from source areas and dispersal barriers. We also found that the response diversity to niche axes was positively correlated with species richness, although local communities with particularly high response diversity were geographically biased. A better understanding of the niche axes of the regional ecological community should help to mitigate the loss of biodiversity and ecosystem services caused by ongoing environmental change.

Tail fluke loss in cetaceans compromises locomotion and impairs social functioning, posing serious welfare challenges. Rehabilitation strategies that address both physical performance and behavioral reintegration are essential for improving quality of life in affected individuals. This study evaluated the outcomes of a structured, two-phase rehabilitation program applied to Sami, an adult Indo-Pacific bottlenose dolphin (Tursiops aduncus) that underwent tail-fluke amputation, with an emphasis on locomotor function, behavioral adaptation, and long-term welfare. The rehabilitation protocol comprised two phases. Phase 1 focused on restoring vertical tail-beat locomotion through a combination of range-of-motion exercises and the use of a custom-designed prosthetic tail fluke. Swimming performance was quantitatively assessed using biologging devices under three conditions: without tail flukes, with the prosthetic tail, and in healthy conspecifics. Phase 2 introduced structured cohabitation with familiar individuals to promote social reintegration. Behavioral data were collected before and after rehabilitation to evaluate affiliative engagement and activity patterns. While maximum swim speed remained lower than in healthy individuals, propulsion per stroke significantly improved with prosthetic use. Notably, the subject dolphin retained species-typical vertical tail-beat motion even after prosthesis discontinuation, indicating motor pattern adaptation. Post-rehabilitation, affiliative behavior increased to 17% of total observed activity-more than twice that of a healthy control-while resting behavior markedly declined. No aggression or abnormal behaviors were observed. This study demonstrates that a welfare-centered, multi-phase rehabilitation framework can effectively promote both functional recovery and social reengagement in dolphins with severe caudal injuries. The long-term retention of adaptive locomotor and social behaviors highlights the potential of integrative approaches to enhance the quality of life in physically compromised cetaceans.

Scleractinian-specific eDNA metabarcoding (eDNA-M), based on amplification of mitochondrial 12S rDNA, has become an effective tool for comprehensive monitoring of zooxanthellate scleractinians at the generic level, but several questions remain about its efficiency. Taking advantage of coral culturing tanks at Okinawa Churaumi Aquarium, Japan, we examined the robustness of this metabarcoding technique. Our eDNA-M system can theoretically identify 53 scleractinian genera. Without knowing genera and numbers of colonies in a large, indoor exhibition tank, eDNA-M identified 29 genera in tank effluent and one genus that requires further bioinformatic improvement for detection. Later, aquarium staff informed us that the tank contains 37 genera. Colony numbers in the tank were also provided. Tank population data revealed that mitochondrial 12S rDNA of the seven missing genera had not been sequenced yet. Those seven taxa were sequenced thereafter, with the result that at the end, 36 of the 37 genera were identified. Even three genera with only one colony in the tank were detected. Surveys of outdoor culture tanks yielded comparable results, with additional genera that may have been detected due to contamination in incurrent natural seawater. We conclude that this scleractinian-specific eDNA metabarcoding is robust for coral monitoring, although further mitochondrial 12S rDNA sequences are needed for additional scleractinian genera.

ABSTRACT Environmental DNA (eDNA) metabarcoding is rapidly becoming an effective tool for biodiversity assessments. However, for taxa such as mesophotic and deep‐sea octocorals, which are difficult to classify based on morphological and molecular grounds and are logistically challenging to sample using conventional SCUBA diving, accurately identified and curated specimens in biological repositories remain under‐represented. This limitation reduces the availability of reliable reference sequences for eDNA detection. Mesophotic and deep‐sea octocorals are key components of mesophotic and cold‐water coral ecosystems that occur at depths > 30 m. Because these habitats are highly vulnerable to anthropogenic disturbances, the ability to monitor them effectively is imperative. This study aimed to expand the 28S rRNA reference database for mesophotic and deep‐sea octocorals in the western Pacific Ocean. A total of 269 samples were sequenced using either Sanger sequencing or low‐coverage genome skimming. Based on expert morphological identifications, the dataset comprised 52 genera spanning 24 families and two orders. Detailed metadata for all samples are provided, including DDBJ accession numbers, sampling locations, depths, collection dates, and repository information. These resources will strengthen biodiversity monitoring and support the conservation of mesophotic and cold‐water coral ecosystems. The detailed metadata and complete dataset are available in MetaCat in JaLTER at https://doi.org/10.20783/DIAS.JLE.91 .

ABSTRACT The barnacle genus Platylepas contains obligate epibionts of marine vertebrates, but the taxonomic status and evolutionary history of the sea-snake specialist, P. ophiophilus , has remained unclear. Here, we reassess the systematics of the genus through an integrative approach, combining morphological examinations with molecular phylogenetic analyses of mitochondrial COI and nuclear H3 genes from specimens collected from sea turtles, sea snakes, and a dugong. Our results unequivocally demonstrate that P. ophiophilus is a valid species, phylogenetically and morphologically distinct from the widespread turtle barnacle, P. hexastylos . Furthermore, we report the first record of P. ophiophilus from a sirenian host ( Dugong dugon ), a discovery that necessitates the re-examination of historical records of barnacles on sirenians worldwide. Our phylogeny places P. decorata , a turtle epibiont, as the earliest diverging lineage within the genus. This strongly suggests that the ancestor of Platylepas was associated with sea turtles, a conclusion supported by the ichnofossil record. The subsequent divergence of the P. ophiophilus clade represents a major macroevolutionary event: an ancient host shift from sea turtles to the taxonomically disparate but ecologically linked inhabitants—sea snakes and sirenians—of seagrass ecosystems. This study not only resolves a long-standing taxonomic problem but also provides a compelling narrative of host-switching that reconciles deep molecular divergence estimates with the sparse body fossil record for this fascinating group of marine symbionts.

Herein, we describe a new species in the genus Hemicorallium Gray, 1867 (Coralliidae), H. ryukyuense sp. nov. An almost complete colony was found at a depth of 860 m approximately 10 km east of Okinawa Island. The colony was identified through the visual and microscopic observations of standard morphological characteristics, including colony size, the diameters of colony base and branches, the diameter and height of autozooid mounds, coenenchyme thickness, and sclerite sizes. The specimen is characterized by large autozooid mounds (1.1–2.0 mm in diameter) and a pinkish-to-reddish cortex and axis. A distinctive feature of this specimen is the absence of commensal burrows on the axis. This is the first described species of precious coral with the Ryukyu Islands as its type locality. Pairwise genetic distances indicate that H. ryukyuense constitutes a distinct evolutionary lineage. However, tree topologies differed among loci, and the interspecific distances within Hemicorallium were smaller than the divergence observed between Pleurocorallium elatius (Ridley, 1882) and P. konojoi (Kishinouye, 1903). Consequently, population-level genomic data will be needed to confirm the species status of H. ryukyuense with greater confidence.

During a recent deep-sea survey around the Okinawa Islands in the Ryukyu Archipelago, southern Japan, two species of commensal gobies, Lobulogobius omanensis Koumans, 1944 and Pleurosicya annandalei Hornell and Fowler, 1922, were observed using remotely operated vehicles (ROVs) on or within marine invertebrates at depths of 95–110 m, and were subsequently collected. This represents the first record of these two species in Japan. This study provides a detailed morphological description of the specimens, including their coloration when alive and fresh. DNA analysis was also performed to further characterize these species. The integration of morphological and genetic approaches is essential for the accurate identification of newly discovered species, particularly in underexplored deep-sea environments.

Monogenean flatworms are pathogenic parasites that infect the skin of marine fish and pose a major problem in aquaculture and aquarium industries. Freshwater baths are the most commonly used method to treat these infections. However, this method is not suitable for certain fish taxa, including hagfish (Agnatha: Myxiniformes: Myxinidae), which have low tolerance to hypoosmotic environments.In the present study, we developed a treatment fluid specifically for use in hagfish. The fluid was prepared by dissolving urea in a mixture of chlorine-free tap water and seawater. A 5-min bath of three captive purple hagfish in the fluid successfully eliminated the parasites, with no apparent side effects. To date, this is the only known effective treatment for monogenean infections in hagfish.•In this study, we developed a method to treat monogenean infections in hagfish.•This method uses a fluid containing a high concentration of urea.•Bathing infected hagfish in the fluid successfully eliminated the parasites without apparent side effects.

Abstract The holotype specimen holds the most authentic characteristics of a species; its features will serve as a foundation for the identification of individuals belonging to this species. The precious coral Pleurocorallium secundum was described in 1846 based on a colony from the Hawaiian Islands. This specimen has been preserved; however, it is decorticated and contains exclusively the axial skeleton, which has hindered its use for accurate species identification. Therefore, the species was redescribed in 1956 based on two lots collected in 1902. Pleurocorallium secundum was considered the most frequently fished precious coral species in the second half of the twentieth century with landings on the total scale of hundred-thousand kilograms, which was followed by its listing on CITES Appendix III. Recently, the conspecificity of the holotype and redescribed colonies was questioned, and specimens labeled in the scientific literature as P. secundum were discovered to be phylogenetically distant from each other. To clarify the identity of P. secundum, we took minimally destructive samples from the century-old holotype and fragments of redescribed colonies and applied techniques conforming to low copy number DNA analyses. DNA sequences of three mitochondrial regions were evaluated in a phylogenetic framework together with DNA sequences retrieved from freshly collected putative P. secundum specimens and sequences from the scientific literature. The results of this study clearly indicate that the holotype and the colony fragments used for the redescription of P. secundum represent the same species. Based on the specimens confirmed to be P. secundum with genetic evidence, the distribution area of P. secundum stretches from the Hawaiian Islands to the South China Sea. At the same time, our analysis uncovered both published and fresh specimens that are in fact not P. secundum. The latter includes the fished Makapuu coral bed in Hawaii, which used to be a significant coral fishing area. Based on the microscopic analysis of redescribed colony fragments, we complement the diagnosis of P. secundum. This, together with our genetic results will aid the identification of coral objects present in the international jewelry trade by providing authentic molecular barcoding markers and morphologic features for the identification of P. secundum.