The complete mitochondrial genome of freshwater gammarid Gammarus nipponensis (Crustacea: Amphipoda: Gammaridae).

This study presents the complete mitochondrial genome sequence of Gammarus nipponensis, a freshwater crustacean found in the western regions of Honshu, Shikoku and Kyushu in Japan. The entire genome is 16,429 bp in length, encoding a standard set of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, as well as the putative control regions. The mitochondrial genome of G. nipponensis is characterized by a high concentration of A and T nucleotides (67.1%). Notably, the mitogenome contains long TATTTTA repeats in the control region 2 at 686 bp long. This newly available genome information will be useful for studying the evolutionary relationships within the genus Gammarus and for understanding diversification among G. nipponensis populations.

Preliminary assessment of genetic variation in the Japanese endemic freshwater crab, Geothelphusadehaani, based on mitochondrial DNA sequences.

Geothelphusadehaani, a freshwater crab species endemic to Japan, has the largest distribution range amongst the 19 known species in the country. Due to its low dispersal capability and restricted habitat to freshwater, it serves as an excellent model for understanding gene flow between geographically isolated populations. In this study, we analysed the genetic relationships of 26 G.dehaani populations collected from different locations in the Japanese archipelago using two mitochondrial DNA regions - cytochrome oxidase subunit I (COI) and cytochrome b (cytB). Our results from the analysis of molecular variance (AMOVA) revealed high genetic variation amongst populations and the phylogenetic analysis identified four geographical groups: Clade I - Honshu and Shikoku, Clade II - north-eastern Kyushu, Clade III - southern Kyushu and Clade IV - north-western Kyushu. Notably, Clade IV exhibited the highest genetic distance amongst the observed groupings. These findings highlight the need for further examination of G.dehaani in Kyushu, including morphological and behavioural traits, to better understand the observed diversity within the species in the region.

Effect of Intertidal Elevation at Tsuyazaki Cove, Fukuoka, Japan on Survival Rate of Horseshoe Crab Tachypleus tridentatus Eggs.

Physical factors affecting the survival of Tachypleus tridentatus eggs were investigated by translocating their eggs between the high intertidal zone and the low intertidal zone of a known spawning site. The mean egg survival rates per day were highest in the mid intertidal zone (45.1%±25.4%) and the lowest in the low intertidal zone (13.3%±27.6%). Differences in the elevation, air exposure time, and water content of the spawning ground were significant factors determining the egg survival rates. Excessive or insufficient air exposure time resulted in inadequate water content at higher and lower intertidal zones and could reduce egg survival. On the other hand, moderate saturation and dehydration were repeated with each tidal movement in the mid intertidal zone. This dynamic is considered as one of the crucial factors for the survival of eggs and is considered optimal for spawning. Therefore, the protection of the mid intertidal zone is imperative for maximizing the egg survival rate in Tsuyazaki Cove where almost all suitable nesting sites have disappeared due to coastal development. By protecting these optimal sites for spawning and recovering other optimal sites on suitable beaches, a positive contribution can be made to future management and conservation. The study also suggests that translocating eggs from marginal to optimal spawning sites might be a recovery strategy for this globally endangered species.

Genetic diversification of the Kanehira bitterling Acheilognathus rhombeus inferred from mitochondrial DNA, with comments on the phylogenetic relationship with its sister species Acheilognathus barbatulus.

The Kanehira bitterling, Acheilognathus rhombeus, is a freshwater fish, discontinuously distributed in western Japan and the Korean Peninsula. Unusually among bitterling it is an autumn-spawning species and shows developmental diapause. Consequently, the characterization of its evolutionary history is significant not only in the context of the fish assemblage of East Asia, but also for understanding life-history evolution. This study aimed to investigate the phylogeography of A. rhombeus and its sister species Acheilognathus barbatulus, distributed in China, using a mitochondrial analysis of the ND1 gene from 311 samples collected from 50 localities in Japan and continental Asia. Phylogenetic analysis revealed that A. barbatulus is included in A. rhombeus and genetically closer to Japanese A. rhombeus than to Korean A. rhombeus. Divergence of Korean A. rhombeus and A. barbatulus from Japanese A. rhombeus was estimated to be from the late Pliocene (3.44 Mya) and the early Pleistocene (1.98 Mya), respectively. Each event closely coincided with the time of the Japan Sea opening. Japanese A. rhombeus comprised seven lineages: three in Honshu and four in Kyushu. One lineage in central Kyushu was genetically closer to the Honshu lineages than to other lineages in northern Kyushu. Divergence of Japanese lineages was estimated to be from the early to middle Pleistocene (0.55-0.93 Mya), during a period of geological and paleoclimatic change, including volcanic activity. Population expansion in the late Pleistocene (<0.10 Ma) was suggested in many of the lineages, which accords with other freshwater fishes. Biogeographically the ancestral A. rhombeus/A. barbatulus was likely to have repeatedly colonized Japan from the continent through land bridges in the late Pliocene and the early Pleistocene. However, the close genetic relationship between Japanese A. rhombeus and A. barbatulus suggests another possibility, with the second colonization occurring in reverse, from Japan to China. The small genetic distance between them indicates that the colonization occurred later than colonization events of other freshwater fishes, including other bitterling species.

Habitat suitability maps for juvenile tri-spine horseshoe crabs in Japanese intertidal zones: A model approach using unmanned aerial vehicles and the Structure from Motion technique.

The tri-spine horseshoe crab, Tachypleus tridentatus, is a threatened species that inhabits coastal areas from South to East Asia. A Conservation management system is urgently required for managing its nursery habitats, i.e., intertidal flats, especially in Japan. Habitat suitability maps are useful in drafting conservation plans; however, they have rarely been prepared for juvenile T. tridentatus. In this study, we examined the possibility of constructing robust habitat suitability models (HSMs) for juveniles based on topographical data acquired using unmanned aerial vehicles and the Structure from Motion (UAV-SfM) technique. The distribution data of the juveniles in the Tsuyazaki and Imazu intertidal flats from 2017 to 2019 were determined. The data were divided into a training dataset for HSM construction and three test datasets for model evaluation. High accuracy digital surface models were built for each region using the UAV-SfM technique. Normalized elevation was assessed by converting the topographical models that consider the tidal range in each region, and the slope was calculated based on these models. Using the training data, HSMs of the juveniles were constructed with normalized elevation and slope as the predictor variables. The HSMs were evaluated using the test data. The results showed that HSMs exhibited acceptable discrimination performance for each region. Habitat suitability maps were built for the juveniles in each region, and the suitable areas were estimated to be approximately 6.1 ha of the total 19.5 ha in Tuyazaki, and 3.7 ha of the total 7.9 ha area in Imazu. In conclusion, our findings support the usefulness of the UAV-SfM technique in constructing HSMs for juvenile T. tridentatus. The monitoring of suitable habitat areas for the juveniles using the UAV-SfM technique is expected to reduce survey costs, as it can be conducted with fewer investigators over vast intertidal zones within a short period of time.

Photo images, 3D/CT data and mtDNA of the freshwater mussels (Bivalvia: Unionidae) in the Kyushu and Ryukyu Islands, Japan, with SEM/EDS analysis of the shell.

BACKGROUND: Freshwater mussels (Bivalvia: Unionidae), which are keystone species of freshwater ecosystems, are in global decline. In addition to ecological/genetic studies, morphological examinations are needed to help provide information for the development of additional freshwater mussel studies and eventually conservation efforts for freshwater ecosystems.The microscopic structure, which can be obtained by scanning electron microscopy (SEM) and elemental composition, which can be obtained with energy dispersive X-ray spectrometry (EDS), of mollusc shells are of interest to malacologists. However, information about freshwater mussels is still limited.Kyushu Island is the southernmost island of the four major islands of Japan. Kyushu Island is a hotspot of bitterling fishes in Japan, which simultaneously means that the island is a hotspot of freshwater mussels. The Ryukyu Islands stretch southwest from Kyushu Island to Taiwan; a freshwater mussel of unknown origin was reported from the Ryukyu Islands.Digital archiving for biology and ecology is a continuing challenge for open science. This data paper describes online published photo images, 3D/CT and mtDNA data and SEM/EDS analyses of the shell of freshwater mussels that inhabit the Kyushu and Ryukyu Islands, Japan. Our data will provide basic information regarding freshwater biology and be of public interest as open science. NEW INFORMATION: Photo images, 3D/CT data, mtDNA data, SEM images and EDS elemental analysis of freshwater mussels that inhabit the Kyushu and Ryukyu Islands (61 individuals, nine species/subspecies) were published online in a local database (http://ffish.asia/Unionidae3D), GBIF (http://ipt.pensoft.net/resource?r=unionidae3d) and DDBJ/EMBL/Genbank (LC431810-LC431840).

A simple SNP genotyping method reveals extreme invasions of non-native haplotypes in pale chub Opsariichthys platypus, a common cyprinid fish in Japan.

Biological invasion by non-native subspecies or populations is one of the most serious threats to ecosystems, because these species might be easily established in the introduced area and can negatively affect native populations through competition and hybridization. Pale chub Opsariichthys platypus, one of the most common fish in East Asia, exhibits clear genetic differentiation among regional populations; however, introgression and subsequent loss of genetic integrity have been occurring throughout Japan due to the artificial introduction of non-native conspecifics. In this study, we developed a simple SNP genotyping method to discriminate between native and non-native mitochondrial DNA (mtDNA) haplotypes in pale chub using real-time PCR assay. We then investigated the distribution patterns of non-native pale chub in Tokai region, located in the center of Honshu Island, Japan and developed a predictive model of the occurrence of non-natives to reveal the factors influencing their invasion. The specificity and accuracy of the genotyping method were confirmed by using samples whose haplotypes were determined previously. Extensive occurrence of non-native haplotypes in Tokai region was detected by this method. In addition, our models suggested that the presence of non-natives varied greatly depending on the river system, and was positively influenced by the impounded water areas. Our method could accurately distinguish between native and non-native haplotypes of pale chub in Japan and suggested key environmental factors associated with the presence of non-natives. This approach can greatly reduce experimental costs be a great contribution for quantitative investigation.

Tributyltin in blood of marine fish collected from a coastal area of northern Kyushu, Japan.

We investigated levels of the pollutant tributyltin (TBT) in blood of pufferfishes (six species), Japanese sea perch, red sea bream, Japanese common goby, Japanese flounder, rockfish, conger eel, and sea mullet collected off the coast of northern Kyushu, Japan. We found considerable levels of TBT (1.4-190 ng/mL) accumulated in the blood of these fish. Blood TBT concentrations were 1.3-22.5 times liver concentrations and 4.9-78 times muscle concentrations, except in conger eel and mullet. We detected TBT (16-111 ng/mL-blood) in the plasma of the fine-patterned puffer (Takifugupoecilonotus) year-round, without any apparent seasonal trend. These results suggest that fish inhabiting coastal areas of Kyushu, Japan, continue to be contaminated with TBT.

Habitat use in irrigation channels by the golden venus chub (Hemigrammocypris rasborella) at different growth stages.

Ecological information on the golden venus chub (Hemigrammocypris rasborella Fowler, 1910) was collected during field surveys and used to analyze habitat use by this species at each growth stage. Surveys were conducted every month for approximately 2 years In an irrigation ditch near the Ushizu River, Kyushu Island, Japan. Based on the characteristic nuptial coloration of males, it was estimated that H. rasborella spawns between spring and summer. Size measurements of 2697 individuals indicated two size classes. The population of age class 1 decreased rapidly after the spawning period. On the basis of growth patterns, the life cycle of H. rasborella was classified into three stages: the growth stage (GS) of age class 0 fish from August to November, the no-growth stage (NGS) of age class 0 fish from December to March, and the growing and spawning stage (GSS) of age class 0 and 1 fish from April to August. Habitat use by GS, NGS, and GSS fish was analyzed with a stepwise multiple linear regression. The average number of fish was negatively correlated with the presence of a concrete revetment in the GS; positively and negatively correlated with minimum water depth and submerged plants, respectively, in the NGS; and positively correlated with maximum water temperature in the GSS. These results suggest that maintenance of the water level in the fallow season and not using concrete revetments are essential for the conservation of this species under the present conditions in Japanese rice fields.

A screening method for toxicity identification evaluation on an industrial effluent using Chelex-100 resin and chelators for specific metals.

Toxicity of an industrial effluent was characterized using a toxicity identification method established at our research institute. Toxicity was evaluated using the Ceriodaphnia dubia survival test. The industrial effluent chosen in the present study had toxic effects on C. dubia before treatment. The effluent was first filtered to remove suspended solids (F-treatment). Activated charcoal was then added to the effluent to adsorb organic substances (AC-treatment), followed by treatment of the supernatant with Chelex-100 resin to remove di- and trivalent cations, including transition metals (C100-treatment). The effluent exhibited a toxic effect on C. dubia even after the AC-treatment, but it was no longer toxic after the C100-treatment, indicating that the effluent contained cations that affect C. dubia survival. To further identify the metals responsible for the toxicity, benzoin-alpha-oxime or dimethylglyoxime was added to the effluent to chelate specific cations. The toxicity of the effluent was eliminated by addition of dimethylglyoxime but not significantly so by addition of benzoin-alpha-oxime, suggesting that the toxicants in the effluent strongly formed complexes with dimethylglyoxime. These results combined with those of metal analysis strongly suggest that nickel might be the noxious agent. The toxicity identification method described in this paper is effective for the identification of metal toxicants in industrial effluents. The method using insoluble chelating resins and chelators for specific metals would serve as a useful addition to the standard toxicity identification evaluation procedure.

Expression analysis of sex-specific and 17beta-estradiol-responsive genes in the Japanese medaka, Oryzias latipes, using oligonucleotide microarrays.

Gene profiling of Japanese medaka (Oryzias latipes) was performed using an oligonucleotide DNA microarray representing 22,587 TIGR O. latipes gene indices (OLGIs). The average correlation coefficients for gene expression between individual mature fish were high (>0.95) for both female and male, indicating that the physiological status of medaka is highly reproducible under prescribed growth conditions. Of the 22,587 OLGIs, 2575 showed significant differences in expression between female and male. Exposure to 17beta-estradiol (E2) revealed 381 E2-responsive OLGIs in male medaka. Feminization and male-dysfunction factors of the E2-treated males calculated using the combination of Pearson correlation coefficient and Euclidean distances indicate that E2 treatment "weakly feminized" male medaka, while male physiological functions were not significantly disrupted. This study demonstrates the possibility of using medaka microarrays to estimate the overall effects of hormonally active chemicals.

Effects of 17beta-estradiol on survival, growth, sexual development and molting cycles of the marine crustacean mysid shrimp, Americamysis bahia.

A 14-day partial life-cycle test was performed to assess the effects of 17beta-estradiol (E2) on the survival, growth, sexual development and molting cycles of a marine crustacean mysid shrimp (Americamysis bahia). Seven-day-old mysids were exposed to the nominal E2 concentrations of 31.3, 62.5, 125, 250 and 500 microg/l for 14 days. The total length and the body weight of mysids significantly decreased relative to the controls when exposed to 62.5, 250 and 500 microg/l E2 for 14 days. Moreover, the carapace length significantly decreased in the 500 microg/l E2 treatment groups. No significant differences were observed in sex ratio with the appearance of secondary sex characteristics in the all treatment groups including the control and solvent control groups. However, the percentage of females with eggs in the oviduct or brood sac decreased significantly in mysids treated with E2 at 62.5, 125, 250 and 500 microg/l. The cumulative total number of molting cycles when exposed to E2 for 14 days significantly decreased in the treatment groups at 500 microg/l relative to the controls. These results suggest that concentrations of E2 over 62.5 microg/l may cause growth suppression in mysid shrimp, and that the disruption of molting cycles may result in alterations in growth due to a sublethal response to toxicant exposure.

Styrene dimers and trimers affect reproduction of daphnid (Ceriodaphnia dubia).

The endocrine disruptor activity of styrene in humans and other vertebrates appears to be negligible. However, offspring numbers were reduced in Ceriodaphnia dubia bred in polystyrene cups. Styrene dimers and trimers were found to be eluted from the polystyrene cups by hexane and methanol with gas chromatography-mass spectrometry. Styrene dimers and trimers at concentrations of 0.04-1.7 microg/l affected C. dubia fertility (25% reduction after seven days), suggesting that styrenes have the potential to impair crustacean populations in the aquatic environment.