Discovery and Genetic Characterization of a Vestimentiferan, Lamellibrachia satsuma, from the Submarine Volcano Omuro Dashi in the Izu-Ogasawara Arc.

Vestimentiferan tube worms (Annelida: Siboglinidae) were discovered in a hydrothermal field at a depth of 195 m in the crater of the submarine volcano Omuro Dashi in the Izu-Ogasawara Arc. Based on the nucleotide sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene in individuals sampled in 2022, they were identified as Lamellibrachia satsuma Miura, Tsukahara & Hashimoto, 1997. STRUCTURE analysis and discriminant analysis of principal components (DAPC) based on 14 microsatellite markers showed a large genetic deviation of the population of Omuro Dashi from those of Kagoshima Bay and the north Mariana Arc (the Nikko and Daikoku Seamounts), whereas the population of Omuro Dashi did not show significant genetic deviation from that of the Nikko Seamount based on the COI gene. All analyses showed that individuals of a methane seep area on the Kanasu-No-Se Bank, the Nankai Trough, which were collected only in 1994, were more closely related to those of Omuro Dashi than to those of other habitats. These results suggest that the ancestors of the Omuro Dashi and Nankai Trough populations originated from migrants from the north Mariana Arc and that there might be undiscovered source population(s) of L. satsuma around the Nankai Trough.

Reproductive Isolation and a Change in the Development Mode of the Tideland Snail Batillaria flectosiphonata (Gastropoda: Batillariidae).

Microsatellite analyses of sympatric populations of a tideland snail endemic to the Nansei Islands, Japan, Batillaria flectosiphonata, and its sister species, Batillaria multiformis, from a tideland on Amami-Oshima Island, indicated that the two species are reproductively isolated from each other, confirming the validity of B. flectosiphonata, whose monophyly was supported only by a low bootstrap probability in the previous molecular phylogenetic analysis. Egg capsules of B. flectosiphonata from Tokunoshima Island of the Amami insular group and Okinawajima Island of the Okinawa insular group were examined, which revealed that this species is a direct developer. Thus, the direct development has evolved twice within batillariids in Japanese waters. The lower genetic diversity of B. flectosiphonata than that of B. multiformis in the sympatric habitat might be attributed to its long-term isolation within the Amami insular group.

The complete mitochondrial genome of the sand bubbler crab Scopimera globosa and its phylogenetic position.

The mitochondrial genome has become commonly used for the molecular phylogenetic analysis of animals. Most phylogenetic studies on brachyurans using mitogenome sequences have indicated the paraphyly of superfamilies Grapsoidea and Ocypodoidea but taxon sampling remains limited. The phylogenetic position of Scopimera has been tested in several previous studies using nuclear and/or mitochondrial DNA sequences, but the phylogenetic relationship within the family remains to be resolved. We newly sequenced the complete mitochondrial genome of the sand bubbler crab Scopimera globosa (Ocypodoidea: Dotillidae). Scopimera globosa was clustered with Ilyoplax despite the morphological similarity between Scopimera and Dotilla. The mitochondrial gene order of S. globosa was unique, whereas that of other genera in the family was the same. These results suggest that phylogenetic analysis based on mitogenome sequences and gene order comparison would provide a more robust phylogeny of Dotillidae.

Cryptic Speciation of a Deep-Sea Demersal Fish of the Genus Bothrocara in the Japan Sea.

Deep-sea demersal fishes of the Bothrocara hollandi species complex are distributed in the Japan Sea, the Okhotsk Sea, and the northwestern Pacific Ocean. Based on the nucleotide sequences of the nuclear Internal Transcribed Spacer 1 (ITS1) region and the microsatellite analysis, cryptic speciation resulting in the existence of two species (sp. 1 and sp. 2) in the Japan Sea was indicated for this species complex. In the Japan Sea off the San-in district, the westernmost part of the Japanese mainland, the frequency of sp. 2 individuals was highest at a depth of ∼400 m and decreased at both greater and lesser depths. Complete genetic deviation was observed between the individuals of the Japan Sea and the other sea areas, with the exception of a single sp. 2 individual, which shared an ITS1 sequence with an individual from the Pacific Ocean. Furthermore, a microsatellite analysis showed that the individuals of the other sea areas were more closely related to sp. 2 individuals. Two species were thought to have deviated from each other after their isolation from the individuals of the sea areas outside of the Japan Sea, through the occurrence of habitat fragmentation and bottleneck events in the Japan Sea during the glacial periods. Group A, one of two mitochondrial haplotype groups that were reported for the Japan Sea individuals in the previous studies, may have evolved within the lineages of sp. 2.

Inbreeding between Deep-Sea Snailfishes Careproctus pellucidus and Careproctus rastrinus in the Northwestern Pacific Ocean.

Genetic deviation between two deep-sea snailfishes, Careproctus pellucidus from the Pacific Ocean and Careproctus rastrinus from the Okhotsk Sea, of the Careproctus rastrinus species complex was analyzed, based on the nucleotide sequences of the mitochondrial cytochrome b (Cytb) gene. Our sampling revealed the occurrence of individuals with C. rastrinus-type Cytb genes off northeastern Japan, in the northwestern Pacific. Most of these individuals were collected from an area off Miyagi Prefecture, while few individuals were collected from areas to its north (off Iwate Prefecture) and south (off Fukushima and Ibaraki Prefectures). Phylogeographic analyses based on nucleotide sequences of the first intron region of the nuclear S7 ribosomal protein gene (S7) and 11 microsatellite loci indicated little genetic deviation between individuals with C. pellucidus-type and C. rastrinus-type Cytb genes in the area off Miyagi Prefecture. Significant genetic differences between the Pacific Ocean and the Okhotsk Sea populations may be attributed to unidirectional migration due to a greater current from the latter to the former. In addition, peritoneum and stomach colors of 10 and 17 specimens collected from the Pacific Ocean and the Okhotsk Sea, respectively, were evaluated quantitatively. The colors were significantly different for the two populations; however, they appeared to overlap. Although only one Pacific individual with a C. rastrinus-type Cytb gene was available for color evaluation, it was more similar to Pacific individuals than to Okhotsk Sea individuals. These results suggest inbreeding between C. pellucidus and C. rastrinus in the Pacific Ocean, off Miyagi Prefecture.

Molecular phylogeny of Maldanidae (Annelida): Multiple losses of tube-capping plates and evolutionary shifts in habitat depth.

Inter-familial relationships of the phylum Annelida have been widely studied using molecular phylogenetic/genomic approaches; however, intra-familial relationships remain scarcely investigated in most annelid families. The Maldanidae (bamboo worms) comprise more than 280 species of 40 genera and six subfamilies that occur in various environments from intertidal to hadal zones. Within this family, the taxon Maldanoplaca, which consists of four subfamilies (Maldaninae, Notoproctinae, Nicomachinae, and Euclymeninae), was proposed based on the presence of cephalic and anal plates. Phylogenetic relationships within the family remain largely undetermined based on molecular data. In this study, we reconstructed a molecular phylogeny using 52 maldanid species from six subfamilies based on two nuclear genes (18S rDNA and 28S rDNA) and two mitochondrial genes (16S rDNA and COI). Our analysis confirmed the monophyly of the subfamilies Rhodininae, Maldaninae, Lumbriclymeninae, and Nicomachinae, but neither Maldanoplaca nor the subfamily Euclymeninae were recovered as monophyletic. Nicomachinae was clustered within Euclymeninae. Ancestral state reconstruction suggested that cephalic plates were lost at least three times, despite the functional importance of capping tubes, and that anal plates were lost once. Mapping habitat depth on the phylogenetic tree suggested that habitat shifts among depth zones frequently occurred in distinct maldanid lineages.

Do larvae from deep-sea hydrothermal vents disperse in surface waters?

Larval dispersal significantly contributes to the geographic distribution, population dynamics, and evolutionary processes of animals endemic to deep-sea hydrothermal vents. Little is known as to the extent that their larvae migrate vertically to shallower waters and experience stronger currents and richer food supplies. Here, we first provide evidence from early life-history traits and population genetics for the surface dispersal of a vent species. Planktotrophic larvae of a red blood limpet, Shinkailepas myojinensis (Gastropoda: Neritimorpha: Phenacolepadidae), were cultured to observe their swimming behavior and to evaluate the effects of temperature on survival and growth. In addition, the population structure was analyzed based on 1.2-kbp mitochondrial DNA sequences from 77 specimens that cover the geographic and bathymetric distributions of the species (northwest Pacific, 442-1,227 m in depth). Hatched larvae constantly swam upward at 16.6-44.2 mm/min depending on temperature. Vertical migration from hydrothermal vents to the surface, calculated to take ~4-43 d, is attainable given their lengthy survival time without feeding. Fed larvae best survived and grew at 25°C (followed by 20°C), which approximates the sea surface temperature in the geographic range of the species. Little or no growth was observed at the temperature of the vent habitat where adult limpets occur (≤15°C). Population genetic analyses showed no differentiation among localities that are <1,350 km apart. The larvae of S. myojinensis most likely migrate to the surface water, where high phytoplankton biomass and strong currents enable their growth and long distance dispersal over many months. Sea surface temperature may represent a critical factor in determining the geographic distribution of many vent endemic species with a planktotrophic early development, and in turn the faunal composition of individual vent sites and regions.

Contrasting population histories of the deep-sea demersal fish, Lycodes matsubarai, in the Sea of Japan and the Sea of Okhotsk.

Recent studies have revealed the impact of the drastic climate change during the last glacial period on coastal marine and anadromous species in the marginal seas of the northwestern Pacific Ocean; however, its influence on deep-sea species remains poorly understood. To compare the effects of the last glacial period on populations from the Sea of Japan and the Sea of Okhotsk, we examined the mitochondrial control region and cytochrome b gene sequences of Lycodes matsubarai, a deepsea demersal fish that inhabits these two seas. Our results showed clear genetic differentiation of populations between the two seas. The populations may have diverged during the last glacial period, probably as a result of vicariance due to the drastic sea level change. The population in the Sea of Okhotsk was larger than that in the Sea of Japan, but suddenly decreased after the last glacial period. However, the Sea of Japan population expanded after the last glacial period, coincident with high levels of oxygenation in deep-sea areas. These results elucidate regional-scale impacts of climate change on deep-sea organisms.

Determination of extremely high pressure tolerance of brine shrimp larvae by using a new pressure chamber system.

Hydrostatic pressure is the only one of a range of environmental parameters (water temperature, salinity, light availability, and so on) that increases in proportion with depth. Pressure tolerance is therefore essential to understand the foundation of populations and current diversity of faunal compositions at various depths. In the present study, we used a newly developed pressure chamber system to examine changes in larval activity of the salt-lake crustacean, Artemia franciscana, in response to a range of hydrostatic pressures. We showed that A. franciscana larvae were able to survive for a short period at pressures of ≤ 60 MPa (approximately equal to the pressure of 6000 m deep). At a pressure of > 20 MPa, larval motor ability was suppressed, but not lost. Meanwhile, at a pressure of > 40 MPa, some of the larval motor ability was lost without recovery after decompression. For all experiments, discordance of movement and timing between right and left appendages, was observed at pressures of > 20 MPa. Our results indicate that the limit of pressure for sustaining active behavior of A. franciscana larvae is ∼20 MPa, whereas the limit of pressure for survival is within the range 30-60 MPa. Thus, members of the genus Artemia possess the ability to resist a higher range of pressures than their natural habitat depth. Our findings demonstrated an example of an organism capable of invading deeper environment in terms of physical pressure tolerance, and indicate the need and importance of pressure study as an experimental method.

Geographic Distribution and Genetic Structures of the Tideland Snails Pirenella nipponica and P.asiatica in Taiwan and Japan.

The tideland snails Pirenellanipponica and Pirenellaasiatica are distributed north of the central Ryukyu Islands and in South Ryukyu, respectively, in Japan. To reveal their distribution and genetic characteristics in Taiwan, we sampled Pirenella snails along the western coast of Taiwan Island and analyzed the nucleotide sequences of their mitochondrial DNAs. Pirenella nipponica and P. asiatica inhabit the northern and southern parts of the western coast of Taiwan, respectively, and coexist only in the central part. Taiwanese and Japanese populations of P. asiatica showed significant genetic differentiation. The former showed higher genetic diversity and a larger effective population size than the latter. However, the Taiwanese population of P. nipponica was not genetically deviated from the local Japanese population on Kyushu Island. Both the Taiwan and Kyushu populations of P. nipponica showed significant genetic differences from local populations in other regions of Japan, namely, Honshu Island (the Japanese mainland) and Central Ryukyu. They also showed higher genetic diversity and a larger effective population size than the others. The Taiwanese populations of both species might be part of a large panmictic population with individuals from the Asian continent and Kyushu Island.

Possible molecular mechanisms of species recognition by barnacle larvae inferred from multi-specific sequencing analysis of proteinaceous settlement-inducing pheromone.

Gregarious settlement is essential for reproduction and survival of many barnacles. A glycoprotein, settlement-inducing protein complex (SIPC) has been recognized as a signal for settlement and it is expressed in both conspecific adults and larvae. Although the settlement-inducing activities of SIPC are species-specific, the molecular-based mechanism by which larvae distinguish conspecific SIPC from the SIPC of other species is still unknown. Here, the complete primary structure of the SIPC of Megabalanus coccopoma, as well as the partial structure of the SIPCs of Balanus improvisus, Megabalanus rosa, and Elminius modestus are reported. These SIPCs contain highly variable regions that possibly modulate the affinity for the receptor, resulting in the species specificity of SIPC. In addition, the distribution patterns of potential N-glycosylation sites were seen to be different among the various species. Differences in such post-translational modifications may contribute to the species specificity of SIPC.

Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species.

Mitogenomes are useful for inferring phylogenetic relationships between organisms. Although the mitogenomes of Annelida, one of the most morphologically and ecologically diverse metazoan groups have been well sequenced, those of several families remain unexamined. This study determined the first mitogenome from the family Travisiidae (Travisia sanrikuensis), analyzed its mitogenomic features, and reconstructed a phylogeny of Sedentaria. The monophyly of the Terebellida + Arenicolida + Travisiidae clade is supported by molecular phylogenetic analysis. The placement of Travisiidae is unclear because of the lack of mitogenomes from closely related lineages. An unexpected intron appeared within the cox1 gene of T. sanrikuensis and in the same positions of five undescribed Travisia spp. Although the introns are shorter (790-1386 bp) than other group II introns, they can be considered degenerate group II introns due to type II intron maturase open reading frames, found in two of the examined species, and motifs characteristic of group II introns. This is likely the first known case in metazoans where mitochondrial group II introns obtained by a common ancestor are conserved in several descendants. Insufficient evolutionary time for intron loss in Travisiidae, or undetermined mechanisms may have helped maintain the degenerate introns.

The mitochondrial genome of the threatened tideland snail Pirenella pupiformis (Mollusca: Caenogastropoda: Potamididae) determined by shotgun sequencing.

The nearly complete mitochondrial genome of the threatened tideland snail Pirenella pupiformis (Mollusca: Cerithioidea: Potamididae) was determined by shotgun next-generation sequencing. The mitogenome is comprised of 13 protein-coding genes (PCGs), two ribosomal RNA (12S and 16S) genes, and 22 transfer RNA genes (tRNAs). This gene order is consistent with the previously published mitochondrial genomes of other species belonging to the family Potamididae. The family Potamididae including P. pupiformis was recovered as a monophyletic group in the superfamily Cerithioidea.

Extensive mitochondrial genome rearrangements between Cerithioidea and Hypsogastropoda (Mollusca; Caenogastropoda) as determined from the partial nucleotide sequences of the mitochondrial DNA of Cerithidea djadjariensis and Batillaria cumingi.

Partial nucleotide sequences ( approximately 8000 bp) of the mitochondrial DNA of two cerithioidean gastropod species-Cerithidea djadjariensis and Batillaria cumingi-were determined. The order of mitochondrial genes (eight protein genes, two ribosomal RNA genes, and nine transfer RNA genes) was identical between these two species. and remarkably different from the previously reported order in other gastropods. The results indicate that the genome structure of the common ancestor of Cerithioidea and its sister group, Hypsogastropoda, is almost identical to that of the common ancestor of Gastropoda; moreover, independent mitochondrial genome rearrangements were identified between the lineages of Cerithioidea and Hypsogastropoda. The rearrangements within Cerithioidea can be explained by the inversion of a single tRNA gene, two translocations of a single tRNA gene, and three translocations of a genome fragment containing a tRNA gene and protein-coding gene(s).

Food sources are more important than biomagnification on mercury bioaccumulation in marine fishes.

Marine animals often accumulate various harmful substances through the foods they ingest. The bioaccumulation levels of these harmful substances are affected by the degrees of pollution in the food and of biomagnification; however, which of these sources is more important is not well-investigated for mercury (Hg) bioaccumulation. Here we addressed this issue in fishes that inhabit the waters around Minamata Bay, located off the west coast of Kyushu Island in Kumamoto Prefecture, Japan. The total Hg concentration (hereafter [THg]) and carbon and nitrogen stable isotope ratios (δ13C and δ15N) were analyzed in the muscle tissue of 10 fish species, of which more than five individuals were caught by gillnet. Except one species, each was separated into two trophic groups with respective lower and higher δ13C values ranging from -17‰ to -16‰ and -15‰ to -14‰, which suggested that the fishes depended more on either phytoplankton- and microphytobenthos-derived foods (i.e., pelagic and benthic trophic pathways), respectively. Linear mixed effects models showed that the Hg levels were significantly associated with both δ15N and the differences in the trophic groups. [THg] increased with δ15N (i.e., indicative of higher trophic levels), but the slopes did not differ between the two trophic groups. [THg] was significantly higher in the group with higher δ13C values than in those with lower δ13C values. The effect size from marginal R squared (R2) values showed that the variation in [THg] was strongly ascribed to the trophic group difference rather than δ15N. These results suggest that the substantial Hg bioaccumulation in the fishes of Minamata Bay is mainly an effect of ingesting the microphytobenthos-derived foods that contain Hg, and that the subsequent biomagnification is secondary.

Population history of deep-sea vent and seep Provanna snails (Mollusca: Abyssochrysoidea) in the northwestern Pacific.

BACKGROUND: Gastropods of the genus Provanna are abundant and widely distributed in deep-sea chemosynthetic environments with seven extant species described in the northwestern Pacific. METHODS: 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. RESULTS: 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). DISCUSSION: Environmental differences, especially depth, appears to have a role in the segregation of Provanna snails. The population of P. clathrata in the Irabu Knoll appears to have expanded after P. subglabra population. The remaining three species, P. lucida, P. kuroshimensis, and P. glabra, are only known from a single site each, all of which were shallower than 1,000 m. These data indicate that Provanna gastropods are vertically segregated, and that their population characteristics likely depend on hydrothermal activities.

The complete mitochondrial genome of the longfin dragonfish Tactostoma macropus (Stomiiformes: Stomiidae).

The complete mitochondrial genome (mitogenome) was determined for the longfin dragonfish Tactostoma macropus, which is the first for the genus and the third within the family Stomiidae. The mitogenome sequence is 17,690 bp in length containing 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and a control region, as in most fishes. The gene order of T. macropus showed an unreported deviation from the typical vertebrate one. Phylogenetic reconstruction using the maximum likelihood method placed T. macropus in the monophyletic Stomiiformes. Three stomiid species were recovered as a moderately supported clade in the phylogenetic tree.

Ecological and genetic impact of the 2011 Tohoku Earthquake Tsunami on intertidal mud snails.

Natural disturbances often destroy local populations and can considerably affect the genetic properties of these populations. The 2011 Tohoku Earthquake Tsunami greatly damaged local populations of various coastal organisms, including the mud snail Batillaria attramentaria, which was an abundant macroinvertebrate on the tidal flats in the Tohoku region. To evaluate the impact of the tsunami on the ecology and population genetic properties of these snails, we monitored the density, shell size, and microsatellite DNA variation of B. attramentaria for more than ten years (2005-2015) throughout the disturbance event. We found that the density of snails declined immediately after the tsunami. Bayesian inference of the genetically effective population size (Ne) demonstrated that the Ne declined by 60-99% at the study sites exposed to the tsunami. However, we found that their genetic diversity was not significantly reduced after the tsunami. The maintenance of genetic diversity is essential for long-term survival of local populations, and thus, the observed genetic robustness could play a key role in the persistence of snail populations in this region which has been devastated by similar tsunamis every 500-800 years. Our findings have significant implications for understanding the sustainability of populations damaged by natural disturbances.

Endemicity of the cosmopolitan mesophilic chemolithoautotroph Sulfurimonas at deep-sea hydrothermal vents.

Rich animal and microbial communities have been found at deep-sea hydrothermal vents. Although the biogeography of vent macrofauna is well understood, the corresponding knowledge about vent microbial biogeography is lacking. Here, we apply the multilocus sequence analysis (MLSA) to assess the genetic variation of 109 Sulfurimonas strains with ⩾98% 16S rRNA gene sequence similarity, which were isolated from four different geographical regions (Okinawa Trough (OT), Mariana Volcanic Arc and Trough (MVAT), Central Indian Ridge (CIR) and Mid-Atlantic Ridge (MAR)). Sequence typing based on 11 protein-coding genes revealed high genetic variation, including some allele types that are widespread within regions, resulting in 102 nucleotide sequence types (STs). This genetic variation was predominantly due to mutation rather than recombination. Phylogenetic analysis of the 11 concatenated genes showed a clear geographical isolation corresponding to the hydrothermal regions they originated from, suggesting limited dispersal. Genetic differentiation among Sulfurimonas populations was primarily influenced by geographical distance rather than gas composition of vent fluid or habitat, although in situ environmental conditions of each microhabitat could not be examined. Nevertheless, Sulfurimonas may possess a higher dispersal capability compared with deep-sea hydrothermal vent thermophiles. This is the first report on MLSA of deep-sea hydrothermal vent Epsilonproteobacteria, which is indicative of allopatric speciation.

Synonymy of Calyptogena solidissima with Calyptogena kawamurai (Bivalvia: Vesicomyidae) and its population structure revealed by mitochondrial DNA sequences.

Nucleotide sequences of part (1,101 bp) of the mitochondrial cytochrome oxidase c subunit I (COI) gene were determined for two specimens of Calyptogena kawamurai collected in Kashima Nada and Suruga Bay, respectively. These sequences were identical to each other and to those from many individuals of Calyptogena solidissima, i.e., 11 of 12 specimens from a seep area in Nankai Trough, two of 20 from hydrothermal-vent fields in Okinawa Trough, and one of 14 from a seep area on Kuroshima Knoll. The nucleotide sequences of the 5' part (about 700 bp) of the first internal transcribed spacer (ITS-1) also showed a close relationship between C. kawamurai and C. solidissima. The radiating threads on the shell surface that were emphasized in describing C. solidissima are not consistent throughout these local populations. Variation in cardinal dentition was confirmed to be intraspecific by observations of a series of specimens. The shell length-height and shell length-width relationships of both species all fit a single regression line. These results suggest that C. solidissima is a junior synonym of C. kawamurai. The populations of Nankai Trough, Okinawa Trough, and Kuroshima Knoll were shown to be diverging genetically from each other. Populations of Okinawa Trough and Kuroshima Knoll are suggested to have derived independently from the most common haplotype of Nankai Trough.