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.

First report of the mitogenome of the invasive reef-building polychaete Ficopomatus enigmaticus (Annelida: Serpulidae) and a cryptic lineage from the Japanese Archipelago.

BACKGROUND: The mitochondrial genomes (mitogenomes) of the family Serpulidae are characterized by a high nucleotide sequence divergence and a significant number of gene order rearrangements compared with other families within the phylum Annelida. However, only two of 50 genera of serpulids have mitogenomes already sequenced. In this study, we report the first sequencing and assembly of the complete mitogenome of Ficopomatus, thus providing further knowledge on mitochondrial gene sequences of Serpulidae. METHODS AND RESULTS: A mitogenome of the invasive reef-building polychaete Ficopomatus enigmaticus was amplified by long PCR and sequenced using the Illumina MiSeq System. It comprised 15,853 bp and consisted of 12 protein-coding genes (atp8 was not found), 23 tRNA, and two rRNA genes. The AT and GC skew values were infrequent when compared to annelid mitogenomes but similar to other serpulids sequenced to date (i.e., Spirobranchus and Hydroides). The mitochondrial gene order of F. enigmaticus was highly rearranged compared to other serpulids. To amplify 16S rRNA gene sequences, we developed a 16S rRNA primer set by modifying the universal primer set 16SarL/16SbrH. We detected the 16S rRNA sequence of F. enigmaticus deposited in GenBank erroneously characterized as of serpulid origin. We reported for the first time the presence of two lineages of F. enigmaticus in Japan, which have already been identified in California, Australia, and the Mediterranean. CONCLUSIONS: The first mitochondrial genome of F. enigmaticus showed a unique gene order rearrangement, corroborating the remarkable diversity in the previously reported mitogenomes of other serpulid species. The presence of the two lineages of F. enigmaticus identified for the first time in Japan represents another case of cryptic invasion. The first 16S rRNA gene sequences of F. enigmaticus obtained in the present study can be used as reference sequences in future DNA metabarcoding studies.

Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes.

Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.

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 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.

First mitochondrial genomes of Capitellidae and Opheliidae (Annelida) and their phylogenetic placement.

The complete mitochondrial genomes of Notomastus sp. (15,776 bp) (Annelida: Capitellidae) and Armandia sp. (18,538 bp) (Annelida: Opheliidae) were assembled for the first time. A group II intron (303 bp) was found in cox1 of Notomastus sp. A phylogenetic analysis revealed that Notomastus sp. and Armandia sp. were monophyletic, and this clade was clustered with echiurans, although the possibility of the effect of long-branch attraction should be considered.

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 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.

The mitochondrial genome and phylogenetic position of a marine snail Nerita (Heminerita) japonica (Gastropoda: Neritimorpha: Neritidae).

The mitochondrial genome of the neritid snail Nerita (Heminerita) japonica (Mollusca: Neritimorpha) from Kumamoto, Japan was determined by whole-genome sequencing. This mitogenome is comprised of 13 protein-coding genes, 2 ribosomal RNA (12S and 16S) genes, and 22 transfer RNA genes, with the same gene order as in the other species of the family Neritidae. A likelihood-based phylogenetic reconstruction recovered the subgenus Heminerita (including N. japonica as its type and N. yoldii from China) as monophyletic and sister to a clade with four species of the subgenera Nerita and Theliostyla.

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.

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.

Prevalence and species richness of trematode parasites only partially recovers after the 2011 Tohoku, Japan, earthquake tsunami.

Trematode parasites have complex life cycles and use a variety of host species across different trophic levels. Thus, they can be used as indicators of disturbance and recovery of coastal ecosystems. Estuaries on the Pacific coast of northeastern Japan were heavily affected by the 2011 Tohoku earthquake tsunami. To evaluate the effect of the tsunami on the trematode community, we examined trematodes in the mud snail, Batillaria attramentaria, at five study sites (three sites severely exposed to the tsunami and two sites sheltered from the tsunami) in Sendai Bay for 2 years prior to and 8 years after the tsunami. While the trematode prevalence decreased at all study sites, the species richness decreased only at the sites exposed to the tsunami. Although parasitism increased over the study period post-tsunami, the community had not fully recovered 8 years after the event. Trematode community structure has changed every year since the tsunami and has not stabilised. This could be explained by the alteration of first and second intermediate host communities. Our study suggests that it will take more time for the recovery of the trematode community and the associated coastal ecosystem in the Tohoku region.

Vertical distribution of particle-associated and free-living ammonia-oxidizing archaea in Suruga Bay, a deep coastal embayment of Japan.

We analyzed the vertical distributions of ammonia-oxidizing archaea (AOA) in terms of abundance in Suruga Bay, Japan. We distinguished particle-associated (PA) from free-living (FL) assemblages. According to quantitative PCR measurements of the ammonia monooxygenase subunit A gene (amoA), most marine AOA were in an FL state. The vertical distributions of PA AOA ecotypes differed from the general trend; the Shallow Marine clade was dominant in both the surface and deep layers. Thus, although PA AOA account for a small percentage of AOA abundance, they have a community structure distinct from that of FL AOA in planktonic environments. Marine particles should be investigated further as an unexplored niche of AOA in the ocean.

The mitochondrial genome of the gold-ringed cowry Monetaria annulus (Mollusca: Gastropoda: Cypraeidae) determined by whole-genome sequencing.

The mitochondrial genome of the cowry snail Monetaria annulus (Caenogastropoda: Cypraeoidea: Cypraeidae) was determined by whole-genome next-generation sequencing. The mitogenome is composed of 13 protein-coding genes (PCGs), 2 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 order Littorinimorpha. The superfamily Cypraeoidea was recovered as a sister clade to the group of Tonnoidea and Neogastropoda.

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.

The complete mitochondrial genome of the stream snail Clithon retropictus (Neritimorpha: Neritidae).

The complete mitochondrial genome of the stream neritid Clithon retropictus was determined by next-generation sequencing. The mitochondrial genome is 15,814 bp in length, comprising two ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes (tRNAs). Of these 37 genes identified, 7 PCGs and 8 tRNAs are encoded on the heavy strand and the other genes on the light strand. This gene order is consistent with the previously published mitochondrial genomes of the other neritid species. This is the first report of a complete mitochondrial genome sequence for the genus and the fourth for the gastropod subclass Neritimorpha.