Abstract Host genetic markers often fail to resolve regional origins in highly connected or panmictic marine species. The Japanese jack mackerel, Trachurus japonicus , is a commercially important fishery species around Japan that shows little or no detectable population structure. Here, we used nationwide multi-omics profiling to compare host genomic variation and gut microbiome composition in wild T. japonicus collected from coastal regions across Japan. We generated MIG-seq data for 43 individuals and 16S rRNA gene profiles for 24 individuals; after quality filtering, 19 individuals remained for matched host–microbiome comparison. Genome-wide host SNP analyses showed weak or absent geographic population structure, consistent with previous evidence of panmixia in Japanese waters. In contrast, gut microbiome composition showed geographic structuring based on Bray-Curtis dissimilarity and PERMANOVA, and this pattern was not explained by proximity to river mouths or host-related variables. Locality- or individual-associated bacterial lineages contributed to the observed differences in the microbiome, while chloroplast-associated and Cyanobacteria-assigned ASVs suggested recent dietary or environmental input. These results indicate that gut microbiome can show regional biological variation not apparent from host genetic markers alone. Our study provides a proof-of-concept example of integrating host genomics and gut microbiome profiling to evaluate regional characteristics and origins in highly connected marine animals. Importance Highly dispersive marine fishes can remain genetically homogeneous across broad regions while encountering strongly contrasting environments. This disconnect limits the ability of host genetic markers to detect regional biological variation and raises a fundamental question: can host-associated microbial communities retain spatial ecological information when host population structure is weak? Using Japanese jack mackerel collected across Japan, we found weak or absent geographic structuring in host SNPs but significant locality-related variation in gut microbiome composition. The microbial pattern included broadly distributed marine-fish-associated taxa together with locally or individually enriched lineages and dietary or plankton-associated signals. These findings show that host-associated microbiomes can respond to regional ecological exposure at spatial scales not resolved by host population genomics. Beyond its potential for seafood traceability, this study establishes a framework for examining how environmental heterogeneity is recorded in animal-associated microbiomes under high host gene flow.

Argonautid octopods (genus Argonauta) possess a unique shell-like biomineralized eggcase, which was suggested to be produced by the first dorsal arms rather than by the mantle tissue, as in typical molluscan shells. In this study, we conducted scanning electron microscopy to investigate the microstructures of both undamaged and post-repair eggcases. Our analysis revealed that a normal eggcase comprises five layers: an outermost organic membrane, an outer spherulitic-fibrous prismatic layer, a middle organic layer, an inner spherulitic-fibrous prismatic layer, and an innermost organic membrane. Both prismatic layers exhibit bidirectional growth from the middle organic layer, a unique feature not observed in typical molluscan shells but, intriguingly, resembles the microstructures of cuttlefish cuttlebones, stony coral calcareous skeletons, and avian eggshells, indicating possible convergence. We propose that the observed eggcase microstructure is formed in four stages: nucleation on the organic scaffold, bidirectional crystal growth from the organic mid-layer, crystal growth perpendicular to the eggcase surface, and organic membrane encapsulation. We also identified two possible repair mechanisms: reattachment of broken fragments and regeneration via new secretions. Our findings thus question the assumed role of the first dorsal arms in calcification. The eggcase also represents the formation of a complex extended phenotype through convergence.

The nautilus ( Nautilus sp.) is an early-branching cephalopod. It retains several conchiferan synapomorphies, including an external planispiral biomineralized shell. The shell's complex structure allows it to withstand hydrostatic pressure, control buoyancy, and protect against external hazards. In this study, we comprehensively examined shell microstructures across different shell components and regions representing various ontogenetic stages in two adult museum shell specimens. We found that the nautilus shell is composed of five microstructural types (spherulitic, prismatic, nacreous, semi-prismatic, and irregularly oriented prismatic structures) organized into layered architectures within individual shell components and coordinated across the shell as an integrated system. Our observations highlight transitions between distinct microstructures within and across shell components and local variation within individual components such as the dorsal and ventral shell walls, suggesting that these patterns may contribute to shell strength and overall mechanical performance. Variation in caecum morphology suggests that this structure may be developmentally plastic and subject to relatively relaxed structural constraints. These findings show that the Nautilus shell is an integrated biomineral system in which diverse microstructures are organized across shell components to meet functional demands and provide the mechanical strength needed for survival.

Ancient evolutionary transitions in animal chromosomal complements and their phenotypic impacts remain understudied. Few systems exist where these events can be dissected into individual steps. In coleoid cephalopods (octopus, squid, cuttlefish), an ancient coleoid chromosomal rearrangement event (ACCRE) resulted in a substantial increase in the chromosome number. However, the discrepancies between extant octopodiform (octopus, ∼30 chromosomes) and decapodiform (squid and cuttlefish, ∼46 chromosomes) karyotypes and the direction of this transition remain unexplained. Through sequencing of the basally branching octopodiform, the vampire squid Vampyroteuthis sp., we reveal its partial retention of the decapodiform karyotype. Together with the chromosome-level assembly of the pelagic octopod Argonauta hians, we show that modern octopod genomes were extensively shaped by chromosomal fusion-with-mixing followed by inter-chromosomal translocations. These irreversible processes have resulted in a more entangled genomic configuration in octopods. Our results offer broader insights into general patterns of chromosomal evolution following large-scale rearrangement in animal genomes.

Despite the rich diversity of marine gastropods, limited taxonomic investigations on edible species raise concerns regarding fisheries management and food safety in Vietnam. In this study, we employed iterative taxonomy by combining morphological identification and DNA barcoding using the COI, 12S-rRNA, 18S-rRNA, 28S-rRNA, and histone H3 gene markers, to confirm the taxonomy of 126 marine gastropod museum specimens collected from various fish markets in Vietnam. Morphological identification assigned 113 of the 126 specimens to 53 species. Sequences were obtained for all samples, although not all genes were successfully sequenced for every specimen. When all gene markers were used, 58 % in 2023 and 79 % in 2025 of the 113 samples were identified at the species level (excluding the morphologically unidentified individuals), compared to only 51 % in 2023 and 62 % in 2025 when only COI was used. The higher match rates in 2025 likely reflect ongoing improvements in public reference databases. Phylogenetic and genetic distance analyses supported these results, revealing monophyletic species and genera. This study revealed that >50 species are part of local diets, emphasizing the importance of fundamental biodiversity studies, including alpha taxonomic surveys, for managing marine gastropod fisheries and highlighting marine gastropods’ potential as novel food resources. By utilizing vouchered museum specimens, this study also contributes to developing a reliable reference database for identification and monitoring edible marine gastropods in Vietnam and Southeast Asia.

Argonautid octopods of the genus Argonauta possess a shell-like biomineralized external structure called an eggcase. A classical behavioral observation suggested that this structure is produced by the first dorsal arms rather than by the mantle tissue as seen in typical molluscan shells. In this study, we performed detailed microstructural analyses using scanning electron microscopy to investigate the characteristics of normal, undamaged eggcases and regions that had undergone post-damage repair. Our analysis revealed that the eggcase comprises five layers: an outermost organic membrane, an outer spherulitic-fibrous prismatic layer, a middle organic layer, an inner spherulitic-fibrous prismatic layer, and an innermost organic membrane. Both prismatic layers exhibit bidirectional growth from the middle organic layer, a unique feature not observed in typical molluscan shells. We propose a four-stage formation sequence to explain the observed microstructural architecture: nucleation on the organic scaffold, bidirectional crystal growth from the organic mid-layer, perpendicular growth relative to the eggcase surface, and final encapsulation by an organic membrane. Interestingly, the growth pattern and crystal shapes in the prismatic layers resemble of the internalized shells of cuttlefish, the calcified skeleton of stony corals, and avian eggshells, suggesting functional convergence. We also identified two repair mechanisms: reattachment of broken fragments and regeneration via new secretions. These findings call into question the previous assumptions about the role of the first dorsal arms in calcification. The eggcase also exemplifies the formation of a functionally and structurally complex extended phenotype through convergence. ### Competing Interest Statement The authors have declared no competing interest. Takeda Science Foundation Life Science Research Grants 2022 Grants-in-aid for Basic Research KIBAN-C, 19K12424, 23K11511, 22K06340 JST SPRING, Grant Sasakawa Scientific Research Grant, 2024-4101 KOSEN GEAR 5.0 of National Institute of Technology

The Japanese turban snail Lunella coreensis is sensitive to ocean currents due to its short pelagic larval stage and moderate dispersal ability, making it an ideal model for studying genetic diversity shaped by paleoclimatic shifts. In this study, we analyzed the mitochondrial genes COI and 12S of museum samples collected from various coasts across Japan and identified 10 haplogroups divided into Pacific Ocean and Japan Sea clades, influenced by Kuroshio and Tsushima currents. Divergence time estimates indicate radiation between 3000 and 77,000 yr ago, coinciding with the last ice age, supported by fossil evidence in Japan. Glaciation cycles likely caused genetic isolation and exchange. Rapid radiation between 18,000 and 1000 yr ago aligns with climatic changes during the last glacial maximum. Effective population size estimates indicate past bottlenecks. These findings reveal how historical environmental events shaped L. coreensis genetic diversity, laying the groundwork for future sclerochronological research on marine biodiversity.

In environmental conservation, mangrove forests play a crucial role. Retransplanting mangrove propagules, however, faces challenges, and success rates are notably low. Achieving an optimal protector for propagules, balancing strength without impeding growth, is challenging. Mangrove propagules require a temporary protector with an optimal balance, neither too weak nor too strong, to shield them from current waves which is difficult. We propose using pervious concrete pots with high-volume fly ash activated with low NaOH concentrations. The investigation focuses on the influence of the mixing procedure on workability, compressive strength, and mineral composition. The novel discovery in this study is the specific sequence of stirring the ingredients using an alkali activator, which adds an interesting dimension to the research. It is recommended to adopt Sequence 2 in pervious concrete production, where NaOH dissolved FA in the mixture forming albite as N-A-S-H gel product. It surely enhanced both workability and the strength confirming uniform application processes. The two recommended variants, PFS-60 and PFBS-50, effectively utilize coal ash, meeting the target compressive strength range of 3-5 MPa and providing support for mangrove pots over a 3-4 year period. Notably, both compositions maintained consistent mechanical properties during exposure to tidal conditions for 240 days.They exhibit high permeability (694 liter/m²/minute), facilitating efficient water passage without sediment entrainment.

The use of seawater in cement-based concrete is debateable because it may increase the hydration rate but significantly decreases the durability. Alternately, seawater can be used as an alkaline activator solution in geopolymer however, very little is currently known about its effects. This study investigated the effect of seawater as alkaline activator mix solution and curing media on the compressive strength of geopolymer paste. The mixtures varied based on the molarity of alkaline activator solution. Alkaline activators were prepared with two solutions: diluted water and seawater. A day after casting, steam curing method was conducted at 65 degrees C for 2 hours and then immersed in seawater or normal water for 28 days. This study revealed that seawater in alkaline activator reduced the compressive strength by up to 25%. Applying temperature resulted the early age strength nearly comparable to the later age strength. Immersion the paste in seawater increased the strength up to 15%. The X-Ray diffraction analysis shown the presence of chloride on the surface, consequently preserving the compressive strength without any reduction at 28 days of immersion. The Scanning Electron Microscopy analysis inside the geopolymer paste prepared with seawater shown the microstructure of quartz, mullite, hematite, and the presence of chloride spread around resulting the disruption of polymerization. The results indicated that seawater has the potential as an alkaline activator mix solution and curing media, compensated by requirement of higher molarity of NaOH.

One of the distinguishing morphological features of conchiferan mollusks is the presence of a calcified exterior shell. Despite being conchiferans, most extant cephalopods have lost, internalized, or degraded their shells, with the exception of the basally divergent nautiloids. We compiled the shell matrix protein (SMP) data from several Nautilus pompilius studies and compared them with publicly available conchiferan SMP data, including those of Sepia pharaonis and Spirula spirula , two decapodiform cephalopods with internalized and partially internalized calcified shells, respectively. The recompilation of N. pompilius data revealed the presence of 85 distinct SMPs. Reciprocal homology searches suggested that N. pompilius shares 27 proteins known for their significant roles in shell formation and biomineralization, such as Pif/Pif-like, with other conchiferans. This is in agreement with our previous results, which suggested that the main functional domains of the SMPs in N. pompilius were also found in the conchiferans, suggesting that the domains were present in the ancestral conchiferans, with some recruited ancestrally, and some taxon-specifically. Meanwhile, 16 N. pompilius proteins are shared among the conchiferans, with only six proteins present in the cephalopods. indicating that some proteins were lost or co-opted in the course of their evolution. Three proteins shared among the conchiferans (CD109 antigen, Chitinase, and Tyrosinase) and one shared among the cephalopods (SOUL Domain-containing protein) apparently have dual functions of immunity and shell biomineralization. Intriguingly, four proteins are shared only between the two decapodiforms, indicating that they were co-opted in the decapodiform lineage with internalized shells.

The paper nautilus or greater argonaut, Argonauta argo, is a species of octopods which is characterized by its pelagic lifestyle and by the presence of a protective spiral-shaped shell-like eggcase in females. To reveal the genomic background of how the species adapted to the pelagic lifestyle and acquired its shell-like eggcase, we sequenced the draft genome of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters, and some gene clusters that could probably be related to the pelagic lifestyle, such as reflectin, tyrosinase, and opsin. The gene models also revealed several homologous genes related to calcified shell formation in Conchiferan mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the shell-less octopus, as well as Nautilus, which has a true outer shell. Therefore, the draft genome sequence of Arg. argo presented here has helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes to form an important, converging extended phenotypic structure such as the shell and the shell-like eggcase. Additionally, it allows us to explore the evolution of from benthic to pelagic lifestyles in cephalopods and octopods.

New specimens of Taeniogyrus japonicus (Marenzeller) were collected from Iwami coast and Sado island of the Sea of Japan. According to detailed observations of external and internal organs, we transferred T. japonicus, T. dendyi (Mortensen), and Scoliorhapis theelii (Heding) to the newly revived genus Scoliodota, with a large retractor organ and hook papillae as major diagnostic characters. We also concluded that Scoliorhapis dianthus Solis-marin et al. is a synonym of T. japonicus. Our molecular phylogeny and genetic distance analysis showed that specimens from Iwami and specimens from Sado of T. japonicus form a monophyletic clade, indicating that they are most likely the same species despite their morphological variation. The phylogenetic analysis also indicated that T. japonicus forms a sister group relationship with Taeniogyrus verruculosus Yamana & Tanaka and Scoliorhapis sesokoensis Yamana & Tanaka, suggesting that Taeniogyrus is not monophyletic. Taken together, these results brought new insights to sea cucumber diversity in Japanese waters.

Phenotypic plasticity in molluscan shell microstructures may be related to environmental changes. The “winter diffusion layer,” a shell microstructure of the Japanese pearl oyster Pinctada fucata, is an example of this phenomenon. In this study, we used P. fucata specimens with shared genetic background to evaluate the seasonal plasticity of shell microstructures, at molecular level. To detect the seasonal changes in shell microstructure and mineral composition, shells of multiple individuals were periodically collected and analyzed using scanning electron microscopy and Raman spectrophotometry. Our observations of the winter diffusion layer revealed that this irregular shell layer, located between the outer and middle shell layers, had a sphenoid shape in radial section. This distinct shape might be caused by the internal extension of the outer shell layer resulting from growth halts. The winter diffusion layer could be distinguished from the calcitic outer shell layer by its aragonitic components and microstructures. Moreover, the components of the winter diffusion layer were irregular simple prismatic (the outer and inner sublayers) and homogeneous structures (the middle sublayer). This irregular formation occurred until April, when the animals resumed their “normal” shell formation after hibernation. To check for a correlation between gene expression and the changes in microstructures, we conducted qPCR of seven major biomineralization-related shell matrix protein-coding genes (aspein, prismalin-14, msi7, msi60, nacrein, n16, and n19) in the shell-forming mantle tissue. Tissue samples were collected from the mantle edge (tissue secreting the outer shell layer) and mantle pallium (where the middle shell layer is constructed) of the same individuals used for microstructural observation and mineral identification that were collected in January (winter growth break period), April (irregular shell formation period), and August (normal shell formation period). Statistically significant differences in gene expression levels were observed between mantle edge and mantle pallium, but no seasonal differences were detected in the seasonal expression patterns of these genes. These results suggest that the formation of the irregular shell layer in P. fucata is caused by a currently unknown genetic mechanism unrelated to the genes targeted in the present study. Further studies using big data (transcriptomics and manipulation of gene expression) are required to answer the questions herein raised. Nevertheless, the results herein presented are essential to unravel the intriguing mystery of the formation of the winter diffusion layer, which may allow us to understand how marine mollusks adapt or acclimate to climate changes.

The patellogastropod limpet genus Nipponacmea is widely distributed in Japan and adjacent East Asia. Species identification within Nipponacmea is challenging due to the high variation in shell morphology. In this study, we examined the taxonomy of this genus represented by nine nominal species from 43 localities (including type localities). Results of the molecular phylogenetic analysis revealed that: (1) N. gloriosa , the sole species in this genus inhabiting the subtidal zone, represents the most basal independent branch; (2) the remaining species are divided into two large clades with lower- and higher-apex shell profiles; and (3) the high-apex morphology was derived from the low-apex type. The terminal clades defined using the molecular data were consistent with nine morphospecies and had 100% bootstrap values, strongly supporting the conventional taxonomy of Nipponacmea . Although morphological similarities do not always reflect phylogeny, the set of morphological characters used in the current taxonomy were proven to be adequate for diagnosis. In conclusion, this study provided solid evidence to uphold the monophyly of known species of Nipponacmea in Japan and demonstrated the usefulness of morphological characters for species diagnosis.

Recruitment of coral juveniles could serve as indicator for potential of coral reef recovery and is a critical process in supporting population as well as facilitating recovery after event of disturbance. However, sediments suspended in the water column and settling on to reef surface can negatively influence the distributions and abundances of reef-building corals, including altering the settlement patterns and survival of coral larvae and new recruits. In this study, we compared the density and diversity of Scleractinian recruits on natural substrate and artificial reef (made of concrete; 2 years after deployment) in the relatively turbid water of Sepulu coastal water, Bangkalan – Madura Island, East Java. Observation of stony coral recruits were conducted in-situ at depth of 3-4 meter in two locations. At the end of the study, we identified 18 species of Scleractinians from 10 genera and 7 families; dominated by Goniopora (F. Poritidae), Galaxea (F. Euphyllidae) and Goniastrea (F. Merulinidae). There was no difference in term of species richness and composition among locations and type of substrate. However, in both locations, more recruits grown in concrete artificial reef (15.2±2.61 - 18.3±2.91 unit/m 2 ) compared to natural substrate (4±1.25 - 4.1±1.29 unit/m 2 ), respectively. These findings suggest that concrete artificial reef is applicable for coral reef restoration and rehabilitation in temporary turbid coastal water by providing suitable substrate for larval recruitments.

A new dendrochirotid sea cucumber, Satsumaocnus kaiyomarui gen. nov., sp. nov. from deep water of southern Japan is herein described. The new species displays the following unique characters : a cylindrical, soft body; mouth surrounded by five oral valves; 10 equal, dendritic tentacles arranged in a single circle, each composed of two tufts; a low, stout, compact, calcareous ring without posterior prolongations; body wall ossicles comprising an external layer of small, x-framed hourglass-shaped cups originally described as "double-faced x-framed cup ossicles" in a previous study reported by Yamana et al. (2019), and an inner layer of scarce dendriform/branched rods, sometimes taking the shape of delicate plate-like deposits. Although the general (external and internal) morphological characters of the new species correspond well with the characters of species within the cucumariid subfamily Colochirinae Panning, 1949, our material lacks any buttons or elaborate plate-like ossicles which characterize all extant genera within this subfamily. We, therefore, describe our material as a new species S. kaiyomarui sp. nov. within the new genus Satsumaocnus. The predominant body wall deposits of the new species strongly resemble the hourglass type ossicles of some species of the psolid genus Lissothuria (Verrill, 1867), but differ in their possession of a supporting x-shaped frame. In addition, it is noteworthy that these hourglass deposits also resemble the table ossicles of some holothuriids and stichopodids, when viewed from the side, especially the small tables of some Labidodemas and/or Stichopus species, while the dendriform rods resemble those of Thelenota.

The full mitogenome of an ethanol-preserved museum specimen of Ceramaster japonicus was determined using the NGS Illumina MiSeq platform. The specimen was collected from Tosa Bay, Japan, facing the Pacific Ocean (33.0781 N 134.0601 E), at 700 m depth in 2011. The mitogenome shows a typical metazoan genomic structure, with all of the 37 genes included in its 16,370 base-long mitogenome. We conducted phylogenetic analyses using a data set including 18 publicly available asteroids rooted against five ophiuroids as outgroups. The result confirms the position of C. japonicus in the order Valvatida. The complete mitogenome of C. japonicus reported here is the first reported for the family Goniasteridae Forbes, 1841.