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AbstractThis 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.

Geothelphusa dehaani, 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.

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.

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.

Geothelphusa dehaani, 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. [ABSTRACT FROM AUTHOR]

The conservation of an endangered horseshoe crab, Tachypleus tridentatus, has been increasingly emphasized worldwide. Although monitoring of T. tridentatus reproduction is effective for its conservation, the conventional monitoring system for spawning has several drawbacks. Thus, our study aimed to examine the environmental DNA (i.e., eDNA) approach to assess T. tridentatus spawning events. Six survey sites were set at the sandy beaches of the Sone tidal flat, Japan. Visual observations of the spawning events, i.e., the presence/absence of adult pairs of T. tridentatus or that of foams, occurring because of their spawning behavior, and water sampling for eDNA assay were conducted 10 times at each site between 2019 and 2020. The spawning events were observed at a total 16 sites during the surveys, and the estimated numbers of T. tridentatus adult pairs were 1--5 per site. T. tridentatus DNA was detected in 15 of the 16 samples at the sites where the spawning events were observed and in 13 of 44 samples where the spawning events were not observed. The estimated number of pairs and the eDNA concentration showed a significantly positive correlation. Moreover, the presence/absence of the spawning events was distinguished with excellent accuracy based on the eDNA concentration. Therefore, our results showed that the spawning events of the species and the eDNA concentration were closely related. In conclusion, we expect that the population of T. tridentatus in spawning grounds can be evaluated more complementarily by combining the conventional observation method with the eDNA approach. [ABSTRACT FROM AUTHOR]

Parapyxidognathus deianira (family Vaninidae) is a rare brackish-water crab, and there is increasing concern about its possible extinction in several region across Japan. We have sampled this species from 20 river estuaries in Kyushu, Japan, from 2014 to 2017. The occurrence of this species in the Sea of Japan coast is being reported for the first time, following the sampling of this species from the Daikon River estuary in Fukuoka Prefecture. Crab and fish fauna at the collection site in the Daikon River suggest that the habitat conditions ofP. deianira at the site are similar to that described in the previous reports of this species. [ABSTRACT FROM AUTHOR]

The invasion of the Asian clam, Corbicula fluminea (O.F. Müller, 1774), has caused serious ecological and economic problems worldwide. In the Japanese archipelago, C. fluminea has been identified using morphological characteristics in most distribution surveys. However, a recent study has shown that morphology alone cannot be used to identify C. fluminea due to its superficial similarity to the related native species C. leana Prime, 1867. Consequently, the present distribution of C. fluminea is still poorly understood. We surveyed the distribution of C. fluminea on Kyushu Island, Japan, by sequencing the cytochrome b region of the mitochondrial DNA, a region that can be used to distinguish the two clam species, and found that C. fluminea was already established throughout the entire island, except at a single site where Corbicula clams comprised solely of C. leana. In response to this serious situation, we suggest using PCR-RFLP method, which was employed here, to distinguish the two clam species for more effective and rapid surveys. [ABSTRACT FROM AUTHOR]

Hybridization between native and non-native fishes is a serious global problem. Thus, there is a need to develop monitoring methods for predicting potential hybridization to evaluate the risk of genetic introgression and to identify important areas for conservation of pure native populations. Here, we developed a prediction model for intersubspecific hybridization, based on distribution and genetic data. We selected Rhodeus ocellatus kurumeus and R. ocellatus ocellatus as the native and non-native subspecies, respectively. First, we developed generalized linear models (GLMs) for the species habitat requirements by using presence/absence data and environmental variables. The best-fit models showed river length gave conflicting effects for the two subspecies. Next, we developed a GLM using the ratio of non-native haplotypes in mitochondrial DNA as an objective variable, with the predicted probabilities of the occurrence of each fish and spatial information as explanatory variables. The best-fit model selected the distance from the center of native distribution and the non-native habitat requirement as key factors. Our findings indicate that hybridization occurs highly and/or initially near the margin of native distribution where non-native habitat requirements are available. Our model could identify sites in native habitats with very low potential risk for genetic invasion as important areas for conservation of pure native populations. [ABSTRACT FROM AUTHOR]

The article presents research which assessed the food changes of dwarf loach or Kichulchoia brevifasciata in relation to their size. The researchers evaluated the size-related changes of the species by examining the contents of the gut of 43 specimens which they have collected from March 2006 to April 2007. They mentioned that the food items in the gut showed rapid changes when the fish reached the approximate length of 35 to 40 millimeters. They found that small subjects were mainly fed on the amoebozoa Difflugia.